Genetic profile of local buffalo (Bubalus bubalis) populations in Pacitan and Tuban, East Java, Indonesia measured by the molecular marker of INRA032 locus
DOI: 10.26740/jrba. v5n1.p.37-42
ABSTRACT. The genetic profile of buffaloes is important information to support their breeding efforts, therefore the assessment of genetic profile needs to be carried out continuously. This study aimed to analyze the application of microsatellite marker at the INRA032 locus for genetic profile assessment in buffalo (Bubalus bubalis) populations in Pacitan and Tuban Regencies, East Java, Indonesia. The total number of samples used was 16, with each population represented by 8 samples. Genetic profile assessment parameters include allele frequency, the Polymorphism Information Content (PIC), and heterozygosity. The results showed that based on the INRA032 locus, the Tuban buffalo population had a higher allele frequency range (0.08 to 0.33) than the Pacitan population (0.18 to 0.31). The average PIC value in both populations was 0.39, so it can be concluded that the INRA032 locus is informative enough to detect polymorphisms in both populations. The percentage heterozygosity of the Pacitan buffalo population is 88%, which is higher than the Tuban population at 50%, suggesting that the genetic diversity of the two populations is still quite high despite the decreasing trend in population numbers. The INRA032 locus was shown to be moderately effective for assessing genetic profile in local buffaloes, but its application in future studies will require an increase in the number of samples representing the population and the addition of other microsatellite markers to obtain a more accurate conclusion.
The molecular approach reveals the relationship among Venus clams (Meretrix s...AbdullaAlAsif1
Molecular study is important to detect variations and similarities among species from the same genus, in case if they do not encompass any morphological or physiological differences. The study was conducted to differentiate among species of Meretrix spp. (Meretrix lyrata, M. meretrix, and M. lusoria) obtained from two locations in Malaysia through the phylogenetic tree. The adductor muscle tissues were used to extract DNA and to perform other procedures; the samples were subjected to analyses using PCR and gel electrophoresis. The multiple sequence comparison was conducted by MUSCLE and the phylogenetic relationships were established using Maximum Likelihood (ML) statistical methods with MEGA 6.0 statistical software. M. lyrata samples showed 99% similarity to the three accessions sequence, where M. lyrata indicated 87% similarities, and M. meretrix showed not more than 89% similarities from the deposited sequence. The nucleotide base composition sequences consisted of the mean of Thiamine (T) 37.9%, Cytosine (C) 15.4%, Adenine (A) 27.4%, and Guanine (G) 19.4%. Maximum Likelihood (ML) analysis was conducted using the Tamura 3-parameter model to establish five major clades on Meretrix spp. and two out-groups clades significantly different from the Meretrix spp. These major clades were closely related to each other at the 50% evidence of bootstrap, which grouped as genus Meretrix. The present study on Meretrix spp. from the Sarawak locality was able to differentiate COI sequences between M. lyrata, M. meretrix, and M. lusoria. M. lusoria was close related to M. meretrix with strong bootstrap supporting evidence at 96% scoring. Moreover, M. lyrata was inferred as the ancestor to M. meretrix, and M. lusoria from Sarawak, Malaysia.
Characterization and Validation of Point Mutation in Breast Cancer 1 (BRCA1) ...paperpublications3
This document summarizes a study that aimed to characterize and validate point mutations in the BRCA1 gene and their relationship to mastitis traits in Sahiwal cattle. The researchers analyzed 120 Sahiwal cattle and targeted a region of intron 6 in the BRCA1 gene. Genotype analysis using PCR-RFLP revealed a monomorphic banding pattern, indicating the sequence was highly conserved in Sahiwal cattle. DNA sequencing also found no significant polymorphisms. Therefore, the reported and in silico screened SNPs could not be considered universal markers for mastitis resistance in all cattle breeds. Further studies with larger sample sizes are needed.
Molecular characterization of rice (Oryza sativa L.) genotypes using target r...Innspub Net
In the present investigation, based on the seven rice putative candidate iron transporter genes, novel TRAP markers were developed. These markers were successfully employed in the molecular diversity study among 30 rice genotypes representing improved rice cultivars and land races with varied grain iron content (7.38 - 30.58 ppm). Totally, thirty TRAP primer combinations were screened, which generated 703 bands out of which 654 were polymorphic (93%) with an average of 21.8 bands per primer combination. The average polymorphic information content (PIC) values ranged from 0.09 (Osysl4b+ME05) to 0.25 (Osnramp5c+ME05, Osnramp1b+ME02 and Osysl4a +ME02). Gene diversity (H ˆ
) ranged from 0.10 (Osysl4b+ME05) to 0.31 (Osnramp1b + ME02 and Osysl4a +ME02). The Jaccard dissimilarity ranged from 0.15 to 0.52, explaining 37% of genetic variation (Table 4). Grouping of genotypes based on UPGMA and principal coordinate analysis (PCoA) were found comparable and grouping of genotypes into a different cluster was found mainly on the basis of pedigree relationships. TRAP markers revealed well resolved relationships among rice genotypes. The information generated from this study will helps to select parental combinations for breeding high iron content
rice varieties.
Biogeography and polyphasic approach of pseudomonas strains from agriculture ...Alexander Decker
This document summarizes a study on the isolation and characterization of Pseudomonas strains from agricultural land in Madhya Pradesh, India. Soil samples were collected from different districts and 50 Pseudomonas strains were isolated. The isolates were characterized using biochemical tests as well as molecular techniques including DNA isolation, PCR-RFLP of 16S rDNA, RAPD-PCR, and REP-PCR fingerprinting. Genetic diversity analysis showed the isolates had genetic similarity with some variation in their genomes. The isolates exhibited potential for use as plant growth-promoting rhizobacteria and biocontrol agents based on their biochemical profiles.
The document summarizes a study that analyzed genetic diversity among 31 maize genotypes based on fodder yield and quality parameters. Key findings include:
- Analysis of variance revealed significant differences between genotypes for various traits measured like plant height, stem diameter, leaf area, fodder yield, protein and fiber content.
- The best performing genotypes identified were DTMA-271, DTMA-15, DTMA-281 and DTMA-295 based on traits like plant height, leaf area, fodder yield and protein content.
- Correlation analysis showed traits like plant height, stem diameter, leaf moisture percentage and fodder yield were significantly correlated with increased fodder yield per plant.
This document describes the development of 160 novel simple sequence repeat (SSR) markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries. Genomic DNA from bitter gourd was used to construct libraries enriched for 10 different repeat motifs. Of the 3,072 clones screened, 93.7% contained microsatellite repeats. Unique primer pairs were designed and validated for 151 loci. Genetic diversity analysis of 51 loci among 54 accessions found 20% were polymorphic. The markers distinguished 15 Indian varieties and 78.4% were transferable across six Momordica species. The new SSR markers will be useful for genetic studies in bitter gourd.
This document characterizes the genetic diversity among four indigenous sheep breeds in Balochistan, Pakistan using random amplified polymorphic DNA (RAPD) analysis. Nineteen RAPD primers were used to analyze DNA samples from 48 sheep across four breeds. A total of 92 DNA fragments were amplified, with 36 showing monomorphism and 56 being polymorphic. The Mengali breed showed the highest genetic diversity and number of polymorphic loci, while the Balochi breed showed the lowest. Genetic similarity was highest between the Balochi, Beverigh and Harnai breeds, likely due to sharing a common habitat. The study demonstrates the presence of genetic diversity both within and among the sheep breeds that can inform conservation and breeding programs
S M Masiul Azam, Md Shahidul Islam, Parvin Shahanaz, Md Shafiqur Rahman and Sarder Md Shahriar Alam. “Molecular Characterization of Brassica Cultivars through RAPD Markers” United International Journal for Research & Technology (UIJRT) 1.3 (2019): 41-45.
The molecular approach reveals the relationship among Venus clams (Meretrix s...AbdullaAlAsif1
Molecular study is important to detect variations and similarities among species from the same genus, in case if they do not encompass any morphological or physiological differences. The study was conducted to differentiate among species of Meretrix spp. (Meretrix lyrata, M. meretrix, and M. lusoria) obtained from two locations in Malaysia through the phylogenetic tree. The adductor muscle tissues were used to extract DNA and to perform other procedures; the samples were subjected to analyses using PCR and gel electrophoresis. The multiple sequence comparison was conducted by MUSCLE and the phylogenetic relationships were established using Maximum Likelihood (ML) statistical methods with MEGA 6.0 statistical software. M. lyrata samples showed 99% similarity to the three accessions sequence, where M. lyrata indicated 87% similarities, and M. meretrix showed not more than 89% similarities from the deposited sequence. The nucleotide base composition sequences consisted of the mean of Thiamine (T) 37.9%, Cytosine (C) 15.4%, Adenine (A) 27.4%, and Guanine (G) 19.4%. Maximum Likelihood (ML) analysis was conducted using the Tamura 3-parameter model to establish five major clades on Meretrix spp. and two out-groups clades significantly different from the Meretrix spp. These major clades were closely related to each other at the 50% evidence of bootstrap, which grouped as genus Meretrix. The present study on Meretrix spp. from the Sarawak locality was able to differentiate COI sequences between M. lyrata, M. meretrix, and M. lusoria. M. lusoria was close related to M. meretrix with strong bootstrap supporting evidence at 96% scoring. Moreover, M. lyrata was inferred as the ancestor to M. meretrix, and M. lusoria from Sarawak, Malaysia.
Characterization and Validation of Point Mutation in Breast Cancer 1 (BRCA1) ...paperpublications3
This document summarizes a study that aimed to characterize and validate point mutations in the BRCA1 gene and their relationship to mastitis traits in Sahiwal cattle. The researchers analyzed 120 Sahiwal cattle and targeted a region of intron 6 in the BRCA1 gene. Genotype analysis using PCR-RFLP revealed a monomorphic banding pattern, indicating the sequence was highly conserved in Sahiwal cattle. DNA sequencing also found no significant polymorphisms. Therefore, the reported and in silico screened SNPs could not be considered universal markers for mastitis resistance in all cattle breeds. Further studies with larger sample sizes are needed.
Molecular characterization of rice (Oryza sativa L.) genotypes using target r...Innspub Net
In the present investigation, based on the seven rice putative candidate iron transporter genes, novel TRAP markers were developed. These markers were successfully employed in the molecular diversity study among 30 rice genotypes representing improved rice cultivars and land races with varied grain iron content (7.38 - 30.58 ppm). Totally, thirty TRAP primer combinations were screened, which generated 703 bands out of which 654 were polymorphic (93%) with an average of 21.8 bands per primer combination. The average polymorphic information content (PIC) values ranged from 0.09 (Osysl4b+ME05) to 0.25 (Osnramp5c+ME05, Osnramp1b+ME02 and Osysl4a +ME02). Gene diversity (H ˆ
) ranged from 0.10 (Osysl4b+ME05) to 0.31 (Osnramp1b + ME02 and Osysl4a +ME02). The Jaccard dissimilarity ranged from 0.15 to 0.52, explaining 37% of genetic variation (Table 4). Grouping of genotypes based on UPGMA and principal coordinate analysis (PCoA) were found comparable and grouping of genotypes into a different cluster was found mainly on the basis of pedigree relationships. TRAP markers revealed well resolved relationships among rice genotypes. The information generated from this study will helps to select parental combinations for breeding high iron content
rice varieties.
Biogeography and polyphasic approach of pseudomonas strains from agriculture ...Alexander Decker
This document summarizes a study on the isolation and characterization of Pseudomonas strains from agricultural land in Madhya Pradesh, India. Soil samples were collected from different districts and 50 Pseudomonas strains were isolated. The isolates were characterized using biochemical tests as well as molecular techniques including DNA isolation, PCR-RFLP of 16S rDNA, RAPD-PCR, and REP-PCR fingerprinting. Genetic diversity analysis showed the isolates had genetic similarity with some variation in their genomes. The isolates exhibited potential for use as plant growth-promoting rhizobacteria and biocontrol agents based on their biochemical profiles.
The document summarizes a study that analyzed genetic diversity among 31 maize genotypes based on fodder yield and quality parameters. Key findings include:
- Analysis of variance revealed significant differences between genotypes for various traits measured like plant height, stem diameter, leaf area, fodder yield, protein and fiber content.
- The best performing genotypes identified were DTMA-271, DTMA-15, DTMA-281 and DTMA-295 based on traits like plant height, leaf area, fodder yield and protein content.
- Correlation analysis showed traits like plant height, stem diameter, leaf moisture percentage and fodder yield were significantly correlated with increased fodder yield per plant.
This document describes the development of 160 novel simple sequence repeat (SSR) markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries. Genomic DNA from bitter gourd was used to construct libraries enriched for 10 different repeat motifs. Of the 3,072 clones screened, 93.7% contained microsatellite repeats. Unique primer pairs were designed and validated for 151 loci. Genetic diversity analysis of 51 loci among 54 accessions found 20% were polymorphic. The markers distinguished 15 Indian varieties and 78.4% were transferable across six Momordica species. The new SSR markers will be useful for genetic studies in bitter gourd.
This document characterizes the genetic diversity among four indigenous sheep breeds in Balochistan, Pakistan using random amplified polymorphic DNA (RAPD) analysis. Nineteen RAPD primers were used to analyze DNA samples from 48 sheep across four breeds. A total of 92 DNA fragments were amplified, with 36 showing monomorphism and 56 being polymorphic. The Mengali breed showed the highest genetic diversity and number of polymorphic loci, while the Balochi breed showed the lowest. Genetic similarity was highest between the Balochi, Beverigh and Harnai breeds, likely due to sharing a common habitat. The study demonstrates the presence of genetic diversity both within and among the sheep breeds that can inform conservation and breeding programs
S M Masiul Azam, Md Shahidul Islam, Parvin Shahanaz, Md Shafiqur Rahman and Sarder Md Shahriar Alam. “Molecular Characterization of Brassica Cultivars through RAPD Markers” United International Journal for Research & Technology (UIJRT) 1.3 (2019): 41-45.
Evaluating fodder quality in sorghum RIL population under contrasting water r...ICRISAT
Drought (midseason or terminal)is a regular and recurring event in arid and semi-arid land, affected by approximately 30% of the world total area and are in habited by 20% of the total world population. The reduction in crop production and yield caused by drought has direct effecton livelihood of farmers(and their families)that inturn affects the yield from livestock (draft capacity/milching).Sorghum is a dual purpose drought resilient crop cultivated in Africa and Asia.
Inter Simple Sequence Repeats (ISSR) markers were utilized to identify the levels of heritable varieties and patterns of the populace structure among the five populaces of Pteris biaurita, a natural fern in India. A comprehensive examination was directed in three replicates at 2013-14 seasons in the Western Ghats, South India. Five wild P. biaurita, accessions (maiden hair) were assessed for genotyping studies. Results demonstrated a pivotal discrepancy among genotypes for they were characterized in view of this uniqueness in four groups by the genetic cluster examination. In this trial, ISSR primers amplified 63 polymorphic groups. In view of the genetic identity data, genotypes were figured and differed from 0.5714 to 0.6984. The percentage of polymorphism indicated predominant genotype that may be utilized for the conservation of species. ISSR appeared to be an obliging marker for prediction of genotype inside a closed group of inter specific populace in the investigation territory.
Inter Simple Sequence Repeats (ISSR) markers were utilized to identify the levels of heritable varieties and patterns of the populace structure among the five populaces of Pteris biaurita, a natural fern in India. A comprehensive examination was directed in three replicates at 2013-14 seasons in the Western Ghats, South India. Five wild P. biaurita, accessions (maiden hair) were assessed for genotyping studies. Results demonstrated a pivotal discrepancy among genotypes for they were characterized in view of this uniqueness in four groups by the genetic cluster examination. In this trial, ISSR primers amplified 63 polymorphic groups. In view of the genetic identity data, genotypes were figured and differed from 0.5714 to 0.6984. The percentage of polymorphism indicated predominant genotype that may be utilized for the conservation of species. ISSR appeared to be an obliging marker for prediction of genotype inside a closed group of inter specific populace in the investigation territory
Molecular Diversity Analysis of Some Local Ginger (Zingiber officinale) Genot...AI Publications
Ginger (Zingiber officinale) rhizomes have been widely used as a spice and flavoring agent in foods and beverages in Bangladesh as well as in all over the world for its economical and medicinal values. The present investigation was undertaken for the assessment of 13 local ginger genotypes collected from different region of Bangladesh through 7 RAPD primers. Genomic DNA was extracted from ginger genotypes using CTAB method. A total of 34 distinct and differential amplification bands ranging from 150-1200 bp were observed with an average of 1.14 polymorphic bands per primer. The overall gene diversity was detected 0.8052 and the value of PIC was detected 0.7532. The RAPD marker generate enough polymorphism for possible use in diversity studies through cluster analysis and principal component analysis (PCA). PCA classified 13 ginger genotypes into four groups and showed in two dimensional scatter plot. The genetic similarity coefficients among genotypes ranged from 0.103 to 0.654. Cluster analysis based on Jaccard’s similarity-coefficient using UPGMA grouped the genotypes into two clusters: Cluster A and Cluster B. The cluster ‘A’ had only one genotype Kaptai local and the second cluster ‘B’ had rest of twelve genotypes. The prevalence level of polymorphism in the local genotypes of ginger will help to breeders for ginger improvement program.
This document describes a DNA marker-based technology developed to identify citrus rootstocks at the seedling stage. Traditionally, Rough lemon and Rangpur lime are preferred rootstocks but are difficult to distinguish from Galgal at an early stage. Galgal is an undesirable rootstock due to susceptibility to diseases. The new technology uses microsatellite markers and PCR to differentiate Rough lemon, Rangpur lime, and Galgal based on presence or absence of DNA fragments. It provides a non-destructive method to ensure nurseries are supplying quality rootstock varieties. The technique has been transferred to agricultural organizations to benefit citrus farmers.
This document describes a study that used molecular methods including PCR and sequencing of the internal transcribed spacer 1 (ITS1) region to analyze the genetic diversity of anaerobic fungi in the gastrointestinal tracts of buffalo. Total DNA was extracted from rumen samples and the ITS1 region was amplified and sequenced. Sequence analysis of 12 clones showed diversity among the anaerobic fungal isolates. The results indicate that analysis of the ITS1 spacer through molecular techniques is a promising approach for comparing rumen fungal populations and diversity.
Genetic variability and phylogenetic relationships studies of Aegilops L. usi...Innspub Net
Studying of genetic relationships among Aegilops L. species is very important for broadening the cultivated wheat genepool, and monitoring genetic erosion, because the genus Aegilops includes the wild relatives of cultivated wheat which contain numerous unique alleles that are absent in modern wheat cultivars and it can contribute to broaden the genetic base of wheat and improve yield, quality and resistance to biotic and abiotic stresses of wheat. The use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant biotechnology and their genetics studies. There are different types of markers, morphological, biochemical and DNA based molecular markers. These DNA-based markers based on PCR (RAPD, AFLP, SSR, ISSR, IRAP), amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Day by day development of such new and specific types of markers makes their importance in understanding the genomic variability and the diversity between the same as well as different species of the plants. In this review, we will discuss about genetic variability and phylogenetic relationships studies of Aegilops L. using some molecular markers, with theirs Advantages, and disadvantages.
Molecular characterization of pea (Pisum sativum L.) using microsatellite mar...IOSR Journals
Nineteen pea (Pisum sativum L.) accessions have been characterized using Simple Sequence Repeats (SSRs). The mains objectives of this study were to examine SSR polymorphism among cultivars and to assess genetic diversity among them. Eight microsatellites, from the Pisum microsatellite consortium (Agrogene ®, France) have been used. Five of the eight SSRs studied gave good electrophoretic profiles and helped us to amplify a number of alleles per locus varying from 3 (PSMPA5 and PSMPA6) to 13 (PSMPSAD126) with a total of 34 and an average number of 6.8 alleles per locus. The Polymorphism Information Content (PIC) varied from 0.18 for PSMPSAD134 to 0.85 for PSMPSAD126, with an average value of 0.62. The five microsatellites analyzed allowed us to separate 18 out of the 19 genotypes studied, and only the two most polymorphic markers (PSMPSAA205 and PSMPSAD126), permit to discriminate among the same genotypes (18) separated using the 5 SSRs. Genetic distances computed have been used to draw the corresponding dendrogram and to distribute genotypes according to their genetic relationship. The genotypes classified within the same group share several agro-morphological characters. Finally, the present study attests that SSR microsatellites are good tools for identifying genotypes and for the assessment of genetic diversity in pea.
This document discusses genetic diversity analysis of grape (Vitis vinifera L.) germplasm in India using microsatellite markers. A total of 42 grape genotypes were analyzed using 7 microsatellite markers. A total of 45 alleles were detected among the genotypes. The microsatellites grouped the genotypes into two main clusters (A and B) based on morphological and genetic characteristics, with subclusters differentiating seeded vs seedless fruits and pigmented vs non-pigmented fruits. The study found high genetic variability among the Indian grape germplasm and that microsatellite markers are a reliable tool for diversity and breeding programs.
Genome wide association studies (GWAS) analysis of karnal bunt resistance in ...Innspub Net
Karnal bunt (KB) disease is one of the most important challenges posed on of wheat (Triticum aestivum L.) industry of Pakistan because of itsinclusionin quarantine list around the globe. This disease is caused by the fungus Tilletia indica M. (Neovossia indica). It affects the grain quality of wheat and hampers its movement in international market resulting in economic losses. Presence of >3% infected grains in wheat lot makes it unsuitable for human consumption. Eradication of this disease is very difficult as no resistant cultivar has been found against KB in Pakistan so far. Genome wide association study (GWAS) was conducted on a set of 199 wheat germplasm collected from Pakistan. In this study 31,000 single nucleotide polymorphism markers were developed by 90K SNP array technology. A linear mixed model in GWAS, accounting for population structure, was fitted to identify significant genomic regions [-log(P) ≥ 4.0] on 6 different chromosomes i.e. 1A, 1D, 2D, 3B, 4A, 5A with novel loci. Candidate genes, through wheat genome assembly, were identified as putative genes related to KB resistance including kinase like protein family. The results of this study can be useful in wheat breeding through marker assisted selection for KB resistant varieties.
This document describes the CarrAgheen Molecular Marker Database (CaMM-Db), a comprehensive database of molecular markers for the red seaweed Chondrus crispus (carragheen). The database contains over 18,000 microsatellites and 12,000 SNPs identified from carragheen genomic sequences. CaMM-Db provides information on different microsatellite types and properties. It also integrates with primer design software to facilitate wet lab experiments. As the first database of its kind for carragheen, CaMM-Db is expected to be a valuable resource for genetic research on carragheen and other red seaweeds.
The document discusses molecular biology research on the fungus Monascus spp. It provides details on:
1) Molecular markers that have been used to classify Monascus spp., including RAPD, D1/D2 regions of LSU rRNA, ITS, IGS, ISSR, and SRAP. These markers revealed genetic diversity and grouped species.
2) Genetic transformation techniques for Monascus spp., such as protoplast transformation, electroporation, bombardment, REMI, and ATMT. Protoplast transformation was successfully used to create mitotically stable transformants of M. aurantiacus and M. purpureus.
3) Cloning of some genes from Mon
The document discusses three case studies related to genetic divergence and bioactive compounds in chickpea (Cicer arietinum L.):
1. The first case study evaluated 100 chickpea genotypes and found significant genetic diversity between clusters. Days to flowering, 100 seed weight, number of seeds per plant, and plant height contributed most to diversity. Six genotypes were identified for hybridization.
2. The second case study used principal component analysis on 434 chickpea genotypes evaluated for 13 traits. Eight components captured 77.68% of variation, with days to flowering and seed yield contributing most. Five genotypes performed well across components.
3. The third case study analyzed correlations and path coefficients in chickpe
This research note describes the development of 17 microsatellite loci for two species of flat periwinkles, Littorina fabalis and L. obtusata. The microsatellites were isolated from L. fabalis using next-generation sequencing and tested on individuals of both species. Seventeen loci were found to reliably amplify in both species. These new nuclear markers can be used to study species discrimination between L. fabalis and L. obtusata, investigate hybridization, and characterize divergence between L. fabalis ecotypes. The microsatellites provide a genetic tool to overcome limitations of morphological identification.
This document summarizes a review on the potential of water buffalo in world agriculture. It discusses water buffalo's role in agriculture, their global population distribution, and phylogenetic classification. It then reviews the current state of knowledge on the molecular determinants of economically important traits in water buffalo like longevity, disease resistance, milk production, and growth. It finds that while knowledge is available, more data is still needed on these traits through genome sequencing and functional genomics to enable precision breeding and farming. Future research using systems approaches can help advance science and technology for sustainable water buffalo production.
Abstract— An experiment stand of clonal orchard of masson pine, which included the 123 plus trees of 8 provenances collected from 8 provinces of Southern China, was founded at Jingshan County of Hubei province. Randomly amplified polymorphic DNA (RAPD) technique was applied to assess genetic diversity and structure for this clonal seed orchard. Total genomic DNA was extracted from fresh needle tissue with Plant Genomic DNA Extraction Miniprep System made by Viotechnology Corporation The results indicated that the clonal seed orchard of masson pine had higher genetic diversity. The average genetic diversity of the clonal seed orchard was 0.3169, the Shannon’s information index was 0.4813 respectively, and the percentage of polymorphic loci was 71.0%. Observed number of alleles (Na), effective number of alleles (Ne), Nei’s gene diversity (H), Shannon’s information index (I) and percentage of polymorphic loci (P) within population of Jiangxi, Hunan and Zhejiang were bigger than those of Guangdong, Guangxi, Anhui and Sichuan. Genetic distances among 8 populations were range from 0.0225 to 0.2175, whereas genetic identities were range from 0.8045 to 0.9777. 8 populations were clustered into 7 clusters, which showed that populations with similar latitude were clustered together and the clustering had nothing to do with geographic distributing. There was not significant correlation between genetic distance and geographic distance, while the correlation between genetic distance and latitude was more significant.
The study aimed to evaluate genetic diversity among 40 aromatic rice genotypes from Odisha, India using microsatellite (SSR) marker analysis. Twenty-two of the 24 SSR primer pairs used were found to be polymorphic. A total of 51 alleles were detected across loci, with an average of 2.3 alleles per locus. Four SSR loci showed high levels of polymorphism information content. Cluster analysis grouped the genotypes into two major clusters corresponding to their eco-geographic regions. Several SSR markers were identified that can help distinguish genotypes and aid future breeding programs. The study demonstrated that SSR markers are useful for evaluating genetic diversity and relationships among aromatic rice germplasm.
Among the large mammals of Africa, elephants are probably the worst affected by human activities. Although they have been listed as endangered and protected since 1989, illegal poaching and habitat destruction continue to diminish and isolate remaining populations that are dispersed widely over 37 sub-Saharan African countries. Their populations currently exist in small isolated habitat, and this threatens elephant genetic diversity. Although literature is available on the taxonomy and phylogeny of African elephant, few studies have focused on codon usage on mitochondrial genomes. To analyze nucleotide diversity, selective pressure and demographic history of African elephants, we used the portion of mitochondrial sequences of 102 individuals available in the genome database. Our data indicated a low codon bias index (CBI) and a relatively high effective number of codons (ENC) value in the mitochondrial genome, suggesting that African elephants are less biased in their codon usage preference. The data also support a strong purifying selection in the mitochondrial genome of African elephants. However, few sites are under positive selection in the mitochondrial genome of African elephants, with Loxodonta africana presenting more sites under positive selection compared to L. cyclotis. The present work supports the idea that different evolutionary rate among nucleotide sites in L. africana and L. cyclotis, attributable to differences in the frequency of positive selection and probably different environmental conditions, are the driving forces for the codon usage bias in African elephants. Further studies are needed to investigate the contribution of different subpopulation in the genetic structure and diversity of African elephants.
Detection of Genetic variation in tissue culture clones of date palm using IS...IJSRD
Date palm is a plant having high nutritional value and long life (yielding up to 100 years). Phoenix dactylifera requires 2-5 males for pollination of 100 females’ plant depending up on genetic and environment factors. Therefore paternity variation expected to very low according to PCR based techniques, Even though we have tried to find out genetic variation among tissue culture cloned plant. Tissue culture technique can be used for genetic improvement of date palm. The main purpose of this study was to evaluate the genetic variation in the tissue culture clones of date palm by using ISSR primers among mother and it’s two clones. The plant DNA was extracted and subjected to detection of genetic variation in two groups of date palm using ISSR primers. In this study ISSR primers produced monomorphic bands within group-1 and group-2. Genetic variation in tissue culture clones of date palm was not detecte by UBC primer series.
22. utilization of ssr markers for seed purity testing in popular rice hybridsVishwanath Koti
This document describes a study that used simple sequence repeat (SSR) markers to identify two popular rice hybrids (KRH-2 and DRRH-2) and their parental lines. Thirty-five SSR markers were tested, and six were found to be polymorphic across the hybrids and parents, allowing unique fingerprints for each hybrid. Five markers (RM 206, RM 276, RM 204, RM 234 and RM 228) differentiated the two hybrids. Analysis of parental lines found residual heterozygosity at two loci, highlighting the importance of SSR markers for maintaining genetic purity. A 20x20 grow-out matrix trial validated that the identified SSR markers effectively detected contaminants in commercial seed lots, comparable to
Peluang gen rbcL sebagai DNA barcode berbasis DNA kloroplas untuk mengungkap ...AbdulBasith222525
Black rice (Oryza sativa L.) is one of germ plasm where there are many found in Indonesia. The popularity of black rice growing in line with public awareness for consuming a functional food. But the scientific study of black rice germ plasm in Indonesia still classified as low, especially the scientific study of the molecular genetik diversity. Information of molecular genetik diversity adequately on black rice germ plasm is one of the cornerstone for the development of action strategies for conservation the varieties of black rice in Indonesia in a sustainable way. The scientific study which is expected to be implemented in the form of research on black rice molecular genetic diversity is an approach of DNA barcode. Most of the genes that utilized as DNA barcode on plants is on chloroplasts DNA (cpDNA). cpDNA having the benefit characteristics for genetic diversity study compared with nuclei DNA (nDNA) and mitochondria mtDNA. Characteristic of these is (1) the cpDNA genome have a small size and stable structure, (2) More conservative with lower average nucleotide substitution and (3) no recombination and uniparental heritable. This article discussed a potential DNA sequences of nucleotides from chloroplast DNA to give information on the genetic diversity of black rice, namely rbcL gene. Until now, NCBI database collected 143 partial sequence of rbcL gene. The number of partial sequence that has been collected is using as comparation facilitate to investigation the genetic diversity of Indonesia black rice. In the future, DNA barcodes expected to be implemented in the research.
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Drought (midseason or terminal)is a regular and recurring event in arid and semi-arid land, affected by approximately 30% of the world total area and are in habited by 20% of the total world population. The reduction in crop production and yield caused by drought has direct effecton livelihood of farmers(and their families)that inturn affects the yield from livestock (draft capacity/milching).Sorghum is a dual purpose drought resilient crop cultivated in Africa and Asia.
Inter Simple Sequence Repeats (ISSR) markers were utilized to identify the levels of heritable varieties and patterns of the populace structure among the five populaces of Pteris biaurita, a natural fern in India. A comprehensive examination was directed in three replicates at 2013-14 seasons in the Western Ghats, South India. Five wild P. biaurita, accessions (maiden hair) were assessed for genotyping studies. Results demonstrated a pivotal discrepancy among genotypes for they were characterized in view of this uniqueness in four groups by the genetic cluster examination. In this trial, ISSR primers amplified 63 polymorphic groups. In view of the genetic identity data, genotypes were figured and differed from 0.5714 to 0.6984. The percentage of polymorphism indicated predominant genotype that may be utilized for the conservation of species. ISSR appeared to be an obliging marker for prediction of genotype inside a closed group of inter specific populace in the investigation territory.
Inter Simple Sequence Repeats (ISSR) markers were utilized to identify the levels of heritable varieties and patterns of the populace structure among the five populaces of Pteris biaurita, a natural fern in India. A comprehensive examination was directed in three replicates at 2013-14 seasons in the Western Ghats, South India. Five wild P. biaurita, accessions (maiden hair) were assessed for genotyping studies. Results demonstrated a pivotal discrepancy among genotypes for they were characterized in view of this uniqueness in four groups by the genetic cluster examination. In this trial, ISSR primers amplified 63 polymorphic groups. In view of the genetic identity data, genotypes were figured and differed from 0.5714 to 0.6984. The percentage of polymorphism indicated predominant genotype that may be utilized for the conservation of species. ISSR appeared to be an obliging marker for prediction of genotype inside a closed group of inter specific populace in the investigation territory
Molecular Diversity Analysis of Some Local Ginger (Zingiber officinale) Genot...AI Publications
Ginger (Zingiber officinale) rhizomes have been widely used as a spice and flavoring agent in foods and beverages in Bangladesh as well as in all over the world for its economical and medicinal values. The present investigation was undertaken for the assessment of 13 local ginger genotypes collected from different region of Bangladesh through 7 RAPD primers. Genomic DNA was extracted from ginger genotypes using CTAB method. A total of 34 distinct and differential amplification bands ranging from 150-1200 bp were observed with an average of 1.14 polymorphic bands per primer. The overall gene diversity was detected 0.8052 and the value of PIC was detected 0.7532. The RAPD marker generate enough polymorphism for possible use in diversity studies through cluster analysis and principal component analysis (PCA). PCA classified 13 ginger genotypes into four groups and showed in two dimensional scatter plot. The genetic similarity coefficients among genotypes ranged from 0.103 to 0.654. Cluster analysis based on Jaccard’s similarity-coefficient using UPGMA grouped the genotypes into two clusters: Cluster A and Cluster B. The cluster ‘A’ had only one genotype Kaptai local and the second cluster ‘B’ had rest of twelve genotypes. The prevalence level of polymorphism in the local genotypes of ginger will help to breeders for ginger improvement program.
This document describes a DNA marker-based technology developed to identify citrus rootstocks at the seedling stage. Traditionally, Rough lemon and Rangpur lime are preferred rootstocks but are difficult to distinguish from Galgal at an early stage. Galgal is an undesirable rootstock due to susceptibility to diseases. The new technology uses microsatellite markers and PCR to differentiate Rough lemon, Rangpur lime, and Galgal based on presence or absence of DNA fragments. It provides a non-destructive method to ensure nurseries are supplying quality rootstock varieties. The technique has been transferred to agricultural organizations to benefit citrus farmers.
This document describes a study that used molecular methods including PCR and sequencing of the internal transcribed spacer 1 (ITS1) region to analyze the genetic diversity of anaerobic fungi in the gastrointestinal tracts of buffalo. Total DNA was extracted from rumen samples and the ITS1 region was amplified and sequenced. Sequence analysis of 12 clones showed diversity among the anaerobic fungal isolates. The results indicate that analysis of the ITS1 spacer through molecular techniques is a promising approach for comparing rumen fungal populations and diversity.
Genetic variability and phylogenetic relationships studies of Aegilops L. usi...Innspub Net
Studying of genetic relationships among Aegilops L. species is very important for broadening the cultivated wheat genepool, and monitoring genetic erosion, because the genus Aegilops includes the wild relatives of cultivated wheat which contain numerous unique alleles that are absent in modern wheat cultivars and it can contribute to broaden the genetic base of wheat and improve yield, quality and resistance to biotic and abiotic stresses of wheat. The use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant biotechnology and their genetics studies. There are different types of markers, morphological, biochemical and DNA based molecular markers. These DNA-based markers based on PCR (RAPD, AFLP, SSR, ISSR, IRAP), amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Day by day development of such new and specific types of markers makes their importance in understanding the genomic variability and the diversity between the same as well as different species of the plants. In this review, we will discuss about genetic variability and phylogenetic relationships studies of Aegilops L. using some molecular markers, with theirs Advantages, and disadvantages.
Molecular characterization of pea (Pisum sativum L.) using microsatellite mar...IOSR Journals
Nineteen pea (Pisum sativum L.) accessions have been characterized using Simple Sequence Repeats (SSRs). The mains objectives of this study were to examine SSR polymorphism among cultivars and to assess genetic diversity among them. Eight microsatellites, from the Pisum microsatellite consortium (Agrogene ®, France) have been used. Five of the eight SSRs studied gave good electrophoretic profiles and helped us to amplify a number of alleles per locus varying from 3 (PSMPA5 and PSMPA6) to 13 (PSMPSAD126) with a total of 34 and an average number of 6.8 alleles per locus. The Polymorphism Information Content (PIC) varied from 0.18 for PSMPSAD134 to 0.85 for PSMPSAD126, with an average value of 0.62. The five microsatellites analyzed allowed us to separate 18 out of the 19 genotypes studied, and only the two most polymorphic markers (PSMPSAA205 and PSMPSAD126), permit to discriminate among the same genotypes (18) separated using the 5 SSRs. Genetic distances computed have been used to draw the corresponding dendrogram and to distribute genotypes according to their genetic relationship. The genotypes classified within the same group share several agro-morphological characters. Finally, the present study attests that SSR microsatellites are good tools for identifying genotypes and for the assessment of genetic diversity in pea.
This document discusses genetic diversity analysis of grape (Vitis vinifera L.) germplasm in India using microsatellite markers. A total of 42 grape genotypes were analyzed using 7 microsatellite markers. A total of 45 alleles were detected among the genotypes. The microsatellites grouped the genotypes into two main clusters (A and B) based on morphological and genetic characteristics, with subclusters differentiating seeded vs seedless fruits and pigmented vs non-pigmented fruits. The study found high genetic variability among the Indian grape germplasm and that microsatellite markers are a reliable tool for diversity and breeding programs.
Genome wide association studies (GWAS) analysis of karnal bunt resistance in ...Innspub Net
Karnal bunt (KB) disease is one of the most important challenges posed on of wheat (Triticum aestivum L.) industry of Pakistan because of itsinclusionin quarantine list around the globe. This disease is caused by the fungus Tilletia indica M. (Neovossia indica). It affects the grain quality of wheat and hampers its movement in international market resulting in economic losses. Presence of >3% infected grains in wheat lot makes it unsuitable for human consumption. Eradication of this disease is very difficult as no resistant cultivar has been found against KB in Pakistan so far. Genome wide association study (GWAS) was conducted on a set of 199 wheat germplasm collected from Pakistan. In this study 31,000 single nucleotide polymorphism markers were developed by 90K SNP array technology. A linear mixed model in GWAS, accounting for population structure, was fitted to identify significant genomic regions [-log(P) ≥ 4.0] on 6 different chromosomes i.e. 1A, 1D, 2D, 3B, 4A, 5A with novel loci. Candidate genes, through wheat genome assembly, were identified as putative genes related to KB resistance including kinase like protein family. The results of this study can be useful in wheat breeding through marker assisted selection for KB resistant varieties.
This document describes the CarrAgheen Molecular Marker Database (CaMM-Db), a comprehensive database of molecular markers for the red seaweed Chondrus crispus (carragheen). The database contains over 18,000 microsatellites and 12,000 SNPs identified from carragheen genomic sequences. CaMM-Db provides information on different microsatellite types and properties. It also integrates with primer design software to facilitate wet lab experiments. As the first database of its kind for carragheen, CaMM-Db is expected to be a valuable resource for genetic research on carragheen and other red seaweeds.
The document discusses molecular biology research on the fungus Monascus spp. It provides details on:
1) Molecular markers that have been used to classify Monascus spp., including RAPD, D1/D2 regions of LSU rRNA, ITS, IGS, ISSR, and SRAP. These markers revealed genetic diversity and grouped species.
2) Genetic transformation techniques for Monascus spp., such as protoplast transformation, electroporation, bombardment, REMI, and ATMT. Protoplast transformation was successfully used to create mitotically stable transformants of M. aurantiacus and M. purpureus.
3) Cloning of some genes from Mon
The document discusses three case studies related to genetic divergence and bioactive compounds in chickpea (Cicer arietinum L.):
1. The first case study evaluated 100 chickpea genotypes and found significant genetic diversity between clusters. Days to flowering, 100 seed weight, number of seeds per plant, and plant height contributed most to diversity. Six genotypes were identified for hybridization.
2. The second case study used principal component analysis on 434 chickpea genotypes evaluated for 13 traits. Eight components captured 77.68% of variation, with days to flowering and seed yield contributing most. Five genotypes performed well across components.
3. The third case study analyzed correlations and path coefficients in chickpe
This research note describes the development of 17 microsatellite loci for two species of flat periwinkles, Littorina fabalis and L. obtusata. The microsatellites were isolated from L. fabalis using next-generation sequencing and tested on individuals of both species. Seventeen loci were found to reliably amplify in both species. These new nuclear markers can be used to study species discrimination between L. fabalis and L. obtusata, investigate hybridization, and characterize divergence between L. fabalis ecotypes. The microsatellites provide a genetic tool to overcome limitations of morphological identification.
This document summarizes a review on the potential of water buffalo in world agriculture. It discusses water buffalo's role in agriculture, their global population distribution, and phylogenetic classification. It then reviews the current state of knowledge on the molecular determinants of economically important traits in water buffalo like longevity, disease resistance, milk production, and growth. It finds that while knowledge is available, more data is still needed on these traits through genome sequencing and functional genomics to enable precision breeding and farming. Future research using systems approaches can help advance science and technology for sustainable water buffalo production.
Abstract— An experiment stand of clonal orchard of masson pine, which included the 123 plus trees of 8 provenances collected from 8 provinces of Southern China, was founded at Jingshan County of Hubei province. Randomly amplified polymorphic DNA (RAPD) technique was applied to assess genetic diversity and structure for this clonal seed orchard. Total genomic DNA was extracted from fresh needle tissue with Plant Genomic DNA Extraction Miniprep System made by Viotechnology Corporation The results indicated that the clonal seed orchard of masson pine had higher genetic diversity. The average genetic diversity of the clonal seed orchard was 0.3169, the Shannon’s information index was 0.4813 respectively, and the percentage of polymorphic loci was 71.0%. Observed number of alleles (Na), effective number of alleles (Ne), Nei’s gene diversity (H), Shannon’s information index (I) and percentage of polymorphic loci (P) within population of Jiangxi, Hunan and Zhejiang were bigger than those of Guangdong, Guangxi, Anhui and Sichuan. Genetic distances among 8 populations were range from 0.0225 to 0.2175, whereas genetic identities were range from 0.8045 to 0.9777. 8 populations were clustered into 7 clusters, which showed that populations with similar latitude were clustered together and the clustering had nothing to do with geographic distributing. There was not significant correlation between genetic distance and geographic distance, while the correlation between genetic distance and latitude was more significant.
The study aimed to evaluate genetic diversity among 40 aromatic rice genotypes from Odisha, India using microsatellite (SSR) marker analysis. Twenty-two of the 24 SSR primer pairs used were found to be polymorphic. A total of 51 alleles were detected across loci, with an average of 2.3 alleles per locus. Four SSR loci showed high levels of polymorphism information content. Cluster analysis grouped the genotypes into two major clusters corresponding to their eco-geographic regions. Several SSR markers were identified that can help distinguish genotypes and aid future breeding programs. The study demonstrated that SSR markers are useful for evaluating genetic diversity and relationships among aromatic rice germplasm.
Among the large mammals of Africa, elephants are probably the worst affected by human activities. Although they have been listed as endangered and protected since 1989, illegal poaching and habitat destruction continue to diminish and isolate remaining populations that are dispersed widely over 37 sub-Saharan African countries. Their populations currently exist in small isolated habitat, and this threatens elephant genetic diversity. Although literature is available on the taxonomy and phylogeny of African elephant, few studies have focused on codon usage on mitochondrial genomes. To analyze nucleotide diversity, selective pressure and demographic history of African elephants, we used the portion of mitochondrial sequences of 102 individuals available in the genome database. Our data indicated a low codon bias index (CBI) and a relatively high effective number of codons (ENC) value in the mitochondrial genome, suggesting that African elephants are less biased in their codon usage preference. The data also support a strong purifying selection in the mitochondrial genome of African elephants. However, few sites are under positive selection in the mitochondrial genome of African elephants, with Loxodonta africana presenting more sites under positive selection compared to L. cyclotis. The present work supports the idea that different evolutionary rate among nucleotide sites in L. africana and L. cyclotis, attributable to differences in the frequency of positive selection and probably different environmental conditions, are the driving forces for the codon usage bias in African elephants. Further studies are needed to investigate the contribution of different subpopulation in the genetic structure and diversity of African elephants.
Detection of Genetic variation in tissue culture clones of date palm using IS...IJSRD
Date palm is a plant having high nutritional value and long life (yielding up to 100 years). Phoenix dactylifera requires 2-5 males for pollination of 100 females’ plant depending up on genetic and environment factors. Therefore paternity variation expected to very low according to PCR based techniques, Even though we have tried to find out genetic variation among tissue culture cloned plant. Tissue culture technique can be used for genetic improvement of date palm. The main purpose of this study was to evaluate the genetic variation in the tissue culture clones of date palm by using ISSR primers among mother and it’s two clones. The plant DNA was extracted and subjected to detection of genetic variation in two groups of date palm using ISSR primers. In this study ISSR primers produced monomorphic bands within group-1 and group-2. Genetic variation in tissue culture clones of date palm was not detecte by UBC primer series.
22. utilization of ssr markers for seed purity testing in popular rice hybridsVishwanath Koti
This document describes a study that used simple sequence repeat (SSR) markers to identify two popular rice hybrids (KRH-2 and DRRH-2) and their parental lines. Thirty-five SSR markers were tested, and six were found to be polymorphic across the hybrids and parents, allowing unique fingerprints for each hybrid. Five markers (RM 206, RM 276, RM 204, RM 234 and RM 228) differentiated the two hybrids. Analysis of parental lines found residual heterozygosity at two loci, highlighting the importance of SSR markers for maintaining genetic purity. A 20x20 grow-out matrix trial validated that the identified SSR markers effectively detected contaminants in commercial seed lots, comparable to
Similar to Genetic profile of local buffalo (Bubalus bubalis) populations in Pacitan and Tuban, East Java, Indonesia measured by the molecular marker of INRA032 locus (20)
Peluang gen rbcL sebagai DNA barcode berbasis DNA kloroplas untuk mengungkap ...AbdulBasith222525
Black rice (Oryza sativa L.) is one of germ plasm where there are many found in Indonesia. The popularity of black rice growing in line with public awareness for consuming a functional food. But the scientific study of black rice germ plasm in Indonesia still classified as low, especially the scientific study of the molecular genetik diversity. Information of molecular genetik diversity adequately on black rice germ plasm is one of the cornerstone for the development of action strategies for conservation the varieties of black rice in Indonesia in a sustainable way. The scientific study which is expected to be implemented in the form of research on black rice molecular genetic diversity is an approach of DNA barcode. Most of the genes that utilized as DNA barcode on plants is on chloroplasts DNA (cpDNA). cpDNA having the benefit characteristics for genetic diversity study compared with nuclei DNA (nDNA) and mitochondria mtDNA. Characteristic of these is (1) the cpDNA genome have a small size and stable structure, (2) More conservative with lower average nucleotide substitution and (3) no recombination and uniparental heritable. This article discussed a potential DNA sequences of nucleotides from chloroplast DNA to give information on the genetic diversity of black rice, namely rbcL gene. Until now, NCBI database collected 143 partial sequence of rbcL gene. The number of partial sequence that has been collected is using as comparation facilitate to investigation the genetic diversity of Indonesia black rice. In the future, DNA barcodes expected to be implemented in the research.
Genetic diversity analysis and phylogenetic reconstruction of groupers Epinep...AbdulBasith222525
Basith A, Abinawanto A, Kusrini E, & Yasman Y. 2021. Biodiversitas, 22(10):4282-4290. DOI: 10.13057/biodiv/d221020
ABSTRACT. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (π). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and π=0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.
DNA barcode characterization of chocolate hind grouper (Cephalopholis boenak)...AbdulBasith222525
Basith A, Abinawanto A, Kusrini E, & Yasman Y. 2022. DNA barcode characterization of chocolate hind grouper (Cephalopholis boenak) in several Indonesia waters with the new squences record from Madura Island. HAYATI Journal of Bioscences, 29(6):733-741.
ABSTRACT. This study aims to describe the molecular characteristics of DNA barcodes in chocolate hind grouper (Cephalopholis boenak) in Indonesian waters with new sequence records from Madura Island waters. Partial sequences of the cytochrome c oxidase 1 (CO1) gene were successfully obtained from two samples of C. boenak in Madura Island waters. In contrast, the other sequences were obtained from the BOLD system database, covering the Islands of Bali, Lombok, and Ambon waters. The overall molecular analysis involved 10 C. boenak sequences with a length of 625 bp. The results indicated that the population of C. boenak in Indonesia waters has high genetic diversity, as evidenced by the value of haplotype diversity (Hd) = 0.956 and nucleotide sequence diversity (Pi) = 0.01746, in which the population is distributed into eight haplotypes. Results of phylogenetic tree reconstruction of neighbor-joining and maximum-likelihood indicate similar topology. The branching of NJ and ML phylogenetic trees of C. boenak in Indonesia waters is grouped into two geographical clades. Clade 1 with the subpopulations of the waters from Madura, Bali, and Lombok Islands. Clade 2 with the subpopulations of the waters from Ambon Island. The results of the median-joining network reconstruction depicted a similar topology with both phylogenetic trees.
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Prosiding seminar nasional MIPA membahas peran ilmu-ilmu MIPA dalam pengembangan teknologi dan pendidikan untuk membangun bangsa yang mandiri. Seminar ini diselenggarakan pada tanggal 13 November 2010 oleh Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Negeri Malang.
Kajian keragaman morfologi, autentikasi molekuler, perkiraan waktu divergensi, dan struktur genetik populasi ikan kerapu (famili Serranidae) dari kawasan perairan Pulau Madura, Jawa Timur, Indonesia
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
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collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
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the last few Gyr, consistent with the body of work surrounding the VRM.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
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Exposé invité Journées Nationales du GDR GPL 2024
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Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
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Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
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https://www.etran.rs/2024/en/home-english/
Genetic profile of local buffalo (Bubalus bubalis) populations in Pacitan and Tuban, East Java, Indonesia measured by the molecular marker of INRA032 locus
1. Jurnal Riset Biologi dan Aplikasinya, Volume 5, Issue 1, March 2023
Genetic profile of local buffalo (Bubalus bubalis) populations in Pacitan and
Tuban, East Java, Indonesia measured by the molecular marker of INRA032 locus
Laily Isnaini Rahmawati1
, Abdul Basith2,4*
, Fitria Lestari3
1SMPN 27 Kota Malang, Jln. Lesanpuro No.24b, Lesanpuro, Kedungkandang District, Malang City, East Java 65138
2Study Program of Biology Education, University of KH. Abdul Wahab Hasbulloh, Jln. Garuda No.9, Tambak Rejo, Jombang
District, Jombang Regency, East Java 61419
3Study Program of Biology Education, University of PGRI Silampari, Jln. Mayor Toha, Air Kuti, Lubuk Linggau Timur I
District, Lubuklinggau City, South Sumatera 31625
4Indonesia Genetic and Biodiversity Community, Jln. Ikan Mujair 1, Lowokwaru District, Malang City, East Java
*Corresponding Author:
e-mail: golden_bee46@yahoo.com
Article History ABSTRACT
Received : 19 December 2022 The genetic profile of buffaloes is important information to support their breeding
efforts, therefore the assessment of genetic profile needs to be carried out
continuously. This study aimed to analyze the application of microsatellite marker
at the INRA032 locus for genetic profile assessment in buffalo (Bubalus bubalis)
populations in Pacitan and Tuban Regencies, East Java, Indonesia. The total
number of samples used was 16, with each population represented by 8 samples.
Genetic profile assessment parameters include allele frequency, the Polymorphism
Information Content (PIC), and heterozygosity. The results showed that based on
the INRA032 locus, the Tuban buffalo population had a higher allele frequency
range (0.08 to 0.33) than the Pacitan population (0.18 to 0.31). The average PIC
value in both populations was 0.39, so it can be concluded that the INRA032 locus
is informative enough to detect polymorphisms in both populations. The
percentage heterozygosity of the Pacitan buffalo population is 88%, which is higher
than the Tuban population at 50%, suggesting that the genetic diversity of the two
populations is still quite high despite the decreasing trend in population numbers.
The INRA032 locus was shown to be moderately effective for assessing genetic
profile in local buffaloes, but its application in future studies will require an
increase in the number of samples representing the population and the addition of
other microsatellite markers to obtain a more accurate conclusion.
Revised : 4 February 2023
Approved : 12 March 2023
Published : 31 March 2023
Keywords
genetic diversity, heterozygosity,
microsatellites, Polymorphism
Information Content
How to cite: Rahmawati, R.I., Basith, A., & Lestari, F. (2023). Genetic profile of local buffalo (Bubalus bubalis) populations
in Pacitan and Tuban, East Java, Indonesia measured by the molecular marker of INRA032 locus. Jurnal Riset Biologi dan
Aplikasinya, 5(1):37-42. DOI: 10.26740/jrba. v5n1.p.37-42.
INTRODUCTION
The need for animal protein consumption is
increasing along with the human population size of
Indonesia, and one of the sources of animal protein
is a large ruminants. One of the large ruminants
that are the main source of animal protein in
Indonesia is buffalo (Bubalus bubalis) (Gunawan &
Romjali, 2009; Komariah et al. 2018; Nuraini et al.
2018). The number of buffaloes in East Java
Province in 2017-2021 has gradually decreased, to
26.622, 24.364, 23994, 22.975, and 22.970,
respectively. The number of buffaloes in East Java
is very small compared to the number of buffaloes in
West Java and Central Java Provinces (Director
General of Livestock and Animal Health, 2021). In
more detail, from 2014 to 2017, the average number
of buffaloes in Pacitan was only 117, while the
average number of buffaloes in Tuban was 1.695
(BPS-statistics of East Java, 2018).
In general, buffaloes are kept by farmers in
rural areas, with an average of 1 to 2 buffalo per
farmer. The decline in buffalo population is due to
various factors, such as limited stock of high-quality
brooders, low quality feed, inbreeding, and despite
farmers have a lot of local wisdom on production
and reproduction, they seem unable to handle large
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2. Jurnal Riset Biologi dan Aplikasinya, 5(1): 27-36, March 2023 | 38
herds of buffalo. The relatively low reproduction
rate may be due to more difficult detection of the
estrous phase in buffaloes with a longer gestation
period compared to cattle (Gunawan & Romjali,
2009). The decline in buffalo population is
associated with an increased in the probability of
negative impacts due to inbreeding. According to
data from BPS-statistics of East Java (2018), the
buffalo population in Pacitan has a higher potential
for inbreeding compared to the Tuban population
because of its smaller population. Based on these
problems, assessments of the buffalo genetic profile
should be conducted regularly, for example by using
the molecular markers of microsatellite.
Microsatellites or short tandem repeats (STRs)
are the most polymorphic DNA molecular markers
and have a high abundance in eukaryotic genomes.
Microsatellites are di-, tri-, or tetra nucleotide of
DNA tandem repeats presented in variable copy
numbers at each locus and throughout the genome.
Microsatellites are one of the popular molecular
markers used to estimate genetic diversity in
livestock. The development of microsatellite
markers in genetics and biotechnology increases
opportunities for livestock selection, health
improvement, and production (Brenig & Schütz,
2016; Viryanski, 2019).
One of the microsatellite markers that has been
widely used in the assessment of genetic diversity in
buffalo populations is the INRA032 locus which is
located on chromosome 11 (Vaiman et al., 1994).
Not only in buffalo, the use of the INRA032 locus in
microsatellite-based genetic diversity assessments
has also been applied to dairy cattle and horses
(Vanessa et al. 2018; Sukri et al. 2022). Several
previous researches have used the INRA032 locus
in microsatellite-based genetic diversity assessment
of buffaloes in Indonesia, specifically in Kudus
(Central Java), East Java, and West Nusa Tenggara
populations (Sukri, 2014; Amin & Lestari, 2014;
Lathifah, 2016). Complementing previous studies,
the investigation of the effectiveness of the
INRA032 locus for genetic profile assessment in
this study focused on local buffalo populations in
Pacitan and Tuban Regencies, East Java.
MATERIALS AND METHODS
The total number of buffalo samples in this
study was 16, obtained through purposive random
sampling, with 8 representing the Pacitan
population and 8 representing the Tuban
population. Samples were obtained from local
farmers in Pacitan and Tuban Regencies. Blood
samples were collected through the jugular vein on
the neck of the buffalo using a venojack and
preserved in EDTA solution and then stored in an
ice box until DNA isolation. Furthermore, DNA
was isolated from blood using the standard
protocols of SDS/proteinase K and
phenol/chloroform method (Sambrook et al. 1989).
The sequence of microsatellite primer pairs of
INRA032 locus, referring to Vaiman et al. (1994) is
presented in Table 1.
Table 1. Primer sequences of INRA032 locus
Primer
position
Primer sequences (5’-3’)
Annealing
temperature
Forward AAACTGTATTCTCTAATAGCAC 57 °C
Reverse GCAAGACATATCTCCATTCCTTT
The DNA amplification process through
Polymerase Chain Reaction (PCR) was composed of
a reaction mixture of 2.5 µl of DNA template
(10mg/µl), 12.5 µl of PCR mix (dNTP, buffer, Taq-
polymerase, H2O), 2.5 µl of dH2O, 2.5 µl of forward
primer, and 2.5 µl of reverse primer. The PCR
process was done for 30 cycles with the following
steps: predenaturation at 95 °C for 2 minutes,
denaturation at 92 °C for 1 minute, annealing at 57
°C for 1 minute, first elongation at 72 °C for 1-
minute, final elongation at 72 °C for 10 minutes,
and the last step at a temperature ranging from 4
°C.
After PCR, DNA separation was carried out
using 10% of Polyacrylamide Gel Electrophoresis
(PAGE), followed by silver staining and
electrophoresis at 135 volts with duration of 60
minutes. Electrophoresis results were documented
in the form of images and analyzed manually with
the help of GelAnalyzer software version 19.1
(www.gelanalyzer.com) by Istvan Lazar Jr., PhD,
and Istvan Lazar Sr., PhD, CSc, to increase the
accuracy of allele observations. All alleles that
appeared were recorded according to size, and then
based on the allele size, allele frequency,
heterozygosity, and polymorphic information
content (PIC), they were calculated using GENPOP
software version 3.1 (Liu et al., 2000).
RESULTS AND DISCUSSION
The maintenance of genetic diversity is a vital
and critical goal in livestock conservation programs
so that livestock populations can adapt to future
environmental challenges and respond to long-term
selection, both natural and engineered, for certain
traits of interest that are important to the economy
3. 39
and culture. According to Putman & Carbone
(2014) the use of highly variable molecular genetic
markers, such as microsatellite, is one of the most
potential ways to assess the genetic diversity due to
their high level of polymorphism, abundance,
random distribution across the genome, co-
dominant inheritance, and neutrality with respect to
selection.
The possibility of detecting polymorphisms is
very important when choosing a molecular marker.
If a molecular marker is unable to detect genetic
differences that exist within a group of individuals,
it is considered ineffective. A molecular marker is
considered polymorphic if it has at least two alleles
and the most frequent allele has a frequency of up to
99% (Shete et al., 2000; Serrote et al., 2020). The
result of this study shows that the INRA032 locus
is moderately effective in detecting polymorphism
between individuals in Pacitan and Tuban buffalo
populations.
Allele frequency is the proportion or ratio of all
gene copies that comprise a particular gene variant.
In other words, allele frequency is the number of
copies of a particular allele divided by the total
number of copies of alleles at a locus in a population.
Allele frequency can be presented as a percentage
(Gillespie, 2004). According to the number of allele
sizes at the INRA032 locus in the two buffalo
populations, the frequency of alleles at the
INRA032 locus in each population was calculated.
The allele frequency of the INRA032 locus in the
Pacitan buffalo population was between 0.18 and
0.31, while in the Tuban buffalo population the
allele frequency was between 0.08 and 0.33. Thus, it
was known that the allele frequency range of the
INRA032 locus in the Tuban buffalo population is
higher than that in the Pacitan population. The
results of the allele frequency analysis of the Pacitan
and Tuban buffalo populations are presented in
Table 2 below. While allele frequencies at the
INRA032 locus in buffalo populations in Kudus
Regency (Central Java) ranged from 0.08 to 0.591,
South Sumatra populations ranged from 0.06 to
0.75, Tana Toraja Regency (South Sulawesi)
populations range from 0.36 to 0.64, and Lombok
(West Nusa Tenggara) populations range from 0.38
to 0.63 (Lestari, 2013; Afrida et al., 2014; Lathifah,
2016). This indicates that the INRA032 locus has
variable allele frequencies, which will be important
preliminary information for the detection of
intrapopulation genetic diversity in buffalo.
Table 2. Allele frequencies of INRA032 locus in
Pacitan and Tuban buffalo populations
Allele size
(base pair)
Populations
Pacitan (%) Tuban (%)
100
110
180
220
230
300
0.31
0.00
0.25
0.18
0.25
0.00
0.16
0.16
0.33
0.25
0.00
0.08
The PIC value indicated that the molecular
marker used was capable of detecting
polymorphisms among individuals in a population,
and the higher that capacity, the greater the value.
PIC values for co-dominant molecular markers
ranged from 0 (monomorphic) to 1 (highly
informative, with multiple alleles of equal
frequency) (Serrote et al. 2020). The PIC values of
the Pacitan and Tuban buffalo populations in this
research are presented in Table 3. Following the
criteria of Botstein et al. (1980), the microsatellite
marker INRA032 locus observed in the study was
highly informative in the Tuban buffalo population
(PIC > 0.5) and less informative (PIC < 0.25) in the
Pacitan population. The mean value of 0.39 for PIC
indicated that the INRA032 locus was moderately
informative (0.25 < PIC < 0.5) for both populations.
Furthermore, higher PIC values indicated the
usefulness of this molecular marker in the
assessment of genetic diversity in a population
(MacHugh et al., 1997) as well as genome mapping
studies (Kayang et al., 2002). For comparison, the
average PIC value of the INRA 032 locus in the
buffalo population in Kudus Regency (Central Java)
is 0.42, the South Sumatra population is 0.41, in the
Tana Toraja Regency population (South Sulawesi)
is 0.35, in the Lombok population (West Nusa
Tenggara) is 0.34, and in the Yogyakarta,
population is 0.29 (Afrida et al. 2014; Limiansi,
2015; Lathifah, 2016). This indicates that the
INRA032 locus is moderately informative for the
detection of genetic diversity in buffalo populations
in different regions of Indonesia. Nevertheless,
based on the analysis, it is recommended to increase
the number of samples and add other microsatellite
markers to ensure the accuracy of the PIC values.
Table 3. Polymorphism information content (PIC)
values in Pacitan and Tuban buffalo populations
Populations
Average
Pacitan Tuban
0.12 0.66 0.39
4. Jurnal Riset Biologi dan Aplikasinya, 5(1): 27-36, March 2023 | 40
Heterozygosity is the probability of an
individual being heterozygous at the location where
the molecular marker is used and depends on the
number of alleles and their frequency in the
population. Heterozygosity values range from 0 (no
heterozygosity) to 1 (high number of alleles with
equal frequency) (Serrote et al. 2020). The
calculated allele frequency values of the INRA032
locus were used to calculate the expected
heterozygosity values, while the observed
heterozygosity values were also obtained from the
observation of heterozygous individuals. The
results of the calculation of heterozygosity values
(observed heterozygosity and expected
heterozygosity) at the INRA032 locus for both
populations are presented in Table 4 below.
Table 4. Heterozygosity of INRA032 locus in Pacitan
and Tuban buffalo populations
Pacitan
(%)
Tuban (%)
Ho He Ho He
88 15.7 50 23.4
Notes: Ho = observed heterozygosity, He = expected
heterozygosity
If observed heterozygosity (Ho) is higher than
expected heterozygosity (He), it indicates that there
is no deviation from Hardy-Weinberg equilibrium
and low probability of inbreeding (Sharma et al.
2016). In both buffalo populations in this research,
Ho value was higher than He value, indicating no
deviation from Hardy-Weinberg equilibrium and
low probability of inbreeding. Interestingly, the Ho
to He value for the Pacitan buffalo population was
higher than the Tuban population, even though the
Pacitan population is much lower than Tuban
population. According to BPS-statistics of East Java
(2018), from 2014 to 2017, the average number of
buffaloes in Pacitan was only 117, while the average
number of buffaloes in Tuban was 1695. Based on
this population size, Pacitan buffalo population has
higher potential for inbreeding compared to Tuban
population, and therefore the heterozygosity of
Pacitan population should be lower than Tuban. In
fact, Tuban is geographically more accessible than
Pacitan, which should increase the potential for
outbreeding in the Tuban buffalo population,
resulting in higher heterozygosity than Pacitan.
The results of this study are in line with the results
of Amin (2012), Afrida et al. (2014), and Lathifah
(2016), which showed that the application of the
INRA032 locus in buffalo populations of Kudus
Regency (Central Java), Tana Toraja Regency
(South Sulawesi), and Lombok (West Nusa
Tenggara) also had higher Ho values than He.
Heterozygosity results in population genetics
research are an important and essential part.
However, homozygosity is not expected. According
to Sharma et al. (2016) if homozygotes are present
in a population, various factors can contribute to the
occurrence of excess homozygotes. First, the
observed locus is under selection. Second, there may
be "null alleles" that lead to incorrect observations
of excess homozygotes. Third, inbreeding may be
common in the observed population. The likelihood
of each of these explanations should be assessed
from extra data, such as demographic information
and population distribution. "Null alleles" are
unlikely to completely segregate the locus. Another
possibility of the high heterozygosity in the Pacitan
and Tuban buffalo populations is the considerable
knowledge of local farmers in the mating
management of their buffalo herds. Hale et al.
(2012) suggest that to improve the accuracy of
microsatellite-based genetic studies, a sample size of
25 to 30 samples per population is required. In line
with this suggestion, we also recommend this
sample size to improve the quality of our future
studies.
Information on allelic variation in
microsatellite DNA indicating genetic diversity in
buffalo is expected to be used as a reference for
determining the genetic quality of buffalo through
the provision of breeding stock for outbreeding
programs or to reduce the effects of inbreeding, so
that genetic quality can be maintained or improved
(Amin & Lestari, 2014). The combination of the
INRA032 locus with other microsatellite loci will
improve the quality of information on the genetic
diversity of local buffalo, thereby increasing the
accuracy of decision-making regarding conservation
measures. In addition, based on previous studies, it
was also explained that the INRA032 locus is
associated with reproductive characteristics (calving
traits) and body conformation (hocks, rear leg set,
rear view) in dairy cattle (Harder et al. 2006;
Buitenhuis et al. 2007; Vanessa et al. 2018).
Therefore, future research needs to investigate the
relationship between the INRA032 locus and other
microsatellite markers to morphological characters
associated with superior traits in local buffaloes in
Indonesia.
CONCLUSION
In general, the INRA032 locus is suitable for
assessing the genetic profile of Pacitan and Tuban
5. 41
buffalo populations in East Java. The number of
alleles at the INRA032 locus in the Pacitan buffalo
population is less than that in the Tuban population.
This was also the same result for the Polymorphism
Information Content (PIC) value of the Pacitan
buffalo population, which was lower than that of the
Tuban population. However, the average PIC value
(0.39) indicated that the INRA032 locus was
moderately informative for the assessment of
genetic diversity in both populations. The
percentage heterozygosity of the Pacitan population
(88%) was higher than that of the Tuban population
(50%), even though the Pacitan population is
smaller than Tuban population. Various factors may
influence the difference in heterozygosity between
the two populations including artificial insemination
program. Future studies need to increase the
number of samples and other microsatellite markers
to improve the accuracy of local buffalo genetic
profile information.
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