Genome Sequencing in Finger Millet
Genome size estimation
SOLiD Sequencing Technology
Illumina Sequencing Technology
Gene prediction and functional annotation of genes
Mining of plant transcription factors and other genes
Zinc finger nucleases (ZFNs) are engineered restriction enzymes
designed to target specific DNA sequences within the genome.
Assembly of zinc finger DNAbinding domain to a DNA-cleavage
domain.
Gene editing application for cancer therapeuticsNur Farrah Dini
The application of TALENs as one of the gene editing tools in order to modify a specific targeted sites on a genome. This method shows a tremendous benefits especially in cancer research.
Role of molecular marker play a significant supplementary role in enhancing yield along with conventional plant breeding methods. the result obtain through molecular method are more accurate and at genotypic level. It had wider applications in field of plant breeding, biotechnology, physiology, pathology, entamology, etc. The mapping information obtained from these markers had created a revolution in the sequencing sector and open many pathways for developments, innovations and research.
A concise and well fabricated presentation the current techniques used for plant genome editing including CRISPER/cas9 system, TALENS, TELES, ZINC FINGER NUCLEASES(ZFN), HEJ (homologous endjoing) and many other high throughout techniques along references.
Zinc finger nucleases (ZFNs) are engineered restriction enzymes
designed to target specific DNA sequences within the genome.
Assembly of zinc finger DNAbinding domain to a DNA-cleavage
domain.
Gene editing application for cancer therapeuticsNur Farrah Dini
The application of TALENs as one of the gene editing tools in order to modify a specific targeted sites on a genome. This method shows a tremendous benefits especially in cancer research.
Role of molecular marker play a significant supplementary role in enhancing yield along with conventional plant breeding methods. the result obtain through molecular method are more accurate and at genotypic level. It had wider applications in field of plant breeding, biotechnology, physiology, pathology, entamology, etc. The mapping information obtained from these markers had created a revolution in the sequencing sector and open many pathways for developments, innovations and research.
A concise and well fabricated presentation the current techniques used for plant genome editing including CRISPER/cas9 system, TALENS, TELES, ZINC FINGER NUCLEASES(ZFN), HEJ (homologous endjoing) and many other high throughout techniques along references.
Genome editing tools form the basis for personalized medicine, especially for therapies requiring change in genome. Currently there are four contenders to this – Meganucleases, ZNF Nucleases, TALENs and CRISPRs. Although, the technologies are many, there are very few commercial providers of this technology. This is attributed to the fact that select few possess the intellectual property rights of turning these technologies to valid form of therapy; for example, ZFN patent with Sangamo BioSciences and TALENs with Cellectis, Transposagen and Life Technologies.
Advanced Genome Engineering Services and Transgenic Model Generation
at MSU’s Transgenic and Genome Editing Facility
Huirong Xie, Elena Demireva, Nate Kauffman, Richard Neubig
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)Akshay Deshmukh
clustered regularly interspaced short palindromic repeats is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria. Now CRISPR use as genome editing tool in different Plant Breeder to manipulate the DNA of the crop
To modifying the structure of a specific gene.
Gene targeting vector introduced into the cell.
Vector modifies the normal chromosomal gene through homologous recombination.
Useful in treating some human genetic disorders – Hemophilia, Duchenne Muscular Dystrophy.
Treating human diseases by genetic approaches – Gene Therapy.
Gene Therapy – Replacing the defective gene by normal copy of the gene.
Expressed sequence tag/EST is a short partial sequence, typically 200-400 bp long, of a complimentary DNA/Cdna.
EST is a short sub-sequence of a cDNA sequence.
Used to identify gene transcripts, and are instrumental in gene discovery and in gene-sequence determination.
Approximately 74.2 million ESTs are available in public databases.
EST results from one-short sequencing of a cloned cDNA.
Low-quality fragments.
Length is approximately 500 to 800 nucleotides.
Genome Editing Techniques by Kainat RamzanKainatRamzan3
Genome technology has revolutionized biological science through techniques of Gene Editing in order to edit any organism's genome.MegNs and zinc-finger nucleases are commonly understood to be used, as is the effector's transcriptional activator-like nucleases. In CRISPR/Cas9, genetic alterations, and gene functionality have become a well-known tool for understanding gene targeting.
Genome editing is a method of making specific changes to the DNA of a cell or organism. An enzyme scissors the DNA at a specific sequence, and when this is repaired by the cell, a change or ‘edit’ is made to the sequence.
https://www.creative-biolabs.com/gene-therapy/approaches-to-genome-editing.htm
Feature story from the Garvan Institute of Medical Research's April 2013 issue of Breakthrough newsletter. More at https://www.garvan.org.au/news-events/newsletters
Genome editing tools form the basis for personalized medicine, especially for therapies requiring change in genome. Currently there are four contenders to this – Meganucleases, ZNF Nucleases, TALENs and CRISPRs. Although, the technologies are many, there are very few commercial providers of this technology. This is attributed to the fact that select few possess the intellectual property rights of turning these technologies to valid form of therapy; for example, ZFN patent with Sangamo BioSciences and TALENs with Cellectis, Transposagen and Life Technologies.
Advanced Genome Engineering Services and Transgenic Model Generation
at MSU’s Transgenic and Genome Editing Facility
Huirong Xie, Elena Demireva, Nate Kauffman, Richard Neubig
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)Akshay Deshmukh
clustered regularly interspaced short palindromic repeats is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria. Now CRISPR use as genome editing tool in different Plant Breeder to manipulate the DNA of the crop
To modifying the structure of a specific gene.
Gene targeting vector introduced into the cell.
Vector modifies the normal chromosomal gene through homologous recombination.
Useful in treating some human genetic disorders – Hemophilia, Duchenne Muscular Dystrophy.
Treating human diseases by genetic approaches – Gene Therapy.
Gene Therapy – Replacing the defective gene by normal copy of the gene.
Expressed sequence tag/EST is a short partial sequence, typically 200-400 bp long, of a complimentary DNA/Cdna.
EST is a short sub-sequence of a cDNA sequence.
Used to identify gene transcripts, and are instrumental in gene discovery and in gene-sequence determination.
Approximately 74.2 million ESTs are available in public databases.
EST results from one-short sequencing of a cloned cDNA.
Low-quality fragments.
Length is approximately 500 to 800 nucleotides.
Genome Editing Techniques by Kainat RamzanKainatRamzan3
Genome technology has revolutionized biological science through techniques of Gene Editing in order to edit any organism's genome.MegNs and zinc-finger nucleases are commonly understood to be used, as is the effector's transcriptional activator-like nucleases. In CRISPR/Cas9, genetic alterations, and gene functionality have become a well-known tool for understanding gene targeting.
Genome editing is a method of making specific changes to the DNA of a cell or organism. An enzyme scissors the DNA at a specific sequence, and when this is repaired by the cell, a change or ‘edit’ is made to the sequence.
https://www.creative-biolabs.com/gene-therapy/approaches-to-genome-editing.htm
Feature story from the Garvan Institute of Medical Research's April 2013 issue of Breakthrough newsletter. More at https://www.garvan.org.au/news-events/newsletters
Presentation1..gymno..non specific markers n microsatellites..by Nikita Patha...NIKITAPATHANIA
NON-SPECIFIC MARKERS-“A cloned random DNA fragment whose function or specific features are not known e.g. AFLP, RAPD, IRAP, SSR etc.
These marker type generally measure apparently neutral DNA variations.
They are generally the PCR based molecular markers.
Determining genetic diversity can be based on morphological, biochemical, and molecular types of information.
However, molecular markers have advantages over other kinds, where they show genetic differences on a more detailed level without interferences from environmental factors, and where they involve techniques that provide fast results detailing genetic diversity.
MOLECULAR MARKERS - In genetics, a molecular marker (identified as genetic marker) is a fragment of DNA that is associated with a certain location within the genome.
MICROSATELLITES : Microsatellites are tandem repeats(TRs) of 1–6 bp and are also known as simple sequence repeats (SSRs). Microsatellites are TRs of base pairs that are widely spread throughout the genome. Microsatellites are located in the coding and non coding regions.
Microsatellite markers are codominant, abundant, and multiallelic and play an important role in the study of molecular population genetics, positional cloning, QTL mapping, disease identification, pathogenesis, and evolutionary studies, etc .
Major molecular markers based on assessment of variability generated by microsatellites sequences are:
STMSs (Sequence Tagged Microsatellite Site), SSLPs (Simple Sequence Length Polymorphism), SNPs (Single Nucleotide Polymorphisms), SCARs (Sequence Characterized Amplified Region) and CAPS (Cleaved Amplified Polymorphic Sequences).
SINGLE COPY NUCLEAR GENE MARKER – Has one physical location in the genome and can have orthologs in different species.
Comprise of a unique sequence that code for proteins and undergo transcription.
Seed plants probably comprise 260,000 to 310,000 extant species. Current seed plants consist of angiosperms and gymnosperms, the latter of which are further sub divided into Cycadidae, Ginkgoidae, Gnetidae, and Pinidae .
In contrast to angiosperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species.
With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants.
Taking advantage of an increasing number of available genomes and transcriptomes, there is identification of single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa.
All studied seed plants shared 1,469 single-copy genes, which are generally involved in functions like DNA metabolism, cell cycle, and photosynthesis.
A plant genome project aims to discover all genes and their function in a particular plant species.
The main objective of genomic research in any species is to sequence the whole genome and functions of all the different coding and non-coding sequences.
These techniques helped in preparation of molecular maps of many plant genomes.
Plant genome projects initially focused on a few model organisms that are characterized by small genomes or their amenability to genetic studies
Since sequencing technologies have moved on, sequencing cost have dropped and bioinformatics tools advanced, the genomes of many plant species including the enormous genome of bread wheat have been assembled
Genome sequencing projects have been carried out on all three plant genomes: the nuclear, chloroplast and mitochondrial genomes
This opened venues for advanced molecular breeding and manipulation of plant species, but also have accelerated phylogenetics studies amongst species
Several excellent curated plant genome databases, besides the general nucleotide data base archives, allow public access of plant genomes
Functional genomics is a general approach toward understanding how the genes of an organism work together by assigning new functions to unknown genes. Information about the hypothesized function of an unknown gene may be deduced from its sequence structure using already known functions of similar genes as the basis for comparison. Gene function analysis therefore necessitates the analysis of temporal and spatial gene expression patterns (Yunbi Xu et al , Plant Molecular Biology (2005) ).
Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in ...Banoth Madhu
Banoth Madhu: Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in Crop Plants. It is a cytogenetic technique that allows the detection and localization of specific nucleic acid sequences on morphologically preserved chromosomes using genomic DNA of donor specie as probe. It is a cytogenetic technique that allows the detection and localization of specific nucleic acid sequences on morphologically preserved chromosomes using genomic DNA of donor specie as probe
When breeding diploid potatoes, tetraploid progeny can result from the union of 2n eggs and 2n pollen in 2x-2x crosses. Thirty-three crosses were made to examine tetraploid progeny frequency in 2x-2x crosses. All crosses were between S. tuberosum dihaploids and diploid self-compatible donors, M6 and DRH S6-10-4P17. Using chloroplast counting for ploidy determination, the frequency of tetraploid progeny was as high as 45% in one of the 33 crosses. Based upon single nucleotide polymorphism (SNP) genotyping, the tetraploid progeny were attributed to bilateral sexual polyploidization (BSP), which is caused by the union of 2n egg and 2n pollen. Dihaploids were identified that produce lower frequencies of 2n eggs. The results of this study suggest that S. tuberosum dihaploids with a high frequency of 2n eggs should be avoided in 2x - 2x crosses for diploid breeding programs.
Genome project of Human and methods of sequencing human genome; Genome project of Rice and its post genome sequencing era; Arabidopsis genome project: Why Rice and Arabidopsis chosen for genome project?
Molecular marker and its application in breed improvement and conservation.docxTrilokMandal2
Molecular markers have revolutionized the field of genetics and genomics by providing valuable tools for studying genetic diversity, identifying individuals, and characterizing traits of interest. This review paper aims to explore the applications of molecular markers in breed improvement and conservation. We discuss the various types of molecular markers commonly used, such as microsatellites, single nucleotide polymorphisms (SNPs), amplified fragment length polymorphisms (AFLPs), and many more. Additionally, we examine their applications in genetic diversity assessment, parentage analysis, marker-assisted selection (MAS), and conservation efforts. The paper highlights the importance of molecular markers in accelerating breed improvement programs and enhancing conservation strategies for maintaining genetic diversity within a population.Molecular markers have had a significant impact on breed development and conservation efforts, transforming genetics and offering vital insights into genetic diversity, lineage tracing, and genotype characterization. The importance of molecular markers in improving genetic gains, facilitating breeding programs, and preserving genetic diversity for the long-term sustainability of the animal population has been underlined in this review paper. Emerging advancements in molecular marker technology show enormous potential for improving and conserving breeds. Deeper insights into the genetic basis of complex traits will be provided through GWAS, CRISPR/Cas9, gene editing technologies, and sequencing technologies, resulting in faster genetic gains. Breeders and conservationists will be able to make more informed judgments thanks to these technologies. In conclusion, molecular markers have had a significant impact on breed conservation and enhancement. Their innovations have changed the industry and given both conservationists and breeders vital knowledge. We can pave the road for more effective and sustainable genetic improvement and the preservation of biodiversity for future generations by combining the power of molecular markers with conventional breeding and conservation techniques.
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.
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
We all have good and bad thoughts from time to time and situation to situation. We are bombarded daily with spiraling thoughts(both negative and positive) creating all-consuming feel , making us difficult to manage with associated suffering. Good thoughts are like our Mob Signal (Positive thought) amidst noise(negative thought) in the atmosphere. Negative thoughts like noise outweigh positive thoughts. These thoughts often create unwanted confusion, trouble, stress and frustration in our mind as well as chaos in our physical world. Negative thoughts are also known as “distorted thinking”.
The Indian economy is classified into different sectors to simplify the analysis and understanding of economic activities. For Class 10, it's essential to grasp the sectors of the Indian economy, understand their characteristics, and recognize their importance. This guide will provide detailed notes on the Sectors of the Indian Economy Class 10, using specific long-tail keywords to enhance comprehension.
For more information, visit-www.vavaclasses.com
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
Welcome to TechSoup New Member Orientation and Q&A (May 2024).pdfTechSoup
In this webinar you will learn how your organization can access TechSoup's wide variety of product discount and donation programs. From hardware to software, we'll give you a tour of the tools available to help your nonprofit with productivity, collaboration, financial management, donor tracking, security, and more.
Ethnobotany and Ethnopharmacology:
Ethnobotany in herbal drug evaluation,
Impact of Ethnobotany in traditional medicine,
New development in herbals,
Bio-prospecting tools for drug discovery,
Role of Ethnopharmacology in drug evaluation,
Reverse Pharmacology.
This is a presentation by Dada Robert in a Your Skill Boost masterclass organised by the Excellence Foundation for South Sudan (EFSS) on Saturday, the 25th and Sunday, the 26th of May 2024.
He discussed the concept of quality improvement, emphasizing its applicability to various aspects of life, including personal, project, and program improvements. He defined quality as doing the right thing at the right time in the right way to achieve the best possible results and discussed the concept of the "gap" between what we know and what we do, and how this gap represents the areas we need to improve. He explained the scientific approach to quality improvement, which involves systematic performance analysis, testing and learning, and implementing change ideas. He also highlighted the importance of client focus and a team approach to quality improvement.
3. 3
CONTENTS
1. Introduction
2. Genome Sequencing in Finger Millet
3. Genome size estimation
4. SOLiD Sequencing Technology
5. Illumina Sequencing Technology
6. Gene prediction and functional annotation of genes
7. Mining of plant transcription factors and other genes
8. Future Perspectives
9. Case study
10. Conclusion
11. Reference
4. 4
GENOME
One complete set of genetic information (total amount of
DNA) from a haploid set of chromosomes of a single cell
in eukaryotes, in a single chromosome in bacteria, or in
the DNA or RNA of viruses.
Basic set of chromosome in a organism.
The whole hereditary information of an organism that is
encoded in the DNA.
In cytogenetics, genome means a single set of
chromosomes.
Denoted by X.
The genome is found inside every cell, and in those that
have nucleus, the genome is situated inside the nucleus.
In Drosophila melanogaster (2n = 2x = 8); genome x = 4.
5. 5
GENOME SEQUENCING
Genome sequencing is the technique that allows
researchers to read the genetic information found in
the DNA of anything from bacteria to plants to
animals.
Sequencing involves determining the order of bases,
the nucleotide subunits found in DNA :-
adenine(A), guanine(G),
cytosine(C), thymine(T).
Genome sequencing is figuring out the order of DNA
nucleotides.
6. 6
WHY GENOME SEQUENCING ?
To understand how the genome as a whole works.
To study gene expression in a specific tissue.
Understand how gene expression is regulated in a
particular Environment.
To find correlations how genome information relates to
susceptibility / resistance to diseases , physiology and
metabolism etc.
To improve the quality and productivity of the crop
plants.
7. 7
FINGER MILLET
Classification :
Kingdom : Plantae
Subkingdom : Tracheobionta
Super division: Spermatophyta
Division : Magnoliophyta
Class : Liliopsida
Subclass : Commelinidae
Order : Cyperales
Family : Poaceae
Genus : Eleusine
Species : Eleusine coracana
DIFFERENT SPECIES :
Diploid species :
1. Eleusine indica
2. E. oligostachya
3. E.tristachya
4. E. poranansis
5. E. jaegeri
6. E. flacifolia
Tetraploid species :
1.Eleusine coracana
2. E. longipoides
3. E. verticillata
4. E. cagopoides
9. 9
FINGER MILLET
It is the fourth most important millet after sorghum, pearl millet and foxtail
millet.
It occupies 12% of global millet’s area and is cultivated in more than 25
countries in African and Asian continents .
High nutraceutical and
antioxidant properties
Gluten-free
Rich in calcium, fiber and
iron
Excellent malting qualities
Low glycemic index
It produces reasonable grain and
fodder yields under low input .
Survives on soils of low fertility.
It has an efficient carbon
concentrating mechanism
through C4 pathway.
In spite of its immense importance in human diet, development of
genomic resources and high throughput breeding efforts have been
limited.
Considering these, the whole genome sequence data was developed.
10. 10
GENOME SEQUENCING IN FINGER MILLET
Genotype used for genome sequencing : ML-365
ML-365 variety was developed and released in 2008.
Features of ML-365 genotype :
Short duration (110– 115 days)
High yielding (5.0–5.5 tonnes/hectare)
Drought tolerant
Blast disease resistant
Good cooking qualities
The genome was sequenced by
SOLiD sequencing technology (Sequencing by
Oligonucleotide Ligation and Detection)
Illumina sequencing technology.
11. 11
Genome size estimation of finger millet and wild species
Seeds of ML-365 (Eleusine coracana subsp. coracana), EC516253 (Eleusine
jaegeri Pilg.), EC516251 (Eleusine multiflora Hochst.), EC516248 (Eleusine tristachya
Lam.), EC516245, EC516243 (Eleusine indica), EC541533, and EC541538 (Eleusine
coracana subsp. africana) were grown in pots containing red soil and fertilizer mix.
Young leaves were collected and chopped into pieces using sterilized blade and
stained using nuclear isolation buffer (NIB).
The liquid was filtered through 30 μm nylon mesh and samples were processed for
ploidy estimation as per the protocol suggested by Krishan .
Stained nuclei were analyzed using BD FACS cell sorter.
Genome sizes of all Eleusine species were estimated by comparing with Pisum
sativum as an internal standard.
The genome size was derived by multiplying the 1C value (pg) with 965 Mb (1pg
equivalent value).
13. 13
Data analysis
SOLiD SEQUENCING TECHNOLOGY
DNA Fragmentation
Adapter Ligation
Hybridization of target DNA with PCR beads
Amplification via PCR
Attaching beads to glass slide
Ligation reaction and imaging
17. 17
Data analysis
Adapter Ligation
Illumina Sequencing Technology
DNA Fragmentation
Adapter Ligation
Hybridization of target DNA with oligos on floor shell
Bridge amplification of DNA
Attaching beads to glass slide
Sequencing reaction and imaging
19. 19
Genome assembly statistics of ML-365
Details Value
Total length of sequence (Mb) 1196.06
No. contigs/scaffolds 525,759
Minimum length of contigs/scaffolds (bp) 200
Maximum length of contigs/scaffolds (bp) 454,778
Average length of contigs/scaffolds (bp) 2274.92
N50 (bp) 23,732
GC content (%) 44.76
No. of genes predicted
a. Non-TE related genes
b. TE related genes
85,243
78,647
6596
Mb - Million bases
Bp - base pairs
Genome sequencing and genome assembly
Shailaja et al. (2017)
20. 20
Gene prediction and functional annotation
The assembled scaffolds were used to predict the genes using
AUGUSTUS by Zea mays as a reference gene model.
In addition, RNA-seq data was incorporated to AUGUSTUS to assist
the gene prediction.
The gene ontology annotation was carried out by performing a BLAST
(Basic Local Alignment Search Tool) with the protein sequences of
Viridiplantae retrieved from UniProt database.
The pathway analysis of genes was carried out by KAAS (KEGG
Automatic Annotation Server) server using Arabidopsis thaliana
(ath), Glycine max (gmx), Oryza sativa japonica (osa), and Vitis
vinifera (vvi) as reference organisms.
The protein domain structures of all protein coding genes were
identified using InterProScan5 software .
21. 21
Gene prediction and functional annotation
Functional annotation confirmed that majority of the genes had
homologs with known functions in UniProt protein database.
The gene ontology (GO) annotation of genes revealed that
more number of genes were involved in molecular function
followed by cellular and biological processes. Majority of the
genes were involved in nucleic acid binding, zinc ion binding,
and ATP binding activities under molecular function.
Similarly, DNA integration and integral components of
membrane were major functions related to biological and
cellular processes, respectively.
The KAAS server based pathway prediction showed that
majority of genes were involved in carbohydrate metabolism,
amino acid metabolism, translation, lipid metabolism and
folding, sorting, and degradation pathways.
23. 23
23
Mining of plant transcription factors (TFs) in finger millet
The protein-protein homology analysis of genes of ML- 365 with
plant TFs protein database revealed 56 various families of TFs
distributed across 11,125 genes in finger millet.
Among them, bHLH, MYB, FAR1, WRKY, NAC, MYB related, B3, ERF,
bZIP, HD-ZIP, C2H2, C3H, G2- like, TALE, GRAS, ARF, M-type,
Trihelix, GATA, WOX, LBD, HSF, MIKC, S1Fa-like, HB other, CPP, and
YABBY were majorly distributed TFs in the finger millet genome.
These 11,125 genes were found to have homology with 75 plant
species and foxtail millet, rice, wild species of rice, apple,
Brachypodium, maize, sorghum, wheat and wild species of wheat
were major among other plant species.
25. 25
25
Repeat content in finger millet genome
Simple sequence repeats (SSRs) play an evolutionary relationship
in genome evolution.
The scaffolds of ML- 365 genome were subjected for identification
of SSRs using MISA.
A total of 114,083 SSRs were distributed across ML-365 genome
signifying the abundance of SSRs, of which 66,805 (58.56%),
40,578 (35.57%), 2179 (1.91%), 3010 (2.64%) and 1511 (1.32%) were
di-, tri-, tetra-, penta-, and hexa- types, respectively.
SSRs identified in this study can be further effectively used in
diversity studies, linkage map construction, association mapping,
QTL mapping of agronomically important traits, and marker
assisted breeding programmes.
28. 28
28
Mining of drought responsive genes
Finger millet is a drought tolerant cereal crop and mining for
drought responsive genes will hasten future breeding activities to
develop varieties for drought prone areas.
The Pfam based identification of drought responsive genes revealed
that 2866 genes were distributed across 19 Pfam domains.
Most of these genes were associated with WRKY, MYB, MYC, ZFHD,
NAC, ABF, AREB, GRF, and NF-Y transcription factors, which are
responsible for drought tolerance .
Utilization of these TFs to study the binding sites of TFs and
analyzing cis-acting elements will enhance further understanding of
drought tolerance in finger millet.
29. 29
29
Pfam ID Pfam domain name Gene count
PF00069 Protein kinase domain 1386
PF07714 Protein tyrosine kinase 546
PF00651 BTB/POZ domain 351
PF01370 NAD dependant epimerase/dehydratase family 175
PF04564 U-box domain 86
PF00582 Universal stress protein family 82
PF00571 CBS domain containing proteins (DCPS) 77
PF05699 hAT family dimerization domain 36
PF08879 WRC 32
PF00999 Sodium/hydrogen exchanger family 20
PF03061 Thioesterase superfamily 19
PF08880 QLQ 16
PF04185 Phosphoesterase family 12
PF07649 C1-like domain 10
PF00257 Dehydrin 10
PF03107 C1-domain 3
PF02637 GatB domain 3
PF04147 Nop 14-like family 2
Shailaja et al. (2017)
30. 30
30
Calcium transport and accumulation genes :
Finger millet grain contains rich sources of nutrients, specifically it possess 5–10
times higher calcium in grains as compared to other cereals.
Homology based analysis identified 330 calcium transport and accumulation related
genes.
Among 330, 28 CaM ATPase, 145 CaMK1, 125 CaMK2, 29 CAX1 and 3 TPC1 genes
were identified.
Out of 330, six genes (g5694.t1, g73960.t1, g89161.t1, g107035.t1, g135510.t1, and
g146823.t1) were found to be homologs to Calcium transport and regulation genes
identified previously.
Genes identified in this study will help in exploring finger millet germplasm for
calcium uptake, translocation and accumulation in various tissues in near future.
31. 31
31
Finger millet remains an important cereal crop in the semi-arid tropics and is likely to
gain more importance as more genomic resources become available and more people
show interest in healthy eating.
The high demand for finger millet in dry areas will require the release of better
yielding varieties coupled with unique resistance to biotic and abiotic stresses.
The current largely conventional breeding approaches in finger millet will not be
sufficient if the full potential of the crop is to be realized.
With the availability of a draft whole genome sequence, research will need to focus
on characterizing important traits and utilizing genomics-assisted breeding for more
efficient release of superior varieties.
Future Perspectives
33. 33
Case Study - 1
Continued….
Seeds of finger millet core collection for ML-365 variety were obtained from All India
Coordinated Research Project on Small Millets, University of Agricultural Sciences (UAS),
Bengaluru.
This project was a competitive grant from World Bank under the Sujala-II funded by
Watershed Development Department, Government of Karnataka, India to Shailaja
Hittalmani as a Principal Investigator.
The funding agency had no role in study design, data collection, analysis and
interpretation, decision to publish, or preparation of the manuscript.
34. 34
Results:
Experimental results from whole genome sequencing and assembling process of
ML-365 finger millet cultivar yielded 1196 Mb covering approximately 82% of total
estimated genome size.
Genome analysis showed the presence of 85,243 genes and one half of the
genome is repetitive in nature.
The finger millet genome was found to have higher colinearity with foxtail millet
and rice as compared to other Poaceae species.
Mining of simple sequence repeats (SSRs) yielded abundance of SSRs within the
finger millet genome.
Functional annotation and mining of transcription factors revealed finger millet
genome harbors large number of drought tolerance related genes.
Transcriptome analysis of low moisture stress and non-stress samples revealed
the identification of several drought-induced candidate genes, which could be
used in drought tolerance breeding.
Conclusions:
This genome sequencing effort will strengthen plant breeders for allele
discovery, genetic mapping, and identification of candidate genes for
agronomically important traits.
Availability of genomic resources of finger millet will enhance the novel breeding
possibilities to address potential challenges of finger millet improvement.
36. 36
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