The document summarizes research on identifying consistent quantitative trait loci (QTLs) for grain yield under drought stress in rice. It describes phenotyping populations of rice under reproductive stage drought stress and genotyping them to identify QTLs. A major QTL, qDTY1.1, was found to increase grain yield by 16-29% in multiple genetic backgrounds. Further research eliminated linkage drag at this QTL locus to develop introgression lines with improved drought tolerance but limited yield penalties under non-stress conditions. Background analysis found that qDTY1.1 alleles from drought tolerant varieties N22 and Dhagaddeshi were similar and distinct from susceptible varieties. Overall, the research aimed to identify stable Q
This document summarizes the current status of hybrid rice research and development at IRRI. It discusses trends in hybrid rice adoption globally, with hybrid rice area growing by 2 million hectares from 2007 to 2011 outside of China. It identifies major challenges for hybrid rice in tropical regions like low yield advantages and heterosis. It outlines IRRI's hybrid rice research priorities and efforts to address challenges through developing new parental lines, disease resistance, and seed production technology. The document also summarizes recommendations from a hybrid rice symposium to increase yields, improve seed production, and strengthen public-private partnerships.
STATUS OF HYBRID RICE BREEDING IN INDIA & ABROADVishal Pandey
Hybrids have the potential of yielding 15-20% more than the best pureline variety grown under similar conditions in Rice by exploiting the phenomenon of hybrid vigour or heterosis
In view of rapidly increasing population and declining natural resources, Hybrid rice is one of the most important and practically feasible technologies for increasing food-grain production, ensuring food security and boosting farmers income.
To further reduce the cost of hybrid rice seeds, Improvement in hybrid rice seed production technology is needed
Hybrid rice seed production technology is labour and knowledge intensive
There is a need for developing Hybrids suited to rainfed lowland as well as of longer duration to replace longer duration mega inbred varieties
GPB 311: Wheat- Centre of origin, distribution of species, wild relatives and major breeding objectives and procedures for development of varieties and hybrids for improvement yield, adoptability, stability, biotic and abiotic stress tolerance and quality in Wheat
" Developing rice varieties with enhanced adaptation to lowland farming syste...ExternalEvents
" Developing rice varieties with enhanced adaptation to
lowland farming systems: Case studies from South Asia " presentation by Abdelbagi Ismail, International Rice Research Institute, Los ernational Rice Research Institute, Los Baños, The Philippines Baños, The Philippines
This document provides an overview of genetically modified cotton in India. It discusses how Bt cotton was developed to express Cry proteins from Bacillus thuringiensis to control the key pest, Helicoverpa armigera. The adoption of Bt cotton in India led to increased yields and reduced pesticide use. Herbicide resistant cotton was also discussed, including glyphosate resistant varieties currently being illegally grown. Overall, the document evaluates the benefits of GM cotton technologies for Indian farmers but notes some concerns around overuse of herbicides and developing weed resistance require ongoing research into more sustainable options.
Introgression breeding for rice submergence tolerance_geetanjaliDr. Geetanjali Baruah
Simplified way of applicability of introgression breeding for submergence tolerance in rice with special emphasis on physiology of submergence tolerance
The document discusses the origin and breeding of various pulse crops including red gram, black gram, and green gram. It provides information on their place of origin, wild relatives, breeding objectives, and methods. The key objectives of red gram breeding are developing long duration varieties for rainfed areas, short duration varieties for irrigated conditions, and varieties with disease resistance, bold grains, and high protein content. Black gram and green gram breeding aims to evolve medium and short duration varieties, varieties resistant to diseases like yellow mosaic virus, and varieties with improved quality. Popular varieties and centers working on pulse improvement are also mentioned.
This document summarizes the current status of hybrid rice research and development at IRRI. It discusses trends in hybrid rice adoption globally, with hybrid rice area growing by 2 million hectares from 2007 to 2011 outside of China. It identifies major challenges for hybrid rice in tropical regions like low yield advantages and heterosis. It outlines IRRI's hybrid rice research priorities and efforts to address challenges through developing new parental lines, disease resistance, and seed production technology. The document also summarizes recommendations from a hybrid rice symposium to increase yields, improve seed production, and strengthen public-private partnerships.
STATUS OF HYBRID RICE BREEDING IN INDIA & ABROADVishal Pandey
Hybrids have the potential of yielding 15-20% more than the best pureline variety grown under similar conditions in Rice by exploiting the phenomenon of hybrid vigour or heterosis
In view of rapidly increasing population and declining natural resources, Hybrid rice is one of the most important and practically feasible technologies for increasing food-grain production, ensuring food security and boosting farmers income.
To further reduce the cost of hybrid rice seeds, Improvement in hybrid rice seed production technology is needed
Hybrid rice seed production technology is labour and knowledge intensive
There is a need for developing Hybrids suited to rainfed lowland as well as of longer duration to replace longer duration mega inbred varieties
GPB 311: Wheat- Centre of origin, distribution of species, wild relatives and major breeding objectives and procedures for development of varieties and hybrids for improvement yield, adoptability, stability, biotic and abiotic stress tolerance and quality in Wheat
" Developing rice varieties with enhanced adaptation to lowland farming syste...ExternalEvents
" Developing rice varieties with enhanced adaptation to
lowland farming systems: Case studies from South Asia " presentation by Abdelbagi Ismail, International Rice Research Institute, Los ernational Rice Research Institute, Los Baños, The Philippines Baños, The Philippines
This document provides an overview of genetically modified cotton in India. It discusses how Bt cotton was developed to express Cry proteins from Bacillus thuringiensis to control the key pest, Helicoverpa armigera. The adoption of Bt cotton in India led to increased yields and reduced pesticide use. Herbicide resistant cotton was also discussed, including glyphosate resistant varieties currently being illegally grown. Overall, the document evaluates the benefits of GM cotton technologies for Indian farmers but notes some concerns around overuse of herbicides and developing weed resistance require ongoing research into more sustainable options.
Introgression breeding for rice submergence tolerance_geetanjaliDr. Geetanjali Baruah
Simplified way of applicability of introgression breeding for submergence tolerance in rice with special emphasis on physiology of submergence tolerance
The document discusses the origin and breeding of various pulse crops including red gram, black gram, and green gram. It provides information on their place of origin, wild relatives, breeding objectives, and methods. The key objectives of red gram breeding are developing long duration varieties for rainfed areas, short duration varieties for irrigated conditions, and varieties with disease resistance, bold grains, and high protein content. Black gram and green gram breeding aims to evolve medium and short duration varieties, varieties resistant to diseases like yellow mosaic virus, and varieties with improved quality. Popular varieties and centers working on pulse improvement are also mentioned.
Novel QTLs for growth angle of seminal roots in wheat (Triticum aestivum L.). PGS
Novel QTLs for growth angle of seminal roots in wheat (Triticum aestivum L.).
Dr. Alhosein Hamada, Associate Professor (Email: a.hamada@aun.edu.eg)
Department of Agronomy, Faculty of Agriculture, Assiut University
This lecuter was presented in Plant Genetics Seminars. The content of this lecture was publised in Plant and Soil 2012
This document provides information on research strategies for rice improvement in India. It discusses the importance of rice as a staple crop, describing how it is cultivated and consumed globally and within India and Tamil Nadu specifically. Statistics on rice production, yield, and varieties are presented for India, Tamil Nadu, and Kerala. The document also summarizes milestones in rice variety development in Tamil Nadu and describes local landraces, hybrid rice research, the system of rice intensification, and mechanization of rice cultivation.
Groundnut is one of the most important cash crops in our country. It is a low- priced commodity but a valuable source of all the nutrients. Groundnut is the sixth most important oilseed crop in the world. It contains 48-50% of oil and 26-28% of protein and is a rich source of dietary fiber, minerals, and vitamins. The production of groundnut is concentrated in Asia and Africa with 56% and 40% of the global area and 68% and 25% of the global production, respectively
This document provides information about rice crops. It discusses the history of rice cultivation in Asia dating back to 3000 BC in China. It describes the botanical classification of rice, including the two cultivated species Oryza sativa and Oryza glaberrima. It also outlines the objectives of rice breeding programs, which include increasing yield, adapting varieties to different growing conditions, and improving grain quality and disease resistance. Finally, it notes that the rice genome was sequenced to further rice research and address production challenges in a sustainable manner.
IRJET- Transgressive Segregation Studies for High Shelling Percentage in Summ...IRJET Journal
1. Two F2 crosses of groundnut (Arachis hypogaea L.), IGSC-11 x SB-XI and TAG-24 x SB-XI, were evaluated to study transgressive segregation. Transgressive segregants exceeding the parental ranges were observed for all evaluated traits including shelling percentage, dry pod yield, and number of mature pods.
2. The highest proportions of transgressive segregants were found for shelling percentage (44 in the first cross and 88 in the second cross).
3. The most promising transgressive segregants for the two crosses exceeded their respective increasing parents for number of mature pods and three to four other traits, producing 23.72% and 23.
This document discusses cassava agronomy research being conducted by IITA. It notes that cassava yields in Africa are typically much lower than potential yields, due to factors like soil degradation, lack of fertilizer recommendations, and insufficient knowledge of optimal planting and intercropping practices. IITA is working on various projects to develop improved agronomic techniques for cassava through on-farm trials evaluating the effects of fertilizers, plant spacing, variety selection, and intercropping. The goal is to close the gap between current and potential yields for this important crop in Africa.
B4FA 2012 Nigeria: Cassava Research in Nigeria - Emmanual Okogbeninb4fa
Presentation by Dr Emmanuel Okogbenin, National Root Crops Research Centre, Umudike, Nigeria
Delivered at the B4FA Media Dialogue Workshop, Ibadan, Nigeria - September 2012
www.b4fa.org
This study investigated the carry-over effect of thidiazuron (TDZ) on banana shoot proliferation under different culture cycles and light conditions. Shoots were initially cultured for 6 weeks on media supplemented with varying TDZ concentrations or benzylaminopurine (BAP, control). Shoots were then transferred to hormone-free media and subcultured for 3 cycles under dark, 8 hr, or 16 hr light. Results showed TDZ had a stronger carry-over effect than BAP, enabling continued shoot proliferation without hormones. Proliferation generally increased with culture cycles and was higher under dark conditions for some cultivars. TDZ concentrations of 7.14 mM produced the highest proliferation for most cultivars
This document discusses speed breeding, a technique to accelerate crop breeding cycles. Traditional breeding can take many years to develop new varieties while meeting future food demands poses challenges. Speed breeding uses controlled environmental conditions like extended photoperiod and supplemental lighting to complete multiple generations in a year. Case studies show this approach led wheat and barley to flower in half the time and generated 5 soybean generations per year. Speed breeding holds potential to rapidly develop climate-resilient varieties on a smaller scale while combining with genomics and other innovations.
Drought molecular breeding in rice, 19 november, 2012 swamyarjunmanju
This document discusses mapping and transferring QTLs for drought tolerance in rice. It begins by providing context on rice production, noting that 45% of rice is grown in rainfed areas with lower productivity. It then discusses strategies for developing drought tolerant rice varieties through conventional breeding and molecular approaches. Key points include using improved lines as donors, direct selection for grain yield under drought, identifying major drought yield QTLs, and introgressing QTLs into improved varieties. Several major effect QTLs for grain yield under drought are identified, including DTY1.1, DTY3.1, and DTY12.1. The consistency of these QTLs across backgrounds, ecosystems, and environments is discussed. The document
The document discusses marker-assisted selection (MAS), which uses genetic markers linked to genes of interest to make selection decisions for genetic improvement. MAS can be applied to traits that are difficult to measure, late-life traits, or those measured on only one sex. The accuracy of MAS depends on the linkage between the marker and gene. Successful MAS requires gene mapping, genotyping, QTL detection, and integrating phenotypic and genotypic data in evaluations. MAS response is limited long-term but benefits of favorable variants continue. Marker-assisted introgression can also be used to transfer genes between breeds faster.
“Agricultural Performance and Food Security in Nepal: Constraints and Challenges” presented by Bishnu Pant, IIDS, Nepal, at the ReSAKSS-Asia Conference, Nov 14-16, 2011, in Kathmandu, Nepal.
The document provides an overview of the Tropical Legumes I (TLI Phase I) project, including its objectives, activities, partners, and achievements. The project aimed to develop genomic resources for tropical legumes like groundnut, cowpea, common bean, and chickpea to improve productivity in marginal environments in sub-Saharan Africa. Key activities included characterizing germplasm and identifying genetic markers for biotic stress resistance and drought tolerance. The project collaborated with national programs and other institutions globally. Achievements included identifying disease resistant sources for various crops and characterizing diversity.
Molecular breeding in legumes for resource-poor farmers: Chickpea for Ethiopi...ExternalEvents
Molecular breeding in legumes for resource-poor farmers: Chickpea for Ethiopia and India presentation by "Douglas Cook, University of California Davis, Davis,
United States of America"
Challenges of agriculture and industrial sector of nepalpraladh timsina
This document outlines the challenges facing the agriculture and industrial sectors in Nepal. For agriculture, key challenges include raising productivity, providing adequate labor, dealing with climate change, developing commercial agriculture, improving marketing research and fertilizer costs. The main industrial challenges are high production costs, unfavorable government policies and regulations, demand for products, access to financing and infrastructure, labor regulations, and obtaining raw materials.
This document discusses marker-assisted selection for improving orphan crops. It provides examples of MAS for cassava, pearl millet, and chickpea. For cassava, markers can be used to select for resistance to cassava mosaic virus and reduce cyanide levels. In pearl millet, markers linked to drought tolerance genes can be introgressed. For chickpea, markers linked to drought tolerance quantitative trait loci and fusarium wilt resistance genes allow selection of these traits. However, limitations include a lack of resources, marker polymorphism, and integration with conventional breeding in orphan crops.
Gene pyramiding in tomato involves combining desirable genes from multiple parents into a single genotype to improve specific traits. It can enhance disease resistance, drought tolerance, yield, and fruit quality. One study found that pyramiding two virus resistance genes (Ty-2 and Ty-3) in tomato improved resistance to three viruses and had higher yields than lines with single genes. Another study found that pyramiding introgressions from wild tomato species S. pennellii improved drought tolerance, yield, soluble solids content, and the ratio of soluble solids to fruit weight. A third study showed that pyramiding quality trait genes increased antioxidant levels, soluble solids, and yield compared to lines with single introgressions. Gene
Marker assisted selection (MAS) uses DNA markers linked to traits of interest to assist plant breeders in selecting desirable plants. MAS can increase the efficiency and precision of plant breeding by allowing selection at early generations or at the seedling stage before phenotypic selection. It also reduces the influence of environmental effects and allows selection of homozygous plants. While MAS has advantages over conventional breeding, its use in actual breeding programs remains limited due to technical and cost constraints. Further optimization and integration of molecular genetics with plant breeding is needed to fully realize the potential of MAS.
Novel QTLs for growth angle of seminal roots in wheat (Triticum aestivum L.). PGS
Novel QTLs for growth angle of seminal roots in wheat (Triticum aestivum L.).
Dr. Alhosein Hamada, Associate Professor (Email: a.hamada@aun.edu.eg)
Department of Agronomy, Faculty of Agriculture, Assiut University
This lecuter was presented in Plant Genetics Seminars. The content of this lecture was publised in Plant and Soil 2012
This document provides information on research strategies for rice improvement in India. It discusses the importance of rice as a staple crop, describing how it is cultivated and consumed globally and within India and Tamil Nadu specifically. Statistics on rice production, yield, and varieties are presented for India, Tamil Nadu, and Kerala. The document also summarizes milestones in rice variety development in Tamil Nadu and describes local landraces, hybrid rice research, the system of rice intensification, and mechanization of rice cultivation.
Groundnut is one of the most important cash crops in our country. It is a low- priced commodity but a valuable source of all the nutrients. Groundnut is the sixth most important oilseed crop in the world. It contains 48-50% of oil and 26-28% of protein and is a rich source of dietary fiber, minerals, and vitamins. The production of groundnut is concentrated in Asia and Africa with 56% and 40% of the global area and 68% and 25% of the global production, respectively
This document provides information about rice crops. It discusses the history of rice cultivation in Asia dating back to 3000 BC in China. It describes the botanical classification of rice, including the two cultivated species Oryza sativa and Oryza glaberrima. It also outlines the objectives of rice breeding programs, which include increasing yield, adapting varieties to different growing conditions, and improving grain quality and disease resistance. Finally, it notes that the rice genome was sequenced to further rice research and address production challenges in a sustainable manner.
IRJET- Transgressive Segregation Studies for High Shelling Percentage in Summ...IRJET Journal
1. Two F2 crosses of groundnut (Arachis hypogaea L.), IGSC-11 x SB-XI and TAG-24 x SB-XI, were evaluated to study transgressive segregation. Transgressive segregants exceeding the parental ranges were observed for all evaluated traits including shelling percentage, dry pod yield, and number of mature pods.
2. The highest proportions of transgressive segregants were found for shelling percentage (44 in the first cross and 88 in the second cross).
3. The most promising transgressive segregants for the two crosses exceeded their respective increasing parents for number of mature pods and three to four other traits, producing 23.72% and 23.
This document discusses cassava agronomy research being conducted by IITA. It notes that cassava yields in Africa are typically much lower than potential yields, due to factors like soil degradation, lack of fertilizer recommendations, and insufficient knowledge of optimal planting and intercropping practices. IITA is working on various projects to develop improved agronomic techniques for cassava through on-farm trials evaluating the effects of fertilizers, plant spacing, variety selection, and intercropping. The goal is to close the gap between current and potential yields for this important crop in Africa.
B4FA 2012 Nigeria: Cassava Research in Nigeria - Emmanual Okogbeninb4fa
Presentation by Dr Emmanuel Okogbenin, National Root Crops Research Centre, Umudike, Nigeria
Delivered at the B4FA Media Dialogue Workshop, Ibadan, Nigeria - September 2012
www.b4fa.org
This study investigated the carry-over effect of thidiazuron (TDZ) on banana shoot proliferation under different culture cycles and light conditions. Shoots were initially cultured for 6 weeks on media supplemented with varying TDZ concentrations or benzylaminopurine (BAP, control). Shoots were then transferred to hormone-free media and subcultured for 3 cycles under dark, 8 hr, or 16 hr light. Results showed TDZ had a stronger carry-over effect than BAP, enabling continued shoot proliferation without hormones. Proliferation generally increased with culture cycles and was higher under dark conditions for some cultivars. TDZ concentrations of 7.14 mM produced the highest proliferation for most cultivars
This document discusses speed breeding, a technique to accelerate crop breeding cycles. Traditional breeding can take many years to develop new varieties while meeting future food demands poses challenges. Speed breeding uses controlled environmental conditions like extended photoperiod and supplemental lighting to complete multiple generations in a year. Case studies show this approach led wheat and barley to flower in half the time and generated 5 soybean generations per year. Speed breeding holds potential to rapidly develop climate-resilient varieties on a smaller scale while combining with genomics and other innovations.
Drought molecular breeding in rice, 19 november, 2012 swamyarjunmanju
This document discusses mapping and transferring QTLs for drought tolerance in rice. It begins by providing context on rice production, noting that 45% of rice is grown in rainfed areas with lower productivity. It then discusses strategies for developing drought tolerant rice varieties through conventional breeding and molecular approaches. Key points include using improved lines as donors, direct selection for grain yield under drought, identifying major drought yield QTLs, and introgressing QTLs into improved varieties. Several major effect QTLs for grain yield under drought are identified, including DTY1.1, DTY3.1, and DTY12.1. The consistency of these QTLs across backgrounds, ecosystems, and environments is discussed. The document
The document discusses marker-assisted selection (MAS), which uses genetic markers linked to genes of interest to make selection decisions for genetic improvement. MAS can be applied to traits that are difficult to measure, late-life traits, or those measured on only one sex. The accuracy of MAS depends on the linkage between the marker and gene. Successful MAS requires gene mapping, genotyping, QTL detection, and integrating phenotypic and genotypic data in evaluations. MAS response is limited long-term but benefits of favorable variants continue. Marker-assisted introgression can also be used to transfer genes between breeds faster.
“Agricultural Performance and Food Security in Nepal: Constraints and Challenges” presented by Bishnu Pant, IIDS, Nepal, at the ReSAKSS-Asia Conference, Nov 14-16, 2011, in Kathmandu, Nepal.
The document provides an overview of the Tropical Legumes I (TLI Phase I) project, including its objectives, activities, partners, and achievements. The project aimed to develop genomic resources for tropical legumes like groundnut, cowpea, common bean, and chickpea to improve productivity in marginal environments in sub-Saharan Africa. Key activities included characterizing germplasm and identifying genetic markers for biotic stress resistance and drought tolerance. The project collaborated with national programs and other institutions globally. Achievements included identifying disease resistant sources for various crops and characterizing diversity.
Molecular breeding in legumes for resource-poor farmers: Chickpea for Ethiopi...ExternalEvents
Molecular breeding in legumes for resource-poor farmers: Chickpea for Ethiopia and India presentation by "Douglas Cook, University of California Davis, Davis,
United States of America"
Challenges of agriculture and industrial sector of nepalpraladh timsina
This document outlines the challenges facing the agriculture and industrial sectors in Nepal. For agriculture, key challenges include raising productivity, providing adequate labor, dealing with climate change, developing commercial agriculture, improving marketing research and fertilizer costs. The main industrial challenges are high production costs, unfavorable government policies and regulations, demand for products, access to financing and infrastructure, labor regulations, and obtaining raw materials.
This document discusses marker-assisted selection for improving orphan crops. It provides examples of MAS for cassava, pearl millet, and chickpea. For cassava, markers can be used to select for resistance to cassava mosaic virus and reduce cyanide levels. In pearl millet, markers linked to drought tolerance genes can be introgressed. For chickpea, markers linked to drought tolerance quantitative trait loci and fusarium wilt resistance genes allow selection of these traits. However, limitations include a lack of resources, marker polymorphism, and integration with conventional breeding in orphan crops.
Gene pyramiding in tomato involves combining desirable genes from multiple parents into a single genotype to improve specific traits. It can enhance disease resistance, drought tolerance, yield, and fruit quality. One study found that pyramiding two virus resistance genes (Ty-2 and Ty-3) in tomato improved resistance to three viruses and had higher yields than lines with single genes. Another study found that pyramiding introgressions from wild tomato species S. pennellii improved drought tolerance, yield, soluble solids content, and the ratio of soluble solids to fruit weight. A third study showed that pyramiding quality trait genes increased antioxidant levels, soluble solids, and yield compared to lines with single introgressions. Gene
Marker assisted selection (MAS) uses DNA markers linked to traits of interest to assist plant breeders in selecting desirable plants. MAS can increase the efficiency and precision of plant breeding by allowing selection at early generations or at the seedling stage before phenotypic selection. It also reduces the influence of environmental effects and allows selection of homozygous plants. While MAS has advantages over conventional breeding, its use in actual breeding programs remains limited due to technical and cost constraints. Further optimization and integration of molecular genetics with plant breeding is needed to fully realize the potential of MAS.
Gene mapping involves three main steps: 1) dividing chromosomes into smaller fragments that can be characterized and propagated, 2) ordering the fragments to correspond to their locations on chromosomes, and 3) determining the base sequence of each fragment. Gene maps describe the order and spacing of genes or markers on each chromosome. There are two main types of maps - genetic linkage maps that show relative locations of DNA markers, and physical maps including low-resolution maps that assign genes to chromosomes and high-resolution maps that depict order and distances between enzyme cleavage sites. Maps are valuable for locating disease genes and enabling analysis of physical traits and disease mechanisms.
This document summarizes research on breeding wheat with improved water use efficiency (WUE) and heat tolerance in China. Researchers identified 70 quantitative trait loci (QTL) markers for drought and heat tolerance traits. They used these markers in marker-assisted recurrent selection of six breeding populations, developing 192 crosses. Elites lines from the Global Crop Diversity Trust (GCP) reference set were crossed over 200 times with Chinese cultivars. Two lines entered national trials and seven entered provincial trials. Next steps include validating additional QTLs, enhancing marker-assisted recurrent selection, delivering drought and heat tolerant lines, and exchanging information to build molecular breeding capacity.
Developing drought resilient crops for improving productivity of drought pron...ICRISAT
1) Drought is a major limitation to crop productivity worldwide and climate change is expected to exacerbate water stress, so developing drought-resilient crops is critical.
2) Water stress during flowering and grain filling causes the most damage, drastically reducing yield through effects on grain number and size.
3) Breeding for drought tolerance focuses on selection environments, criteria, and methods including empirical selection and molecular breeding. Empirical breeding involves direct selection under drought stress while molecular breeding uses markers linked to drought resistance traits.
4) Integrating drought-tolerant landraces with high-yielding varieties through hybridization combines stress adaptation and productivity to develop resilient crops for drought-prone regions.
Root genetic research and its application in plant breeding or crop improvementOm Prakash Patidar
UNIVERSITY OF AGRICULTURAL SCIENCES, DHARWAD
DEPARTMENT OF GENETICS AND PLANT BREEDING Master’s seminar-II
Root genetic research and its applications in plant breeding
Speaker: Om Prakash Patidar Date: 20/03/2015 ID No.: PGS13AGR6140 Time: 3:00 PM
Synopsis
Roots play an essential role in the acquisition of water and minerals from soils. Root system architecture (RSA), the spatial configuration of a root system in the soil, is used to describe the shape and structure of root system. Its importance in plant productivity lies in the fact that major soil resources are heterogeneously distributed in the soil, so that the spatial deployment of roots will substantially determine the ability of a plant to secure edaphic resources. Measuring crop root architecture and assaying for changes in function can be challenging, but examples have emerged showing that modifications to roots result in higher yield and increased stress tolerance.1
A marker-assisted back-crossing (MABC) breeding programme was conducted to improve the root morphological traits, and thereby drought tolerance, of the Indian upland rice variety, Kalinga III. The donor parent was Azucena, an upland japonica variety from Philippines. Five segments on different chromosomes were targeted for introgression; four segments carried QTLs for improved root morphological traits and the fifth carried a recessive QTL for aroma. It significantly increased root length under both irrigated and drought stress treatments.2
Alteration of root system architecture improves drought avoidance through the cloning and characterization of DEEPER ROOTING 1 (DRO1), a rice quantitative trait locus controlling root growth angle. Higher expression of DRO1 increases the root growth angle, whereby roots grow in a more downward direction. Introducing DRO1 into a shallow-rooting rice cultivar by backcrossing enabled the resulting line to avoid drought by increasing deep rooting, which maintained high yield performance under drought conditions relative to the recipient cultivar.3
GmEXPB2, A vegetative -expansin gene, clone from a Pi starvation-induced soybean cDNA library. GmEXPB2 was found to be primarily expressed in roots, and was highly induced by Pi starvation, and the induction pattern was confirmed by GUS staining in transgenic soybean hairy roots. Results from intact soybean composite showed that GmEXPB2 is involved in hairy root elongation, and subsequently affects plant growth and P uptake, especially at low P levels.4
Candidate Aluminum tolerance proteins include organic acid efflux transporters, with the organic acids forming non-toxic complexes with rhizosphere aluminum. ge
Genetic mapping involves using genetic techniques like examining family histories and cross-breeding to construct maps showing the location of genes on a genome. It has been used successfully to identify genes responsible for rare single-gene disorders. Genetic maps provide clues about which chromosome contains a disease gene and its precise location. They are also useful for guiding research on more common multi-gene disorders. Physical mapping directly examines DNA to map sequence features, while genetic mapping looks for co-inheritance of diseases and genetic markers in family studies.
Marker assisted breeding of biotic stress resistance in Rice Senthil Natesan
A marker is a DNA sequence which serves as a signpost/flag post
linked to the trait/gene of interest and is co-inherited along with
the trait
Presence of specific allele of marker = Presence of specific allele of target gene based on the concept the MAS practiced -R.M. Sundaram
Directorate Rice of Research, Hydrabad , July 3rd 2009, CPMB&B, TNAU presentation
Wheat is the most important cereal crop grown in Afghanistan. There are two main types of wheat - spring wheat, which is planted in the spring, and winter wheat, which is planted in the fall. Wheat is classified by time of planting, color, and kernel hardness. The main cultural practices for wheat production include selecting an appropriate variety, properly planting at the right time and depth, applying fertilizer, and managing pests and diseases. Wheat is harvested when the heads are mature but before shattering to maximize yields.
Breeding for Drought tolerance in Pearl MilletSatish Patel
This document summarizes a presentation given by Patel Satishkumar on drought tolerance in pearl millet. The presentation covered introduction to pearl millet, mechanisms of drought tolerance, screening methods, case studies on physiological and biochemical responses to drought, and breeding approaches for drought tolerance. Key points included that 36% of India's land area is drought-prone, screening criteria focus on yield under stress conditions and secondary traits with high heritability and correlation to yield, and case studies demonstrated effects of drought on growth, yield, and physiological traits in various pearl millet genotypes.
This document summarizes updates from the 2010 PABRA SC meeting in South Africa.
1. The PABRA framework involves 11 member countries in southern Africa collaborating on bean research.
2. Key outcomes of the meeting included developing bean varieties resistant to environmental stresses and increasing nutrient-rich varieties to improve nutrition.
3. Activities involved identifying sources of stress resistance, distributing germplasm, developing integrated soil and pest management options, and breeding beans with higher iron and zinc content.
The official concern for food productivity stagnation calls for a Second Green Revolution involving new hybrid rice and transgenic rice varieties. However, traditional rice landraces prove to be fine tuned to local soil and climatic conditions. Traditional farmer landraces can yield significantly greater in marginal environmental conditions than any modern hybrid variety. Traditional agoecological knowledge and farmer innovations are the best bet to address the food security issue.
The document provides a summary of activities in 2012 and plans for 2013 regarding the collection, conservation and use of crop wild relatives (CWR). It discusses (1) closing the global system project, ramping up the CWR project, and initiating CRP Genebanks in 2012; (2) progress made in 2012 including regeneration of accessions, safety duplication, evaluation projects and results; and (3) plans for 2013 including CWR research, collecting, prebreeding and evaluation, and increasing information sharing and use of CWR. The overall aim is to collect, conserve and utilize important CWR diversity to help crops adapt to climate change.
1) Marker assisted breeding is being used at IRRI to introgress major effect drought tolerance QTLs from donors into popular rice varieties like IR64 and Swarna.
2) Several introgression lines have been developed that contain up to 4 drought tolerance QTLs and yield well under drought with grain quality similar to the recipient parent.
3) The protocol for pyramiding QTLs involves foreground and background selection across multiple generations followed by phenotyping of selected lines.
On June 14 - 15, on the occasion of 27th foundation day of U.P. Council of Agricultural Research, Lucknow, a two day National Conference was held on Mass Communication as an effective tool for Agriculture Development, Prof B. N. Singh delivered his lecture on On-farm Research on Aerobic rice Technology Testing and Dissemination in the said conference.
LEAD Trust is collaborating in digital propagation of his lecture slides, which are available here.
Technical Programme of P.h.D Experiment on Maize shikharverma26
This document provides details of a proposed PhD experiment on the effects of nano zinc, inorganic fertilizers, and organic manures on the growth and yield of maize. The experiment will have 21 treatments in a split plot design with 3 replications. Treatments will evaluate the effects of farmyard manure, vermicompost, and different combinations of recommended NPK doses with zinc sulfate and nano zinc on maize growth parameters, yield, nutrient uptake, and soil properties. Economic analysis of treatments will also be conducted.
The document discusses the System of Rice Intensification (SRI), an agricultural method that indicates a path toward post-modern agriculture. SRI was developed in Madagascar in the 1980s and aims to produce more rice with less water and other inputs through changes in plant, soil, and water management rather than external inputs. The document summarizes evidence that SRI leads to higher yields, less water use, lower costs, and greater resilience compared to conventional rice production methods. SRI practices have now spread to over 38 countries across Asia, Africa, and Latin America.
Presenter: T.M. Thiyagarajan
Institution: Agricultural College & Research Institute Killikulam, Vallanadu 628 252 Tamil Nadu
Presented at: World Rice Research Conference, Tsukuba, Japan
Subject Country: Tamil Nadu, India
Rijsberman cgiar science overview funders forum 2-11-2012CGIAR
The document provides an update on CGIAR Research and Results. It discusses that food security is the greatest challenge facing humanity in coming decades. CGIAR aims to increase sustainable food production through sustainable intensification while addressing ongoing issues of food insecurity, undernutrition, and micronutrient deficiencies. It summarizes the research focus and expected impacts of various CGIAR Research Programs such as MAIZE, WHEAT, Dryland Cereals, and Water, Land and Ecosystems. The document also highlights some early results and success stories from the research.
Presented by: Norman Uphoff, CIIFAD, Cornell University, USA
Presented at: International Conference on Sustainable Development in the Context of Climate Change- Asian Institute of Technology
Presented on: September 24, 2009
The document discusses CGIAR reform efforts to address global food security challenges. It notes that CGIAR reform has accomplished much in recent years, including establishing the CGIAR Consortium and Fund to better coordinate research across centers. However, it says the "last mile" of reform is critical to ensure the CGIAR is equipped to tackle the immense challenge of sustainably increasing food production to feed a growing global population. It emphasizes the importance of continued performance management, partnerships, and investments in areas like gender, agrobiodiversity and capacity building.
The document discusses updates on reforms to the CGIAR, a global agricultural research partnership. Key points include:
- Major achievements have been made in CGIAR reform, but more work remains in the "last mile" to ensure the reforms fully deliver on their promise.
- The reforms have established a CGIAR Consortium, Fund, and portfolio of CRPs (Collaborative Research Programs) to better coordinate research.
- Performance management systems still need improvement to set clear priorities and metrics for measuring outcomes of the CRPs.
- Partnerships also need more fulfillment of expectations through improved alignment and perception surveys.
- Continued priority issues are making the CRPs focused on clear outcomes and impact
Development of drought tolerant maize cultivars is prerequisite to achieving stable grain yield in
drought–prone ecologies of Nigeria’s Guinea savanna. However, success has been limited mainly due
to lack of maize genotypes that show clear differences in response to well defined moisture deficit
condition. Two sets of drought tolerant (DT) maize germplasm were evaluated under screenhouse and
field conditions between 1999 and 2002. In the screenhouse study, performances of the genotypes
were compared under well-watered condition and moisture deficit imposed at different growth stages.
Under field conditions, the first set comprising 11 accessions along with a check were evaluated for 4
growing seasons while the second set which comprised 3 DT varieties were evaluated along with 2
check varieties using monthly plantings between April and August of 2001 and 2002, respectively. In
the first set, post anthesis moisture deficit significantly reduced grain yield by 25 to 73.5% in the open
pollinated varieties (OPVs) and by 20 to 64% in the hybrids. Grain yield under field conditions ranged
from 2.48 to 3.49, 2.82 to 3.73 and 3.58 to 4.76 tons/ha-1 for 1999, 2000 and 2001 full growing seasons,
respectively, and 2.03 to 2.50 tons/ha-1 for 2000 late growing season. In the second set, pre and post
anthesis moisture deficits reduced grain yield by 77.6 and 95.8%, respectively, of well watered
condition while in the field, grain yields in the genotypes were highest for plantings made in April and
July (1.90 - 2.5 t/ha), lowest for August (0.7 -1.8 t/ha) when moisture deficit coincided with
reproductive phase. Yield stability exhibited under moisture deficit and on the field by 8522-2, Oba
super 2 and AK9943-DMRSR in the first set as well as DT-SR-Y C0 and DT-SR-W C0 in the second set,
indicates their suitability either as cultivars per se or as potential source of DT alleles for
development of DT maize varieties for Nigeria’s savanna ecologies.
Agronomic performance and farmers perception on zinc enriched rice brri dhan62Md. Julfiker Rahman
Newly developed zinc enriched rice variety BRRI dhan62 was evaluated along with three other short maturing Transplanted Aman (wet season) rice varieties namely BINA dhan7, BRRI dhan33 and BRRI dhan56 at six different locations of Bangladesh during 2014. The study was laid out in randomized complete block design where each of the six dispersedly located locations act as replications. Agronomic performance, yield and yield components were determined at maturity. Economic performance and farmer’s perceptions on the newly developed zinc enriched rice BRRI dhan62 were measured after harvest. Maximum genotypic difference was 12% in plant height, ranging from 122 to 109 cm among the tested varieties where BRRI dhan62 was the shortest and BRRI dhan56 was the tallest plant. The maximum grain yield was obtained from BINA dhan7 (5.70 ton h-1) which was similar with BRRI dhan33 and minimum grain yield was obtained from BRRI dhan62 (4.78 ton h-1) that was statistically similar with BRRI dhan56. BINA dhan7 gave maximum yield compared to other because of its maximum panicle number m-2. The highest yielding variety BINA dhan7 produced highest productivity day-1 (55 kg) which was statistically similar with BRRI dhan62 (51 kg) and lowest productivity day-1 was found BRRI dhan56 (48 kg). BRRI dhan33 produced highest benefit cost ratio (2.33) compared to other variety and BRRI dhan62 and BRRI dhan56 produced lowest benefit cost ratio (2.16). The short maturing characteristic of BRRI dhan62 was most preferred attribute by the farmers rather than higher yield or higher zinc content.
Utkur DJANIBEKOV "Cooperative institutions for increasing rural livelihood un...Global Risk Forum GRFDavos
Cooperative institutions for increasing rural livelihood under CDM forestation on marginal croplands.
The study examines afforesting marginal croplands in Uzbekistan through cooperative institutions between farmers and a clean development mechanism (CDM) project. Three scenarios are modeled: business as usual, individual farmer afforestation, and a CDM cooperative. The cooperative scenario produces the highest total outputs of food, fuelwood, and tree products by efficiently allocating water across farms. However, some individual farms may lose profits in a cooperative. Compensating disadvantaged farms from gains by others ensures all farms benefit. Cooperation allows complementarity across heterogeneous farm types to maximize livelihoods and carbon sequestration.
This summary provides the key details from the document in 3 sentences:
This document discusses a study evaluating an integrated disease management (IDM) approach for controlling foliar diseases in groundnuts. The study was conducted on farms in India over two growing seasons with the involvement of farmers. Results showed that combining moderate host plant resistance with seed treatment and one fungicide application led to higher yields compared to using susceptible varieties or relying only on chemical control.
Conservation agriculture for resource use efficiency and sustainability BASIX
The Green Revolution era focused on enhancing the production and productivity of crops. New challenges demand that the issues of efficient resource use and resource conservation receive high priority to ensure that past gains can be sustained and further enhanced to meet the emerging needs. Extending some of the resource-conserving interventions developed for the agricultural crops are the major challenges for researchers and farmers alike. The present paper shares recent research experiences on resource conservation technologies involving tillage and crop establishment options and associated agronomic practices which enable farmers in reducing production costs, increase profitability and help them move forward in the direction of adopting conservation agriculture.
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A workshop hosted by the South African Journal of Science aimed at postgraduate students and early career researchers with little or no experience in writing and publishing journal articles.
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A Survey of Techniques for Maximizing LLM Performance.pptx
Division seminar august 1,2012 prashant vikram
1. Major and consistent drought grain
yield QTLs for marker assisted
breeding in rice
Prashant Vikram
Visiting Research Fellow
PBGB Division, IRRI, Los Baños, Laguna
2. Outline
Introduction
qDTY1.1 : A QTL effective in multiple genetic backgrounds
Phenotyping & Genotyping strategies
qDTY1.1 : QTL effects
qDTY1.1 : Elimination of linkage drag
qDTY1.1 : Allelic analysis
qDTY1.1 :Candidate gene analysis
qDTY3.2 : A loci with interaction effects
qDTY12.1 : QTL stability across ecosystems and environments
qDTY8.1 : Mapping QTLs with basmati variety
Marker Assisted QTL Pyramiding (MAQP) for grain yield under drought
stress
Conclusions
3. Global Water Resource & Rice
• Estimated water resource: 43750 km3/year
• 70% of fresh water resource is consumed in Agriculture
• Water resource per inhabitant is least in Asia where 90% world’s rice is
grown
• Rice is a semi-aquatic plant and 1Kg rice consumes 3000-5000 Kg water
• 20% of global calorie intake; 35-60% calories source in Asia alone
Water resource Rice Calorie intake
4. Rice Cultivation and Water regimes
Rice
Irrigated Rainfed
(55%)
Rainfed Rainfed
upland lowland
(9%) (34%)
Bouman, 2007
Sub-Saharan Africa: ~80% rice area is rainfed
South Asia: 50% harvested rice area is rainfed (Dawe, 2010)
Drought tolerant rice is a felt need
Rice field affected by drought in India; June, 2010
(Source, Channel Asia, Times of India)
5. Drought breeding approaches : Conventional & Molecular
Drought is a complex trait & improvement of drought tolerance
through indirect selection of secondary traits did not yield satisfactory
results
Direct selection for grain yield under drought is a well proven
India
criterion and several varieties have been released using this approach in
last 3 years:
Sahbhagi dhan (India);
Sukha dhan-1, Sukha dhan-2 & Sukha dhan-3 (Nepal);
BRRI Dhan-56 (Bangladesh);
Bangladesh
Sahod ulan-3, 5, 6, 8 & Katihan-8 (Philippines)
Fast track improvement for drought tolerance : MAB
Marker products in pipeline (Swamy and Kumar, 2011) Nepal
MAB: Enhancing efficiency of drought breeding
(for grain yield under drought)
Philippines
6. MAB: Drought QTLs identified in rice
1. Literature Search:
2. Pub Med Search:
Drought: 7072
Drought + rice: 525
Drought +rice +QTLs: 48
Drought +rice +grain yield+ QTLs: 16
8 papers related to GY under drought
3. Gramene Search:
Drought + QTLs : 77
Drought + QTLs + rice: 42
Drought +rice + QTLs + grain yield: 0
Vikram et al. 2012
QTLs identified in past: Mostly secondary traits
Specific to genetic backgrounds & Seldom used for MAS
Consistent drought grain yield QTLs worthy for MAS
7. Are drought grain yield QTLs real ?
qDTY3.2 qDTY6.1
(Vikram et al. 2011) (Venuprasad et
al. 2012)
qDTY12.1
(Bernier et al.
2007)
qDTY1.1 qDTY3.1
(Venuprasad et al.
(Vikram et al. 2011)
2009)
Drought grain yield QTLs are real !
Several genomic regions harbour consistent QTLs: Across backgrounds
Consistent drought grain yield QTLs :
Potential candidates for MAB
8. qDTY1.1: A QTL effective in multiple genetic
backgrounds
QTL Mapping Strategy
Populations: common donor & multiple recipient parents
Phenotyping: GY under reproductive stage drought stress
Genotyping: WPG & BSA
9. Development of mapping populations
N22 × IR64 Target varieties F1 F2
N22 × Swarna
N22 × MTU1010
Selected single seed of
each F2 plant
F3:4 plants were phenotyped for grain yield under
lowland reproductive stage drought stress. Single F3 plants were grown
and harvested individually.
Target varieties F1 F2
Dhagaddeshi × IR64
Dhagaddeshi × Swarna
Selected single seed of
each F2 plant
F3:4 lines of Dhagaddeshi derived populations were Single F3 plants were grown
grown for seed increase. and harvested individually.
F3:5 & F3:6 lines phenotyped & genotyped for grain yield under drought stress.
Populations with common donor and multiple recipients
10. Phenotyping: Larger populations required
1. Distribution of genotypes for grain yield under stress in N22 x IR64 population
2. Distribution of genotypes for grain yield under stress in N22 x Swarna population
3. Distribution of genotypes for grain yield under stress in N22 x MTU1010 population
Populations were large enough to show normal distribution
11. QTL identification for grain yield under drought: Population size
300-350 population size is good
enough for identification of
drought grain yield QTLs
Vikram et al. 2012 (FCR)
12. Phenotyping: Screening for grain yield under drought
Drought stress experiment
• All mapping populations planted in two replications 5m
single row plot in two consecutive Dry seasons
• Water stress was given 50 days after sowing
• Grain Yield and yield related trait data were recorded
• Days to 50% flowering
• Plant height
• Biomass
• Grain yield
• HI
Non Stress/ Irrigated experiment
•Same trial was repeated under non stress condition
•Under non stress a 5cm water maintained till maturity
Lines must be under stress
at least 2 weeks before flowering
13. Phenotyping: Characterization for grain yield under drought Stress
Depleting water level under drought stress
Water table goes below 80 KPa
Mild stress: ≤ 30% yield reduction
Moderate stress: 31-65 % yield reduction
Rainfall relative to meat trial flowering Severe stress: 65-85 % yield reduction
DS2010 RAINFALL mm
DS2011 RAINFALL mm Rainless days during flowering
Water table Rainfall
March 1-10
March 21-31
March 11-20
January 1-10
January 21-31
January 11-20
February 1-10
February 21-28
February 11-20
Flowering
DS2010
DS2011
FLOWERING RANGE
14. Genotyping: Whole population genotyping Vs BSA
BSA
Powerful and cost effective approach
Applicable to multiple populations simultaneously
Useful in identifying major and consistent QTLs
16. BSA: genotype multiple populations simultaneously
BSA
RM212 Identify few markers
BSA with adjoining markers
RM431 of the identified one.
Validation of BSA results
RM315
BSA can be validated through
genotyping of phenotypic tails with
DHAGADDESHI
DHAGADDESHI
BULK HIGH
BULK HIGH
BULK LOW
BULK LOW
BULK HIGH BSA markers (Kanagaraj et al. 2010)
SWARNA
BULK LOW
SWARNA
SWARNA
N22
RM11943 RM431 RM231
17. BSA: QTL Effects
Selective genotyping lead to an upward estimation of QTL effects
BSA doesn’t lead to an upward estimation of QTL effects
Vikram et al. 2012 (FCR)
18. Drought grain yield QTLs in N22 populations
N22 *
N22
N22 *
qDTY2.3
qDTY1.1
N22 x IR64
N22 x Swarna
qDTY3.2
N22 x IR64
N22 x MTU1010 N22 x Swarna
19. QTL qDTY1.1 on tail end of chromosome 1
qDTY1.1 located at the distal
end of chromosome 1
RM212
RM3825
RM315
RM11943
RM431
RM12023
RM12091
RM12146
RM12233
21. QTL identification: Contrasting parents Vs Target variety
qDTY3.2 effect under
moderate stress only
Vikram et al. 2011 (BMC Genetics)
qDTY2.3 effect under
severe stress only
Days to flowering
loci from MTU1010
•QTL effect depends on contrast of the parents Additive effect
•Large effect QTL in one background may not work in other
Swarna > IR64 > MTU1010
•Target variety should be used in QTL identification and MAB
Drought tolerance
22. Co-variate analysis for DTF and Plant height
Co-variate adjustment of DTF and plant height
qDTY1.1: Significant for grain yield under drought after the co-variate adjustment
Single-marker analysis after covariance adjustment for DTF under drought stress
Mean grain yield of N22 Mean grain yield of IR64, Swarna,
Population Marker p-value
homozygote (kg/ha) MTU1010 homozygote (kg/ha)
RM431 1273 761 <0.001
N22/IR64
RM11943 1239 878 <0.001
RM431 1517 926 <0.01
N22/Swarna
RM11943 1484 927 <0.01
RM431 1543 1149 <0.01
N22/MTU1010
RM11943 1531 1199 <0.01
Single-marker interval analysis after covariance adjustment for PH under drought stress
Mean grain yield of N22 Mean grain yield of IR64/,
Population p-value
homozygote Swarna/, MTU1010 homozygote
N22/Swarna 1448 1267 <0.01
N22/IR64 1330 1073 <0.01
N22/MTU1010 1470 1381 NS
Vikram et al. 2011 (BMC Genetics)
23. Elimination of linkage drag: N22/Swarna
N22 × Swarna
FG X FG
217 dwarf 2 Plants segregating for
BC3F1 Selected 21 F1s ~3000 BC3F2 qDTY1.1
plants
X FG X Ratooned and
Screened under ROS in WS2011 Full & partial QTL ~180 BC3F3
split planted
lines
Selected recombinants
X
Single plant selected and
Screened in DS2012 Full QTL lines
genotyped for foreground
Plants selected for Swarna plant
type and grain type
Background genotyping Six introgressed Markers run on
regions identified N22/Swarna RIL
population
Plants with clear background
Phenotypically and genotypically
No effect on GY
under RS
Being screened at IRRI Being screened at Hazaribagh,
under ROS India under ROS
Dwarf qDTY1.1 lines in Swarna background
25. 115 Days after sowing
STRESS
Swarna BIL
NON STRESS
Swarna BIL
April, 16,2012
Dwarf qDTY1.1 lines in Swarna background
Non stress: they had similar flowering time as Swarna
26. Elimination of linkage drag: N22/IR64 & N22/MTU1010
N22/IR64 & N22/MTU1010 RILs
•segregating for qDTY1.1 ,
F5, F6 and
•<130 cm under non stress,
F7 planted
•Better yield under drought
stress
All these plants are grown
under rainfed situation
800 semi-dwarf (~400 from both
population) plants tagged and
genotyped.
RILs with qDTY1.1 and height comparable
to IR64/ MTU1010 identified
27. qDTY1.1: Allelic study
•qDTY1.1 tolerant allele contributed by traditional donors: (1) N22 (2) Apo (3)
Dhagaddeshi
RM431 in random varieties
qDTY1.1 was significant in more than 50% of drought QTL panel lines (Swamy et al. 2011)
RM431 in random varieties
0.06
N22
landraces
Dhagaddeshi
N22 & Dhagaddeshi are Samba Mahsuri
closer phylogenetically Sw arna
Apo Variety
MTU1010
IR 64
Basmat i 334
28. Closeness of N22 & Dhagaddeshi
67 %
Marker loci where drought-tolerant varieties Dhagaddeshi and N22 have similar alleles,
different from the alleles in susceptible varieties Swarna and IR64
30. Candidate gene analysis for qDTY1.1
SNPs among N22, IR64 and Swarna, qDTY1.1 region were compared.
Based on available reports differentially expressed genes in qDTY1.1
region between N22 and IR64 were annotated.
31. SNPs in qDTY1.1 region: a region specific to N22
N22
Swarna
IR64
1 TBGI065107 40298480 C T T
1 TBGI065108 40298598 T C C
1 TBGI065127 40329203 A G G
1 TBGI065129 40329319 C T T
1 TBGI065130 40329422 G A A
1 TBGI065133 40330056 G T T
1 TBGI065139 40332364 T G G
A 90 Kb block specific to N22
1 TBGI065142 40332797 G A A in qDTY1.1 region
1 TBGI065146 40333650 A C C
1 TBGI065154 40334497 C T T
1 TBGI065155 40334597 C T T
1 TBGI065156 40334719 T C C
1 TBGI065158 40334855 G T T
1 TBGI065161 40335346 T C C
1 TBGI065169 40373741 G C C
SNP ID Position
32. Differentially expressed genes between N22 & IR64 in
qDTY1.1 : Candidate genes
RM212
1. LOC_Os01g65690
2. LOC_Os01g65780
3. LOC_Os01g66010 RM315
4. LOC_Os01g66290 RM11943
5. LOC_Os01g66860
(4,5-DOPA dioxygenase extradiol,
RM431
glycosyl transferase,
amino acid transporters, RM104
MADS-box family gene, RM529
serine/threonine protein kinase)
RM2182
RM2227
(Lenka et al. 2011) RM2289
Vikram et al. 2011 (BMC Genetics)
33. qDTY1.1 peak marker RM431: A marker from Gene
containing zing finger
RM431
Peak marker in most studies
Meta-QTL analysis
34. qDTY3.2 : A loci with interaction effects
qDTY3.2: First identified in N22 x Swarna population for grain yield under drought
(Vikram et al. 2012-BMC Genetics)
Located on the proximal end (top) of the chromosome 3
This QTL showed significant interaction with qDTY1.1 in N22 × Swarna as well as N22
× IR64 populations
qDTY3.2 : interaction with qDTY12.1 (Dixit et al. 2012- Mol. breed)
qDTY3.2 : Significant effect for GY under drought in IR77298-5-6-18/Sabitri population.
Additive interaction of qDTY1.1 & qDTY3.2
: advantage for MAB
35. qDTY3.2 – qDTY1.1 interaction
qDTY3.2 qDTY3.2
qDTY1.1 qDTY1.1
N22/IR64 RIL population N22/Swarna RIL population
36. qDTY12.1: QTL stability across ecosystems and
environments
IR74371-46-1-1/ Sabitri BIL population
Sabitri is popular variety of Nepal
Screened under lowland drought stress at IRRI and Nepal
Genotyped through BSA
qDTY12.1 was found consistent at both locations
37. Phenotyping at IRRI
Duration
WATER TABLE DATA OF DS2011
DS2011, IRRI
Water table (cm)
Rainfall (mm)
RAINFALL DATA OF DS2011
flowering (days)
Days to 50%
FLOWERING RANGE
38. Phenotyping at Nepal
Duration
WATER TABLE DATA OF DS2011
WS2011, Nepal
Water table (cm)
RAINFALL DATA OF DS2011
Rainfall (mm)
flowering (days)
Days to 50%
FLOWERING RANGE
39. qDTY12.1: QTL across ecosystems, environments & backgrounds
Peak marker : RM28166
Additive effect: 47.7%
Phenotypic variance: 24.6%
qDTY12.1
(18.15Mb)
(15.41Mb)
RM28199
RM28089
•Ecosystem: lowland and upland drought stress
•Environments: IRRI and Nepal
•Backgrounds –Vandana and Sabitri
Mishra et al. Unpublished
40. qDTY12.1: Interaction effect analysis
V/W
•qDTY12.1 showed significant interaction with two other loci W Yield advantage
qDTY12.1 Under drought
(qDTY2.3 and qDTY3.2) Dixit et al. 2012 (Mol. Breed)
•No interaction was observed in lowland drought stress in +
IR74371-46-1-1/ Sabitri population V V/W Enhanced
qDTY2.3 yield advantage
Population qDTY12.1 qDTY2.3 qDTY3.2 qDTY3.2 Under drought
Interaction Ecosystem
QTL (29-41%)
V-W W V V √ Upland
I-S I I/S I/S × Lowland IR74371-46-1-1 (I) is
derivative of Wayrarem (W)
•Under upland qDTY12.1 W allele interacts with qDTY2.3 & I/S
I Yield advantage
qDTY3.2 allele of Vandana (V) qDTY12.1 Under drought
•Under lowland I/W allele of qDTY12.1 is effective alone
+
•Vandana is drought tolerant upland adapted variety
S I/S No additional
•Sabitri is drought susceptible lowland adapted variety qDTY2.3 yield advantage
qDTY3.2 Under drought
qDTY12.1 effect vary with backgrounds and ecosystems
Use of target variety in QTL study
41. qDTY8.1: Mapping QTLs with basmati variety
Basmati334:traditional Basmati cultivar of Punjab (India and Pakistan)
• F3:5 Basmati334/ Swarna population was
screened for yield under drought stress
in Dry Season 2010.
• qDTY8.1 was identified as significant loci
for yield under drought through BSA.
Additive effect -160.53
Population mean 621.12
AE (%) -25.84 %
Marker interval RM210-RM447
44. Marker assisted Pyramiding in Swarna background
Basmati334-Swarna F4 X Apo-Swarna BC3F1 WS 2008
qDTY8.1 qDTY3.1
F1 X N22 x Swarna F4 WS 2009
qDTY1.1
qDTY1.1 + qDTY3.1 +qDTY8.1
F1
DS 2010
F1 plants with 3 QTLs X Swarna
WS 2010
F1 plants individual QTLs X Swarna
F1s with qDTY3.1 X F1s with qDTY1.1+qDTY8.1 DS 2011
Four F1 plants selected with qDTY1.1+qDTY3.1+qDTY8.1
WS 2011
X
Four F2 families with qDTY1.1+qDTY3.1+qDTY8.1 planted DS 2012
T RE QT L S RE
H E L INE ADY FOR PH NOT IC SCRE NING
E YP E
45. Marker assisted Pyramiding in Sabitri background
IR74371-46-1-1/Sabitri X IR77298-5-6-18/Sabitri WS 2011
BC1F5 BC1F5
qDTY12.1 qDTY3.2
F1
F2 qDTY12.1 + qDTY3.2
DS 2012
1000F2
Genotyping of F2 contd….
46. CONCLUSIONS……
• A large effect QTL on chromosome 1 was identified in multiple
populations simultaneously through WPG/BSA.
• Bulked segregant Analysis is a powerful and cost-effective
strategy in identifying drought grain yield QTLs
• QTL effects depend on ecosystems, environments and
backgrounds. Target varieties should be used in QTL studies.
• DTY-QTLs showed interactions with other regions. Additive
interactions are useful for MAB.
• qDTY1.1 linked with plant height. Linkage broken for product
development.
• qDTY1.1 positive alleles are likely to be conserved in landraces
• qDTY1.1 harbors candidate genes –AA transporters, PK & ZFP.
• qDTY12.1 was consistent across-ecosystems, environments &
backgrounds.
• Marker Assisted QTL Pyramiding (MAQP) is a preferred
strategy for improving rice varieties for rainfed environments.
47. Acknowledgements
Funding Agencies Team Leader
•Generation Challenge program (GCP) • Dr. Arvind Kumar
•Bill and Melinda Gates Foundation (STRASA)
PDF /VRF Collaborating IRRI scientists
• Dr. BPM Swamy • Dr. Amelia Henry
• Dr. Ajay Kohli
• Dr. Shalabh Dixit
Collaborators (NARS)
Assistant Scientists • Dr. N. K. Singh, NRCPB, IARI, India
• Jennylyn Trinidad • Dr.N.P.Mandal, Hazaribagh, India
• Paul C. Maturan • Dr.P.Swain, CRRI, Cuttack, India
• MT Sta. Cruz • Dr.O.N.Singh, CRRI, Cuttack, India
Researchers • Krishna Kumar Mishra, Nepal
• Ruth E Carpio • Ram Baran Yadaw, Nepal
• Guevarra Jocelyn
Technicians
• Teody, Loui, Orly