The Experts below are selected from a list of 6993 Experts worldwide ranked by ideXlab platform
Rajeev K Varshney - One of the best experts on this subject based on the ideXlab platform.
-
genomics assisted breeding for Pigeonpea improvement
Theoretical and Applied Genetics, 2020Co-Authors: Abhishek Bohra, K B Saxena, Rajeev K Varshney, Rachit K SaxenaAbstract:The review outlines advances in Pigeonpea genomics, breeding and seed delivery systems to achieve yield gains at farmers’ field. Pigeonpea is a nutritious and stress-tolerant grain legume crop of tropical and subtropical regions. Decades of breeding efforts in Pigeonpea have resulted in development of a number of high-yielding cultivars. Of late, the development of CMS-based hybrid technology has allowed the exploitation of heterosis for yield enhancement in this crop. Despite these positive developments, the actual on-farm yield of Pigeonpea is still well below its potential productivity. Growing needs for high and sustainable Pigeonpea yields motivate scientists to improve the breeding efficiency to deliver a steady stream of cultivars that will provide yield benefits under both ideal and stressed environments. To achieve this objective in the shortest possible time, it is imperative that various crop breeding activities are integrated with appropriate new genomics technologies. In this context, the last decade has seen a remarkable rise in the generation of important genomic resources such as genome-wide markers, high-throughput genotyping assays, saturated genome maps, marker/gene–trait associations, whole-genome sequence and germplasm resequencing data. In some cases, marker/gene–trait associations are being employed in Pigeonpea breeding programs to improve the valuable yield and market-preferred traits. Embracing new breeding tools like genomic selection and speed breeding is likely to improve genetic gains. Breeding high-yielding Pigeonpea cultivars with key adaptation traits also calls for a renewed focus on systematic selection and utilization of targeted genetic resources. Of equal importance is to overcome the difficulties being faced by seed industry to take the new cultivars to the doorstep of farmers.
-
breeding Pigeonpea cultivars for intercropping synthesis and strategies
Breeding Science, 2018Co-Authors: K B Saxena, A K Choudhary, Rachit K Saxena, Rajeev K VarshneyAbstract:Pigeonpea [Cajanus cajan (L.) Millsp.] is an ideal pulse crop of rainfed tropics and sub-tropics due to its high nutritive value and ability to survive various biotic and abiotic stresses. Thus it has continued to be cultivated on marginal land mostly under rainfed situation where the risk of crop failure is very high. To have insurance against crop failures and harvest more food in time and space, most farmers grow Pigeonpea as an intercrop with short-aged cereals and other crops. Presently, intercropping system accounts for over 70% of the Pigeonpea area. However, yield of Pigeonpea in this system is very low (400-500 kg/ha). The non-availability of improved cultivars adapted specifically to the intercropping environments is perhaps the major constraint that accounts for low yield. Considering the food and nutritional needs of the ever increasing population, productivity enhancement of this high-protein pulse is highly indispensable. In this review, the authors critically examine the technical difficulties encountered by breeders in developing high yielding cultivars for intercropping systems and discuss the strategies to overcome these constraints.
-
single nucleotide polymorphism genotyping for breeding and genetics applications in chickpea and Pigeonpea using the beadxpress platform
The Plant Genome, 2013Co-Authors: Manish Roorkiwal, Rachit K Saxena, S L Sawargaonkar, Annapurna Chitikineni, Mahendar Thudi, Hari D Upadhyaya, Isabel M Vales, Oscar Rieralizarazu, Rajeev K VarshneyAbstract:Single nucleotide polymorphisms (SNPs) are ideal molecular markers due to their higher abundance. Although several types of genotyping platforms for assaying large number of SNPs are available, in cases such as marker-assisted selection, where few markers are required for genotyping a set of potential lines, highthroughput SNP genotyping platforms (e.g., iScan or Infinium) may not be cost effective. In this scenario, GoldenGate assays based on VeraCode technology using Illumina BeadXpress seems to be the most cost-effective platform. The objective of this study was to develop cost-effective SNP genotyping platforms in chickpea (Cicer arietinum L.) and Pigeonpea (Cajanus cajan L.). Two sets of SNPs, one each for chickpea (96 SNPs) and Pigeonpea (48 SNPs), were developed and tested by genotyping 288 diverse genotypes from respective reference sets. The SNPs selected for the oligo pool assays had high transferability to crop wild relative species. The mean polymorphism information content value of assayed SNP markers was 0.31 and 0.32 in chickpea and Pigeonpea, respectively. No unique pattern was observed in the chickpea reference set whereas two major groups were observed in the case of the Pigeonpea reference set. The Illumina BeadXpress platform assays developed for chickpea and Pigeonpea are highly informative and cost effective for undertaking genetic studies in these legume species.
-
advances in genetics and molecular breeding of three legume crops of semi arid tropics using next generation sequencing and high throughput genotyping technologies
Journal of Biosciences, 2012Co-Authors: Rachit K Saxena, Rajeev K Varshney, Himabindu Kudapa, Manish Roorkiwal, Mahendar Thudi, Manish K Pandey, Siva K Chamarthi, Murali Mohan S, Nalini MallikarjunaAbstract:Molecular markers are the most powerful genomic tools to increase the efficiency and precision of breeding practices for crop improvement. Progress in the development of genomic resources in the leading legume crops of the semi-arid tropics (SAT), namely, chickpea (Cicer arietinum), Pigeonpea (Cajanus cajan) and groundnut (Arachis hypogaea), as compared to other crop species like cereals, has been very slow. With the advances in next-generation sequencing (NGS) and high-throughput (HTP) genotyping methods, there is a shift in development of genomic resources including molecular markers in these crops. For instance, 2,000 to 3,000 novel simple sequence repeats (SSR) markers have been developed each for chickpea, Pigeonpea and groundnut. Based on Sanger, 454/FLX and Illumina transcript reads, transcriptome assemblies have been developed for chickpea (44,845 transcript assembly contigs, or TACs) and Pigeonpea (21,434 TACs). Illumina sequencing of some parental genotypes of mapping populations has resulted in the development of 120 million reads for chickpea and 128.9 million reads for Pigeonpea. Alignment of these Illumina reads with respective transcriptome assemblies have provided >10,000 SNPs each in chickpea and Pigeonpea. A variety of SNP genotyping platforms including GoldenGate, VeraCode and Competitive Allele Specific PCR (KASPar) assays have been developed in chickpea and Pigeonpea. By using above resources, the first-generation or comprehensive genetic maps have been developed in the three legume species mentioned above. Analysis of phenotyping data together with genotyping data has provided candidate markers for drought-tolerance-related root traits in chickpea, resistance to foliar diseases in groundnut and sterility mosaic disease (SMD) and fertility restoration in Pigeonpea. Together with these trait-associated markers along with those already available, molecular breeding programmes have been initiated for enhancing drought tolerance, resistance to fusarium wilt and ascochyta blight in chickpea and resistance to foliar diseases in groundnut. These trait-associated robust markers along with other genomic resources including genetic maps and genomic resources will certainly accelerate crop improvement programmes in the SAT legumes.
-
genetic patterns of domestication in Pigeonpea cajanus cajan l millsp and wild cajanus relatives
PLOS ONE, 2012Co-Authors: Mulualem T Kassa, Rajeev K Varshney, Varma R Penmetsa, Noelia Carrasquillagarcia, B K Sarma, Subhojit Datta, H D Upadhyaya, Eric J B Von WettbergAbstract:Pigeonpea (Cajanus cajan) is an annual or short-lived perennial food legume of acute regional importance, providing significant protein to the human diet in less developed regions of Asia and Africa. Due to its narrow genetic base, Pigeonpea improvement is increasingly reliant on introgression of valuable traits from wild forms, a practice that would benefit from knowledge of its domestication history and relationships to wild species. Here we use 752 single nucleotide polymorphisms (SNPs) derived from 670 low copy orthologous genes to clarify the evolutionary history of Pigeonpea (79 accessions) and its wild relatives (31 accessions). We identified three well-supported lineages that are geographically clustered and congruent with previous nuclear and plastid sequence-based phylogenies. Among all species analyzed Cajanus cajanifolius is the most probable progenitor of cultivated Pigeonpea. Multiple lines of evidence suggest recent gene flow between cultivated and non-cultivated forms, as well as historical gene flow between diverged but sympatric species. Evidence supports that primary domestication occurred in India, with a second and more recent nested population bottleneck focused in tropical regions that is the likely consequence of Pigeonpea breeding. We find abundant allelic variation and genetic diversity among the wild relatives, with the exception of wild species from Australia for which we report a third bottleneck unrelated to domestication within India. Domesticated C. cajan possess 75% less allelic diversity than the progenitor clade of wild Indian species, indicating a severe “domestication bottleneck” during Pigeonpea domestication.
Rachit K Saxena - One of the best experts on this subject based on the ideXlab platform.
-
genomics assisted breeding for Pigeonpea improvement
Theoretical and Applied Genetics, 2020Co-Authors: Abhishek Bohra, K B Saxena, Rajeev K Varshney, Rachit K SaxenaAbstract:The review outlines advances in Pigeonpea genomics, breeding and seed delivery systems to achieve yield gains at farmers’ field. Pigeonpea is a nutritious and stress-tolerant grain legume crop of tropical and subtropical regions. Decades of breeding efforts in Pigeonpea have resulted in development of a number of high-yielding cultivars. Of late, the development of CMS-based hybrid technology has allowed the exploitation of heterosis for yield enhancement in this crop. Despite these positive developments, the actual on-farm yield of Pigeonpea is still well below its potential productivity. Growing needs for high and sustainable Pigeonpea yields motivate scientists to improve the breeding efficiency to deliver a steady stream of cultivars that will provide yield benefits under both ideal and stressed environments. To achieve this objective in the shortest possible time, it is imperative that various crop breeding activities are integrated with appropriate new genomics technologies. In this context, the last decade has seen a remarkable rise in the generation of important genomic resources such as genome-wide markers, high-throughput genotyping assays, saturated genome maps, marker/gene–trait associations, whole-genome sequence and germplasm resequencing data. In some cases, marker/gene–trait associations are being employed in Pigeonpea breeding programs to improve the valuable yield and market-preferred traits. Embracing new breeding tools like genomic selection and speed breeding is likely to improve genetic gains. Breeding high-yielding Pigeonpea cultivars with key adaptation traits also calls for a renewed focus on systematic selection and utilization of targeted genetic resources. Of equal importance is to overcome the difficulties being faced by seed industry to take the new cultivars to the doorstep of farmers.
-
breeding Pigeonpea cultivars for intercropping synthesis and strategies
Breeding Science, 2018Co-Authors: K B Saxena, A K Choudhary, Rachit K Saxena, Rajeev K VarshneyAbstract:Pigeonpea [Cajanus cajan (L.) Millsp.] is an ideal pulse crop of rainfed tropics and sub-tropics due to its high nutritive value and ability to survive various biotic and abiotic stresses. Thus it has continued to be cultivated on marginal land mostly under rainfed situation where the risk of crop failure is very high. To have insurance against crop failures and harvest more food in time and space, most farmers grow Pigeonpea as an intercrop with short-aged cereals and other crops. Presently, intercropping system accounts for over 70% of the Pigeonpea area. However, yield of Pigeonpea in this system is very low (400-500 kg/ha). The non-availability of improved cultivars adapted specifically to the intercropping environments is perhaps the major constraint that accounts for low yield. Considering the food and nutritional needs of the ever increasing population, productivity enhancement of this high-protein pulse is highly indispensable. In this review, the authors critically examine the technical difficulties encountered by breeders in developing high yielding cultivars for intercropping systems and discuss the strategies to overcome these constraints.
-
genomics assisted breeding for boosting crop improvement in Pigeonpea cajanus cajan
Frontiers in Plant Science, 2015Co-Authors: Lekha T Pazhamala, Rachit K Saxena, Vikas Singh, C V Sameerkumar, Vinay Kumar, Pallavi Sinha, Kishan Patel, Jimmy Obala, Seleman R KaonekaAbstract:Pigeonpea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although Pigeonpea growing area has considerably increased, yield has remained stagnant for the last six decades mainly due to the exposure of the crop to various biotic and abiotic constraints. In addition, low level of genetic variability and limited genomic resources have been serious impediments to Pigeonpea crop improvement through modern breeding approaches. In recent years, however, due to the availability of next generation sequencing and high-throughput genotyping technologies, the scenario has changed tremendously. The reduced sequencing costs resulting in the decoding of the Pigeonpea genome has led to the development of various genomic resources including molecular markers, transcript sequences and comprehensive genetic maps. Mapping of some important traits including resistance to Fusarium wilt and sterility mosaic disease, fertility restoration, determinacy with other agronomically important traits have paved the way for applying genomics-assisted breeding (GAB) through marker assisted selection as well as genomic selection (GS). This would accelerate the development and improvement of both varieties and hybrids in Pigeonpea. Particularly for hybrid breeding programme, mitochondrial genomes of cytoplasmic male sterile (CMS) lines, maintainers and hybrids have been sequenced to identify genes responsible for cytoplasmic male sterility. Furthermore, several diagnostic molecular markers have been developed to assess the purity of commercial hybrids. In summary, Pigeonpea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in Pigeonpea breeding.
-
candidate gene analysis for determinacy in Pigeonpea cajanus spp
Theoretical and Applied Genetics, 2014Co-Authors: K B Saxena, Rachit K Saxena, Sarwar Azam, Reyazul Rouf Mir, Himabindu Kudapa, Sandhya Srikanth, Ashutosh Sharma, Varma R PenmetsaAbstract:Pigeonpea (Cajanus cajan) is the sixth most important legume crop grown on ~5 million hectares globally. Determinacy is an agronomically important trait selected during Pigeonpea domestication. In the present study, seven genes related to determinacy/flowering pattern in Pigeonpea were isolated through a comparative genomics approach. Single nucleotide polymorphism (SNP) analysis of these candidate genes on 142 Pigeonpea lines found a strong association of SNPs with the determinacy trait for three of the genes. Subsequently, QTL analysis highlighted one gene, CcTFL1, as a likely candidate for determinacy in Pigeonpea since it explained 45–96 % of phenotypic variation for determinacy, 45 % for flowering time and 77 % for plant height. Comparative genomics analysis of CcTFL1 with the soybean (Glycine max) and common bean (Phaseolus vulgaris) genomes at the micro-syntenic level further enhanced our confidence in CcTFL1 as a likely candidate gene. These findings have been validated by expression analysis that showed down regulation of CcTFL1 in a determinate line in comparison to an indeterminate line. Gene-based markers developed in the present study will allow faster manipulation of the determinacy trait in future breeding programs of Pigeonpea and will also help in the development of markers for these traits in other related legume species.
-
single nucleotide polymorphism genotyping for breeding and genetics applications in chickpea and Pigeonpea using the beadxpress platform
The Plant Genome, 2013Co-Authors: Manish Roorkiwal, Rachit K Saxena, S L Sawargaonkar, Annapurna Chitikineni, Mahendar Thudi, Hari D Upadhyaya, Isabel M Vales, Oscar Rieralizarazu, Rajeev K VarshneyAbstract:Single nucleotide polymorphisms (SNPs) are ideal molecular markers due to their higher abundance. Although several types of genotyping platforms for assaying large number of SNPs are available, in cases such as marker-assisted selection, where few markers are required for genotyping a set of potential lines, highthroughput SNP genotyping platforms (e.g., iScan or Infinium) may not be cost effective. In this scenario, GoldenGate assays based on VeraCode technology using Illumina BeadXpress seems to be the most cost-effective platform. The objective of this study was to develop cost-effective SNP genotyping platforms in chickpea (Cicer arietinum L.) and Pigeonpea (Cajanus cajan L.). Two sets of SNPs, one each for chickpea (96 SNPs) and Pigeonpea (48 SNPs), were developed and tested by genotyping 288 diverse genotypes from respective reference sets. The SNPs selected for the oligo pool assays had high transferability to crop wild relative species. The mean polymorphism information content value of assayed SNP markers was 0.31 and 0.32 in chickpea and Pigeonpea, respectively. No unique pattern was observed in the chickpea reference set whereas two major groups were observed in the case of the Pigeonpea reference set. The Illumina BeadXpress platform assays developed for chickpea and Pigeonpea are highly informative and cost effective for undertaking genetic studies in these legume species.
K B Saxena - One of the best experts on this subject based on the ideXlab platform.
-
genomics assisted breeding for Pigeonpea improvement
Theoretical and Applied Genetics, 2020Co-Authors: Abhishek Bohra, K B Saxena, Rajeev K Varshney, Rachit K SaxenaAbstract:The review outlines advances in Pigeonpea genomics, breeding and seed delivery systems to achieve yield gains at farmers’ field. Pigeonpea is a nutritious and stress-tolerant grain legume crop of tropical and subtropical regions. Decades of breeding efforts in Pigeonpea have resulted in development of a number of high-yielding cultivars. Of late, the development of CMS-based hybrid technology has allowed the exploitation of heterosis for yield enhancement in this crop. Despite these positive developments, the actual on-farm yield of Pigeonpea is still well below its potential productivity. Growing needs for high and sustainable Pigeonpea yields motivate scientists to improve the breeding efficiency to deliver a steady stream of cultivars that will provide yield benefits under both ideal and stressed environments. To achieve this objective in the shortest possible time, it is imperative that various crop breeding activities are integrated with appropriate new genomics technologies. In this context, the last decade has seen a remarkable rise in the generation of important genomic resources such as genome-wide markers, high-throughput genotyping assays, saturated genome maps, marker/gene–trait associations, whole-genome sequence and germplasm resequencing data. In some cases, marker/gene–trait associations are being employed in Pigeonpea breeding programs to improve the valuable yield and market-preferred traits. Embracing new breeding tools like genomic selection and speed breeding is likely to improve genetic gains. Breeding high-yielding Pigeonpea cultivars with key adaptation traits also calls for a renewed focus on systematic selection and utilization of targeted genetic resources. Of equal importance is to overcome the difficulties being faced by seed industry to take the new cultivars to the doorstep of farmers.
-
Natural cross-pollination is both a boon and bane for Pigeonpea breeders
2019Co-Authors: R Sultana, K B SaxenaAbstract:Natural cross-pollination in Pigeonpea, mediated by insects, is a universal phenomenon with the first report appearing in 1919. Considerable information is now available on various aspects of this biological phenomenon including degree of out-crossing and pollinating agents in different parts of the world. A large variation (0-60%) has been recorded in 30 different environments across 11 countries. The role of cross-pollination in rapid deterioration of the genetic purity of cultivars and elite genetic stocks is well understood and documented by breeders and seed producers. Pigeonpea breeders have converted this constraint into an opportunity by way of visually selecting natural hybrids from landraces in farmers’ fields and deriving high yielding cultivars. In a key development, the occurrence of natural cross-pollination in the wild relatives of Pigeonpea has also been recorded; and in three wild species such natural hybrids have yielded valuable cytoplasmic male sterility systems. This has encouraged breeders to develop a hybrid breeding technology with natural out-crossing playing a key role in the large-scale seed production of commercial Pigeonpea hybrids.
-
breeding Pigeonpea cultivars for intercropping synthesis and strategies
Breeding Science, 2018Co-Authors: K B Saxena, A K Choudhary, Rachit K Saxena, Rajeev K VarshneyAbstract:Pigeonpea [Cajanus cajan (L.) Millsp.] is an ideal pulse crop of rainfed tropics and sub-tropics due to its high nutritive value and ability to survive various biotic and abiotic stresses. Thus it has continued to be cultivated on marginal land mostly under rainfed situation where the risk of crop failure is very high. To have insurance against crop failures and harvest more food in time and space, most farmers grow Pigeonpea as an intercrop with short-aged cereals and other crops. Presently, intercropping system accounts for over 70% of the Pigeonpea area. However, yield of Pigeonpea in this system is very low (400-500 kg/ha). The non-availability of improved cultivars adapted specifically to the intercropping environments is perhaps the major constraint that accounts for low yield. Considering the food and nutritional needs of the ever increasing population, productivity enhancement of this high-protein pulse is highly indispensable. In this review, the authors critically examine the technical difficulties encountered by breeders in developing high yielding cultivars for intercropping systems and discuss the strategies to overcome these constraints.
-
development and commercialization of cms Pigeonpea hybrids
2018Co-Authors: K B Saxena, D Sharma, M I ValesAbstract:The role of heterosis in enhancing productivity in food crops is well known. Legume breeders have not been able, however, to take advantage of this genetic phenomenon for a long time, due to biological restrictions, such as the requirement of high seeding rate and the inability to produce large quantities of F1 hybrid seed. Recently, in Pigeonpea (Cajanus cajan (L.) Millsp.), a breakthrough has been realized with the development and marketing of the world’s first legume hybrid, ICPH 2671. The key for this achievement was breeding and using a stable cytoplasmic nuclear male sterility (CMS) system obtained from the cross between C. cajanifolius, a wild relative of Pigeonpea, and the cultivated type. The inherent partial natural out‐crossing of Pigeonpea was knitted with this CMS system to facilitate economically‐viable large‐scale hybrid seed production. These developments provided opportunities to overcome the historic stagnant low yield (0.6–0.8 t ha–1) through heterosis breeding. Among hundreds of hybrid combinations tested, a cross between ICPA 2043 and ICPL 87119 (=ICPR 2671), designated as ICPH 2671, was the most promising, with >40% yield superiority (reaching yields above 3 t ha–1) over the prevalent cultivar ‘Maruti’, in multi‐location, multi‐year, on‐station trials, as well as on‐farm evaluations. The outstanding performance of ICPH 2671 led to its release in 2010 as the first medium duration commercial Pigeonpea hybrid in India. Subsequently, two additional Pigeonpea hybrids, ICPH 3762 and ICPH 2740 were also released for commercial cultivation in India in 2014 and 2015, respectively. According to recent estimates, in 2015 the CMS‐based Pigeonpea hybrids were grown over 150,000 hectares in central and southern India. In this review, we summarize the research efforts that led to the milestone of developing the first commercial hybrid in food legumes.
-
nectarivore aided hybridization and its exploitation for productivity enhancement in Pigeonpea
International journal of scientific and research publications, 2016Co-Authors: K B Saxena, A K Choudhary, A N Tikle, R Kumar, B BahadurAbstract:A record of out-crossing in Pigeonpea (Cajanus cajan (L.) Millsp.) from 32 locations indicated a large variation within and across 12 countries of Asia, Africa, and Americas. Pigeonpea breeders have exploited the natural hybrids within landraces for developing high yielding inbred cultivars in different countries. Similarly, natural hybrids selected from wild relatives of Pigeonpea have been used to breed male sterility systems. During the last 40 years the importance of natural out-crossing in genetic enhancement of yield in Pigeonpea has been well recognized, particularly in developing commercial hybrid technology; and it has allowed thousands of Indian farmers to harvest 30-40% more grains. This review provides an update on various aspects of natural out-crossing such as pollinating agents, extent of outcrossing, factors influencing out-crossing; besides this, the successful role of out-crossing in the genetic enhancement of yield in Pigeonpea has also been discussed.
Abhishek Bohra - One of the best experts on this subject based on the ideXlab platform.
-
genomics assisted breeding for Pigeonpea improvement
Theoretical and Applied Genetics, 2020Co-Authors: Abhishek Bohra, K B Saxena, Rajeev K Varshney, Rachit K SaxenaAbstract:The review outlines advances in Pigeonpea genomics, breeding and seed delivery systems to achieve yield gains at farmers’ field. Pigeonpea is a nutritious and stress-tolerant grain legume crop of tropical and subtropical regions. Decades of breeding efforts in Pigeonpea have resulted in development of a number of high-yielding cultivars. Of late, the development of CMS-based hybrid technology has allowed the exploitation of heterosis for yield enhancement in this crop. Despite these positive developments, the actual on-farm yield of Pigeonpea is still well below its potential productivity. Growing needs for high and sustainable Pigeonpea yields motivate scientists to improve the breeding efficiency to deliver a steady stream of cultivars that will provide yield benefits under both ideal and stressed environments. To achieve this objective in the shortest possible time, it is imperative that various crop breeding activities are integrated with appropriate new genomics technologies. In this context, the last decade has seen a remarkable rise in the generation of important genomic resources such as genome-wide markers, high-throughput genotyping assays, saturated genome maps, marker/gene–trait associations, whole-genome sequence and germplasm resequencing data. In some cases, marker/gene–trait associations are being employed in Pigeonpea breeding programs to improve the valuable yield and market-preferred traits. Embracing new breeding tools like genomic selection and speed breeding is likely to improve genetic gains. Breeding high-yielding Pigeonpea cultivars with key adaptation traits also calls for a renewed focus on systematic selection and utilization of targeted genetic resources. Of equal importance is to overcome the difficulties being faced by seed industry to take the new cultivars to the doorstep of farmers.
-
an intra specific consensus genetic map of Pigeonpea cajanus cajan l millspaugh derived from six mapping populations
Theoretical and Applied Genetics, 2012Co-Authors: K B Saxena, Rachit K Saxena, B N Gnanesh, Abhishek Bohra, M Byregowda, Abhishek Rathore, P B KavikishorAbstract:Pigeonpea (Cajanus cajan L.) is an important food legume crop of rainfed agriculture. Owing to exposure of the crop to a number of biotic and abiotic stresses, the crop productivity has remained stagnant for almost last five decades at ca. 750 kg/ha. The availability of a cytoplasmic male sterility (CMS) system has facilitated the development and release of hybrids which are expected to enhance the productivity of Pigeonpea. Recent advances in genomics and molecular breeding such as marker-assisted selection (MAS) offer the possibility to accelerate hybrid breeding. Molecular markers and genetic maps are pre-requisites for deploying MAS in breeding. However, in the case of Pigeonpea, only one inter- and two intra-specific genetic maps are available so far. Here, four new intra-specific genetic maps comprising 59–140 simple sequence repeat (SSR) loci with map lengths ranging from 586.9 to 881.6 cM have been constructed. Using these four genetic maps together with two recently published intra-specific genetic maps, a consensus map was constructed, comprising of 339 SSR loci spanning a distance of 1,059 cM. Furthermore, quantitative trait loci (QTL) analysis for fertility restoration (Rf) conducted in three mapping populations identified four major QTLs explaining phenotypic variances up to 24 %. To the best of our knowledge, this is the first report on construction of a consensus genetic map in Pigeonpea and on the identification of QTLs for fertility restoration. The developed consensus genetic map should serve as a reference for developing new genetic maps as well as correlating with the physical map in Pigeonpea to be developed in near future. The availability of more informative markers in the bins harbouring QTLs for sterility mosaic disease (SMD) and Rf will facilitate the selection of the most suitable markers for genetic analysis and molecular breeding applications in Pigeonpea.
-
analysis of bac end sequences bess and development of bes ssr markers for genetic mapping and hybrid purity assessment in Pigeonpea cajanus spp
BMC Plant Biology, 2011Co-Authors: Rachit K Saxena, Varma R Penmetsa, Abhishek Bohra, Anuja Dubey, K N Poornima, Naresh KumarAbstract:Background: Pigeonpea [Cajanus cajan (L.) Millsp.] is an important legume crop of rainfed agriculture. Despite of concerted research efforts directed to Pigeonpea improvement, stagnated productivity of Pigeonpea during last several decades may be accounted to prevalence of various biotic and abiotic constraints and the situation is exacerbated by availability of inadequate genomic resources to undertake any molecular breeding programme for accelerated crop improvement. With the objective of enhancing genomic resources for Pigeonpea, this study reports for the first time, large scale development of SSR markers from BAC-end sequences and their subsequent use for genetic mapping and hybridity testing in Pigeonpea. Results: A set of 88,860 BAC (bacterial artificial chromosome)-end sequences (BESs) were generated after constructing two BAC libraries by using HindIII (34,560 clones) and BamHI (34,560 clones) restriction enzymes. Clustering based on sequence identity of BESs yielded a set of >52K non-redundant sequences, comprising 35 Mbp or >4% of the Pigeonpea genome. These sequences were analyzed to develop annotation lists and subdivide the BESs into genome fractions (e.g., genes, retroelements, transpons and non-annotated sequences). Parallel analysis of BESs for microsatellites or simple sequence repeats (SSRs) identified 18,149 SSRs, from which a set of 6,212 SSRs were selected for further analysis. A total of 3,072 novel SSR primer pairs were synthesized and tested for length polymorphism on a set of 22 parental genotypes of 13 mapping populations segregating for traits of interest. In total, we identified 842 polymorphic SSR markers that will have utility in Pigeonpea improvement. Based on these markers, the first SSR-based genetic map comprising of 239 loci was developed for this previously uncharacterized genome. Utility of developed SSR markers was also demonstrated by identifying a set of 42 markers each for two hybrids (ICPH 2671 and ICPH 2438) for genetic purity assessment in commercial hybrid breeding programme. Conclusion: In summary, while BAC libraries and BESs should be useful for genomics studies, BES-SSR markers, and the genetic map should be very useful for linking the genetic map with a future physical map as well as for molecular breeding in Pigeonpea.
Damaris Achieng Odeny - One of the best experts on this subject based on the ideXlab platform.
-
new microsatellite markers for Pigeonpea cajanus cajan l millsp
BMC Research Notes, 2009Co-Authors: Damaris Achieng Odeny, B Jayashree, Christiane Gebhardt, Jonathan H CrouchAbstract:Pigeonpea is a nutritious tropical legume with several desirable characteristics but has been relatively neglected in terms of research. More efficient improvement can be achieved in this crop through molecular breeding but adequate molecular markers are lacking and no linkage map has been developed so far. Microsatellites remain the markers of choice due to their high polymorphism and their transferability from closely related genera. The overall objective of this study was to develop microsatellite markers from an enriched library of Pigeonpea as well as testing the transferability of soybean microsatellites in Pigeonpea. Primers were designed for 113 Pigeonpea genomic SSRs, 73 of which amplified interpretable bands. Thirty-five of the primers revealed polymorphism among 24 Pigeonpea breeding lines. The number of alleles detected ranged from 2 to 6 with a total of 110 alleles and an average of 3.1 alleles per locus. GT/CA and GAA class of repeats were the most abundant di-nucleotide and tri-nucleotide repeats respectively. Additionally, 220 soybean primers were tested in Pigeonpea, 39 of which amplified interpretable bands. Despite the observed morphological diversity, there is little genetic diversity within cultivated Pigeonpea as revealed by the developed microsatellites. Although some of the tested soybean microsatellites may be transferable to Pigeonpea, lack of useful polymorphism may hinder their full use. A robust set of markers will still have to be developed for Pigeonpea genome if molecular breeding is to be achieved.
-
new microsatellite markers for Pigeonpea cajanus cajan l millsp
BMC Research Notes, 2009Co-Authors: Damaris Achieng Odeny, B Jayashree, Christiane Gebhardt, Jonathan H CrouchAbstract:Background Pigeonpea is a nutritious tropical legume with several desirable characteristics but has been relatively neglected in terms of research. More efficient improvement can be achieved in this crop through molecular breeding but adequate molecular markers are lacking and no linkage map has been developed so far. Microsatellites remain the markers of choice due to their high polymorphism and their transferability from closely related genera. The overall objective of this study was to develop microsatellite markers from an enriched library of Pigeonpea as well as testing the transferability of soybean microsatellites in Pigeonpea.
-
the potential of Pigeonpea cajanus cajan l millsp in africa
Natural Resources Forum, 2007Co-Authors: Damaris Achieng OdenyAbstract:Pigeonpea is a tropical grain legume grown mainly in India. Though largely considered an orphan crop, Pigeonpea has a huge untapped potential for improvement both in quantity and quality of production in Africa. More than any other legume adapted to the region, Pigeonpea uniquely combines optimal nutritional profiles, high tolerance to environmental stresses, high biomass productivity and most nutrient and moisture contributions to the soil. The legume can be utilized in several diverse ways while the high genetic variability that exists within the cultivated and wild relatives remains to be explored for further uses. This article highlights the need for popularizing Pigeonpea as a major legume crop in Africa. The main constraints to productivity are discussed and recent breeding efforts in Africa highlighted. Important opportunities for improvement are further provided.
-
development characterization and utilization of microsatellite markers in Pigeonpea
Plant Breeding, 2007Co-Authors: Damaris Achieng Odeny, B Jayashree, Jonathan H Crouch, David A Hoisington, Morag Ferguson, Christiane GebhardtAbstract:Pigeonpea is a major legume of the semi-arid tropics that has been neglected in terms of molecular breeding. The objectives of this study were to develop microsatellite markers and evaluate their potential for use in Pigeonpea genetics and breeding. Two hundred and eight microsatellite loci were isolated by screening a non-enriched partial genomic library. Primers were designed for 39 microsatellite loci, 20 of which amplified polymerase chain reaction products of the expected size. Nineteen of the primer pairs were polymorphic amongst 15 cultivated and nine wild Pigeonpea accessions providing evidence for cross-species transferability within the genus Cajanus. A total of 98 alleles were detected at the 19 polymorphic loci with an average of 4.9 alleles per locus. The observed heterozygosity ranged from 0.17 to 0.80 with a mean of 0.42 per locus. Less allelic variation (31 alleles) was observed within the cultivated species than across the wild species (92 alleles). The diversity analysis readily distinguished all wild relatives from each other and from the cultivated germplasm. Development of more microsatellites is recommended for future genomic studies in Pigeonpea.