Browsing by Author "Singh, Vikas K."

Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    Development of sequence-based markers for seed protein content in pigeonpea
    (Molecular Genetics and Genomics, 2019) Obala, Jimmy; Saxena, Rachit K.; Singh, Vikas K.; Sameer Kumar, C. V.; Saxena, K. B.; Tongoona, Pangirayi; Sibiya, Julia; Varshney, Rajeev K.
    Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F2 population of the cross ICP 5529 (high SPC) × ICP 11605 (low SPC), resulted in four of the CAPS/dCAPS markers significantly (P < 0.05) co-segregated with SPC. In summary, four markers derived from mutations in four genes will be useful for enhancing/regulating SPC in pigeonpea crop improvement programs.
  • Thumbnail Image
    Item
    Genomics-assisted breeding for boosting crop improvement in pigeon pea (Cajanus cajan)
    (Frontiers in plant science, 2015) Pazhamala, Lekha; Saxena, Rachit K.; Singh, Vikas K.; Sameerkumar, C.V.; Kumar, Vinay; Sinha, Pallavi; Patel, Kishan; Obala, Jimmy; R.Kaoneka, Seleman; Tongoona, P.; Shimelis, Hussein A.; Gangarao, N.V.P.R.; Odeny, Damaris; Rathore, Abhishek; Dharmaraj, P.S.; Yamini, K. N.; Varshney, Rajeev K.
    Pigeon pea is an important pulse crop grown predominantly in the tropical and sub-tropical regions of the world. Although pigeon pea 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 pigeon pea 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 pigeon pea 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 pigeon pea. 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, pigeon pea has become a genomic resources-rich crop and efforts have already been initiated to integrate these resources in pigeon pea breeding.
  • Thumbnail Image
    Item
    Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic effects QTLs
    (Scientific reports, 2020) Obala, Jimmy; Saxena, Rachit K.; Singh, Vikas K.; Kale, Sandip M.; Garg, Vanika; Sameer Kumar, C. V.; Saxena, K. B.; Tongoona, Pangirayi; Sibiya, Julia; Varshney, Rajeev K.
    The genetic architecture of seed protein content (SPC) and its relationships to agronomic traits in pigeonpea is poorly understood. Accordingly, five F2 populations segregating for SPC and four agronomic traits (seed weight (SW), seed yield (SY), growth habit (GH) and days to first flowering (DFF)) were phenotyped and genotyped using genotyping-by-sequencing approach. Five high-density population-specific genetic maps were constructed with an average inter-marker distance of 1.6 to 3.5 cM, and subsequently, integrated into a consensus map with average marker spacing of 1.6 cM. Based on analysis of phenotyping data and genotyping data, 192 main effect QTLs (M-QTLs) with phenotypic variation explained (PVE) of 0.7 to 91.3% were detected for the five traits across the five populations. Major effect (PVE ≥ 10%) M-QTLs included 14 M-QTLs for SPC, 16 M-QTLs for SW, 17 M-QTLs for SY, 19 M-QTLs for GH and 24 M-QTLs for DFF. Also, 573 epistatic QTLs (E-QTLs) were detected with PVE ranging from 6.3 to 99.4% across traits and populations. Colocalization of M-QTLs and E-QTLs explained the genetic basis of the significant (P < 0.05) correlations of SPC with SW, SY, DFF and GH. The nature of genetic architecture of SPC and its relationship with agronomic traits suggest that genomics-assisted breeding targeting genome-wide variations would be effective for the simultaneous improvement of SPC and other important traits.