Development of sequence-based markers for seed protein content in pigeonpea

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dc.contributor.authorObala, Jimmy
dc.contributor.authorSaxena, Rachit K.
dc.contributor.authorSingh, Vikas K.
dc.contributor.authorSameer Kumar, C. V.
dc.contributor.authorSaxena, K. B.
dc.contributor.authorTongoona, Pangirayi
dc.contributor.authorSibiya, Julia
dc.contributor.authorVarshney, Rajeev K.
dc.date.accessioned2023-09-06T17:37:03Z
dc.date.available2023-09-06T17:37:03Z
dc.date.issued2019
dc.description.abstractPigeonpea 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.en_US
dc.identifier.citationObala, J., Saxena, R. K., Singh, V. K., Kumar, C. S., Saxena, K. B., Tongoona, P., ... & Varshney, R. K. (2019). Development of sequence-based markers for seed protein content in pigeonpea. Molecular Genetics and Genomics, 294, 57-68. https://doi.org/10.1007/s00438-018-1484-8en_US
dc.identifier.urihttps://doi.org/10.1007/s00438-018-1484-8
dc.identifier.urihttps://nru.uncst.go.ug/handle/123456789/9183
dc.language.isoenen_US
dc.publisherMolecular Genetics and Genomicsen_US
dc.subjectSeed protein contenten_US
dc.subjectCajanus cajanen_US
dc.subjectWhole-genome resequencingen_US
dc.subjectNext generation sequencingen_US
dc.subjectSequence variantsen_US
dc.subjectCommon variant analysisen_US
dc.titleDevelopment of sequence-based markers for seed protein content in pigeonpeaen_US
dc.typeArticleen_US
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