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

J. Obala; R.K. Saxena; V.K. Singh; C.V.S. Kumar; K.B. Saxena; P. Tongoona; J. Sibiya; R.K. Varshney

doi:10.1007/s00438-018-1484-8

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

Journal article

Peer reviewed

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

J. Obala, R.K. Saxena, V.K. Singh, C.V.S. Kumar, K.B. Saxena, P. Tongoona, J. Sibiya and R.K. Varshney

Molecular Genetics and Genomics, Vol.294(1), pp.57-68

2019

DOI: https://doi.org/10.1007/s00438-018-1484-8

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Abstract

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.

Details

Title: Development of sequence-based markers for seed protein content in pigeonpea
Authors/Creators: J. Obala (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
R.K. Saxena (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
V.K. Singh (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
C.V.S. Kumar (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
K.B. Saxena (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
P. Tongoona (Author/Creator) - University of KwaZulu-Natal
J. Sibiya (Author/Creator) - University of KwaZulu-Natal
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
Publication Details: Molecular Genetics and Genomics, Vol.294(1), pp.57-68
Publisher: Springer
Identifiers: 991005540805307891
Copyright: © 2021 Springer Nature Switzerland AG.
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Biochemistry & Molecular Biology; Genetics & Heredity
ESI research areas: Molecular Biology & Genetics