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Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea


This study has identified single-nucleotide polymorphism (SNP) markers associated with nine yield-related traits in pigeonpea by using two backcross populations (BP) developed through interspecific crosses and evaluating them at two locations and 3 years. In both the populations, markers have shown strong segregation distortion; therefore, a quantitative trait locus (QTL) mapping mixed model was used. A total of 86 QTLs explaining 12–21% phenotypic variation were detected in BP-1. On the other hand, 107 QTLs explaining 11–29% phenotypic variation were detected in BP-2. Although most QTLs were environment and trait specific, few stable and consistent QTLs were also detected. Interestingly, 11 QTLs in BP-2 were associated with more than one trait. Among these QTLs, eight QTLs associated with days to 50% flowering and days to 75% maturity were located on CcLG07. One SNP “S7_14185076” marker in BP-2 population has been found associated with four traits, namely days to 50% flowering, days to 75% maturity, primary branches per plant and secondary branches per plant with positive additive effect. Hence, the present study has not only identified QTLs for yield-related traits, but also discovered novel alleles from wild species, which can be used for improvement of traits through genomics-assisted breeding.

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Authors are thankful for the Department of Agriculture Cooperation & Farmers’ Welfare, Ministry of Agriculture & Farmers Welfare, Government of India and United States Agency for International Development (USAID). This work is also partially funded as part of the initiative “Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives,” which is supported by the Government of Norway. The project is managed by the Global Crop Diversity Trust. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC). ICRISAT is a member of CGIAR Consortium.

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RKV, RRM and RKS designed the experiments; NM led and RKV, RRM and RKS contributed to develop backcross populations; CVSK, NM, MS, AG, YN and RKS generated phenotyping data; RKV, RKS and SK generated genotyping data; RRD and AR analysed the phenotyping data; SK, PY, JM analysed the genotyping data and performed QTL analysis with support of RKS and RKV. All authors reviewed and approved the submission.

Correspondence to Rajeev K. Varshney.

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Saxena, R.K., Kale, S., Mir, R.R. et al. Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea. Theor Appl Genet 133, 737–749 (2020). https://doi.org/10.1007/s00122-019-03504-z

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