Discovery of genomic regions and candidate genes controlling shelling percentage using QTL ‐seq approach in cultivated peanut ( Arachis hypogaea L.)

Luo, H and Pandey, M K and Khan, A W and Guo, J and Wu, B and Cai, Y and Huang, L and Zhou, X and Chen, Y and Chen, W and Liu, N and Lei, Y and Liao, B and Varshney, R K and Jiang, H (2019) Discovery of genomic regions and candidate genes controlling shelling percentage using QTL ‐seq approach in cultivated peanut ( Arachis hypogaea L.). Plant Biotechnology Journal (TSI), 17 (7). pp. 1248-1260. ISSN 1467-7644

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Abstract

Cultivated peanut (Arachis hypogaea L.) is an important grain legume providing high‐quality cooking oil, rich proteins and other nutrients. Shelling percentage (SP) is the 2nd most important agronomic trait after pod yield and this trait significantly affects the economic value of peanut in the market. Deployment of diagnostic markers through genomics‐assisted breeding (GAB) can accelerate the process of developing improved varieties with enhanced SP. In this context, we deployed the QTL‐seq approach to identify genomic regions and candidate genes controlling SP in a recombinant inbred line population (Yuanza 9102 × Xuzhou 68‐4). Four libraries (two parents and two extreme bulks) were constructed and sequenced, generating 456.89–790.32 million reads and achieving 91.85%–93.18% genome coverage and 14.04–21.37 mean read depth. Comprehensive analysis of two sets of data (Yuanza 9102/two bulks and Xuzhou 68‐4/two bulks) using the QTL‐seq pipeline resulted in discovery of two overlapped genomic regions (2.75 Mb on A09 and 1.1 Mb on B02). Nine candidate genes affected by 10 SNPs with non‐synonymous effects or in UTRs were identified in these regions for SP. Cost‐effective KASP (Kompetitive Allele‐Specific PCR) markers were developed for one SNP from A09 and three SNPs from B02 chromosome. Genotyping of the mapping population with these newly developed KASP markers confirmed the major control and stable expressions of these genomic regions across five environments. The identified candidate genomic regions and genes for SP further provide opportunity for gene cloning and deployment of diagnostic markers in molecular breeding for achieving high SP in improved varieties.

Item Type:	Article
Divisions:	Research Program : Genetic Gains
CRP:	CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords:	peanut, shelling percentage, QTL‐seq, genomic regions, candidate genes, groundnut, phenotyping, genome resequencing, genomics
Subjects:	Mandate crops > Groundnut Others > Genetics and Genomics
Depositing User:	Mr Ramesh K
Date Deposited:	13 Aug 2019 06:05
Last Modified:	13 Aug 2019 06:05
URI:	http://oar.icrisat.org/id/eprint/11237
Official URL:	https://doi.org/10.1111/pbi.13050
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	This study was supported by the National Natural Science Foundations of China (31471534, 31601340, 31571713, 31761143005 and 31461143022), the Natural Science Foundation of Hubei Province (2017CFB540) and the Youth Chenguang Project of Science and Technology of Wuhan City (2017050304010285). 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. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.
Links:	Google Scholar

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