Whole‐genome resequencing‐based QTL ‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut

Kumar, R and Janila, P and Vishwakarma, M K and Khan, A W and Manohar, S S and Gangurde, S S and Variath, M T and Shasidhar, Y and Pandey, M K and Varshney, R K (2019) Whole‐genome resequencing‐based QTL ‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut. Plant Biotechnology Journal(TSI). pp. 1-12. ISSN 1467-7644

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The subspecies fastigiata of cultivated groundnut lost fresh seed dormancy (FSD) during domestication and human‐made selection. Groundnut varieties lacking FSD experience precocious seed germination during harvest imposing severe losses. Development of easy‐to‐use genetic markers enables early‐generation selection in different molecular breeding approaches. In this context, one recombinant inbred lines (RIL) population (ICGV 00350 × ICGV 97045) segregating for FSD was used for deploying QTL‐seq approach for identification of key genomic regions and candidate genes. Whole‐genome sequencing (WGS) data (87.93 Gbp) were generated and analysed for the dormant parent (ICGV 97045) and two DNA pools (dormant and nondormant). After analysis of resequenced data from the pooled samples with dormant parent (reference genome), we calculated delta‐SNP index and identified a total of 10,759 genomewide high‐confidence SNPs. Two candidate genomic regions spanning 2.4 Mb and 0.74 Mb on the B05 and A09 pseudomolecules, respectively, were identified controlling FSD. Two candidate genes—RING‐H2 finger protein and zeaxanthin epoxidase—were identified in these two regions, which significantly express during seed development and control abscisic acid (ABA) accumulation. QTL‐seq study presented here laid out development of a marker, GMFSD1, which was validated on a diverse panel and could be used in molecular breeding to improve dormancy in groundnut.

Item Type: Article
Divisions: Research Program : Genetic Gains
Research Program : Asia
CRP: CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords: Abscisic acid, Candidate genes, Groundnut, Fresh Seed dormancy, QTL-seq, RILs, single nucleotide polymorphism, whole-genome sequencing
Subjects: Others > Plant Breeding
Mandate crops > Groundnut
Others > Genetics and Genomics
Others > Legume Crops
Depositing User: Mr Arun S
Date Deposited: 08 Nov 2019 06:26
Last Modified: 08 Nov 2019 06:32
URI: http://oar.icrisat.org/id/eprint/11331
Official URL: https://doi.org/10.1111/pbi.13266
Acknowledgement: This research was supported by the MARS-Wrigley, USA, and CGIAR Research Program on Grain Legumes and Dryland Cereals(GLDC). ICRISAT is a member of the CGIAR. RK was supported by Science and Engineering Research Board (SERB), Department of Science and Technology (DST), and SSG acknowledges DST, Govt. of India, for being supported by DST-INSPIRE fellowship for his doctoral studies
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