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

OAR@ICRISAT

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Relation http://oar.icrisat.org/11331/
https://doi.org/10.1111/pbi.13266
doi:10.1111/pbi.13266
 
Title Whole‐genome resequencing‐based QTL ‐seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut
 
Creator Kumar, R
Janila, P
Vishwakarma, M K
Khan, A W
Manohar, S S
Gangurde, S S
Variath, M T
Shasidhar, Y
Pandey, M K
Varshney, R K
 
Subject Plant Breeding
Groundnut
Genetics and Genomics
Legume Crops
 
Description 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.
 
Publisher Wiley Open Access
 
Date 2019-10
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Identifier http://oar.icrisat.org/11331/1/pbi.13266.pdf
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