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Discovery of two novel and adjacent QTLs on chromosome B02 controlling resistance against bacterial wilt in peanut variety Zhonghua 6
Saturday, 2020/03/28 | 07:21:47

Huaiyong LuoManish K. PandeyYe ZhiHuan ZhangSiliang XuJianbin GuoBei WuHaiwen ChenXiaoping RenXiaojing ZhouYuning ChenWeigang ChenLi HuangNian LiuHari K. SudiniRajeev K. VarshneyYong LeiBoshou Liao & Huifang Jiang 

Theoretical and Applied Genetics April 2020;  133:1133–1148

Key message

Two novel and adjacent genomics and candidate genes for bacterial wilt resistance were identified on chromosome B02 in peanut variety Zhonghua 6 using both traditional QTL mapping and QTL-seq methods.

Abstract

Peanut (Arachis hypogaea) is an important oilseed crop worldwide. Utilization of genetic resistance is the most economic and effective approach to control bacterial wilt, one of the most devastating plant diseases, in peanut production. To accelerate the genetic improvement of bacterial wilt resistance (BWR) in peanut breeding programs, quantitative trait locus (QTL) mapping has been conducted for two resistant varieties. In this context, we deployed linkage mapping as well as sequencing-based mapping approach, QTL-seq, to identify genomic regions and candidate genes for BWR in another highly resistant variety Zhonghua 6. The recombination inbred line population (268 progenies) from the cross Xuhua 13 × Zhonghua 6 was used in BWR evaluation across five environments. QTL mapping using both SSR- and SNP-based genetic maps identified a stable QTL (qBWRB02-1) on chromosome B02 with 37.79–78.86% phenotypic variation explained (PVE) across five environments. The QTL-seq facilitated further dissection of qBWRB02-1 into two adjacent genomic regions, qBWRB02-1-1 (2.81–4.24 Mb) and qBWRB02-1-2 (6.54–8.75 Mb). Mapping of newly developed Kompetitive allele-specific PCR (KASP) markers on the genetic map confirmed their stable expressions across five environments. The effects of qBWRB02-1-1 (49.43–68.86% PVE) were much higher than qBWRB02-1-2 (3.96–6.48% PVE) and other previously reported QTLs. Nineteen putative candidate genes affected by 49 non-synonymous SNPs were identified for qBWRB02-1-1, and ten of them were predicted to code for disease resistance proteins. The major and stable QTL qBWRB02-1-1 and validated KASP markers could be deployed in genomics-assisted breeding (GAB) to develop improved peanut varieties with enhanced BWR.

 

Co-localization of the major QTL identified by SSR- and SNP-based genetic map for bacterial wilt resistance on chromosome B02. B02_SSR indicates the linkage map B02 constructed based on SSR markers. B02_SNP indicates the reversed linkage map B02 constructed based on SNP loci by Liu et al. (2019). B02_FHS indicates the estimated physical positions of SSR and SNP loci on the genomic sequence of chromosome B02 of Fuhuasheng. The positions of QTL intervals were highlighted in blue and green color, respectively (color figure online).

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