Abstract
Key messageTwo 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.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.
Highlights
The cultivated peanut (Arachis hypogaea L.), known as groundnut, is an important legume crop grown in more than 100 countries with 47.10 million tonnes global production in 2017 (FAOSTAT 2019)
The average survival rate of recombination inbred line (RIL) with the aaBB genotypes was higher than RILs with the aabb genotype but not significantly. These results indicated that the resistance against bacterial wilt of Zhonghua 6 was mainly controlled by the qBWRB02-1-1
The genetic and genomic quantitative trait locus (QTL) analyses of bacterial wilt resistance (BWR) were performed for two resistant sources namely Yueyou 92 (Zhao et al 2016) and Yuanza 9102 (Luo et al 2019), the genetic basis of the majority resistant germplasm could not be dissected
Summary
The cultivated peanut (Arachis hypogaea L.), known as groundnut, is an important legume crop grown in more than 100 countries with 47.10 million tonnes global production in 2017 (FAOSTAT 2019). Bacterial wilt disease poses a serious threat to peanut production in China, the highest peanut producer in the world, in addition to Vietnam, Indonesia, Uganda and other Southeast Asian countries This disease usually causes 10–30% yield losses and can cause up to 50–100% in severe circumstances (Jiang et al 2017). The breeding of new resistant varieties faces challenges due to the inability of conducting large-scale screening in conventional breeding programs (Jiang et al 2017) Under such circumstances, it is essential to identify QTLs and linked markers for bacterial wilt resistance (BWR), which could be deployed in genomics-assisted breeding (GAB) to accelerate the breeding process (Janila et al 2016; Varshney et al 2014)
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