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Background  Spotted wilt, caused by  tomato spotted wilt virus  (TSWV), has been one of major diseases in cultivated peanut grown in the southeastern United States (US) since 1990. Previously a major quantitative trait locus (QTL) controlling spotted wilt disease resistance was mapped to an interval of 2.55 cM genetic distance corresponding to a physical distance of 14.4 Mb on chromosome A01 of peanut by using a segregating F 2  population. The current study focuses on refining this major QTL region and evaluating its contributions in the US peanut mini-core germplasm.    Results  Two simple sequence repeat (SSR) markers associated with the major QTL were used to genotype F 5  individuals, and 25 heterozygous individuals were selected and developed into an F 6  segregating population. Based on visual evaluation in the field, a total of 194 susceptible F 6  individuals were selected and planted into F 7  generation for phenotyping. Nine SSR markers were used to genotype the 194 F 6  individuals, and QTL analysis revealed that a confidence interval of 15.2 Mb region had the QTL with 22.8% phenotypic variation explained (PVE). This QTL interval was further genotyped using the Amplicon-seq method. A total of 81 non-redundant single nucleotide polymorphism (SNP) and eight InDel markers were detected. No recombinant was detected among the F 6  individuals. Two InDel markers were integrated into the linkage group and helped to refine the confidence interval of this QTL into a 0.8 Mb region. To test the QTL contributes to the resistance variance in US peanut mini-core germplasm, two flanking SSR markers were used to genotype 107 mini-core germplasm accessions. No statistically significant association was observed between the genotype at the QTL region and spotted wilt resistance in the mini-core germplasm, which indicated that the resistance allelic region at this QTL didn’t contribute to the resistance variance in the US peanut mini-core germplasm, thus was a unique resistance source.    Conclusion  A major QTL related to spotted wilt disease resistance in peanut was refined to a 0.8 Mb region on A01 chromosome, which didn’t relate to spotted wilt disease resistance in the US peanut mini-core germplasm and might be a unique genetic source.    Electronic supplementary material  The online version of this article (10.1186/s12863-018-0601-3) contains supplementary material, which is available to authorized users.

bmc genomic data

Refining a major QTL controlling spotted wilt disease resistance in cultivated peanut (Arachis hypogaea L.) and evaluating its contribution to the resistance variations in peanut germplasm