Development of SSR markers and identification of major quantitative trait loci controlling shelling percentage in cultivated peanut (Arachis hypogaea L.)

Abstract

Key message A total of 204,439 SSR markers were developed in diploid genomes, and 25 QTLs for shelling percentage were identified in a RIL population across 4 years including five consistent QTLs. AbstractCultivated peanut (Arachis hypogaea L.) is an important grain legume providing edible oil and protein for human nutrition. Genome sequences of its diploid ancestors, Arachis duranensis and A. ipaensis, were reported, but their SSRs have not been well exploited and utilized hitherto. Shelling percentage is an important economic trait and its improvement has been one of the major objectives in peanut breeding programs. In this study, the genome sequences of A. duranensis and A. ipaensis were used to develop SSR markers, and a mapping population (Yuanza 9102 × Xuzhou 68-4) with 195 recombinant inbred lines was used to map QTLs controlling shelling percentage. The numbers of newly developed SSR markers were 84,383 and 120,056 in the A. duranensis and A. ipaensis genomes, respectively. Genotyping of the mapping population was conducted with both newly developed and previously reported markers. QTL analysis using the phenotyping data generated in Wuhan across four consecutive years and genotyping data of 830 mapped loci identified 25 QTLs with 4.46–17.01% of phenotypic variance explained in the four environments. Meta-analysis revealed five consistent QTLs that could be detected in at least two environments. Notably, the consistent QTL cqSPA09 was detected in all four environments and explained 10.47–17.01% of the phenotypic variance. The segregation in the progeny of a residual heterozygous line confirmed that the cpSPA09 locus had additive effect in increasing shelling percentage. These consistent and major QTL regions provide opportunity not only for further gene discovery, but also for the development of functional markers for breeding.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-017-2915-3) contains supplementary material, which is available to authorized users.

Next‐generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut (Arachis hypogaea L.)

“…In addition, the traditional QTL analysis was conducted using the same phenotyping data and the previously published SSR‐based genetic linkage map with 830 loci (Luo et al ., ). CIM identified five additive QTLs with 4.63%–40.19% PVE across three environments (Table S5).…”

Discovery of genomic regions and candidate genes controlling shelling percentage using QTL‐seq approach in cultivated peanut (Arachis hypogaea L.)

“…The RIL population (Yuanza 9102 × Xuzhou 68‐4) had high phenotypic variability for SP (Figures and S1). Based on the phenotyping data generated in Wuhan in four consecutive years (Luo et al ., ), the SP of Yuanza 9102 was 81.65 ± 0.44%, whereas that of Xuzhou 68‐4 was 75.81 ± 0.29% (Table S1). The SP of the RIL population showed continuous distributions skewed towards higher values in all of the four environments (Figure S2), ranging from 67.83% to 83.36% on average.…”

“…(d) Δ SNP index plot using the Xuzhou assembly as reference, from outside to inside: upper probability values at 99% confidence, upper probability values at 95% confidence, Δ SNP index, lower probability values at 95% confidence, lower probability values at 99% confidence. (e) Physical position of earlier mapped QTL (Luo et al ., ) for shelling percentage through traditional mapping approach. The physical position of QTL was estimated through blast the flanking primers into the A. duranensis and A. ipaensis genome.…”

“…The present study successfully identified two genomic regions responsible for SP with stable expressions across five environments. The genomic region (66.75–69.50 Mb) on chromosome A09 was mapped on the same location with the previously identified major QTL cqSPA09 through classical SSR marker‐based genetic mapping (Luo et al ., ). This study has also successfully narrowed down the QTL region mapped on A09 from 44 Mb (26–70 Mb, identified through genetic mapping) to 2.75 Mb.…”

“…This study has also successfully narrowed down the QTL region mapped on A09 from 44 Mb (26–70 Mb, identified through genetic mapping) to 2.75 Mb. Similarly, the genomic region (5.85–6.95 Mb) on chromosome B02 identified in this study also harboured the previously identified major QTL cqSPB02 through classical SSR marker‐based genetic mapping (Luo et al ., ). This study successfully narrowed down the second genomic region mapped on B02 from 3.18 Mb (5.95–9.13 Mb) to 1.1 Mb.…”