Abstract
Key messageA 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.Cultivated 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.
Highlights
Cultivated peanut (Arachis hypogaea L.), known as groundnut, is an allotetraploid (AABB, 2n = 4x = 40) grain legume native to South America, but grown in diverse environments in six continents between latitudes 40°N and 40°S (Sharma and Bhatnagar-Mathur 2006)
Cultivated peanut was formed through the natural hybridization of its two diploid ancestors, A. duranensis (AA, 2n = 2x = 20) and A. ipaensis (BB, 2n = 2x = 20)
The recombinant inbred lines (RILs) population was used as mapping population to validate the quality of newly developed SSR markers, to construct a dense genetic map and to conduct Quantitative trait locus (QTL)
Summary
Cultivated peanut (Arachis hypogaea L.), known as groundnut, is an allotetraploid (AABB, 2n = 4x = 40) grain legume native to South America, but grown in diverse environments in six continents between latitudes 40°N and 40°S (Sharma and Bhatnagar-Mathur 2006). It provides edible oil and protein for human nutrition. Shelling percentage (SP) is an important economic trait in peanut production. Peanut pod has two parts: kernel and hull (Fig. 1a). Shelling percentage (weight of kernels/weight of pods) significantly varied among peanut varieties. There is a great potential in the genetic improvement of shelling percentage in peanut breeding
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