High-density genetic map development and QTL mapping for concentration degree of floret flowering date in cultivated peanut (Arachis hypogaea L.)

Abstract

The concentration degree of floret flowering date (CDFFD) is an important selection index for earliness breeding of peanut, while the genetic basis of CDFFD-related traits in peanut is poorly understood. The aim of this study was to develop a high-density genetic linkage map of cultivated peanut by combining SLAF-seq (specific locus amplified fragment sequencing) with SSR (simple sequence repeat) techniques and to identify QTL (quantitative trait loci) controlling CDFFD. A RIL population derived from a cross between Silihong and Jinonghei 3 was sequenced by the HiSeq 2500 platform. A total of 1262.02 M high-quality paired-end reads were obtained, and 1,328,966 SNPs (single nucleotide polymorphisms) were developed from parents and progenies, of which 754,499 SNPs were successfully encoded and genotyping. The resulting map consisted of 3326 genetic markers (2996 SNPs and 330 SSRs) distributed in 20 linkage groups (LGs), spanning 1822.83 cM with an average distance of 0.55 cM between adjacent markers. These assigned SNP markers had average sequencing depths of 16.94-, 15.66-, and 20.94-fold in the male parent, female parent, and their progenies, respectively. Based on phenotyping in 4 environments, 15 significant QTL for the CDFFD were identified. And one major QTL for days to accumulation of 25 flowers (DA25F), qDA25F6.2, located on chromosome 6 was obtained, with a phenotypic variance explanation (PVE) of 12.49%. This map exhibited higher resolution and accuracy, which will facilitate more QTL discovery for interested agronomic and quality traits in cultivated peanut.