High-density genetic map development and QTL mapping for concentration degree of floret flowering date in cultivated peanut (Arachis hypogaea L.)
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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.
KeywordsGenetic map SLAF-seq SNP SSR Concentration degree of floret flowering date (CDFFD) QTL mapping
We thank Zhanying Zhang, Xingming Sun, Jianyin Xie, Haifeng Guo, and Dongdong Li (College of Agronomy, China Agricultural University, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education) for providing important advice during manuscript preparation. And we also thank Zhenzhen Wang and Jian Li (Beijing Biomarker Technologies Corporation, China) for providing sequencing technical support.
L.L. (Lifeng Liu) and Z.L. conceived the original research plans. X.Y. and S.C. designed the experiments. N.Z. and L.L. (Li Li) performed part of the experiments. L.W., M.H., and G.M. analyzed the data. L.W. wrote the manuscript. All authors listed have revised and approved the manuscript.
This work was supported by the China Agriculture Research System (CARS-13), the National Natural Science Foundation of China (31771833), the Science and Technology Supporting Plan Project of Hebei Province, China (16226301D), and the Key Projects of Science and Technology Research in Higher Education Institution of Hebei Province, China (ZD2015056).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by the any authors.
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