Table_6_Fine mapping of a QTL and identification of candidate genes associated with cold tolerance during germination in peanut (Arachis hypogaea L.) on chromosome B09 using whole genome re-sequencing.xlsx

Low temperatures significantly affect the growth and yield of peanuts. Temperatures lower than 12 °C are generally detrimental for the germination of peanuts. To date, there has been no report on precise information on the quantitative trait loci (QTL) for cold tolerance during the germination in peanuts. In this study, we developed a recombinant inbred line (RIL) population comprising 807 RILs by tolerant and sensitive parents. Phenotypic frequencies of germination rate low-temperature conditions among RIL population showed normally distributed in five environments. Then, we constructed a high density SNP-based genetic linkage map through whole genome re-sequencing (WGRS) technique and identified a major quantitative trait locus (QTL), qRGRB09, on chromosome B09. The cold tolerance-related QTLs were repeatedly detected in all five environments, and the genetic distance was 6.01 cM (46.74 cM - 61.75 cM) after taking a union set. To further confirm that qRGRB09 was located on chromosome B09, we developed Kompetitive Allele Specific PCR (KASP) markers for the corresponding QTL regions. A regional QTL mapping analysis, which was conducted after taking the intersection of QTL intervals of all environments into account, confirmed that qRGRB09 was between the KASP markers, G22096 and G220967 (chrB09:155637831–155854093), and this region was 216.26 kb in size, wherein a total of 15 annotated genes were detected. This study illustrates the relevance of WGRS-based genetic maps for QTL mapping and KASP genotyping that facilitated QTL fine mapping of peanuts. The results of our study also provided useful information on the genetic architecture underlying cold tolerance during germination in peanuts, which in turn may be useful for those engaged in molecular studies as well as crop improvement in the cold-stressed environment.

低温对花生生长和产量产生显著影响。花生发芽过程中，低于12°C的温度通常对发芽有害。迄今为止，尚未有关于花生发芽过程中耐寒性数量性状基因座（QTL）的精确信息报道。在本研究中，我们通过耐寒和敏感亲本，培育了一个包含807个重组自交系（RIL）的群体。在五个环境中，RIL群体中发芽速率在低温条件下的表型频率表现出正态分布。随后，我们利用全基因组重测序（WGRS）技术构建了一个高密度单核苷酸多态性（SNP）基因连锁图谱，并在B09染色体上识别到一个主要的数量性状基因座（QTL），即qRGRB09。在所有五个环境中均重复检测到与耐寒性相关的QTLs，经过并集处理后，遗传距离为6.01 cM（46.74 cM - 61.75 cM）。为进一步确认qRGRB09位于B09染色体上，我们开发了针对相应QTL区域的竞争性等位基因特异性PCR（KASP）标记。考虑到所有环境中QTL区间的交集，进行区域QTL定位分析，证实qRGRB09位于KASP标记G22096和G220967之间（chrB09:155637831–155854093），该区域大小为216.26 kb，其中检测到总计15个注释基因。本研究阐述了基于WGRS的遗传图谱在QTL定位和KASP基因分型中的作用，这些作用有助于花生QTL精细定位。我们研究的结果还提供了有关花生发芽过程中耐寒性遗传结构的宝贵信息，这对于从事分子研究和在冷胁迫环境下作物改良的研究者而言可能具有重要价值。