Data from: Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US]) from the second generation of the two divergently selected populations and an unselected control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD) decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist) by LOSITAN and hierarchical structure model using ARLEQUIN detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

低温是严重影响多年生黑麦草（Lolium perenne L.）生长的非生物胁迫之一。解析其耐寒性的遗传调控机制，将有助于培育出更适应霜冻环境的多年生黑麦草品种。本研究从两个定向选育群体的二代群体及一个未选择对照群体中共计选取80份个体：高耐寒（High Frost, HF）群体24份、低耐寒（Low Frost, LF）群体29份、未选择（Unselected, US）对照群体27份，并利用基于多年生黑麦草转录组序列开发的278个全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点对其进行基因分型分析。研究结果表明，经过耐寒性定向选择后，HF与LF群体间已出现显著遗传分化，而HF与US群体的遗传相似性较高。连锁不平衡（Linkage Disequilibrium, LD）衰减在7条染色体上呈现异质性，且HF与LF群体间显著的LD模式进一步证实了二者在耐寒性上的遗传分化。此外，本研究采用两种固定指数（Fixation Index, Fst）异常位点检测方法：分别是基于LOSITAN的有限岛屿模型（fdist）以及基于ARLEQUIN的层级结构模型，共检测到6个受定向选择的位点。这些异常位点极有可能与参与耐寒性调控、低温适应及非生物胁迫响应的基因连锁，可作为培育高耐寒多年生黑麦草品种的潜在分子标记资源。