Marrano Annarita, Micheletti Diego, Lorenzi Silvia, Neale David, Grando M Stella
1Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all 'Adige (TN), Italy.
2Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all 'Adige (TN), Italy.
Hortic Res. 2018 Jul 1;5:34. doi: 10.1038/s41438-018-0041-2. eCollection 2018.
The application of population genetic methods in combination with gene mapping strategies can help to identify genes and mutations selected during the evolution from wild plants to crops and to explore the considerable genetic variation still maintained in natural populations. We genotyped a grapevine germplasm collection of 44 wild ( subsp. ) and 48 cultivated ( subsp. ) accessions at 54 K single-nucleotide polymorphisms (SNPs) to perform a whole-genome comparison of the main population genetic statistics. The analysis of Wright Fixation Index () along the whole genome allowed us to identify several putative "signatures of selection" spanning over two thousand SNPs significantly differentiated between and . Many of these genomic regions included genes involved in the adaptation to environmental changes. An overall reduction of nucleotide diversity was observed across the whole genome within , supporting a small effective population size of the wild grapevine. Tajima's D resulted positive in both wild and cultivated subgroups, which may indicate an ongoing balancing selection. Association mapping for six domestication-related traits was performed in combination with population genetics, providing further evidence of different perception and response to environmental stresses between and .
将群体遗传学方法与基因定位策略相结合加以应用，有助于识别从野生植物进化到作物过程中被选择的基因和突变，并探索自然群体中仍然保留的大量遗传变异。我们对一个包含44份野生（亚种）和48份栽培（亚种）种质的葡萄种质资源库进行了54K单核苷酸多态性（SNP）基因分型，以对主要群体遗传统计数据进行全基因组比较。对全基因组的赖特固定指数（）分析使我们能够识别出跨越两千多个在野生和栽培种质之间显著分化的SNP的几个假定“选择特征”。这些基因组区域中有许多包含参与适应环境变化的基因。在野生种质中观察到全基因组范围内核苷酸多样性总体降低，这支持了野生葡萄有效群体规模较小的观点。塔吉玛D值在野生和栽培亚组中均为正值，这可能表明正在进行平衡选择。结合群体遗传学对六个驯化相关性状进行了关联作图，进一步证明了野生和栽培种质对环境胁迫的不同感知和反应。
