Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA.
Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA.
Genome Biol. 2021 Sep 3;22(1):254. doi: 10.1186/s13059-021-02467-z.
Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine (V. vinifera) rootstocks.
By creating a reference genome assembly from one wild species, V. arizonica, and by resequencing 130 accessions, we focus on identifying putatively introgressed regions (pIRs) between species. We find six species pairs with signals of introgression between them, comprising up to ~ 8% of the extant genome for some pairs. The pIRs tend to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explore SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierce's disease (Xylella fastidiosa). pIRs are enriched for SNPs associated with both climate and bacterial levels, suggesting that introgression is driven by adaptation to biotic and abiotic stressors.
Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the evolutionary history of economically important wild relatives of a critical crop.
渐渗杂交可以将遗传变异重新组合成有利的组合，从而使生物适应新的生态位。为了评估有助于渐渗的进化模式和动态，我们研究了原产于美国西南部的六种野生葡萄属物种，这些物种对于培育葡萄(Vitis vinifera)砧木很有用。
通过从一个野生物种——V. arizonica 中创建参考基因组组装，并对 130 个样本进行重测序，我们专注于鉴定物种间的推定渐渗区(pIR)。我们发现了六对具有渐渗信号的物种对，其中一些对的 pIR 约占现存基因组的 8%。pIR 往往基因较少，位于高重组区域，富含与疾病抗性功能相关的基因。为了评估潜在的 pIR 功能，我们探索了 SNP 与生物气候变量的关联，以及感染李痘病病原菌(Xylella fastidiosa)后细菌水平的关联。pIR 富含与气候和细菌水平相关的 SNP，表明渐渗是由对生物和非生物胁迫的适应驱动的。
总的来说，这项研究深入了解了渐渗的基因组范围、塑造适应性渐渗的潜在压力，以及经济上重要的关键作物野生亲缘的进化历史。
