Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Heredity (Edinb). 2024 Aug;133(2):67-77. doi: 10.1038/s41437-024-00693-2. Epub 2024 Jun 4.
Good understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into 'hardy' and 'not hardy' cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 Mb of chromosome 1 among apple cultivars in the 'hardy' group. Using phased genotypic data from the 20 K apple Infinium® SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.
了解苹果适应北方气候的基因组区域对于促进当地适应的苹果品种的高效选育至关重要。表型分析和评估的适当基础设施对于鉴定适应相关性状和解析其遗传组成至关重要。然而，这种基础设施成本高昂，目前在瑞典北部的北方地区不可用。因此，我们利用了 59 个苹果品种的气候适应历史园艺数据和全基因组测序，来鉴定在推荐在瑞典北部种植的苹果品种中经历了历史选择的基因组区域。我们发现，苹果品种的收集由两个祖先群体组成，这些群体在很大程度上与根据园艺文献对“耐寒”和“不耐寒”品种的分组一致。使用多个全基因组扫描来寻找选择信号，我们在“耐寒”品种群体的 1 号染色体约 29Mb 的基因组区域获得了强烈的正选择信号。利用来自 20K 苹果 Infinium®SNP 阵列的相位基因型数据，我们鉴定了与两个品种群体相关的单倍型，并追踪了这些单倍型在一些苹果品种系谱中的传递。这表明，来自园艺文献的历史数据可以通过群体基因组学方法进行分析，作为揭示园艺小生境关键性状的基因组控制的一步。这种知识对于促进未来当地适应的苹果品种的高效选育策略非常重要。本研究说明了气候因素对树木作物产生的非常强烈的选择压力的响应，以及遗传研究在这方面的重要性以及在当前气候变化背景下开展选育工作的可行性。
