Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia.
Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia.
Int J Mol Sci. 2020 May 31;21(11):3952. doi: 10.3390/ijms21113952.
A defining challenge of the 21st century is meeting the nutritional demands of the growing human population, under a scenario of limited land and water resources and under the specter of climate change. The Vavilov seed bank contains numerous landraces collected nearly a hundred years ago, and thus may contain 'genetic gems' with the potential to enhance modern breeding efforts. Here, we analyze 407 landraces, sampled from major historic centers of chickpea cultivation and secondary diversification. Genome-Wide Association Studies (GWAS) conducted on both phenotypic traits and bioclimatic variables at landraces sampling sites as extended phenotypes resulted in 84 GWAS hits associated to various regions. The novel haploblock-based test identified haploblocks enriched for single nucleotide polymorphisms (SNPs) associated with phenotypes and bioclimatic variables. Subsequent bi-clustering of traits sharing enriched haploblocks underscored both non-random distribution of SNPs among several haploblocks and their association with multiple traits. We hypothesize that these clusters of pleiotropic SNPs represent co-adapted genetic complexes to a range of environmental conditions that chickpea experienced during domestication and subsequent geographic radiation. Linking genetic variation to phenotypic data and a wealth of historic information preserved in historic seed banks are the keys for genome-based and environment-informed breeding intensification.
二十一世纪面临的一个重大挑战是，在土地和水资源有限且气候变化的情况下，满足不断增长的人口的营养需求。瓦维洛夫种子银行保存了近百年来收集的大量地方品种，因此其中可能蕴藏着具有增强现代育种工作潜力的“遗传瑰宝”。在这里，我们分析了 407 份地方品种，这些品种取自鹰嘴豆主要的历史种植中心和次要的多样化中心。对地方品种采样点的表型性状和生物气候变量进行全基因组关联研究（GWAS），作为扩展表型的结果，发现了 84 个与各种区域相关的 GWAS 命中。基于单倍型块的新型测试确定了与表型和生物气候变量相关的单核苷酸多态性（SNP）富集的单倍型块。随后对共享富集单倍型块的性状进行双聚类，突出了多个单倍型块中 SNP 的非随机分布及其与多个性状的关联。我们假设，这些多效 SNP 簇代表了对一系列环境条件的共同适应遗传复合物，这些条件是鹰嘴豆在驯化和随后的地理辐射过程中经历的。将遗传变异与表型数据以及历史种子库中保存的大量历史信息联系起来，是基于基因组和环境信息的强化育种的关键。
