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群体基因组分析揭示了从美国、波多黎各和哥伦比亚的大豆和干豆中分离出的[具体研究对象未给出]的地理结构和气候多样性。

Population genomic analysis reveals geographic structure and climatic diversification for isolated from soybean and dry bean across the United States, Puerto Rico, and Colombia.

作者信息

Ortiz Viviana, Chang Hao-Xun, Sang Hyunkyu, Jacobs Janette, Malvick Dean K, Baird Richard, Mathew Febina M, Estévez de Jensen Consuelo, Wise Kiersten A, Mosquera Gloria M, Chilvers Martin I

机构信息

Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States.

Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, United States.

出版信息

Front Genet. 2023 Jun 7;14:1103969. doi: 10.3389/fgene.2023.1103969. eCollection 2023.

Abstract

causes charcoal rot, which can significantly reduce yield and seed quality of soybean and dry bean resulting from primarily environmental stressors. Although charcoal rot has been recognized as a warm climate-driven disease of increasing concern under global climate change, knowledge regarding population genetics and climatic variables contributing to the genetic diversity of is limited This study conducted genome sequencing for 95  isolates from soybean and dry bean across the continental United States, Puerto Rico, and Colombia. Inference on the population structure using 76,981 single nucleotide polymorphisms (SNPs) revealed that the isolates exhibited a discrete genetic clustering at the continental level and a continuous genetic differentiation regionally. A majority of isolates from the United States (96%) grouped in a clade with a predominantly clonal genetic structure, while 88% of Puerto Rican and Colombian isolates from dry bean were assigned to a separate clade with higher genetic diversity. A redundancy analysis (RDA) was used to estimate the contributions of climate and spatial structure to genomic variation (11,421 unlinked SNPs). Climate significantly contributed to genomic variation at a continental level with temperature seasonality explaining the most variation while precipitation of warmest quarter explaining the most when spatial structure was accounted for. The loci significantly associated with multivariate climate were found closely to the genes related to fungal stress responses, including transmembrane transport, glycoside hydrolase activity and a heat-shock protein, which may mediate climatic adaptation for . On the contrary, limited genome-wide differentiation among populations by hosts was observed. These findings highlight the importance of population genetics and identify candidate genes of that can be used to elucidate the molecular mechanisms that underly climatic adaptation to the changing climate.

摘要

引发炭腐病,这会因主要的环境压力源而显著降低大豆和干豆的产量及种子质量。尽管炭腐病已被认为是一种受温暖气候驱动的疾病,在全球气候变化背景下日益受到关注,但关于其种群遗传学以及影响其遗传多样性的气候变量的知识有限。本研究对来自美国大陆、波多黎各和哥伦比亚的95株大豆和干豆分离株进行了基因组测序。利用76981个单核苷酸多态性(SNP)对种群结构进行推断,结果显示这些分离株在大陆水平上呈现出离散的遗传聚类,在区域水平上呈现出连续的遗传分化。美国的大多数分离株(96%)聚集在一个具有主要克隆遗传结构的分支中,而来自波多黎各和哥伦比亚的干豆分离株中88%被分配到一个具有更高遗传多样性的单独分支中。采用冗余分析(RDA)来估计气候和空间结构对基因组变异(11421个非连锁SNP)的贡献。在大陆水平上,气候对基因组变异有显著贡献,温度季节性解释的变异最多,而在考虑空间结构时最暖季度的降水量解释的变异最多。发现与多变量气候显著相关的位点与真菌应激反应相关基因紧密相邻,包括跨膜运输、糖苷水解酶活性和一种热休克蛋白,这些基因可能介导了对气候的适应性。相反,观察到不同宿主种群之间在全基因组水平上的分化有限。这些发现凸显了种群遗传学的重要性,并确定了可用于阐明气候适应变化气候的分子机制的候选基因。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/213f/10282554/054e74280ee0/fgene-14-1103969-g001.jpg

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