Common bean pan-genome reveals abundant variation patterns and relationships of stress response genes and pathways
Xu Wang,
Ming Yan,
Shanshan Cui,
Fang Li,
Qingqing Zhao,
Qingnan Wang,
Bin Jiang,
Yixin Huang,
Yang Sun,
Xiangdong Kong
Affiliations
Xu Wang
Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University
Ming Yan
Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University
Shanshan Cui
Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University
Fang Li
Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University
Qingqing Zhao
Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University
Qingnan Wang
Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University
Bin Jiang
Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University
Yixin Huang
Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded By Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University
Yang Sun
Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University
Abstract Long-term geographical isolation and the different directions of domestication can cause a large number of genome variations. Population genetic analysis based on a single reference genome cannot capture all the variation information. Pan-genome construction is an effective way to overcome this problem. Resequencing data from 683 common bean landraces and breeding lines provided a pan-genome construction data resource. For the first time, for common bean pan-genome construction, 305 Mb non-reference contigs and 10,452 novel genes were identified. Among these new genes, 373 resistance gene analogs containing 372 variable genes were identified and used to narrow down the candidate genes in Pseudomonas syringae pv. phaseolicola resistance quantitative trait locus interval of the common bean. Transcriptome analysis of multiple biotic and abiotic stresses reveals that gene expression patterns are organ-, stress-, and gene conservation-specific. Core and shell genes may be co-expressed in all samples and may have functional complementarity to maintain the stability of plant growth. Within pathways, 8990 and 30,272 mutual exclusivity and co-occurrence gene presence-absence variations (PAVs) were discovered respectively, providing further insights into the functional complementarity of genes. In conclusion, our study provides a comprehensive genome resource, which will be useful for further common bean breeding and study.
