Transcriptome and association mapping revealed functional genes respond to drought stress in Populus

Fangyuan Song; Jiaxuan Zhou; Mingyang Quan; Liang Xiao; Wenjie Lu; Shitong Qin; Yuanyuan Fang; Dan Wang; Peng Li; Qingzhang Du; Yousry A El-Kassaby; Deqiang Zhang

doi:10.3389/fpls.2022.829888

Transcriptome and association mapping revealed functional genes respond to drought stress in Populus

Front Plant Sci. 2022 Jul 29:13:829888. doi: 10.3389/fpls.2022.829888. eCollection 2022.

Authors

Fangyuan Song^{1

2}, Jiaxuan Zhou^{1

2}, Mingyang Quan^{1

2}, Liang Xiao^{1

2}, Wenjie Lu^{1

2}, Shitong Qin^{1

2}, Yuanyuan Fang^{1

2}, Dan Wang^{1

2}, Peng Li^{1

2}, Qingzhang Du^{1

2}, Yousry A El-Kassaby³, Deqiang Zhang^{1

2}

Affiliations

¹ National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
² Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
³ Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada.

Abstract

Drought frequency and severity are exacerbated by global climate change, which could compromise forest ecosystems. However, there have been minimal efforts to systematically investigate the genetic basis of the response to drought stress in perennial trees. Here, we implemented a systems genetics approach that combines co-expression analysis, association genetics, and expression quantitative trait nucleotide (eQTN) mapping to construct an allelic genetic regulatory network comprising four key regulators (PtoeIF-2B, PtoABF3, PtoPSB33, and PtoLHCA4) under drought stress conditions. Furthermore, Hap_01PtoeIF-2B, a superior haplotype associated with the net photosynthesis, was revealed through allelic frequency and haplotype analysis. In total, 75 candidate genes related to drought stress were identified through transcriptome analyses of five Populus cultivars (P. tremula × P. alba, P. nigra, P. simonii, P. trichocarpa, and P. tomentosa). Through association mapping, we detected 92 unique SNPs from 38 genes and 104 epistatic gene pairs that were associated with six drought-related traits by association mapping. eQTN mapping unravels drought stress-related gene loci that were significantly associated with the expression levels of candidate genes for drought stress. In summary, we have developed an integrated strategy for dissecting a complex genetic network, which facilitates an integrated population genomics approach that can assess the effects of environmental threats.

Keywords: Populus; association genetics; co-expression; drought tolerance; eQTN; epistasis.