Compressed variance component mixed model reveals epistasis associated with flowering in Arabidopsis

Le Han; Bolin Shen; Xinyi Wu; Jin Zhang; Yang-Jun Wen

doi:10.3389/fpls.2023.1283642

Compressed variance component mixed model reveals epistasis associated with flowering in Arabidopsis

Front Plant Sci. 2024 Jan 8:14:1283642. doi: 10.3389/fpls.2023.1283642. eCollection 2023.

Authors

Le Han^#¹, Bolin Shen^#¹, Xinyi Wu¹, Jin Zhang^{1

2}, Yang-Jun Wen^{1

2}

Affiliations

¹ College of Science, Nanjing Agricultural University, Nanjing, China.
² State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China.

^# Contributed equally.

Abstract

Introduction: Epistasis is currently a topic of great interest in molecular and quantitative genetics. Arabidopsis thaliana, as a model organism, plays a crucial role in studying the fundamental biology of diverse plant species. However, there have been limited reports about identification of epistasis related to flowering in genome-wide association studies (GWAS). Therefore, it is of utmost importance to conduct epistasis in Arabidopsis.

Method: In this study, we employed Levene's test and compressed variance component mixed model in GWAS to detect quantitative trait nucleotides (QTNs) and QTN-by-QTN interactions (QQIs) for 11 flowering-related traits of 199 Arabidopsis accessions with 216,130 markers.

Results: Our analysis detected 89 QTNs and 130 pairs of QQIs. Around these loci, 34 known genes previously reported in Arabidopsis were confirmed to be associated with flowering-related traits, such as SPA4, which is involved in regulating photoperiodic flowering, and interacts with PAP1 and PAP2, affecting growth of Arabidopsis under light conditions. Then, we observed significant and differential expression of 35 genes in response to variations in temperature, photoperiod, and vernalization treatments out of unreported genes. Functional enrichment analysis revealed that 26 of these genes were associated with various biological processes. Finally, the haplotype and phenotypic difference analysis revealed 20 candidate genes exhibiting significant phenotypic variations across gene haplotypes, of which the candidate genes AT1G12990 and AT1G09950 around QQIs might have interaction effect to flowering time regulation in Arabidopsis.

Discussion: These findings may offer valuable insights for the identification and exploration of genes and gene-by-gene interactions associated with flowering-related traits in Arabidopsis, that may even provide valuable reference and guidance for the research of epistasis in other species.

Keywords: 3VmrMLM; Arabidopsis thaliana; GWAS; epistasis; flowering-related traits.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The work was supported by the National Natural Science Foundation of China (32070688 and 32270694), the Postdoctoral Science Foundation of Jiangsu (2020Z330), and the Fundamental Research Funds for the Central Universities (JCQY202108).