AUTHOR=Han Le , Shen Bolin , Wu Xinyi , Zhang Jin , Wen Yang-Jun 

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

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1283642

DOI=10.3389/fpls.2023.1283642

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p>Epistasis is currently a topic of great interest in molecular and quantitative genetics. <italic>Arabidopsis thaliana</italic>, 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 <italic>Arabidopsis</italic>.</p></sec><sec><title>Method</title><p>In this study, we employed <italic>Levene’s</italic> 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 <italic>Arabidopsis</italic> accessions with 216,130 markers.</p></sec><sec><title>Results</title><p>Our analysis detected 89 QTNs and 130 pairs of QQIs. Around these loci, 34 known genes previously reported in <italic>Arabidopsis</italic> were confirmed to be associated with flowering-related traits, such as <italic>SPA4</italic>, which is involved in regulating photoperiodic flowering, and interacts with <italic>PAP1</italic> and <italic>PAP2</italic>, affecting growth of <italic>Arabidopsis</italic> 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 <italic>AT1G12990</italic> and <italic>AT1G09950</italic> around QQIs might have interaction effect to flowering time regulation in <italic>Arabidopsis</italic>.</p></sec><sec><title>Discussion</title><p>These findings may offer valuable insights for the identification and exploration of genes and gene-by-gene interactions associated with flowering-related traits in <italic>Arabidopsis</italic>, that may even provide valuable reference and guidance for the research of epistasis in other species.</p></sec>