Combined genome‐wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice

Abstract

AbstractPlant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of thesemi‐dwarf1(SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome‐wide association study (GWAS) and identified 12 non‐repetitive QTL/genes regulating PH variation in 619 Asian cultivated rice accessions. One of these was anSD1structural variant, not normally detected in standard GWAS analyses. Given the strong effect ofSD1on PH, we also divided 619 accessions into subgroups harbouring distinctSD1haplotypes, and found a further 85 QTL/genes for PH, revealing genetic heterogeneity that may be missed by analysing a broad, diverse population. Moreover, we uncovered two epistatic interaction networks of PH‐associated QTL/genes in thejaponica(Geng)‐dominantSD1NIPsubgroup. In one of them, the hub QTL/geneqphSN1.4/GAMYBinteracted withqphSN3.1/OsINO80,qphSN3.4/HD16/EL1,qphSN6.2/LOC_Os06g11130, andqphSN10.2/MADS56. Sequence variations inGAMYBandMADS56were associated with their expression levels and PH variations, and MADS56 was shown to physically interact with MADS57 to coregulate expression of gibberellin (GA) metabolic genesOsGA2ox3andElongated Uppermost Internode1(EUI1). Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi‐dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.