Genome-Wide Association Study of the Genetic Basis of Effective Tiller Number in Rice

作者：Mengmeng Ren, Minghan Huang, Haiyang Qiu, Yan Chun, Lu Li, Ashmit Kumar, Jingjing Fang, Jinfeng Zhao, Hang He, Xueyong Li · 发表于：Rice · 年份：2021 · DOI：10.1186/s12284-021-00495-8 · 被引用次数：45 · 研究领域：Genetic Mapping and Diversity in Plants and Animals、Rice Cultivation and Yield Improvement、Plant Molecular Biology Research

BACKGROUND: Effective tiller number (ETN) has a pivotal role in determination of rice (Oryza sativa L.) grain yield. ETN is a complex quantitative trait regulated by both genetic and environmental factors. Despite multiple tillering-related genes have been cloned previously, few of them have been utilized in practical breeding programs. RESULTS: In this study, we conducted a genome-wide association study (GWAS) for ETN using a panel of 490 rice accessions derived from the 3 K rice genomes project. Thirty eight ETN-associated QTLs were identified, interestingly, four of which colocalized with the OsAAP1, DWL2, NAL1, and OsWRKY74 gene previously reported to be involved in rice tillering regulation. Haplotype (Hap) analysis revealed that Hap5 of OsAAP1, Hap3 and 6 of DWL2, Hap2 of NAL1, and Hap3 and 4 of OsWRKY74 are favorable alleles for ETN. Pyramiding favorable alleles of all these four genes had more enhancement in ETN than accessions harboring the favorable allele of only one gene. Moreover, we identified 25 novel candidate genes which might also affect ETN, and the positive association between expression levels of the OsPILS6b gene and ETN was validated by RT-qPCR. Furthermore, transcriptome analysis on data released on public database revealed that most ETN-associated genes showed a relatively high expression from 21 days after transplanting (DAT) to 49 DAT and decreased since then. This unique expression pattern of ETN-associated genes may contribute to the transition fr...