Dissection of the Genetic Architecture of Rice Tillering using a Genome-wide Association Study

Abstract

Background Rice tiller number (TN) is one of the most important components associated with rice grain yield. Around one hundred rice TN genes have been identified, but dissecting the genetic architecture of rice TN variations remains difficult because of its complex trait and control by both major genes and quantitative trait loci (QTLs). Results In this study, we used a subset of the rice diversity population II (S-RDP-II), genotyped with 700,000 single nucleotide polymorphisms (SNPs), to identify the loci associated with tiller number variations (LATNs) through a genome-wide association study (GWAS). The analysis revealed that 23 LATNs are significantly associated with TN variations. Among the 23 LATNs, eight are co-localized with previously cloned TN genes, and the remaining 15 LATNs are novel. DNA sequence analysis of the 15 novel LATNs led to the identification of five candidate genes using the accessions with extreme TN phenotypes. Genetic variations in two of the genes are mainly located in the promoter regions. qRT-PCR analysis showed that the expression levels of these two genes are also closely associated with TN variations. Conclusions We identified 15 novel LATNs that contribute significantly to the genetic variation of rice TN. Of these 15, the five identified TN-associated candidate genes will enhance our understanding of rice tillering and can be used as molecular markers for improving rice yield. Electronic supplementary material The online version of this article (10.1186/s12284-019-0302-1) contains supplementary material, which is available to authorized users.

Molecular mapping of QTLs for yield related traits in recombinant inbred line (RIL) population derived from the popular rice hybrid KRH-2 and their validation through SNP genotyping

“…The first step is the axillary meristem formation and the second being axillary buds' growth. Three important monoculm genes namely MOC1 , MOC2 and MOC3 controlling the axillary bud formation and its outgrowth have been identified in rice 35 . Molecular characterization of these three genes MOC1 ( Os06g40780 ), MOC2 ( Os01g64660 ) and MOC3 ( Os04g56780)/TAB1/OsWUS was delineated as reported by earlier studies 36 – 38 .…”

“…Negative regulator of axillary bud growth was identified to be an amino acid transporter gene, OsAAP3 (Os06g36180) 45 and gene OsHAP2E (Os03g29760) positively regulated the TN by increasing photosynthesis 46 . The genome wide association study (GWAS) associated with tiller number variations (LATNs) in rice identified four candidate genes Os07g28890, Os11g15130, Os01g28690 and Os05g32120 which might have a role in tiller number variation and are awaiting validation 35 . Another study used a combination of association studies and pedigree-based analysis for deciphering the genetic architecture of yield and grain quality using a MAGIC population 47 .…”

Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential

“…GWAS has been proved to be a new strategy for explaining the genetic basis of complex traits, which has the advantage of improving the e ciency of detecting natural variations (Li et al 2018). Most GWAS studies focused on dissecting the genetic basis of single yield traits (Ta et al 2018;Jiang et al 2019), but the study on clarifying the genetic basis of the relationship between the yield and component traits of rice is few. Here we carried out meta-analyses of GWAS results from two populations (575 + 1495 F 1 ) in different environments, and adopted an MR design to further estimated the causal relationship between rice yield and component traits of rice.…”

Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies

“…More recently, a GWAS using 700,000 SNPs revealed 23 loci associated with tiller number at the later tillering stage of 350 RDP-2 accessions [23]. However, these previous GWASs have focused on tiller number at a single stage, without considering alterations during different stages.…”