Abstract
BackgroundRice 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).ResultsIn 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.ConclusionsWe 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.
Highlights
Rice tiller number (TN) is one of the most important components associated with rice grain yield
Temperate Japonica (TEJ) rice belongs to the northern ecotype in China, and subtropical indica (IND) rice belongs to the southern ecotype
A previous study showed that the single tiller mutant moc3 is caused by one single nucleotide polymorphisms (SNPs) mutation (Lu et al, 2015b); we subsequently investigated whether the association at loci associated with tiller number variations (LATNs)-10 was due to MOC3’s sequence polymorphism or not
Summary
Rice tiller number (TN) is one of the most important components associated with rice grain yield. Tiller number (TN) and panicle morphology are two key factors associated with rice grain yields (Wang & Li 2011). Three important monoculm genes have been identified far in rice: MOC1, MOC2, and MOC3. MOC1 (Os06g40780) on chromosome 6 is a member of the GRAS (GAI, RGA and SCR) family of proteins that promotes axillary bud outgrowth. A 1.9kb retrotransposon inserted in MOC1 interrupts the gene and leads to a single main culm phenotype (Li et al 2003). MOC2 (Os01g64660) on chromosome 1 encodes a fructose-1,6-bisphosphatase (FBP1), which is imperative for tiller bud outgrowth in rice.
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