Abstract
BackgroundEffective 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.ResultsIn 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 from vegetative to reproductive growth of tillers.ConclusionsOur results revealed that GWAS is a feasible way to mine ETN-associated genes. The candidate genes and favorable alleles identified in this study have the potential application value in rice molecular breeding for high ETN and grain yield.
Highlights
Effective tiller number (ETN) has a pivotal role in determination of rice (Oryza sativa L.) grain yield
Colocalization of ETN-Associated Quantitative trait locus (QTL) with Previously Reported Rice Tillering Genes To evaluate the reliability of our genome-wide association study (GWAS) results, we examined whether the detected ETN-associated QTLs could colocalize with some known genes involved in rice tillering
Our results showed that Hap5 of OsAAP1, Hap3 and Hap6 of DWL2, Hap3 and Hap4 of WRKY74 are favorable alleles for ETN (Fig. 3 and Fig. 4), and the 18 accessions harboring favorable alleles of all these four genes showed an apparent increase in ETN (Additional file 5: Fig. S2), indicating that pyramiding multiple favorable alleles may contribute to high ETN
Summary
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. Effective tiller number (ETN) per plant is an essential yield component for rice and affected by both genetic and environmental factors (Xing & Zhang 2010). Rice tiller derives from two processes, axillary meristem (AM) formation and tiller bud outgrowth (Wang & Li 2011), which are regulated by many genes. MOC1, encoding a GRAS domain transcription factor, plays a pivotal role in AM formation, and the loss-of-function moc mutant shows a monoculm phenotype (Li et al 2003). MOC3/ OsWUS/TILLERS ABSENT1 (TAB1) is indispensable for tiller bud formation (Lu et al 2015b), which may promote AM initiation by inducing the expression of OSH1 (Tanaka et al 2015). Typical SL mutants display dwarf and increased tillering, such as d27 (Lin et al 2009), htd1/d17 (Zou et al 2006), and d10 (Arite et al 2007; Yuan et al 2013), whose responsible genes are involved in SL synthesis; htd2/d14 (Liu et al 2009), d3 (Yasuno et al 2009; Zhao et al 2014) and d53 (Zhou et al 2013; Jiang et al 2013), whose responsible genes are involved in SL signaling
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