Genetic architecture to cause dynamic change in tiller and panicle numbers revealed by genome‐wide association study and transcriptome profile in rice

Abstract

Panicle number (PN) is one of the three yield components in rice. As one of the most unstable traits, the dynamic change in tiller number (DCTN) may determine the final PN. However, the genetic basis of DCTN and its relationship with PN remain unclear. Here, 377 deeply re-sequenced rice accessions were used to perform genome-wide association studies (GWAS) for tiller/PN. It was found that the DCTN pattern rather than maximum tiller number or effective tiller ratio is the determinant factor of high PN. The DCTN pattern that affords more panicles exhibits a period of stable tillering peak between 30 and 45 days after transplant (called DT30 and DT45, respectively), which was believed as an ideal pattern contributing to the steady transition from tiller development to panicle development (ST-TtP). Consistently, quantitative trait loci (QTL) expressed near DT30−DT45 were especially critical to the rice DCTN and in supporting the ST-TtP. The spatio-temporal expression analysis showed that the expression pattern of keeping relatively high expression in root at 24:00 (R24-P2) from about DT30 to DT45 is a typical expression pattern of cloned tiller genes, and the candidate genes with R24-P2 can facilitate the prediction of PN. Moreover, gene OsSAUR27 was identified by an integrated approach combining GWAS, bi-parental QTL mapping and transcription. These findings related to the genetic basis underlying the DCTN will provide the genetic theory in making appropriate decisions on field management, and in developing new varieties with high PN and ideal dynamic plant architecture.

Rice receptor kinase FLR7 regulates rhizosphere oxygen levels and enriches the dominant Anaeromyxobacter that improves submergence tolerance in rice

“…S8B ), consistent with previous studies [ 43–45 ]. We found that PSR-1 significantly decreased the expression levels of the positive growth regulator OsGPAT1 [ 46 ] and significantly increased the expression levels of the negative growth regulator OsSAUR27 [ 47 ] compared to the uninoculated mock and E. coli treatment when rice was submerged for 4 days ( Fig. 4C ; Fig.…”

Natural variation in Tiller Number 1 affects its interaction with TIF1 to regulate tillering in rice

“…A panel of 2154 cultivated and 221 wild rice varieties was used to construct a phylogenetic tree of the TN1 gene sequence according to previously described methods (Li et al, 2021). A minimum spanning tree of haplotypes using the same data was calculated following a previously described method (Guo et al, 2020).…”

“…It was recently found that tiller‐regulating genes usually showed high expression in the root at 24:00. Based on this expression pattern and a genome‐wide association study (GWAS), a small auxin‐UP RNA gene, OsSAUR27 , was identified in natural populations and has been proven to affect tiller number and plant architecture (Ma et al ., 2020 ).…”

Co-Overexpression of Two Key Source Genes, OsBMY4 and OsISA3, Improves Multiple Key Traits of Rice Seeds

“…10,11 In addition, the number of genes controlling the panicle number and size that have been cloned is also increasing, and examples are IPA1, 12 PANDA, 13 and OsSAUR27. 14 Studies on rice quality improvement, especially ECQ and appearance quality, have been focused on the enzymes involved in the biosynthesis of amylose and amylopectin, the constituent starch polymers in seeds. Nevertheless, most of these cloned genes can only improve limited aspects of the target traits, without positive contributions and even causing possible negative effects on other nontarget traits.…”

“…For example, scientists usually seek to clone novel target genes involved in controlling the panicle number, grain number, and grain weight and size, using them to generate rice varieties with more panicles and grains, larger and heavier grains, and finally increased rice yield. − In general, the majority of these cloned genes in rice are related to sink organs. It is impressive that more than 80 grain size-related genes have been cloned, , including GS3 , DEP1 , GW2 , and qGL3 / OsPPKL1 . , In addition, the number of genes controlling the panicle number and size that have been cloned is also increasing, and examples are IPA1 , PANDA , and OsSAUR27 . Studies on rice quality improvement, especially ECQ and appearance quality, have been focused on the enzymes involved in the biosynthesis of amylose and amylopectin, the constituent starch polymers in seeds.…”