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

Abstract

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 from vegetative to reproductive growth of tillers. Conclusions Our 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.

Developing Novel Rice Genotypes Harboring Specific QTL Alleles Associated with High Grain Yield under Water Shortage Stress

“…It is obvious that the water shortage stress has delayed the flowering time for all the newly developed lines, as it has for their parents and the checks. This symptom was previously observed by [ 28 , 29 , 30 ]. According to some studies, the delayed flowering under water stress is a good indicator of plant responses to water stress and may explain the plants’ adaptability to tolerate the stress [ 31 ].…”

Development of adaptive rice variety to non-tidal swamp: Growth evaluation of backcrossed progenies (BC1F1) and its parents, Inpago 5 and Inpara 8

“…The plant height of BC1F1 (Table 2) indicates that the population of backcross was genetically affected by the parents. (Ren et al 2021) stated that performance of progenies influenced by genetics of both parents, although the plants were grew in same condition.…”

“…Takai et al (2021) suggested that rice crops have a potential to increase its production along with the number of tillers. Tillering ability of rice greatly influenced by genetic (Ren et al 2021) and environmental factors (Gao et al 2019). Tiller productivity was categorized into 4 groups, (1) Low (less than 10 tillers), ( 2) Medium (11-15 tillers), ( 3) High (16-20 tillers), and (4) Very high (more than 20 tillers) (IRRI, 2013).…”

Novel quantitative trait loci for yield and yield related traits identified in Basmati rice (Oryza sativa)

“…Bian et al, 2015, reported 21 QTLs for the number of tillers (NT) in an introgression line. Similarly, in a genome‐wide association study (GWAS) 38 marker‐trait associations for the effective number of tillers were identified (Ren et al, 2021). The next important component of yield, the grain weight was found to be associated with a gene TGW6 encoding a protein having indole‐3‐acetic acid (IAA)‐glucose hydrolase activity, and positively regulates free IAA in grains.…”