The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice (Oryza sativa L.)

Abstract

Background Direct seeding is an efficient cultivation technique in rice. However, poor low temperature germinability (LTG) of modern rice cultivars limits its application. Identifying the genes associated with LTG and performing molecular breeding is the fundamental way to address this issue. However, few LTG QTLs have been fine mapped and cloned so far. Results In the present study, the LTG evaluation of 375 rice accessions selected from the Rice Diversity Panel 2 showed that there were large LTG variations within the population, and the LTG of Indica group was significantly higher than that of Japonica and Aus groups (p < 0.01). In total, eleven QTLs for LTG were identified through genome-wide association study (GWAS). Among them, qLTG_sRDP2–3/qLTG_JAP-3, qLTG_AUS-3 and qLTG_sRDP2–12 are first reported in the present study. The QTL on chromosome 10, qLTG_sRDP2–10a had the largest contribution to LTG variations in 375 rice accessions, and was further validated using single segment substitution line (SSSL). The presence of qLTG_sRDP2–10a could result in 59.8% increase in LTG under 15 °C low temperature. The expression analysis of the genes within qLTG_sRDP2–10a region indicated that LOC_Os10g22520 and LOC_Os10g22484 exhibited differential expression between the high and low LTG lines. Further sequence comparisons revealed that there were insertion and deletion sequence differences in the promoter and intron region of LOC_Os10g22520, and an about 6 kb variation at the 3′ end of LOC_Os10g22484 between the high and low LTG lines, suggesting that the sequence variations of the two genes could be the cause for their differential expression in high and low LTG lines. Conclusion Among the 11 QTLs identified in this study, qLTG_sRDP2–10a could also be detected in other three studies using different germplasm under different cold environments. Its large effect and stable expression make qLTG_sRDP2–10a particularly valuable in rice breeding. The two genes, LOC_Os10g22484 and LOC_Os10g22520, were considered as the candidate genes underlying qLTG_sRDP2–10a. Our results suggest that integrating GWAS and SSSL can facilitate identification of QTL for complex traits in rice. The identification of qLTG_sRDP2–10a and its candidate genes provide a promising source for gene cloning of LTG and molecular breeding for LTG in rice.

Identification of OsPK5 involved in rice glycolytic metabolism and GA/ABA balance for improving seed germination via genome-wide association study

“…The mean GR and GI values were lowest in AUS among the rice sub-groups in both years ( Fig. 1 ), similar to the results regarding low-temperature germination reported by Wang et al (2018) and Yang et al (2020) . In addition, a few accessions of AUS showed very low GRs below 10%, even at 7 DAI ( Supplementary Table S1 ), possibly due to the strong seed dormancy of these accessions of AUS , similar to wild rice ( Oryza rufipogon ).…”

QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study

“…Using a core collection (Rice Diversity Panel 1, RDP1) of rice, a total of 42 QTLs were identified as being associated with cold tolerance during the germination and seedling stages ( Shakiba et al, 2017 ). Through a GWAS, 11 QTLs were found to be associated with LTG among Rice Diversity Panel 2 (RDP2) and two candidate genes were narrowed down ( Yang et al, 2020c ). OsSAP16 was cloned using 187 natural accessions by GWAS in rice ( Wang et al, 2018b ).…”

Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

“…In the past 20 years, researchers have identified more than 100 QTLs for LTG on the 12 rice chromosomes using bi-parental mapping methods based on phenotypic traits such as germination percentage and germination index (Chen et al 2006 ; Fujino et al 2004 ; Ji et al 2009 ; Jiang et al 2006 , 2017 ; Miura et al 2001 ; Wang et al 2011 ; Xie et al 2014 ). Besides, as an alternative strategy, genome-wide association study (GWAS) has increasingly applied for LTG genetic research to dissect the variation of natural rice accessions (Fujino et al 2015 ; Sales et al 2017 ; Wang et al 2018b ; Yang et al 2020 ).…”