The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice (Oryza sativa L.)
Tifeng Yang1,2†, Lian Zhou1,2†, Junliang Zhao1,2, Jingfang Dong1,2, Qing Liu1,2, Hua Fu1,2, Xingxue Mao1,2, Wu Yang1,2, Yamei Ma1,2, Luo Chen1,2, Jian Wang1,2, Song Bai1,2, Shaohong Zhang1,2* and Bin Liu1,2*
RICE
Abstract
Background:Direct seeding is an efficient cultivation technique in rice. However, poor low temperaturegerminability (LTG) of modern rice cultivars limits its application. Identifying the genes associated with LTG andperforming molecular breeding is the fundamental way to address this issue. However, few LTG QTLs have beenfine mapped and cloned so far.
Results:In the present study, the LTG evaluation of 375 rice accessions selected from the Rice Diversity Panel 2showed that there were large LTG variations within the population, and the LTG of Indica group was significantlyhigher than that of Japonica and Aus groups (p < 0.01). In total, eleven QTLs for LTG were identified throughgenome-wide association study (GWAS). Among them, qLTG_sRDP2–3/qLTG_JAP-3, qLTG_AUS-3 and qLTG_sRDP2–12are first reported in the present study. The QTL on chromosome 10, qLTG_sRDP2–10a had the largest contributionto LTG variations in 375 rice accessions, and was further validated using single segment substitution line (SSSL). Thepresence of qLTG_sRDP2–10a could result in 59.8% increase in LTG under 15 °C low temperature. The expressionanalysis of the genes within qLTG_sRDP2–10a region indicated that LOC_Os10g22520 and LOC_Os10g22484exhibited differential expression between the high and low LTG lines. Further sequence comparisons revealed thatthere were insertion and deletion sequence differences in the promoter and intron region of LOC_Os10g22520, andan about 6 kb variation at the 3′ end of LOC_Os10g22484 between the high and low LTG lines, suggesting that thesequence 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 threestudies using different germplasm under different cold environments. Its large effect and stable expression makeqLTG_sRDP2–10a particularly valuable in rice breeding. The two genes, LOC_Os10g22484 and LOC_Os10g22520, wereconsidered as the candidate genes underlying qLTG_sRDP2–10a. Our results suggest that integrating GWAS andSSSL can facilitate identification of QTL for complex traits in rice. The identification of qLTG_sRDP2–10a and itscandidate genes provide a promising source for gene cloning of LTG and molecular breeding for LTG in rice.
Keywords:Rice (Oryza sativa L.), Low temperature germinability, Quantitative trait locus, Candidate gene, Genomewideassociation study
