Natural variation reveals that OsSAP16 controls low-temperature germination in rice

Abstract

A genome-wide-association study of rice natural varieties identifies a stress-associated protein, OsSAP16, as a positive regulator of low-temperature germination in rice.

Genetic Dissection of Germinability under Low Temperature by Building a Resequencing Linkage Map in japonica Rice

“…qLTG12a was mapped near qLTG-12a [37] and qLTG-12 [38]. qLTG12b was identified near the region of qCTGERM12-1 [31], qGR-12 [10], qLTG-12 [36], and qLTG-12 [39]. The above comparison results reflect the accuracy of this study, as well as the complexity of cold tolerance during germination.…”

“…qLTG7a was mapped near qCTGERM7-1 [31], qLTG-7 [34], qGR-7, and qGI-7 [35]. Furthermore, qLTG7b was found to be mapped near qCTGERM7-4 [31], qLTG-7 [36], and OsSAP16 [10]. At the germination stage, there was a correlation between the cold tolerance of qLTG9b and the qLTG-9 region [32,33].…”

“…The QTL named qLTG3 was located in the interval of the LTG gene described as qLTG3-1, with a 4.71 LOD value and 14.02% phenotype variance [9]. The QTL named qLTG7b had a 7.39 LOD value and 21.04% phenotypic variation and was located on OsSAP16, a rice LTG gene that has already been identified by the association study method [10]. PCR amplification and sequencing were conducted to screen out the causal polymorphisms of qLTG3-1 and OsSAP-16, which determined that LTH has two cold-tolerant genes ( Figure 3E,F).…”

“…Among all the QTLs for low-temperature germination in rice, only qLTG3-1 and OsSAP16 were cloned. qLTG3-1 encodes a protein with glycine-rich and lipid trans-protein domain structures [9], and OsSAP16 encodes a zinc-finger protein that positively regulates germination under low temperatures [10]. The QTLs qCTS7, LTG1, COLD1, qCTS9, bZIP73, qPSR10, and HAN1 control the pathways for cold tolerance in rice.…”

Quantitative Trait Locus Analysis of Seed Germination and Early Seedling Growth in Rice

“…Seed germination is a complex process that can be influenced by many factors, such as seed size, genotype, seed development, storage time and environment (Sun et al, 2007;Milošević et al, 2010). To date, numerous quantitative trait loci (QTLs) for seed germination have been reported in rice (Miura et al, 2002;Fujino et al, 2004;Jiang et al, 2006;Fujino et al, 2008;Wang et al, 2010;Li et al, 2013;Liu et al, 2014;Xie et al, 2014;Cheng et al, 2015;Hsu and Tung, 2015;Kretzschmar et al, 2015;Jiang et al, 2017;Wang et al, 2017;Jin et al, 2018). However, cloned genes related to the control of rice seed germination are still rare.…”