Mapping QTL for Seed Germinability under Low Temperature Using a New High-Density Genetic Map of Rice

Abstract

Mapping major quantitative trait loci (QTL) responsible for rice seed germinability under low temperature (GULT) can provide valuable genetic source for improving cold tolerance in rice breeding. In this study, 124 rice backcross recombinant inbred lines (BRILs) derived from a cross indica cv. Changhui 891 and japonica cv. 02428 were genotyped through re-sequencing technology. A bin map was generated which includes 3057 bins covering distance of 1266.5 cM with an average of 0.41 cM between markers. On the basis of newly constructed high-density genetic map, six QTL were detected ranging from 40 to 140 kb on Nipponbare genome. Among these, two QTL qCGR8 and qGRR11 alleles shared by 02428 could increase GULT and seed germination recovery rate after cold stress, respectively. However, qNGR1 and qNGR4 may be two major QTL affecting indica Changhui 891germination under normal condition. QTL qGRR1 and qGRR8 affected the seed germination recovery rate after cold stress and the alleles with increasing effects were shared by the Changhui 891 could improve seed germination rate after cold stress dramatically. These QTL could be a highly valuable genetic factors for cold tolerance improvement in rice lines. Moreover, the BRILs developed in this study will serve as an appropriate choice for mapping and studying genetic basis of rice complex traits.

Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

“…Among these populations, a few major QTLs have been identified by Andaya and Mackill (2003b), Fujino et al (2004), Lou et al (2007), Baruah et al (2009), Shinada et al (2014), Fig. 4 Depicted representation of the distribution pattern of lowtemperature stress (LTS) tolerance QTLs associated with phenotypic traits on 12 chromosomes, The total phenotypic variance explained (PVE) of different QTL indicates in the middle part with black color font, and percentage of number QTLs (%) distributed on 12 chromosomes were shown at the outter boundary of pie chart (Chr = chromosome; PVE = phenotypic variation explained; LTG = low-temperature germination; LTGS = low-temperature germination stress index; BMSI = biomass stress index; SL = shoot length; RL = root length; SLSI = shoot length stress index; RLSI = root length stress index; SGI = shoot growth index; SVI = seedling vigor index) Jiang et al (2017), andShakiba et al (2017). However, there are no significant main-effect QTLs related to the interaction of different QTLs for germination and seedling growth traits.…”

“…LTS tolerance in rice is a very complex and polygenic trait that is genetically controlled by multiple QTLs. Several LTS tolerance QTLs have been mapped on different genomic regions distributed on all 12 rice chromosomes using various types of molecular markers such as RFLP, AFLP, SSR, STS, and SNP, which has facilitated the identification of chromosomal regions associated with tolerance of low temperature (Andaya and Tai 2006;Lou et al 2007;Ji et al 2010;Ye et al 2010;Jena et al 2012;Verma et al 2014;Satoh et al 2016;Wang et al 2016a;Jiang et al 2017).…”

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.…”

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

“…However, the long-term cultivation method of seedling-transplantation has led to a loss of expressions of some low-temperature-tolerant genes, which are usually expressed at the germination stage. Poor germinability remains one of the major problems [5,21,29,30]. Therefore, screening cultivars with high germination abilities under low-temperature stress is necessary to sustain rice yield and ensure the application of direct seeding cultivation in the NEC region.…”

“…Advances in genome-wide sequencing technology have provided an effective method to detect DNA sequencing differences among closely related rice materials and to ensure the presence of sufficient markers for a genetic mapping analysis. A genotype calling method for RILs that utilizes resequencing data was developed [19], which determined the construction of resequencing bin maps and accelerated genetics-based studies for many crops, including cereals [19][20][21][22][23][24][25][26][27]. Based on the above discussions, many important advances have been achieved in the study of rice cold stress, but we still need to use high-throughput sequencing technology to mine further cold-tolerance genes from japonica rice, especially cold tolerance genes at the germination stage for breeding practice.…”