Fine mapping of qRC10-2, a quantitative trait locus for cold tolerance of rice roots at seedling and mature stages

• Published in: PloS one 2014-05, Vol.9 (5), p.e96046-e96046
• Main Authors: Xiao, Ning, Huang, Wei-Nan, Zhang, Xiao-Xiang, Gao, Yong, Li, Ai-Hong, Dai, Yi, Yu, Ling, Liu, Guang-Qing, Pan, Cun-Hong, Li, Yu-Hong, Dai, Zheng-Yuan, Chen, Jian-Min
• Format: Article
• Language: English
• Subjects: Adaptation, Biological - genetics; Biology and Life Sciences; Biotechnology; Chromosome 10; Chromosome Mapping; Chromosomes, Plant; Cold; Cold Temperature; Cold tolerance; Cold weather construction; Conductivity; Correlation coefficient; Correlation coefficients; Developmental biology; Ecology and Environmental Sciences; Electric properties; Electrical conductivity; Electrical resistivity; Gene expression; Gene loci; Gene mapping; Genetic Linkage; Genetics; Genomes; High altitude; High-altitude environments; Laboratories; Loci; Low temperature; Mapping; Marker-assisted selection; Markers; Oryza - genetics; Oryza - growth & development; Phenotype; Physical Chromosome Mapping; Physiology; Plant Roots - genetics; Plant Roots - growth & development; Polymorphism; Population; Quantitative genetics; Quantitative Trait Loci; Research and Analysis Methods; Rice; Seedlings; Seedlings - genetics; Seedlings - growth & development; Temperature tolerance
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0096046

Cold stress causes various injuries to rice seedlings in low-temperature and high-altitude areas and is therefore an important factor affecting rice production in such areas. In this study, root conductivity (RC) was used as an indicator to map quantitative trait loci (QTLs) of cold tolerance in Oryza rufipogon Griff., Dongxiang wild rice (DX), at its two-leaf stage. The correlation coefficients between RC and the plant survival rate (PSR) at the seedling and maturity stages were -0.85 and -0.9 (P = 0.01), respectively, indicating that RC is a reliable index for evaluating cold tolerance of rice. A preliminary mapping group was constructed from 151 BC2F1 plants using DX as a cold-tolerant donor and the indica variety Nanjing 11 (NJ) as a recurrent parent. A total of 113 codominant simple-sequence repeat (SSR) markers were developed, with a parental polymorphism of 17.3%. Two cold-tolerant QTLs, named qRC10-1 and qRC10-2 were detected on chromosome 10 by composite interval mapping. qRC10-1 (LOD = 3.1, RM171-RM1108) was mapped at 148.3 cM, and qRC10-2 (LOD = 6.1, RM25570-RM304) was mapped at 163.3 cM, which accounted for 9.4% and 32.1% of phenotypic variances, respectively. To fine map the major locus qRC10-2, NJ was crossed with a BC4F2 plant (L188-3), which only carried the QTL qRC10-2, to construct a large BC5F2 fine-mapping population with 13,324 progenies. Forty-five molecular markers were designed to evenly cover qRC10-2, and 10 markers showed polymorphisms between DX and NJ. As a result, qRC10-2 was delimited to a 48.5-kb region between markers qc45 and qc48. In this region, Os10g0489500 and Os10g0490100 exhibited different expression patterns between DX and NJ. Our results provide a basis for identifying the gene(s) underlying qRC10-2, and the markers developed here may be used to improve low-temperature tolerance of rice seedling and maturity stages via marker-assisted selection (MAS). With root electrical conductivity used as a cold-tolerance index, the quantitative trait locus qRC10-2 was fine mapped to a 48.5-kb candidate region, and Os10g0489500 and Os10g0490100 were identified as differently expressed genes for qRC10-2.