Abstract
BackgroundCold stress is an important factor limiting rice yield in many areas of high latitude and altitude. Considerable efforts have been taken to genetically dissect cold tolerance (CT) in rice using DNA markers. Because of possible epistasis and gene × environment interactions associated with identified quantitative trait loci, the results of these genetic studies have unfortunately not been directly applicable to marker-assisted selection for improved rice CT. In this study, we demonstrated the utility of a selective introgression strategy for simultaneous improvement and genetic dissection of rice seedling CT.ResultsA set of japonica introgression lines (ILs) with significantly improved seedling CT were developed from four backcross populations based on two rounds of selection. Genetic characterization of these cold-tolerant ILs revealed two important aspects of genome-wide responses to strong phenotypic selection for rice CT: (1) significant over-introgression of donor alleles at 57 loci in 29 functional genetic units (FGUs) across the rice genome and (2) pronounced non-random associations between or among alleles at many unlinked CT loci. Linkage disequilibrium analyses of the detected CT loci allowed us to construct putative genetic networks (multi-locus structures) underlying the seedling CT of rice. Each network consisted of a single FGU, with high introgression as the putative regulator plus two to three groups of highly associated downstream FGUs. A bioinformatics search of rice genomic regions harboring these putative regulators identified a small set of candidate regulatory genes that are known to be involved in plant stress response.ConclusionsOur results suggest that CT in rice is controlled by multiple pathways. Genetic complementarity between parental-derived functional alleles at many loci within a given pathway provides an appropriate explanation for the commonly observed hidden diversity and transgressive segregation of CT and other complex traits in rice.
Highlights
Cold stress is an important factor limiting rice yield in many areas of high latitude and altitude
Progeny testing of the 177 derived BC2F2:6 Introgression line (IL) to confirm their cold tolerance (CT) under more severe cold stress in a growth chamber revealed that 68 BC2F6 ILs derived from 30 of the 41 selected BC2F2 plants had significantly higher survival percentage (SP) and Cold response index (CRI) values than C418 (Table 2; Additional file 2: Figure S1)
Strong phenotypic selection for rice seedling CT in four rice BC populations resulted in the development of 30 cold-tolerant ILs
Summary
Cold stress is an important factor limiting rice yield in many areas of high latitude and altitude. Because of possible epistasis and gene × environment interactions associated with identified quantitative trait loci, the results of these genetic studies have not been directly applicable to marker-assisted selection for improved rice CT. The development of high-yielding, coldtolerant cultivars is the most efficient way to overcome the problem of low-temperature stress Because of their generally superior CT compared with that of indica rice, subsp. Two major QTLs for CT, qCTS4 and qCTS12, have been finemapped onto rice chromosome 4 and the short arm of chromosome 12, respectively [1,18] Results from these genetic studies have not been directly applicable to marker-assisted selection for improved rice CT owing to possible epistasis and gene × environment interactions associated with the identified QTLs [19]
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