Identification of QTLs for Rice Cold Tolerance at Plumule and 3-Leaf-Seedling Stages by Using QTLNet

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A doubled haploid (DH) population consisted of 120 lines,derived from a cross between an indica variety,TN1,and a japonica variety,Chunjiang 06,was used to identify QTLs controlling rice cold tolerance at the plumule and 3-leaf-seedling stages by using the QTLNetwork software.The percentages of normal plumules after 4℃ treatments for 7 d,9 d,11 d,and 14 d,as well as the cold stress tolerance index (CSTI) and the withering index (WI) of rice seedling were investigated.A total of five single-effect QTLs,each for percentages of normal plumules after 4℃ treatments for 9 d,11 d and 14 d,and CSTI and WI,respectively were identified.The QTLs for the percentages of normal plumules after Iow temperature treatments for 9 d,11 d and 14 d were on chromosomes 4,2 and 11,accounting for 14.1%,17.3% and 21.5% of the phenotypic variation,respectively.QTLs for CSTI and WI were on chromosomes 10 and 1,respectively.Two pairs of epistatic loci were identified,but none of the epistatic loci involved the single-effect QTLs.The RM528-RM340 interval on chromosome 6 interacted with the RM278-RM3919B interval on chromosome 9 for CSTI,and the epistatic interaction accounted for 17.7% of the phenotypic variation.A pair of epistatic loci was identified for WI,the RM246-RM5461 interval on chromosome 1 interacted with the ISA-RM447 interval on chromosome 8,which accounted for 22.6% of the phenotypic variation.
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