Detection of QTLs controlling cold tolerance at bud bursting stage by using a high-density SNP linkage map in japonica rice

Abstract

China Abstract: Direct seeded rice (DSR) has received much attention because of its time- and labour-saving and low-input demand. However, the long-term cultivation method of seedling-transplantation has led to loss of some low-temperature-tolerant genes expressed at the bud stage. It has made many currently popular rice varieties unsuitable a recombinant inbred line population constructed by cross of Lijiangxintuanheigu Shennong 265 (SN265) and its linkage map containing 2818 markers to detect cold tolerance QTLs at the bud stage. A total of five QTLs were detected on rice chromosomes 1, 3, 9, and 11. All the cold tolerance alleles were from the cold-tolerant parent LTH. The LOD values of these QTLs ranged from 3.05 to 24.01, and the phenotypic variations ranged from 8.0% to 53.5%. Among them, the major QTL qCTB11b was located in a 790 kb interval of 21.24 Mb to 22.03 Mb on the long arm of chromosome 11. Subsequently, the “selective mapping” strategy was used for QTL verification and pyramiding effect analysis. Genetic improvement of cold tolerance at the bud stage would be achieved through pyramiding more QTLs. These results not only promote people’s understanding of the genetic basis for cold tolerance at the bud stage in rice but also provide theoretical basis and techni-cal guidance for genetic improvement of DSR varieties.