Construction of Chromosome Fragment Replacement Lines and QTLs Identification of Plant Height and Tiller in Annual Wild Rice (Oryza nivara)
JIANG Jia-Huan1,2,3, CAI Qiu-Hua1,2,3, WEI Yi-Dong1,2,3, LIU Feng4, CHEN Li-Ping1,2,3, ZHU Yong-Sheng1,2,3, ZHANG Jian-Fu1,2,3,*
1 Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350019, China; 2 State Key Laboratory for Ecological Control of Crop Pests between Fujian and Taiwan, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China; 3 National Engineering Laboratory of Rice/South China Research Base of State Key Laboratory of Hybrid Rice/Incubating Base of State Key Laboratory of Crop Germplasm Innovation and Molecular Breeding between Fujian Province and Ministry of Science and Technology/Fuzhou Branch of National Rice Improvement Center/South China Key Laboratory of Hybrid Rice Germplasm innovation and Molecular Breeding of Ministry of Agriculture and Rural Areas/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China; 4 Fujian Youxi County Agriculture and Rural Bureau Agricultural Extension Center, Youxi 365107, China
Abstract：Wild rice has nearly 1 times more alleles than cultivated rice (Oryza sativa), so it is of great significance to improve rice yield and quality by using wild rice excellent genes. In this study, a set of rice chromosome fragment replacement lines were constructed using annual wild rice (Oryza nivara) as donor parent and indica hybrid rice 'Fuhui 676' ('FH676') as recipient parent. After one hybridization, three backcrosses, and multiple generations of self-cross, 502 BC3F7 individuals were selected for whole genome detection using rice high density whole genome SNP chip. Finally, 474 lines containing the genome fragments of the donor parents were used as the establishment population. The results showed that the homozygosity of the whole line was high, and the number of SNP markers in the genetic map was up to 1 429, and the average number of SNP markers in each chromosome was 119. Seventy-two imported lines containing ≤4 fragments were selected as the coverage map of the whole genome, and the imported fragments basically covered the whole genome. The total length of target segment substitution in overlay map substitution line population was 581.84 Mb. The total length of the substitution fragment in the whole genome was 306.56 Mb, covering 82.75% of the genome. Plant height and effective tiller spike of the whole line were investigated in Sanya, Hainan province and Youxi, Fujian province. Combined with genotype, QTL analysis of plant height and effective tiller spike was performed by using complete interval mapping. A total of 9 QTLs affecting plant height were detected in the 2 environments, distributed on chromosomes 2, 3, 7, 8 and 11. Only qPH-3 on chromosome 3 was detected in both environments; A QTL qPH-8-1 significantly correlated with plant height was identified, with LOD value of 16.79 and phenotypic contribution rate of 9.16%. Fourteen effective tiller QTLs were detected, distributed on chromosomes 2, 3, 4, 5, 6 and 7, and qETN-7-3, qETN-7-4 and qETN-7-8 were detected in both environments. A QTL, qETN-7-6, with a LOD value of 58.28 and a phenotypic contribution rate of 32.86%, significantly correlated with the number of effective tillers was identified. This study provides the theoretical basis for fine QTL localization of plant height and tiller.
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