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Identification of QTL for kernel number-related traits in a rice chromosome segment substitution line and fine mapping of qSP1

Ma, Fuying, Zhu, Xiaoyan, Wang, Hui, Wang, Shiming, Cui, Guoqing, Zhang, Ting, Yang, Zhenglin, He, Guanghua, Ling, Yinghua, Wang, Nan, Zhao, Fangming
The crop journal 2019
Arabidopsis thaliana, DNA, alleles, branches, chromosomes, inheritance (genetics), mutation, nucleotide sequences, panicles, phenotypic variation, quantitative trait loci, rice, seed set, seeds, spikelets, substitution lines, tissues
A chromosome segment substitution line (CSSL) is a powerful tool for combining quantitative trait locus (QTL) mapping with the pyramiding of desirable alleles. The rice CSSL Z1364 with increased kernel number was identified in a BC3F8 population derived from a cross of Nipponbare as the recipient with Xihui 18 as the donor parent. Z1364 carried three substitution segments distributed on chromosomes 1, 6, and 8. The mean substitution length was 1.19 Mb. Of 17 QTL identified on the substitution segments, qSP1 for spikelets per panicle, qSSD1 for seed-set density, and qNSB1 for number of secondary branches explained respectively 57.34%, 87.7%, and 49.44% of the corresponding phenotypic variance and were all linked to RM6777. Chi-square analysis showed that the increased kernel number in Z1364 was inherited recessively by a single gene. By fine mapping, qSP1 was delimited to a 50-kb region on the short arm of chromosome 1. Based on DNA sequence, a previously uncharacterized rice homolog of Arabidopsis thaliana AT4G32551 was identified as a candidate gene for qSP1 in which mutation increases the number of spikelets and kernels in Z1364. qSP1 was expressed in all tissues, but particularly in 1-cm panicles. The expression levels of OsMADS22, GN1A, and DST were upregulated and those of LAX2, GNP1, and GHD7 were downregulated in Nipponbare. These results provide a foundation for functional research on qSP1.