Identification of grain trait QTLs in introgression lines derived from Guangxi common wild rice based on high-density genetic map

【Objective】Based on the high-density genetic map, the QTLs of the grain trait of the introgression line of common wild rice in Guangxi was located, and key candidate genes were screened to provide theoretical reference for the fine localization of genes related to rice grain traits and breeding improvement. 【Method】Taking the common wild rice Y11 from Guangxi as the male parent and the indica conventional restorer line Guanghui 998（GH998） as the female parent, a BC₃F₉ introgression line population containing 281 lines was constructed. Grain trait analysis and genome sequencing were conducted on it. The QTLs related to grain length, grain width, length-to-width ratio and 1000-grain weight were located through high-density genetic mapping. Then, key candidate genes were screened out through gene function annotation and detection of the relative expression levels of candidate genes. 【Result】In the 281 progeny lines,the coefficient of variation for grain length was the smallest（3.41%）,while that for grain width was the largest（9.73%）. Grain length was significantly and positively correlated with 1000-grain weight（P＜0.05, the same below）,grain width was significantly and positively correlated with 1000-grain weight,significantly and negatively correlated with the length-towidth ratio. A total of 119 grain-related trait QTLs were detected,including 22 major-effect QTLs（10 for grain length,5 for grain width,3 for length-to-width ratio,and 4 for 1000-grain weight）,distributed on 12 rice chromosomes,with LOD values ranging from 6.72 to 13.32 and phenotypic contribution rates ranging from 10.75% to-20.19%. Five pleiotropic QTL intervals were identified:qGL2.2 and qTGW2.1（26626185-34078363 bp） on chromosome 2,associated with grain length and 1000-grain weight; qGW2.1 and qGLWR2.1（10595289-18845781 bp） on chromosome 2,associated with grain width and length-to-width ratio; qGL3.1 and qGLWR3.1（21022358-21038343 bp） on chromosome 3 as well as qGL6.2 and qTGW6.1 26793010-28240073 bp) on chromosome 6,both associated with grain length; and qGW7.2 and qTGW7.1（17771510-18372657 bp） on chromosome 7,associated with grain width and 1000-grain weight. Additionally,referring to the gene function of the homologous sequence of Nipponbare, a total of 10 genes that might be related to grain traits were screened out from the qGL6.1 and qGW7.1 intervals. The LOC＿Os06g01670 gene（MYB transcription factor gene） in the qGL6.1 interval was an ideal candidate gene affec-ting rice grain length. This gene was highly expressed in the young panicles of short grain lines, and it was speculated that it negatively regulated grain length by affecting endosperm development. The LOC＿Os07g01740（cysteine protease gene） and LOC＿Os07g01940（chromatid cohesion gene） in the qGW7.1 interval were highly expressed in the narrow grain lines and might regulate grain width by affecting cell division. These 2 genes were listed as candidate genes affecting grain width in rice. 【Conclusion】The population genetic effect of the introgression line of common wild rice in Guangxi constructed is relatively stable. From it, 22 major QTLs of grain traits are identified, among which qGL6.1 on chromosome 6 and qGW7.1 on chromosome 7 are new QTL of grain traits. The LOC＿Os06g01670 gene in the qGL6.1 interval is related to grain length, and the LOC＿Os07g01740 and LOC＿Os07g01940 genes in the qGW7.1 interval are related to grain width. It is preliminarily speculated that the three are candidate genes affecting grain traits.