基于高密度遗传图谱定位广西普通野生稻导入系籽粒性状QTLs

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

  • 摘要: 【目的】基于高密度遗传图谱定位广西普通野生稻导入系籽粒性状QTLs,筛选关键候选基因,为水稻籽粒性状相关基因精细定位及育种改良提供理论参考。【方法】以广西普通野生稻Y11为父本、籼型常规恢复系广恢998(GH998)为母本,构建包含281个株系的BC3F9导入系群体,对其进行籽粒性状分析及基因组测序,通过高密度遗传图谱定位粒长、粒宽、长宽比、千粒重相关QTLs,再通过基因功能注释、候选基因相对表达量检测筛选出关键候选基因。【结果】281个子代株系中,粒长的变异系数最小(3.41%),粒宽的变异系数最大(9.73%)。粒长与千粒重呈显著正相关(P<0.05,下同),粒宽与千粒重呈显著正相关,与长宽比呈显著负相关。从281个子代株系中共检测到119个籽粒相关性状QTLs,有22个为主效QTLs,其中粒长相关QTLs 10个、粒宽相关QTLs 5个、长宽比相关QTLs 3个、千粒重相关QTLs 4个,分布于水稻12条染色体,LOD为6.72~13.32,表型贡献率为10.75%~20.19%。筛选出5个多效性QTLs:2号染色体上的qGL2.2和qTGW2.1(26626185~34078363 bp)与粒长和千粒重相关;2号染色体上的qGW2.1和qGLWR2.1(10595289~18845781 bp)与粒宽和长宽比相关;3号染色体qGL3.1和qGLWR3.1(21022358~21038343 bp)及6号染色体上的qGL6.2和qTGW6.1(26793010~28240073 bp)与粒长相关;7号染色体上的qGW7.2和qTGW7.1(17771510~18372657 bp)与粒宽和千粒重相关。参考日本晴基因组同源序列的基因功能,从qGL6.1和qGW7.1区间共筛选出10个可能与籽粒性状相关的基因。qGL6.1区间的LOC_Os06g01670基因(MYB转录因子基因)作为影响水稻粒长的理想候选基因,该基因在短粒株系幼穗中高表达,推测其通过影响胚乳发育负调控粒长;qGW7.1区间的LOC_Os07g01740(半胱氨酸蛋白酶基因)和LOC_Os07g01940(染色单体粘连蛋白基因)在窄粒株系中高表达,推测其通过影响细胞分裂调控粒宽,将这2个基因列为影响水稻粒宽的候选基因。【结论】构建的广西普通野生稻导入系群体遗传效应较稳定,从中定位到22个籽粒性状主效QTLs,其中6号染色体上的qGL6.1和7号染色体上的qGW7.1是新的籽粒性状QTL,qGL6.1区间的LOC_Os06g01670基因与粒长相关,qGW7.1区间的LOC_Os07g01740和LOC_Os07g01940基因与粒宽相关,初步推测三者为影响籽粒性状的候选基因。

     

    Abstract: 【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.

     

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