玉米灌浆期茎秆抗推力的全基因组关联分析

Genome-Wide Association Analysis of Maize Stalk Anti-Thrust

【目的】通过基因型与表型数据关联分析,检测出与玉米茎秆抗推力相关的SNP位点,发掘出控制茎秆抗推力的候选基因。【方法】以292份玉米自交系组成的自然群体为材料,2015年和2016年在菏泽、枣庄、青州、胶州等地进行茎秆抗推力的测定,并且对株高、穗位高、雄穗长和雄穗柄长进行测定。另一方面,对材料进行取样并提取DNA,由美国先锋良种有限公司利用Maize SNP50基因芯片进行基因分型,该芯片包括55 126个单核苷酸多态性(SNP)标记,去除杂合率大于10%、缺失率大于20%和最小等位基因频率低于0.05的标记,剩余25 331个SNP,运用farm CPU结合基因型对茎秆抗推力表型数据进行全基因组关联分析,检测出与茎秆抗推力显著相关SNP位点,根据SNP所处的物理位置,对标记所在的区间进行定位,从而获得相对应的候选基因。运用SPSS statistics 20.0数据分析软件对株高、穗位高、雄穗长和雄穗柄长进行相关性分析,确定茎秆抗推力与4个性状的相关性。【结果】共检测出16个与茎秆抗推力显著相关的SNP(P<0.0001),分别位于染色体框3.06、5.02、4.08、6.04、8.03和9.03。在多个环境中检测到的SNP位点位于相同的染色体框,例如,位于染色体框8.03中的PZE_108026930、SYN19532、PZE_108048987和PZE_108050769,在2015年枣庄和2016年枣庄分别被检测到。位于染色体框3.06的PZE_103111295和PZE_103125327,在2015年青州和2016年枣庄分别被检测到。共获得GRMZM2G504401、GRMZM2G062974、GRMZM2G053767、GRMZM2G348551和GRMZM2G024260 5个候选基因,分别编码几丁质酶A、b ZIP转录因子超家族的蛋白、核糖体40S亚基S4类蛋白X1、可溶性淀粉合成酶2-3、腺嘌呤核苷酸水解酶超家族蛋白。此外,发现茎秆抗推力与株高、穗位高、雄穗长和雄穗柄长有显著或极显著相关性,但是在各个环境中相关关系不稳定,环境可能具有一定的影响。【结论】GRMZM2G062974参与植物在逆境下的表达调控,响应多种非生物胁迫。GRMZM2G348551参与糖代谢途径,调控支链淀粉的合成,与细胞壁的形成有关。GRMZM2G504401在植物中表达受到生物或者非生物胁迫的诱导,从而发挥作用。倒伏会受到自身或多种胁迫的影响。

【Objective】SNP loci related to stalk anti-thrust were detected by association analysis between genotype and phenotype data, so that various candidate genes related to stalk anti-thrust were explored.【Method】At present, genome-wide association analysis is widely used in the study of various traits in plants. In this study, 292 maize inbred lines were used as experimental materials, the determination of stalk anti-thrust was carried out in Heze, Zaozhuang, Qingzhou, Jiaozhou in 2015 and 2016. Besides, the plant height, ear height, tassel length and male spike length were measured. On the other hand, the DNA samples of the materials were extracted and then sent to Pioneer seed Products Ltd for genotyping by using Maize SNP50 gene chip. The chip includes 55126 single nucleotide polymorphism（SNP） markers, after removing the markers whose heterozygous ratio was greater than 10%, loss rate was more than 20% and minimum allele frequency was less than 0.05, there were 25331 SNPs left.Combined with the use of farm CPU, genome-wide association analysis was carried out for analyzing stalk anti-thrust phenotype data, the SNP loci which were significantly related to thrust resistance of stem were detected. According to the physical location of the SNP, the region of the marker was located and then the corresponding candidate genes were obtained. Using SPSS statistics 20 data analysis software, the correlation analysis of plant height, ear height, tassel length and male spike length was carried out to determine the correlation between stem thrust resistance and the 4 traits. In addition, stalk anti-thrust was found to have a significant or extremely significant correlation with plant height, ear height, tassel length and male spike length, but the correlation in each environment was instable, which means that the environment might have a certain impact on the correlation.【Result】A total of 16 SNPs were found to be significantly correlated with stalk anti-thrust, which were located on chromosome box 3.06, 5.02, 4.08, 6.04 and 9.03. SNP loci detected in multiple environments were found to be located on the same chromosome box, for example, SNP loci PZE_108026930, SYN19532, PZE_108048987 and PZE_108050769 which were all found to be located on chromosome 8.03 were detected in Zaozhuang in 2015 and 2016. Moreover, PZE_103111295 and PZE_103125327 found to be located on chromosome 3.06 were detected in Qingzhou in 2015 and Zaozhuang in 2016. A total of 5 candidate genes GRMZM2 G504401, GRMZM2 G062974, GRMZM2 G053767, GRMZM2 G348551 and GRMZM2 G024260 which encode basic endochitinase A, b ZIP transcription factor superfamily protein, 40 S ribosomal protein S4-like protein isoform X1, soluble starch synthase 2-3, adenine nucleotide alpha hydrolase-like superfamily protein were also obtained, respectively. 【Conclusion】GRMZM2 G062974 is involved in the expression regulation of plants under stress and responds to a variety of abiotic stresses. GRMZM2 G348551 participates in the pathway of glucose metabolism and regulates the synthesis of amylopectin, which is involved in the formation of cell walls. GRMZM2 G504401 is induced by biotic or abiotic stresses in plant. Lodging is affected by its own or a variety of stresses, and the functions of these genes are compatible with lodging resistance, so future studies should focus on the function of these genes.