Genome-wide Association Analysis of Maize (Zea mays) Grain Quality Related Traits Based on Four Test Cross Populations
GUO Jin-Jie1, *, LIU Wen-Si1, *, ZHENG Yun-Xiao1, LIU Han2, ZHAO Yong-Feng1, ZHU Li-Ying, JIA Xiao-Yan1, CHEN Jing-Tang1, **
1 College of Agronomy, Hebei Agricultural University/Hebei Sub-center of National Maize Improvement Center/Key Laboratory for Crop Germplasm Resources of Hebei, Baoding 071000, China; 2 National Maize Improvement Center of China/State Key Laboratory of Agrobiotechnology/China Agricultural University, Beijing 100193, China
摘要玉米(Zea mays)生产上利用的是杂交种,利用不同遗传背景的测交群体来定位杂种当代控制品质性状的遗传位点,是对前人定位研究的有益补充。本实验以100份遗传背景丰富的玉米骨干自交系作为母本,分别以Mo17、E28、昌7-2、郑58作为测验种,按照NCⅡ设计,组配400份杂交组合,构建4个F1群体,每个F1群体各100份杂交组合。对4个测交群体的籽粒品质相关性状进行统计分析和全基因组关联分析(genome-wide association study, GWAS)。研究结果表明,蛋白质含量在E28和昌7-2测交群体显著高于其他群体(P<0.05);油分含量在E28测交群体显著高于其他群体(P<0.05);赖氨酸含量在Mo17测交群体显著高于其他群体(P<0.05)。Mo17测交群体在蛋白质含量、油分含量、赖氨酸含量中分别定位到2、5、17个显著关联的SNP位点,E28测交群体在蛋白质含量、油分含量、赖氨酸含量中分别定位到11、7、54个SNP位点,昌7-2测交群体在蛋白质含量、油分含量、赖氨酸含量中分别定位到8、8、6个SNP位点,郑58测交群体在蛋白质含量、油分含量、赖氨酸含量中分别定位到38、79、11个SNP位点。4个测交群体的定位结果差异很大,对4个测交群体的同一性状SNP位点进行比较,仅得到7个共位点。分别在蛋白质含量、油分含量、赖氨酸含量中定位到2、4、1个共位点,共挖掘到6个候选基因。本研究结果为玉米品质相关性状的传统连锁分析和关联分析提供了有益补充,为进一步玉米籽粒品质改良提供了参考。
Abstract：Hybrids are used in maize (Zea mays) production.Based on natural populations, recombination inbred line (RIL), doubled haploid (DH), F2, backcrossing (BC) and other traditional loci or regions can only reflect the contemporary genetic effects of F1 indirectly.The genetic effects of F1 could be studied directly by locating the genetic loci or regions of hybrids that control the target traits.In this study, 100 maize inbred lines with rich genetic background were used as female parents, and four lines, Mo17, E28, Zheng58, and Chang7-2 were used as test parents.According to the NCⅡ experiment, 400 hybrids (100 females×4 males) were constructed.Statistical analysis and genome-wide association study (GWAS) of grain quality-related traits, protein (Pro) content, oil content , and lysine (Lys) content, in 4 test cross populations were performed.The kernel quality traits were significant differences in F1, because of the influence of 4 different genetic background test parents.The results showed that the Pro content in the test cross populations with pollens from E28 (E28s) and Chang7-2 (Chang7-2s) was significantly higher than other populations (P<0.05); the oil content in the test cross population with pollens from E28 was significantly higher than other populations (P<0.05); Lys content in the test cross population with pollens from Mo17 (Mo17s) was significantly higher than other populations (P<0.05).For Pro, Oil, and Lys, 2, 5, and 17 significantly associated SNPs were detected in Mo17s, respectively.The phenotype variation range that can be explained by a single locus was 1.99%~21.83%, 1.15%~16.83%, 1.48%~29.91%.And in populations of E28s, Chang7-2s, and Zheng58s, the correspondingly detected SNP loci associated Pro/Oil/Lys were 11/7/54, 8/8/6, and 38/79/11, respectively.The phenotype variation range that can be explained by a single locus was 1.15%~38.60%/4.01%~26.35%/0.25%~46.10%, 7.32%~34.63%/1.25%~8.08%/2.53%~18.64% and 1.07%~61.14%/1.00%~31.04%/1.02%~21.15%, respectively.The total shared SNPs detected for Pro, Oil, and Lys were 7, 2 for Pro, 4 for Oil, and 1 for Lys.The phenotype variation range that could be explained by a single locus was 0.12%~2.51%, 3.18%~11.59%, 0.25%~14.63%.These 7 SNPs were located on the Chr1, Chr4, Chr5, Chr6, Chr9, Chr10 and donated 6 candidate genes.The candidate genes were GRMZM2G143817, GRMZM2G446313, GRMZM2G146346, GRMZM2G104920, GRMZM2G083886, GRMZM2G148400, respectively.These results provided informative references for loci mining associated with maize kernel quality-related traits via QTL mapping or GWAS pathways, and also provided practical references for kernel quality improvement in maize breeding procedures.
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