玉米叶绿素含量的全基因组关联分析

史大坤,姚天茏,刘楠楠,邓敏,段海洋,王路林,万炯,高炯浩,谢惠玲,汤继华,张雪海

Genome-Wide Association Study of Chlorophyll Content in Maize

SHI DaKun,YAO TianLong,LIU NanNan,DENG Min,DUAN HaiYang,WANG LuLin,WAN Jiong,GAO JiongHao,XIE HuiLing,TANG JiHua,ZHANG XueHai

表3 玉米棒三叶叶绿素含量候选基因及功能注释

Table 3 Candidate genes and their annotation of chlorophyll content in maize three ear leaves at six environments

位点a Loci 染色 Chr. 环境 Enviro. 性状 Trait 峰值SNP Peak SNP 物理位置b Posi. (bp) P值c P value 贡献率d R2(%) 候选基因e Candidate gene 功能注释 Annotation 1 1 2018年长沙 Changsha, 2018 穗位叶 Uppermost ear leaf Chr.1.S_33879839 33879839 1.05E-06 5.89 GRMZM2G110023 ATP结合亚基CLPT1叶绿体 ATP-dependent Clp protease ATP-binding subunit CLPT1 chloroplastic GRMZM2G110004 NA GRMZM2G035552 ACR8 GRMZM2G035461 自噬蛋白9Autophagy protein 9 2 1 2017年三亚 Sanya, 2017 穗位叶 Uppermost ear leaf Chr.1.S_249417295 249417295 2.65E-06 5.43 GRMZM2G031771 NA GRMZM2G031788 NA GRMZM2G058057 同源线粒体导入受体亚基 Mitochondrial import receptor subunit TOM5 homolog TOM5 GRMZM2G058227 甘油磷酰二元酸酯磷酸二酯酶Glycerophosphoryl diester phosphodiesterase GRMZM2G058244 UDP -葡萄糖6脱氢酶UDP-glucose 6-dehydrogenase GRMZM2G172512 未知Unknown GRMZM2G172584 未知Unknown 2 1 2017年三亚 Sanya, 2017 穗位叶 Uppermost ear leaf Chr.1.S_249417300 249417300 2.65E-06 5.43 GRMZM2G031771 NA GRMZM2G031788 NA GRMZM2G058057 TOM5同源线粒体导入受体亚基 Mitochondrial import receptor subunit TOM5 homolog GRMZM2G058227 甘油磷酰二元酸酯磷酸二酯酶Glycerophosphoryl diester phosphodiesterase GRMZM2G058244 UDP -葡萄糖6脱氢酶UDP-glucose 6-dehydrogenase GRMZM2G172512 未知Unknown GRMZM2G172584 未知Unknown 2 1 2017年三亚 Sanya, 2017 穗位叶 Uppermost ear leaf Chr.1.S_249417301 249417301 2.65E-06 5.43 GRMZM2G031771 NA GRMZM2G031788 NA GRMZM2G058057 TOM5同源线粒体导入受体亚基 Mitochondrial import receptor subunit TOM5 homolog GRMZM2G058227 甘油磷酰二元酸酯磷酸二酯酶Glycerophosphoryl diester phosphodiesterase GRMZM2G058244 UDP -葡萄糖6脱氢酶UDP-glucose 6-dehydrogenase 位点a Loci 染色 Chr. 环境 Enviro. 性状 Trait 峰值SNP Peak SNP 物理位置b Posi. (bp) P值c P value 贡献率d R2(%) 候选基因e Candidate gene 功能注释 Annotation GRMZM2G172512 未知Unknown GRMZM2G172584 未知Unknown 3 3 2012年鹤壁 Hebi, 2012 穗下叶Below the uppermost ear leaf Chr.3.S_167437401 167437401 2.88E-07 6.52 GRMZM2G701895 NA GRMZM2G044055 甲酸精蛋白1Formin-like protein 1 GRMZM2G044092 葡萄糖苷酶42Beta-glucosidase 42 GRMZM2G118362 含五肽复合物的线粒体蛋白 Pentatricopeptide repeat-containing protein mitochondrial 4 3 综合Blup 穗上叶Above the uppermost ear leaf PZE-103136749 192318356 6.48E-07 5.10 GRMZM2G038953 54 kD蛋白3信号识别粒子Signal recognition particle 54 kD protein 3 5 5 综合Blup 穗上叶Above the uppermost ear leaf PZE-105049606 41552842 1.46E-06 4.80 GRMZM2G007185 β13-半乳糖基转移酶4 Probable beta-13-galactosyltransferase 4 5 5 综合Blup 穗上叶Above the uppermost ear leaf PZE-105049607 41552873 2.58E-06 4.53 GRMZM2G007185 β13-半乳糖基转移酶4 Probable beta-13-galactosyltransferase 4 6 5 2012年鹤壁 Hebi, 2012 穗位叶 Uppermost ear leaf Chr.5.S_174139937 174139937 2.23E-06 5.36 GRMZM5G836353 单氧酶1 Monooxygenase 1 GRMZM2G339523 单氧酶1 Monooxygenase 1 GRMZM2G087169 单氧酶1 Monooxygenase 1 GRMZM2G087068 类Cmc1细胞色素c氧化酶生物发生蛋白 Cytochrome c oxidase biogenesis protein Cmc1-like GRMZM2G388099 未知Unknown GRMZM2G087040 乙烯反应转录因子ERF021Ethylene-responsive transcription factor ERF021 GRMZM2G086946 TPX2（靶向蛋白为Xklp2）蛋白家族 TPX2 (targeting protein for Xklp2) protein family 7 5 综合Blup 穗下叶Below the uppermost ear leaf Chr.5.S_216586758 216586758 2.75E-06 5.03 GRMZM2G014116 26S蛋白酶体非ATP酶调节亚基 26S proteasome non-ATPase regulatory subunit 12 homolog B GRMZM2G014793 O-岩藻糖转移酶家族蛋白O-fucosyltransferase family protein GRMZM2G015090 植物细胞内ras -group相关LRR蛋白 Plant intracellular Ras-group-related LRR protein 9 GRMZM2G145061 脯氨酰4羟化酶亚基α2 Prolyl 4-hydroxylase alpha-2 subunit GRMZM2G145107 蔗糖转运2 Sucrose transporter2 GRMZM2G145128 含有重复PPR的线粒体蛋白Pentatricopeptide repeat-containing protein 位点a Loci 染色 Chr. 环境 Enviro. 性状 Trait 峰值SNP Peak SNP 物理位置b Posi. (bp) P值c P value 贡献率d R2(%) 候选基因e Candidate gene 功能注释 Annotation GRMZM2G145133 未知Unknown GRMZM2G445944 转录因子TCP21Transcription factor TCP21 GRMZM2G445958 复制蛋白a32 kD亚基A Replication protein A 32 kD subunit A GRMZM2G145473 未知Unknown 8 7 2012年鹤壁 Hebi, 2012 穗下叶Below the uppermost ear leaf Chr.7.S_9204823 9204823 4.39E-07 6.37 GRMZM2G704349 Pumilio同源3 Pumilio homolog 3 GRMZM2G046776 Pumilio同源3 Pumilio homolog 3 GRMZM2G046750 脂质转运蛋白Lipid-transfer protein 种子贮藏2S白蛋白超家族蛋白Seed storage 2S albumin superfamily protein GRMZM2G046529 叶绿体中蛋白质脂肪酸输出1 Protein FATTY ACID EXPORT 1 chloroplastic GRMZM2G004301 Ⅳ型肌醇多磷酸酶Type Ⅳ inositol polyphosphate 9 7 2017年三亚 Sanya, 2017 穗下叶Below the uppermost ear leaf Chr.7.S_145681493 145681493 1.72E-06 5.54 GRMZM2G168913 RNA聚合酶Ⅱ的中介体亚单位8 Mediator of RNA polymerase Ⅱtranscription subunit 8 GRMZM2G168858 NADPH-细胞色素P450还原酶NADPH--cytochrome P450 reductase 2 GRMZM2G357688 锌指蛋白2 Zinc finger protein 2 GRMZM2G436511 BTB/POZ蛋白域 BTB/POZ domain-containing protein GRMZM2G135651 环核苷酸封闭通道Cyclic nucleotide-gated ion channel 14 9 7 2017年三亚 Sanya, 2017 穗下叶Below the uppermost ear leaf Chr.7.S_145682189 145682189 5.85E-07 6.07 GRMZM2G168913 RNA聚合酶Ⅱ的中介体亚单位8 Mediator of RNA polymeraseⅡ transcription subunit 8 GRMZM2G168858 NADPH-细胞色素P450还原酶2 NADPH--cytochrome P450 reductase 2 GRMZM2G357688 锌指蛋白2Zinc finger protein 2 GRMZM2G436511 BTB/POZ蛋白域BTB/POZ domain-containing protein GRMZM2G135651 环核苷酸封闭通道Cyclic nucleotide-gated ion channel 14 10 8 2012年鹤壁 Hebi, 2012 穗上叶Above the uppermost ear leaf Chr.8.S_1454124 1454124 1.32E-06 5.55 GRMZM2G378906 外被体蛋白β亚基Coatomer subunit beta GRMZM2G110368 未知Unknown 11 8 综合Blup 穗位叶 Uppermost ear leaf Chr.8.S_1454124 1454124 3.95E-06 4.70 GRMZM2G378906 外被体蛋白β亚基Coatomer subunit beta GRMZM2G110368 未知Unknown 位点a Loci 染色 Chr. 环境 Enviro. 性状 Trait 峰值SNP Peak SNP 物理位置b Posi. (bp) P值c P value 贡献率d R2(%) 候选基因e Candidate gene 功能注释 Annotation 12 9 综合Blup 穗上叶Above the uppermost ear leaf Chr.9.S_9638369 9638369 1.32E-06 4.86 GRMZM2G159402 假定锌指蛋白Putative zinc finger protein GRMZM2G033130 DUF1296结构域蛋白家族 Putative DUF1296 domain containing family protein 12 9 综合Blup 穗上叶Above the uppermost ear leaf Chr.9.S_9639904 9639904 1.32E-06 4.86 GRMZM2G159402 假定锌指蛋白Putative zinc finger protein GRMZM2G033130 DUF1296结构域蛋白家族Putative DUF1296 domain containing family protein 12 9 综合Blup 穗上叶Above the uppermost ear leaf chr9.S_9642472 9642472 1.32E-06 4.86 GRMZM2G159402 假定锌指蛋白Putative zinc finger protein GRMZM2G033130 DUF1296结构域蛋白家族Putative DUF1296 domain containing family protein 12 9 综合Blup 穗上叶Above the uppermost ear leaf Chr.9.S_9643507 9643507 1.32E-06 4.86 GRMZM2G159402 假定锌指蛋白Putative zinc finger protein GRMZM2G033130 DUF1296结构域蛋白家族Putative DUF1296 domain containing family protein 12 9 综合Blup 穗上叶Above the uppermost ear leaf Chr.9.S_9644832 9644832 1.32E-06 4.86 GRMZM2G159402 假定锌指蛋白Putative zinc finger protein GRMZM2G033130 DUF1296结构域蛋白家族Putative DUF1296 domain containing family protein 13 9 2017年三亚 Sanya, 2017 穗位叶 Uppermost ear leaf Chr.9.S_151327393 151327393 1.72E-06 6.01 GRMZM2G178787 叶绿体蛋白激酶Protein kinase 2B chloroplastic GRMZM2G178826 脱氢奎尼酸合酶3-dehydroquinate synthase GRMZM2G479529 未知Unknown GRMZM2G178847 未知Unknown GRMZM2G178859 原血红素Ⅸ法氏转移酶Protoheme Ⅸ farnesyltransferase GRMZM2G178880 甘露聚糖合酶7 Probable mannan synthase 7 GRMZM2G178916 含有重复PPR的线粒体蛋白 Pentatricopeptide repeat-containing protein mitochondrial GRMZM2G479581 未知Unknown GRMZM2G178945 O-岩藻糖转移酶家族蛋白O-fucosyltransferase family protein GRMZM2G178960 核酮糖磷酸3-表异构酶Ribulose-phosphate 3-epimerase GRMZM2G057950 核糖体蛋白L32含有蛋白质的异构体1%3B核糖体蛋白L32,含有蛋白质的异构体 2Ribosomal protein L32 containing protein isoform 1%3B, Ribosomal protein L32 containing protein isoform 2 位点a Loci 染色 Chr. 环境 Enviro. 性状 Trait 峰值SNP Peak SNP 物理位置b Posi. (bp) P值c P value 贡献率d R2(%) 候选基因e Candidate gene 功能注释 Annotation GRMZM2G058037 类HVA22蛋白Ⅰ HVA22-like proteinⅠ GRMZM2G361256 ATP结合盒（ABC)蛋白家族3 ABC transporter C family member 3 14 9 2017年三亚 Sanya, 2017 穗位叶 Uppermost ear leaf Chr.9.S_153737236 153737236 7.91E-07 6.59 GRMZM2G382537 未知Unknown GRMZM2G382534 羟化酶5 Hydroxylase5 GRMZM2G060564 PLAC8 家族蛋白PLAC8 family protein GRMZM2G060507 假定类结转录因子家族蛋白Putative knotted-like transcription factor family protein GRMZM2G064005 Protein FIZZY-RELATED 1 FIZZY-RELATED蛋白 GRMZM2G063931 假定泛素连接酶酶家族,E2泛素连接酶 Putative ubiquitin-conjugating enzyme family%3B, ubiquitin-conjugating enzyme E2 15 10 2012年鹤壁 Hebi, 2012 穗位叶 Uppermost ear leaf Chr.10.S_45404195 45404195 2.81E-06 4.76 NO - 16 10 2012年鹤壁 Hebi, 2012 穗位叶 Uppermost ear leaf Chr.10.S_46780569 46780569 2.76E-06 4.75 GRMZM2G135800 NA GRMZM2G371316 未知Unknown GRMZM2G371345 黄酮醇3-O-葡糖基转移酶Flavonol 3-O-glucosyltransferase 16 10 2012年鹤壁 Hebi, 2012 穗位叶 Uppermost ear leaf Chr.10.S_46780652 46780652 2.76E-06 4.75 GRMZM2G135800 NA GRMZM2G371316 未知Unknown GRMZM2G371345 黄酮醇3-O-葡糖基转移酶Flavonol 3-O-glucosyltransferase 17 10 2018年长沙 Changsha, 2018 穗位叶 Uppermost ear leaf Chr.10.S_148643242 148643242 3.04E-06 5.30 GRMZM2G074787 DNA错配修复蛋白MSH3 DNA mismatch repair protein MSH3 GRMZM2G074773 核转录因子Y亚基C-4 Nuclear transcription factor Y subunit C-4 GRMZM2G074759 酰基活化酶3 Acyl activating enzyme3 GRMZM2G074754 C2钙/脂结合植物磷脂酰转移酶家族蛋白 C2 calcium/lipid-binding plant phosphoribosyltransferase family protein GRMZM2G074718 表达蛋白Expressed protein GRMZM2G074107 DNA结合蛋白DNA binding protein 位点a Loci 染色 Chr. 环境 Enviro. 性状 Trait 峰值SNP Peak SNP 物理位置b Posi. (bp) P值c P value 贡献率d R2(%) 候选基因e Candidate gene 功能注释 Annotation 17 10 2018年长沙 Changsha, 2018 穗位叶 Uppermost ear leaf Chr.10.S_148643247 148643247 3.87E-06 5.27 GRMZM2G074787 DNA错配修复蛋白MSH3 DNA mismatch repair protein MSH3 GRMZM2G074773 核转录因子Y亚基C-4 Nuclear transcription factor Y subunit C-4 GRMZM2G074759 酰基活化酶3 Acyl activating enzyme3 GRMZM2G074754 C2钙/脂结合植物磷脂酰转移酶家族蛋白 C2 calcium/lipid-binding plant phosphoribosyltransferase family protein GRMZM2G074718 表达蛋白Expressed protein GRMZM2G074107 DNA结合蛋白DNA binding protein 17 10 2018年长沙 Changsha, 2018 穗位叶 Uppermost ear leaf Chr.10.S_148643249 148643249 1.78E-07 6.71 GRMZM2G074787 DNA错配修复蛋白MSH3 DNA mismatch repair protein MSH3 GRMZM2G074773 核转录因子Y亚基C-4 Nuclear transcription factor Y subunit C-4 GRMZM2G074759 酰基活化酶3 Acyl activating enzyme3 GRMZM2G074754 C2钙/脂结合植物磷脂酰转移酶家族蛋白 C2 calcium/lipid-binding plant phosphoribosyltransferase family protein GRMZM2G074718 表达蛋白Expressed protein GRMZM2G074107 DNA结合蛋白DNA binding protein 18 10 2018年长沙 Changsha, 2018 穗上叶Above the uppermost ear leaf Chr.10.S_148643249 148643249 1.58E-06 5.80 GRMZM2G074787 DNA错配修复蛋白MSH3 DNA mismatch repair protein MSH3 GRMZM2G074773 核转录因子Y亚基C-4 Nuclear transcription factor Y subunit C-4 GRMZM2G074759 酰基活化酶3 Acyl activating enzyme3 GRMZM2G074754 C2钙/脂结合植物磷脂酰转移酶家族蛋白 C2 calcium/lipid-binding plant phosphoribosyltransferase family protein GRMZM2G074718 表达蛋白Expressed protein GRMZM2G074107 DNA结合蛋白DNA binding protein