基于极端混合池全基因组重测序的茄子萼下果色基因预测

doi:10.16420/j.issn.0513-353x.2021-0018

摘要/Abstract

摘要：

以茄子萼下紫色稳定遗传的圆茄自交系Y5与萼下绿色圆茄自交系Y73杂交,结果发现F₂代的萼下果色分离呈正态分布。在F₂群体中选取30个萼下紫色和30个萼下绿色单株构建极端混合池,对混合池和双亲开展30×和10×覆盖度的全基因组重测序,定位萼下果色性状关联区间,并根据其对应的参考基因组共线性区段和基因注释信息预测候选基因。重测序得到7 747 547个单核苷酸多态性（SNP）标记和569 796个插入缺失标记（InDel）标记,用于萼下果色性状的全基因组定位。定位结果获得7个显著关联区间,分布于茄子第4、10和11号染色体,根据通路富集和基因功能注释,筛选到候选基因EGP21397、EGP21400、EGP21491、EGP22288和EGP22289,这5个候选基因与光合作用密切相关,分别编码钙调素结合家族蛋白、C2H2型锌指蛋白、类胡萝卜素异构酶、2Fe-2S铁氧还蛋白样超家族蛋白和脂质转运蛋白。同时预测到与细胞色素P450和光敏色素合成有关的候选基因共6个,位于10号染色体关联区间,这些蛋白和光敏色素均与光合作用和逆境发育有关,从一定程度上揭示了茄子萼下果色发育的分子机理。

关键词: 茄子, 萼下果色, 基因定位, 极端混合池, 全基因组重测序

Abstract:

Stably genetic purple under the calyx,round eggplant inbred line Y5 was crossed with green under the calyx,round eggplant inbred line Y73. The segregation of fruit color under the calyx of F₂ progeny had a normal distribution,which could be analyzed by bulk segregant analysis（BSA）. In the F₂ population,30 purple and 30 green under the calyx plants were selected to construct separated mixed pools. Whole-genome resequencing of 30× and 10× coverage was carried out in the mixed pools and parents to locate the correlation interval of fruit color under the calyx. Candidate genes were predicted according to the collinear region and gene annotation information of the eggplant genome. A total of 7 747 547 single nucleotide polymorphisms（SNP）and 569 796 insertion deletion markers（InDel）were obtained from the hybrid pools and parents,which were used for genome-wide mapping of fruit color traits under the calyx. According to pathway enrichment and gene function annotation,candidate genes EGP21397,EGP21400,EGP21491,EGP22288,and EGP22289 were obtained. The five candidate genes were closely related to cell photosynthesis and encoded calmodulin-binding family proteins,the C2H2 zinc finger protein,carotenoid isomerase,2Fe-2S ferredoxin-like superfamily proteins,and the lipid transfer protein. At the same time,six candidate genes related to cytochrome P450 and phytochrome synthesis were predicted,which were located in the association regions of chromosomes 10. These proteins and pigments were related to photosynthesis and stress development,which revealed the molecular mechanism of fruit color in eggplant.

Key words: eggplant, fruit color under the calyx, gene mapping, extreme mixing pool, whole-genome resequencing

中图分类号:

S641.1

乔军, 刘婧, 李素文, 王利英. 基于极端混合池全基因组重测序的茄子萼下果色基因预测[J]. 园艺学报, 2022, 49(3): 613-621.

QIAO Jun, LIU Jing, LI Suwen, WANG Liying. Prediction of Fruit Color Genes Under the Calyx of Eggplant Based on Genome-wide Resequencing in an Extreme Mixing Pool[J]. Acta Horticulturae Sinica, 2022, 49(3): 613-621.

图/表 4

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预测基因 Predicted gene	染色体 Chr.	关联区间/Mb Correlation interval	突变位置 Mutation location	突变碱基 Mutant base	突变区域 Mutation region	是否同义突变 Synonymous mutation（Y/N）	基因注释 Gene annotation
EGP21397	10	1.9 ~ 5.1	2 045 972	G→A	外显子区 Extron	否N	C2H2型锌指蛋白 C2HC zinc fingers superfamily protein
EGP21400	10	1.9 ~ 5.1	2 112 411	A→T	外显子区 Extron	否N	钙调素结合家族蛋白 Calmodulin-binding family protein
EGP21491	10	1.9 ~ 5.1	3 244 885	T→C	外显子区 Extron	否N	类胡萝卜素异构酶 Carotenoid isomerase
EGP21416	10	1.9 ~ 5.1	2 279 620	A→G	基因间 Intergenic	否N	细胞色素P450,家族96,亚家族A,多肽1 Cytochrome P450,family 96,subfamily A,polypeptide 1
EGP21417	10	1.9 ~ 5.1	2 279 620	A→G	基因间 Intergenic	否N	细胞色素P450,家族96,亚家族A,多肽1 Cytochrome P450,family 96,subfamily A,polypeptide 1
EGP21480	10	1.9 ~ 5.1	3 107 257	G→A	基因间 Intergenic	否N	细胞色素P450,家族82,亚家族C,多肽4 Cytochrome P450,family 82,subfamily C,polypeptide 4
EGP21561	10	1.9 ~ 5.1	3 901 677	G→A	基因间 Intergenic	否N	细胞色素P450,家族94,亚家族C,多肽1 Cytochrome P450,family 94,subfamily C, polypeptide 1
EGP21596	10	1.9 ~ 5.1	4 258 708	C→A	基因间 Intergenic	否N	细胞色素P450,家族76,亚家族C,多肽7 Cytochrome P450,family 76,subfamily C, polypeptide 7
EGP21891	10	7.3 ~ 14.1	8 710 042	G→A	基因间 Intergenic	否N	光敏色素 Phytochrome
EGP22288	10	14.5 ~ 23.7	17 833 364	A→G	基因间 Intergenic	否N	2Fe-2S铁氧还蛋白样超家族蛋白 2Fe-2S ferredoxin-like superfamily protein
EGP22289	10	14.5 ~ 23.7	17 833 364	A→G	基因间 Intergenic	否N	脂质转运蛋白 Lipid transfer protein

预测基因 Predicted gene	染色体 Chr.	关联区间/Mb Correlation interval	突变位置 Mutation location	突变碱基 Mutant base	突变区域 Mutation region	是否同义突变 Synonymous mutation（Y/N）	基因注释 Gene annotation
EGP21397	10	1.9 ~ 5.1	2 045 972	G→A	外显子区 Extron	否N	C2H2型锌指蛋白 C2HC zinc fingers superfamily protein
EGP21400	10	1.9 ~ 5.1	2 112 411	A→T	外显子区 Extron	否N	钙调素结合家族蛋白 Calmodulin-binding family protein
EGP21491	10	1.9 ~ 5.1	3 244 885	T→C	外显子区 Extron	否N	类胡萝卜素异构酶 Carotenoid isomerase
EGP21416	10	1.9 ~ 5.1	2 279 620	A→G	基因间 Intergenic	否N	细胞色素P450,家族96,亚家族A,多肽1 Cytochrome P450,family 96,subfamily A,polypeptide 1
EGP21417	10	1.9 ~ 5.1	2 279 620	A→G	基因间 Intergenic	否N	细胞色素P450,家族96,亚家族A,多肽1 Cytochrome P450,family 96,subfamily A,polypeptide 1
EGP21480	10	1.9 ~ 5.1	3 107 257	G→A	基因间 Intergenic	否N	细胞色素P450,家族82,亚家族C,多肽4 Cytochrome P450,family 82,subfamily C,polypeptide 4
EGP21561	10	1.9 ~ 5.1	3 901 677	G→A	基因间 Intergenic	否N	细胞色素P450,家族94,亚家族C,多肽1 Cytochrome P450,family 94,subfamily C, polypeptide 1
EGP21596	10	1.9 ~ 5.1	4 258 708	C→A	基因间 Intergenic	否N	细胞色素P450,家族76,亚家族C,多肽7 Cytochrome P450,family 76,subfamily C, polypeptide 7
EGP21891	10	7.3 ~ 14.1	8 710 042	G→A	基因间 Intergenic	否N	光敏色素 Phytochrome
EGP22288	10	14.5 ~ 23.7	17 833 364	A→G	基因间 Intergenic	否N	2Fe-2S铁氧还蛋白样超家族蛋白 2Fe-2S ferredoxin-like superfamily protein
EGP22289	10	14.5 ~ 23.7	17 833 364	A→G	基因间 Intergenic	否N	脂质转运蛋白 Lipid transfer protein