基于极端混合池全基因组重测序的茄子果实硬度基因定位

doi:10.7668/hbnxb.20195535

摘要/Abstract

摘要：

为系统研究果实硬度相关基因,通过基因组重测序BSA方法定位果实硬度关联区间,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,为下一步基因克隆奠定基础。以稳定遗传的软肉自交系C18与硬肉自交系LE4杂交,F₂后代的果实硬度分离呈正态分布。在F₂群体中分别选取30株软肉和30株硬肉单株构建极端混合池,对混合池样本和双亲材料分别开展30×和10×覆盖度的全基因组重测序。重测序共获得1 891 040个单核苷酸多态性(SNPs)标记及376 603个插入缺失(InDels)标记,用于果实硬度性状的全基因组定位。BSA定位峰值位于茄子第6号染色体,从72 610 411到75 329 951 bp,共计2.71 Mb。根据通路富集和基因功能注释,筛选到候选基因Smechr0601726.1 和Smechr0601735.1。综上,通过基因组重测序BSA分析可知,茄子果实硬度可能由2个重要的候选基因进行调控,Smechr0601726.1编码多聚半乳糖醛酸酶基因,与果实硬度直接相关;Smechr0601735.1与抗坏血酸和阿糖二酸代谢密切相关,编码抗坏血酸过氧化物酶,与果实发育和硬度形成有关,可以延缓果实软化。

关键词: 茄子, 极端混合池, 全基因组重测序, 果实硬度, 基因定位

Abstract:

To systematically study genes related to fruit hardness,genome resequencing BSA method was used to locate the fruit hardness association interval,and predict candidate genes based on their corresponding reference genome collinearity segments and gene annotation information,to lay the foundation for the next step of gene localization and cloning.The fruit hardness separation of F₂ offspring from stable genetic soft flesh inbred line C18 and hard flesh inbred line LE4 crosses followed a normal distribution.30 soft fleshed and 30 hard fleshed individual plants were selected from the F₂ population to construct extreme mixed pools,and whole genome resequencing with 30×and 10×coverage on the mixed pools and parents was conducted.A total of 1 891 040 single nucleotide polymorphisms(SNPs)and 376 603 insertion deletion markers(InDels)were obtained from the hybrid pools and parents,which were used for genome-wide mapping of fruit hardness traits.The peak of BSA localization was distributed within a total of 2.71 Mb between 72 610 411 and 75 329 951 bp on eggplant chromosome 6.Based on pathway enrichment and gene function annotation,candidate genes Smechr0601726.1 and Smechr0601735.1 were obtained.In summary,through genome resequencing BSA analysis,eggplant fruit hardness may be regulated by two important candidate genes.Smechr0601726.1 encodes a polygalacturonase gene,which is directly related to fruit hardness;Smechr0601735.1 is closely related to the metabolism of ascorbic acid and arabic acid,encoding ascorbate peroxidase,and is associated with fruit development and hardness formation,which can delay fruit softening.

Key words: Eggplant, Extreme mixing pool, Whole-genome resequencing, Fruit hardness, Gene mapping

中图分类号:

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果实硬度基因定位[J]. 华北农学报, 2025, 40(3): 44-50. doi: 10.7668/hbnxb.20195535.

QIAO Jun, LIU Jing, LI Suwen, WANG Liying. Prediction of Fruit Hardness Genes of Eggplant Based on Genome-wide Resequencing in an Extreme Mixing Pool[J]. Acta Agriculturae Boreali-Sinica, 2025, 40(3): 44-50. doi: 10.7668/hbnxb.20195535.

http://www.hbnxb.net/CN/Y2025/V40/I3/44

图/表 6

表1 亲本及F₁果实硬度值

Tab.1 Fruit hardness index in parents and F₁kg/cm²

序号 Number	P₁(C18)	F₁(C18×LE4)	P₂(LE4)
1	2.9	3.8	5.3
2	3.5	3.6	4.9
3	3.7	4.1	5.4
4	3.9	5.0	5.6
5	3.4	3.6	5.7
6	3.6	5.0	5.4
7	2.7	4.0	5.3
8	3.0	4.2	5.4
9	3.4	4.1	5.7
10	3.6	3.6	4.9
平均	3.37±0.12a	4.10±0.17b	5.36±0.09c
Average

图1 杂交组合F₂果实硬度分布

Fig.1 Distribution of fruit hardness index in F₂ population

表2 测序深度及覆盖度统计

Tab.2 Statistics of sequencing depth and coverage

样本 Sample	数据总条数/Gb Total bases	比对数据条数/Gb Mapped bases	比对率/% Mapping rate	平均深度/× Average depth	至少有1个碱基覆盖的位点占基因组的百分比/% Coverage at least 1×	至少有5个碱基覆盖的位点占基因组的百分比/% Coverage at least 5×
硬肉极端池 Hard extreme pool	30.19	30.11	99.74	26.19	0.91	0.88
硬肉亲本 Hard parents	33.05	33.00	99.86	28.91	0.90	0.87
软肉极端池 Soft extreme pool	29.92	29.85	99.76	25.95	0.91	0.88
软肉亲本 Soft parents	12.76	12.74	99.89	11.06	0.89	0.81

图2 茄子基因组中显著关联区间的分布

Fig.2 Distribution of significant association intervals in the eggplant genome

图3 候选基因参与的生物过程、细胞组分和分子功能生物过程图:1.钙代谢过程;2.杜松烯生物合成过程;3.法尼二磷酸代谢过程;4.倍半萜代谢;5.倍半萜生物合成工艺;6.萜烯生物合成工艺;7.萜烯代谢过程;8.萜类代谢过程;9.异戊二烯生物合成过程;10.异戊二烯代谢过程;11.磷脂代谢过程;12.脂质生物合成过程;13.有机磷代谢过程;14.小RNA组装异染色质;15.细胞修饰氨基酸代谢过程;16.mRNA多聚腺苷酸化;17.RNA聚腺苷酸化;18.水溶性维生素生物合成过程;19.支链氨基酸代谢过程;20.mRNA 3'末端加工。细胞组分图:1.染色质;2.过时的染色体部分;3.线粒体基质;4.染色体;5.过时的线粒体部分;6.微管;7.纤维素合酶复合体;8.聚合物细胞骨架纤维;9.叶绿体类囊体膜;10.质体类囊体膜;11.线粒体蛋白复合物;12.超分子聚合物;13.超分子纤维;14.超分子复合物;15.类囊体膜;16.光合膜;17.皮质微管;18.活动纤毛;19.精子鞭毛;20.9+2活动纤毛。分子功能图:1.(+)-δ-杜松烯合酶活性;2.倍半萜合酶活性;3.萜合酶活性;4.作用于磷酸盐的碳氧裂合酶活性;5.碳氧裂合酶活性;6.裂合酶活性;7.天冬氨酸型内肽酶活性;8.天冬氨酸型肽酶活性;9.分子内氧化还原酶活性;10.异构酶活性;11.过氧化物酶活性;12.作用于受体的过氧化物氧化还原酶活性;13.细胞色素C过氧化物酶活性;14.醛脱氢酶活性;15.作用于供体CH-NH2基团,氧气作为受体的氧化还原酶活性;16.醛糖和酮糖相互转化的氧化还原酶活性;17.组蛋白赖氨酸N-甲基转移酶活性;18.作用于供体的CH-OH基团,NAD或NADP作为受体的氧化还原酶活性;19.激酶结合跨膜受体蛋白质丝氨酸/苏氨酸;20.作用于供体醛基或氧基,NAD或NADP作为受体的氧化还原酶活性。

Fig.3 Biological processes,cellular component,and molecular function involved in candidate genes Biological processes:1.Cadinene metabolic process;2.Cadinene biosynthetic process;3.Farnesyl diphosphate metabolic process;4.Sesquiterpene metabolic process;5.Sesquiterpene biosynthetic process;6.Terpene biosynthetic process;7.Terpene metabolic process;8.Terpenoid metabolic process;9.Isoprenoid biosynthetic process;10.Isoprenoid metabolic process;11.Phospholipid metabolic process;12.Lipid biosynthetic process;13.Organophosphate metabolic process;14.Heterochromatin assembly by small RNA;15.Cellular modified amino acid metabolic process;16.mRNA polyadenylation;17.RNA polyadenylation;18.Water-soluble vitamin biosynthetic process;19.Branched-chain amino acid metabolic process;20.mRNA 3'-end processing.Cellular component:1.Chromatin;2.Obsolete chromosomal part;3.Mitochondrial matrix;4.Chromosome;5.Obsolete mitochondrial part;6.Microtubule;7.Cellulose synthase complex;8.Polymeric cytoskeletal fiber;9.Chloroplast thylakoid membrane;10.Plastid thylakoid membrane;11.Mitochondrial protein-containing complex;12.Supramolecular polymer;13.Supramolecular fiber;14.Supramolecular complex;15.Thylakoid membrane;16.Photosynthetic membrane;17.Cortical microtubule;18.Motile cilium;19.Sperm flagellum;20.9+2 motile cilium.Molecular function:1.(+)-delta-cadinene synthase activity;2.Sesquiterpene synthase activity;3.Terpene synthase activity;4.Carbon-oxygen lyase activity,acting on phosphates;5.Carbon-oxygen lyase activity;6.Lyase activity;7.Aspartic-type endopeptidase activity;8.Aspartic-type peptidase activity;9.Intramolecular oxidoreductase activity;10.Isomerase activity;11.Peroxidase activity;12.Oxidoreductase activity,acting on peroxide as acceptor;13.Cytochrome-c peroxidase activity;14.Aldehyde dehydrogenase activity;15.Oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor;16.Oxidoreductase activity, interconverting aldoses and ketoses;17.Histone-lysine N-methyltransferase activity;18.Oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;19.Transmembrane receptor protein serine/threonine;20.Oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor.

表3 茄子果实硬度候选基因详细信息

Tab.3 Detailed information on candidate genes for eggplant fruit hardness

基因名称 Gene name	染色体名称 Chr	起始位置/bp Start	终止位置/bp End	正负链 Strand	基因长度/bp Gene length	基因类型 Gene biotype	基因功能描述 Gene description
Smechr0601726.1	E06	74 969 809	74 978 410	-	8 602	蛋白编辑	多聚半乳糖醛酸酶
Smechr0601735.1	E06	75 184 728	75 194 390	+	9 663	蛋白编辑	抗坏血酸过氧化物酶

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