Prediction of Fruit Hardness Genes of Eggplant Based on Genome-wide Resequencing in an Extreme Mixing Pool

doi:10.7668/hbnxb.20195535

Abstract

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

CLC Number:

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.

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Figures/Tables 6

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

Fig.1 Distribution of fruit hardness index in F₂ population

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

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

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.

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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