基于GBS技术开展柚类资源群体遗传评价并发掘酸含量相关基因

doi:10.3864/j.issn.0578-1752.2023.08.010

Abstract

Abstract:

【Objective】 To reveal the phylogeny, population genetic structure and diversity level of pomelo (Citrus grandis (L.) Osbeck) germplasm, and to efficiently utilize them to explore genes related to important fruit quality traits, this research provided an insight into the population genetic structure and phylogeny of pomelo germplasm and facilitated the pomelo varieties innovation.【Method】 A total of 282 pomelo accessions including landraces from different geographical regions and hybrid offspring of kiyomi tangor and pomelo were contained in this study. GBS library was constructed with genomic DNAs digested by EcoR I restriction endonuclease and sequenced on Illumina HiSeq PE150 platform, the clean short reads were then mapped to pomelo reference genome by BWA, and SNPs were called out with SAMTOOLS pipeline. Based on 121 726 SNPs genotyping data, principal component analysis (PCA) and population genetic structure analysis were carried out and phylogenetic trees were constructed with Neighbor-joining method. Furthermore, two sub-populations containing high-acid accessions (32) and low-acid accessions (23) were used to identify candidate genes related to fruit acidity by Fst and XP-CLR selective sweeping analysis. Meanwhile, the genotype data of 282 pomelo accessions and the phenotypic data of titratable acid content in fruit were used for GWAS.【Result】 A total of 201.66 Gb original reads were generated from 282 pomelo germplasm by GBS approach, in average each sample produced 0.72 Gb reads. After the screening conditions of sequencing depth of dp5, the miss less than 0.2 and minor alleles frequency (MAF)>0.01, and a total of 121 726 SNPs were selected out for subsequent analysis. The PCA, structure and phylogenetic analysis all supported that the 282 pomelo germplasm could be divided into 6 subgroups, among which pomelo and kiyomi hybrid population, grapefruits and other pomelo hybrid populations could be obviously different from true-to-type pomelo populations, pomelos originated from different geographical region displayed unique genetic feature. The pomelo germplasm from Thailand and Vietnam formed a relatively unique group different from other domestic groups, such as ShaTian pomelo, Wen Dan pomelo, and Dian Jiang pomelo in China. The genetic introgression from Vietnam pomelos were exhibited in most pomelo germplasm in southern China, suggested that Vietnam was the origin center for pomelo. In addition, some pomelo germplasm with unknown origin have been identified accurately by GBS technology. This study showed that different geographical distribution and artificial selection pressure had great effect on the genomic composition of pomelo. Besides, Fst, XP-CLR selective sweeping analysis revealed a strong selection signal region on chromosome 7 contained genes annotated as dihydrolipoyl transacetylase (DLT-E2) of pyruvate dehydrogenase complex (PDC) and aluminum-activated malate transporter (ALMT9), which involved in the synthesis and transportation of citric acid. In additional GWAS genome-wide association analysis identified another region on chromosome 2, which was also highly associated with fruit acidity. 【Conclusion】GBS technology provided reliable and efficient method for studying the phylogeny and evolution of pomelo. The study showed that artificial cross breeding, long-term artificial selection, geography isolation and domestication were the major driving forces for the formation of different types of pomelo germplasm. In addition, it clearly showed that Southeast Asian was primary center for pomelo origin and China mainland was secondary evolutionary center. Several candidate genes related to citric acid content in pomelo fruits were identified by Fst, XP-CLR selective sweeping and GWAS. This study provided important gene resources for the further genetic improvement and breeding of pomelo fruits.

Key words: GBS, pomelo phylogeny, genes related to fruit acidity, GWAS

JIANG Dong, WANG Xu, LI RenJing, ZHAO XiaoDong, DAI XiangSheng, LIU ZhengWei. Population Genomic Structure of Pomelo Germplasm and Fruit Acidity Associated Genes Identification by Genotyping-by-Sequencing Technology[J].Scientia Agricultura Sinica, 2023, 56(8): 1547-1560.

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References 45

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亚群 Sub_population	π值范围 Range of π	平均π值 Average value of π	平均Tajima’s D Average value of Tajima’s D
沙田柚类 Shatian pomelo group	0.04—0.51	0.129	-0.15
文旦柚类 Wendan pomelo group	0.02—0.51	0.130	0.41
垫江柚类 Dianjiang pomelo group	0.03—0.51	0.134	0.45
越南泰国柚类 Vietnam and Thailand pomelo group	0.01—0.50	0.155	0.17
‘清见’杂交柚类 Pomelo and Kiyomi crossing group	0.01—0.50	0.233	1.12
葡萄柚类 Grapefruit group	0.03—0.51	0.259	0.92

Population Genomic Structure of Pomelo Germplasm and Fruit Acidity Associated Genes Identification by Genotyping-by-Sequencing Technology

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