Population Genetic Characteristics of the Cultivated <i>Coffea arabica</i> with Whole-Genome Resequencing
<i>Coffea arabica</i> L. (<i>C. arabica</i>) is an economically important agricultural crop and the most popular beverage worldwide. To analyze genetic diversity and provide genetic resources for the selection and breeding of superior varieties of <i>C. arabica</i>...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2024-10-01
|
| Series: | Horticulturae |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2311-7524/10/11/1153 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850227265816756224 |
|---|---|
| author | Qin Zhang Dongxiao Ma Yang Yang Faguang Hu Xingfei Fu Guiping Li Xiaofang Zhang Na Wang Dexin Liu Ruirui Wu Xiaofei Bi Yuqiang Lou Yaqi Li Haohao Yu Wei Yan Yanan Li |
| author_facet | Qin Zhang Dongxiao Ma Yang Yang Faguang Hu Xingfei Fu Guiping Li Xiaofang Zhang Na Wang Dexin Liu Ruirui Wu Xiaofei Bi Yuqiang Lou Yaqi Li Haohao Yu Wei Yan Yanan Li |
| author_sort | Qin Zhang |
| collection | DOAJ |
| description | <i>Coffea arabica</i> L. (<i>C. arabica</i>) is an economically important agricultural crop and the most popular beverage worldwide. To analyze genetic diversity and provide genetic resources for the selection and breeding of superior varieties of <i>C. arabica</i>, 61 cultivated Arabica coffee accessions were analyzed in the study, including 12 resequencing accessions from previous research and 49 accessions that were resequenced in this study. Single nucleotide polymorphisms (SNPs) and insertion–deletions (InDels) were statistically analyzed. Based on SNP variations, a genetic structure analysis, phylogenetic tree construction, and principal component analysis were performed for the 61 coffee accessions. The results showed that a total of 805.46 Gb of raw whole-genome resequencing data was obtained from the 61 coffee accessions, with 781.29 Gb of high-quality sequencing data after filtering. In total, 7,013,820 SNP sites and 1,074,329 InDel sites were detected. The average sequencing depth ranged from 6.69× to 19.35×, and the coverage ranged from 85.49% to 96.43%. The population genetic structure and phylogenetic analysis of the 61 coffee accessions revealed four lineages, suggesting that they had at least four ancestral genetic components. Catimor exhibited the highest genetic diversity, while Geisha had the lowest genetic diversity. The selective sweep analysis indicated that among the selected genes in Catimor, disease-resistance genes were significantly more numerous than in other coffee varieties. The genome resequencing data and genetic markers identified from the 61 cultivated Arabica coffee materials provided insights into the genetic variation in Arabica coffee germplasm and facilitated extensive genetic research. |
| format | Article |
| id | doaj-art-3222ceeb41e045dfbbdf4235532290c9 |
| institution | OA Journals |
| issn | 2311-7524 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Horticulturae |
| spelling | doaj-art-3222ceeb41e045dfbbdf4235532290c92025-08-20T02:04:52ZengMDPI AGHorticulturae2311-75242024-10-011011115310.3390/horticulturae10111153Population Genetic Characteristics of the Cultivated <i>Coffea arabica</i> with Whole-Genome ResequencingQin Zhang0Dongxiao Ma1Yang Yang2Faguang Hu3Xingfei Fu4Guiping Li5Xiaofang Zhang6Na Wang7Dexin Liu8Ruirui Wu9Xiaofei Bi10Yuqiang Lou11Yaqi Li12Haohao Yu13Wei Yan14Yanan Li15Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, ChinaInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China<i>Coffea arabica</i> L. (<i>C. arabica</i>) is an economically important agricultural crop and the most popular beverage worldwide. To analyze genetic diversity and provide genetic resources for the selection and breeding of superior varieties of <i>C. arabica</i>, 61 cultivated Arabica coffee accessions were analyzed in the study, including 12 resequencing accessions from previous research and 49 accessions that were resequenced in this study. Single nucleotide polymorphisms (SNPs) and insertion–deletions (InDels) were statistically analyzed. Based on SNP variations, a genetic structure analysis, phylogenetic tree construction, and principal component analysis were performed for the 61 coffee accessions. The results showed that a total of 805.46 Gb of raw whole-genome resequencing data was obtained from the 61 coffee accessions, with 781.29 Gb of high-quality sequencing data after filtering. In total, 7,013,820 SNP sites and 1,074,329 InDel sites were detected. The average sequencing depth ranged from 6.69× to 19.35×, and the coverage ranged from 85.49% to 96.43%. The population genetic structure and phylogenetic analysis of the 61 coffee accessions revealed four lineages, suggesting that they had at least four ancestral genetic components. Catimor exhibited the highest genetic diversity, while Geisha had the lowest genetic diversity. The selective sweep analysis indicated that among the selected genes in Catimor, disease-resistance genes were significantly more numerous than in other coffee varieties. The genome resequencing data and genetic markers identified from the 61 cultivated Arabica coffee materials provided insights into the genetic variation in Arabica coffee germplasm and facilitated extensive genetic research.https://www.mdpi.com/2311-7524/10/11/1153<i>Coffea arabica</i>resequencingphylogenetic analysisvariation detectiondiversity |
| spellingShingle | Qin Zhang Dongxiao Ma Yang Yang Faguang Hu Xingfei Fu Guiping Li Xiaofang Zhang Na Wang Dexin Liu Ruirui Wu Xiaofei Bi Yuqiang Lou Yaqi Li Haohao Yu Wei Yan Yanan Li Population Genetic Characteristics of the Cultivated <i>Coffea arabica</i> with Whole-Genome Resequencing Horticulturae <i>Coffea arabica</i> resequencing phylogenetic analysis variation detection diversity |
| title | Population Genetic Characteristics of the Cultivated <i>Coffea arabica</i> with Whole-Genome Resequencing |
| title_full | Population Genetic Characteristics of the Cultivated <i>Coffea arabica</i> with Whole-Genome Resequencing |
| title_fullStr | Population Genetic Characteristics of the Cultivated <i>Coffea arabica</i> with Whole-Genome Resequencing |
| title_full_unstemmed | Population Genetic Characteristics of the Cultivated <i>Coffea arabica</i> with Whole-Genome Resequencing |
| title_short | Population Genetic Characteristics of the Cultivated <i>Coffea arabica</i> with Whole-Genome Resequencing |
| title_sort | population genetic characteristics of the cultivated i coffea arabica i with whole genome resequencing |
| topic | <i>Coffea arabica</i> resequencing phylogenetic analysis variation detection diversity |
| url | https://www.mdpi.com/2311-7524/10/11/1153 |
| work_keys_str_mv | AT qinzhang populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT dongxiaoma populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT yangyang populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT faguanghu populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT xingfeifu populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT guipingli populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT xiaofangzhang populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT nawang populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT dexinliu populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT ruiruiwu populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT xiaofeibi populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT yuqianglou populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT yaqili populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT haohaoyu populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT weiyan populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing AT yananli populationgeneticcharacteristicsofthecultivatedicoffeaarabicaiwithwholegenomeresequencing |