Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome
Potato is one of the world’s most important food crops, with a time-consuming breeding process. In this study, we performed a genome-wide association (GWAS) analysis of the two important traits of potato tuber shape and eye depth, using the tetraploid potato genome (2n=4x=48) as a reference. A total...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1080666/full |
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| author | Long Zhao Long Zhao Long Zhao Meiling Zou Ke Deng Ke Deng Ke Deng Chengcai Xia Sirong Jiang Chenji Zhang Yongzhen Ma Yongzhen Ma Xiaorui Dong Miaohua He Tiancang Na Tiancang Na Tiancang Na Tiancang Na Tiancang Na Jian Wang Jian Wang Jian Wang Jian Wang Jian Wang Zhiqiang Xia Fang Wang Fang Wang Fang Wang Fang Wang Fang Wang |
| author_facet | Long Zhao Long Zhao Long Zhao Meiling Zou Ke Deng Ke Deng Ke Deng Chengcai Xia Sirong Jiang Chenji Zhang Yongzhen Ma Yongzhen Ma Xiaorui Dong Miaohua He Tiancang Na Tiancang Na Tiancang Na Tiancang Na Tiancang Na Jian Wang Jian Wang Jian Wang Jian Wang Jian Wang Zhiqiang Xia Fang Wang Fang Wang Fang Wang Fang Wang Fang Wang |
| author_sort | Long Zhao |
| collection | DOAJ |
| description | Potato is one of the world’s most important food crops, with a time-consuming breeding process. In this study, we performed a genome-wide association (GWAS) analysis of the two important traits of potato tuber shape and eye depth, using the tetraploid potato genome (2n=4x=48) as a reference. A total of 370 potatoes were divided into three subgroups based on the principal component analysis and evolutionary tree analysis. The genetic diversity within subgroups is low (5.18×10-5, 4.36×10-5 and 4.24×10-5). Genome-wide linkage disequilibrium (LD) analysis showed that their LD is about 60 Kb. GWAS analysis identified that 146 significant single nucleotide polymorphism (SNP) loci at Chr01A1:34.44−35.25 Mb and Chr02A1:28.35−28.54 Mb regions are significantly associated with potato tuber shape, and that three candidate genes that might be related to potato tuber traits, PLATZ transcription factor, UTP-glucose-1-phosphate uridylyltransferase and FAR1 DNA-binding domain, are in the association region of Chr02A1. GWAS analysis identified 53 significant SNP loci at Chr05A2: 49.644-50.146 Mb and Chr06A2: 25.866-26.384 Mb regions with robust associations with potato tuber eye depth. Hydrolase and methyltransferases are present in the association region of Chr05A2, and three CYPs are present in the association region of Chr06A2. Our findings suggested that these genes are closely associated with potato tuber shape and eye depth. Our study identified molecular markers and candidate genes for improving tetraploid potato tuber shape and eye depth and provided ideas and insights for tetraploid potato breeding. |
| first_indexed | 2024-04-09T21:23:02Z |
| format | Article |
| id | doaj.art-bd694c6027be42dfb1b4ba86250fdaf8 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-09T21:23:02Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-bd694c6027be42dfb1b4ba86250fdaf82023-03-28T04:49:54ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-03-011410.3389/fpls.2023.10806661080666Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genomeLong Zhao0Long Zhao1Long Zhao2Meiling Zou3Ke Deng4Ke Deng5Ke Deng6Chengcai Xia7Sirong Jiang8Chenji Zhang9Yongzhen Ma10Yongzhen Ma11Xiaorui Dong12Miaohua He13Tiancang Na14Tiancang Na15Tiancang Na16Tiancang Na17Tiancang Na18Jian Wang19Jian Wang20Jian Wang21Jian Wang22Jian Wang23Zhiqiang Xia24Fang Wang25Fang Wang26Fang Wang27Fang Wang28Fang Wang29Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, ChinaNational Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, ChinaCollege of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, ChinaCollege of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, ChinaAcademy of Agriculture and Forestry Sciences, Qinghai University, Xining, ChinaNational Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, ChinaCollege of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, ChinaCollege of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, ChinaCollege of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, ChinaCollege of Agronomy and Biotechnology, China Agricultural University, Beijing, ChinaAcademy of Agriculture and Forestry Sciences, Qinghai University, Xining, ChinaNational Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, ChinaCollege of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, ChinaCollege of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, ChinaAcademy of Agriculture and Forestry Sciences, Qinghai University, Xining, ChinaNational Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, ChinaKey Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Qinghai University, Xining, ChinaQinghai Provincial Key Laboratory of Potato Breeding, Qinghai University, Xining, ChinaLaboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, ChinaAcademy of Agriculture and Forestry Sciences, Qinghai University, Xining, ChinaNational Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, ChinaKey Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Qinghai University, Xining, ChinaQinghai Provincial Key Laboratory of Potato Breeding, Qinghai University, Xining, ChinaLaboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, ChinaCollege of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, ChinaAcademy of Agriculture and Forestry Sciences, Qinghai University, Xining, ChinaNational Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, ChinaKey Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Qinghai University, Xining, ChinaQinghai Provincial Key Laboratory of Potato Breeding, Qinghai University, Xining, ChinaLaboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, ChinaPotato is one of the world’s most important food crops, with a time-consuming breeding process. In this study, we performed a genome-wide association (GWAS) analysis of the two important traits of potato tuber shape and eye depth, using the tetraploid potato genome (2n=4x=48) as a reference. A total of 370 potatoes were divided into three subgroups based on the principal component analysis and evolutionary tree analysis. The genetic diversity within subgroups is low (5.18×10-5, 4.36×10-5 and 4.24×10-5). Genome-wide linkage disequilibrium (LD) analysis showed that their LD is about 60 Kb. GWAS analysis identified that 146 significant single nucleotide polymorphism (SNP) loci at Chr01A1:34.44−35.25 Mb and Chr02A1:28.35−28.54 Mb regions are significantly associated with potato tuber shape, and that three candidate genes that might be related to potato tuber traits, PLATZ transcription factor, UTP-glucose-1-phosphate uridylyltransferase and FAR1 DNA-binding domain, are in the association region of Chr02A1. GWAS analysis identified 53 significant SNP loci at Chr05A2: 49.644-50.146 Mb and Chr06A2: 25.866-26.384 Mb regions with robust associations with potato tuber eye depth. Hydrolase and methyltransferases are present in the association region of Chr05A2, and three CYPs are present in the association region of Chr06A2. Our findings suggested that these genes are closely associated with potato tuber shape and eye depth. Our study identified molecular markers and candidate genes for improving tetraploid potato tuber shape and eye depth and provided ideas and insights for tetraploid potato breeding.https://www.frontiersin.org/articles/10.3389/fpls.2023.1080666/fulltetraploid potatoGWAStuber shapeeye depthpopulation structuregenetic diversity |
| spellingShingle | Long Zhao Long Zhao Long Zhao Meiling Zou Ke Deng Ke Deng Ke Deng Chengcai Xia Sirong Jiang Chenji Zhang Yongzhen Ma Yongzhen Ma Xiaorui Dong Miaohua He Tiancang Na Tiancang Na Tiancang Na Tiancang Na Tiancang Na Jian Wang Jian Wang Jian Wang Jian Wang Jian Wang Zhiqiang Xia Fang Wang Fang Wang Fang Wang Fang Wang Fang Wang Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome Frontiers in Plant Science tetraploid potato GWAS tuber shape eye depth population structure genetic diversity |
| title | Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome |
| title_full | Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome |
| title_fullStr | Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome |
| title_full_unstemmed | Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome |
| title_short | Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome |
| title_sort | insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome |
| topic | tetraploid potato GWAS tuber shape eye depth population structure genetic diversity |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1080666/full |
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