Genome-Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz)
Cassava (Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromos...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-04-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fpls.2018.00503/full |
| _version_ | 1819045314072412160 |
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| author | Shengkui Zhang Shengkui Zhang Xin Chen Cheng Lu Jianqiu Ye Meiling Zou Kundian Lu Subin Feng Jinli Pei Chen Liu Xincheng Zhou Ping’an Ma Zhaogui Li Cuijuan Liu Qi Liao Zhiqiang Xia Wenquan Wang |
| author_facet | Shengkui Zhang Shengkui Zhang Xin Chen Cheng Lu Jianqiu Ye Meiling Zou Kundian Lu Subin Feng Jinli Pei Chen Liu Xincheng Zhou Ping’an Ma Zhaogui Li Cuijuan Liu Qi Liao Zhiqiang Xia Wenquan Wang |
| author_sort | Shengkui Zhang |
| collection | DOAJ |
| description | Cassava (Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromosome were in agreement. Population structure analysis indicated that this panel can be divided into three subgroups. Genetic diversity analysis indicated that the average nucleotide diversity of the panel was 1.21 × 10-4 for all sampled landraces. This average nucleotide diversity was 1.97 × 10-4, 1.01 × 10-4, and 1.89 × 10-4 for subgroups 1, 2, and 3, respectively. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about ∼8 kb. We evaluated 158 cassava varieties under 11 different environments. Finally, we identified 36 loci that were related to 11 agronomic traits by genome-wide association analyses. Four loci were associated with two traits, and 62 candidate genes were identified in the peak SNP sites. We found that 40 of these genes showed different expression profiles in different tissues. Of the candidate genes related to storage roots, Manes.13G023300, Manes.16G000800, Manes.02G154700, Manes.02G192500, and Manes.09G099100 had higher expression levels in storage roots than in leaf and stem; on the other hand, of the candidate genes related to leaves, Manes.05G164500, Manes.05G164600, Manes.04G057300, Manes.01G202000, and Manes.03G186500 had higher expression levels in leaves than in storage roots and stem. This study provides basis for research on genetics and the genetic improvement of cassava. |
| first_indexed | 2024-12-21T10:26:36Z |
| format | Article |
| id | doaj.art-12f6a6d40e824b8ea10a370200a14bc4 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-21T10:26:36Z |
| publishDate | 2018-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-12f6a6d40e824b8ea10a370200a14bc42022-12-21T19:07:18ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-04-01910.3389/fpls.2018.00503341121Genome-Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz)Shengkui Zhang0Shengkui Zhang1Xin Chen2Cheng Lu3Jianqiu Ye4Meiling Zou5Kundian Lu6Subin Feng7Jinli Pei8Chen Liu9Xincheng Zhou10Ping’an Ma11Zhaogui Li12Cuijuan Liu13Qi Liao14Zhiqiang Xia15Wenquan Wang16College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, ChinaInstitute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, ChinaInstitute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, ChinaInstitute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, ChinaTropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, ChinaInstitute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, ChinaWuming Agricultural Technology Extension Center, Nanning, ChinaInstitute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, ChinaInstitute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, ChinaInstitute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, ChinaInstitute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, ChinaInstitute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, ChinaWuming Agricultural Technology Extension Center, Nanning, ChinaHepu Institute of Agricultural Science, Beihai, ChinaHepu Institute of Agricultural Science, Beihai, ChinaInstitute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, ChinaInstitute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, ChinaCassava (Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromosome were in agreement. Population structure analysis indicated that this panel can be divided into three subgroups. Genetic diversity analysis indicated that the average nucleotide diversity of the panel was 1.21 × 10-4 for all sampled landraces. This average nucleotide diversity was 1.97 × 10-4, 1.01 × 10-4, and 1.89 × 10-4 for subgroups 1, 2, and 3, respectively. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about ∼8 kb. We evaluated 158 cassava varieties under 11 different environments. Finally, we identified 36 loci that were related to 11 agronomic traits by genome-wide association analyses. Four loci were associated with two traits, and 62 candidate genes were identified in the peak SNP sites. We found that 40 of these genes showed different expression profiles in different tissues. Of the candidate genes related to storage roots, Manes.13G023300, Manes.16G000800, Manes.02G154700, Manes.02G192500, and Manes.09G099100 had higher expression levels in storage roots than in leaf and stem; on the other hand, of the candidate genes related to leaves, Manes.05G164500, Manes.05G164600, Manes.04G057300, Manes.01G202000, and Manes.03G186500 had higher expression levels in leaves than in storage roots and stem. This study provides basis for research on genetics and the genetic improvement of cassava.http://journal.frontiersin.org/article/10.3389/fpls.2018.00503/fullManihot esculenta Crantzsingle-nucleotide polymorphism (SNP)genetic diversitypopulation structuregenome-wide association analysis (GWAS) |
| spellingShingle | Shengkui Zhang Shengkui Zhang Xin Chen Cheng Lu Jianqiu Ye Meiling Zou Kundian Lu Subin Feng Jinli Pei Chen Liu Xincheng Zhou Ping’an Ma Zhaogui Li Cuijuan Liu Qi Liao Zhiqiang Xia Wenquan Wang Genome-Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz) Frontiers in Plant Science Manihot esculenta Crantz single-nucleotide polymorphism (SNP) genetic diversity population structure genome-wide association analysis (GWAS) |
| title | Genome-Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz) |
| title_full | Genome-Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz) |
| title_fullStr | Genome-Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz) |
| title_full_unstemmed | Genome-Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz) |
| title_short | Genome-Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz) |
| title_sort | genome wide association studies of 11 agronomic traits in cassava manihot esculenta crantz |
| topic | Manihot esculenta Crantz single-nucleotide polymorphism (SNP) genetic diversity population structure genome-wide association analysis (GWAS) |
| url | http://journal.frontiersin.org/article/10.3389/fpls.2018.00503/full |
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