Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.)
Abstract Background Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely distributed across the entire plant genome and can be used to develop SSR markers, which can then be used to conduct genetic analyses and molecular breeding. Cultivated peanut (...
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BMC
2019-11-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-019-6148-5 |
| _version_ | 1818339182765932544 |
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| author | Qing Lu Yanbin Hong Shaoxiong Li Hao Liu Haifen Li Jianan Zhang Haofa Lan Haiyan Liu Xingyu Li Shijie Wen Guiyuan Zhou Rajeev K. Varshney Huifang Jiang Xiaoping Chen Xuanqiang Liang |
| author_facet | Qing Lu Yanbin Hong Shaoxiong Li Hao Liu Haifen Li Jianan Zhang Haofa Lan Haiyan Liu Xingyu Li Shijie Wen Guiyuan Zhou Rajeev K. Varshney Huifang Jiang Xiaoping Chen Xuanqiang Liang |
| author_sort | Qing Lu |
| collection | DOAJ |
| description | Abstract Background Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely distributed across the entire plant genome and can be used to develop SSR markers, which can then be used to conduct genetic analyses and molecular breeding. Cultivated peanut (A. hypogaea L.), an important oil crop worldwide, is an allotetraploid (AABB, 2n = 4× = 40) plant species. Because of its complex genome, genomic marker development has been very challenging. However, sequencing of cultivated peanut genome allowed us to develop genomic markers and construct a high-density physical map. Results A total of 8,329,496 SSRs were identified, including 3,772,653, 4,414,961, and 141,882 SSRs that were distributed in subgenome A, B, and nine scaffolds, respectively. Based on the flanking sequences of the identified SSRs, a total of 973,984 newly developed SSR markers were developed in subgenome A (462,267), B (489,394), and nine scaffolds (22,323), with an average density of 392.45 markers per Mb. In silico PCR evaluation showed that an average of 88.32% of the SSR markers generated only one in silico-specific product in two tetraploid A. hypogaea varieties, Tifrunner and Shitouqi. A total of 39,599 common SSR markers were identified among the two A. hypogaea varieties and two progenitors, A. duranensis and A. ipaensis. Additionally, an amplification effectiveness of 44.15% was observed by real PCR validation. Moreover, a total of 1276 public SSR loci were integrated with the newly developed SSR markers. Finally, a previously known leaf spot quantitative trait locus (QTL), qLLS_T13_A05_7, was determined to be in a 1.448-Mb region on chromosome A05. In this region, a total of 819 newly developed SSR markers were located and 108 candidate genes were detected. Conclusions The availability of these newly developed and public SSR markers both provide a large number of molecular markers that could potentially be used to enhance the process of trait genetic analyses and improve molecular breeding strategies for cultivated peanut. |
| first_indexed | 2024-12-13T15:22:57Z |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T15:22:57Z |
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| series | BMC Genomics |
| spelling | doaj.art-4a0b232f9bc7416fa0dd00a77813a82c2022-12-21T23:40:29ZengBMCBMC Genomics1471-21642019-11-012011910.1186/s12864-019-6148-5Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.)Qing Lu0Yanbin Hong1Shaoxiong Li2Hao Liu3Haifen Li4Jianan Zhang5Haofa Lan6Haiyan Liu7Xingyu Li8Shijie Wen9Guiyuan Zhou10Rajeev K. Varshney11Huifang Jiang12Xiaoping Chen13Xuanqiang Liang14Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic ImprovementCrops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic ImprovementCrops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic ImprovementCrops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic ImprovementCrops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic ImprovementMolBreeding Biotechnology Co., Ltd.MolBreeding Biotechnology Co., Ltd.Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic ImprovementCrops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic ImprovementCrops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic ImprovementCrops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic ImprovementCenter of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesCrops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic ImprovementCrops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic ImprovementAbstract Background Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely distributed across the entire plant genome and can be used to develop SSR markers, which can then be used to conduct genetic analyses and molecular breeding. Cultivated peanut (A. hypogaea L.), an important oil crop worldwide, is an allotetraploid (AABB, 2n = 4× = 40) plant species. Because of its complex genome, genomic marker development has been very challenging. However, sequencing of cultivated peanut genome allowed us to develop genomic markers and construct a high-density physical map. Results A total of 8,329,496 SSRs were identified, including 3,772,653, 4,414,961, and 141,882 SSRs that were distributed in subgenome A, B, and nine scaffolds, respectively. Based on the flanking sequences of the identified SSRs, a total of 973,984 newly developed SSR markers were developed in subgenome A (462,267), B (489,394), and nine scaffolds (22,323), with an average density of 392.45 markers per Mb. In silico PCR evaluation showed that an average of 88.32% of the SSR markers generated only one in silico-specific product in two tetraploid A. hypogaea varieties, Tifrunner and Shitouqi. A total of 39,599 common SSR markers were identified among the two A. hypogaea varieties and two progenitors, A. duranensis and A. ipaensis. Additionally, an amplification effectiveness of 44.15% was observed by real PCR validation. Moreover, a total of 1276 public SSR loci were integrated with the newly developed SSR markers. Finally, a previously known leaf spot quantitative trait locus (QTL), qLLS_T13_A05_7, was determined to be in a 1.448-Mb region on chromosome A05. In this region, a total of 819 newly developed SSR markers were located and 108 candidate genes were detected. Conclusions The availability of these newly developed and public SSR markers both provide a large number of molecular markers that could potentially be used to enhance the process of trait genetic analyses and improve molecular breeding strategies for cultivated peanut.http://link.springer.com/article/10.1186/s12864-019-6148-5Genome sequenceSimple sequence repeatsMolecular breedingPeanut (Arachis hypogaea L.) |
| spellingShingle | Qing Lu Yanbin Hong Shaoxiong Li Hao Liu Haifen Li Jianan Zhang Haofa Lan Haiyan Liu Xingyu Li Shijie Wen Guiyuan Zhou Rajeev K. Varshney Huifang Jiang Xiaoping Chen Xuanqiang Liang Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.) BMC Genomics Genome sequence Simple sequence repeats Molecular breeding Peanut (Arachis hypogaea L.) |
| title | Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.) |
| title_full | Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.) |
| title_fullStr | Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.) |
| title_full_unstemmed | Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.) |
| title_short | Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.) |
| title_sort | genome wide identification of microsatellite markers from cultivated peanut arachis hypogaea l |
| topic | Genome sequence Simple sequence repeats Molecular breeding Peanut (Arachis hypogaea L.) |
| url | http://link.springer.com/article/10.1186/s12864-019-6148-5 |
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