Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array
Polypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-02-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fpls.2018.00104/full |
| _version_ | 1818117249235419136 |
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| author | Qian You Qian You Xiping Yang Ze Peng Liping Xu Jianping Wang Jianping Wang Jianping Wang |
| author_facet | Qian You Qian You Xiping Yang Ze Peng Liping Xu Jianping Wang Jianping Wang Jianping Wang |
| author_sort | Qian You |
| collection | DOAJ |
| description | Polypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide polymorphism (SNP) array is considered to be one of, high-throughput, relatively cost-efficient and automated genotyping approaches. However, there are significant challenges for SNP identification in complex, polyploid genomes, which has seriously slowed SNP discovery and array development in polyploid species. Ploidy is a significant factor impacting SNP qualities and validation rates of SNP markers in SNP arrays, which has been proven to be a very important tool for genetic studies and molecular breeding. In this review, we (1) discussed the pros and cons of SNP array in general for high throughput genotyping, (2) presented the challenges of and solutions to SNP calling in polyploid species, (3) summarized the SNP selection criteria and considerations of SNP array design for polyploid species, (4) illustrated SNP array applications in several different polyploid crop species, then (5) discussed challenges, available software, and their accuracy comparisons for genotype calling based on SNP array data in polyploids, and finally (6) provided a series of SNP array design and genotype calling recommendations. This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes. |
| first_indexed | 2024-12-11T04:35:24Z |
| format | Article |
| id | doaj.art-6f2eb57558f142b5ad29b87a644d060d |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-11T04:35:24Z |
| publishDate | 2018-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-6f2eb57558f142b5ad29b87a644d060d2022-12-22T01:20:45ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-02-01910.3389/fpls.2018.00104297846Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) ArrayQian You0Qian You1Xiping Yang2Ze Peng3Liping Xu4Jianping Wang5Jianping Wang6Jianping Wang7Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, ChinaAgronomy Department, University of Florida, Gainesville, FL, United StatesAgronomy Department, University of Florida, Gainesville, FL, United StatesAgronomy Department, University of Florida, Gainesville, FL, United StatesKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, ChinaAgronomy Department, University of Florida, Gainesville, FL, United StatesPlant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL, United StatesKey Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, ChinaPolypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide polymorphism (SNP) array is considered to be one of, high-throughput, relatively cost-efficient and automated genotyping approaches. However, there are significant challenges for SNP identification in complex, polyploid genomes, which has seriously slowed SNP discovery and array development in polyploid species. Ploidy is a significant factor impacting SNP qualities and validation rates of SNP markers in SNP arrays, which has been proven to be a very important tool for genetic studies and molecular breeding. In this review, we (1) discussed the pros and cons of SNP array in general for high throughput genotyping, (2) presented the challenges of and solutions to SNP calling in polyploid species, (3) summarized the SNP selection criteria and considerations of SNP array design for polyploid species, (4) illustrated SNP array applications in several different polyploid crop species, then (5) discussed challenges, available software, and their accuracy comparisons for genotype calling based on SNP array data in polyploids, and finally (6) provided a series of SNP array design and genotype calling recommendations. This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes.http://journal.frontiersin.org/article/10.3389/fpls.2018.00104/fullpolyploidySNPSNP arraygenotype callinghigh throughput genotyping |
| spellingShingle | Qian You Qian You Xiping Yang Ze Peng Liping Xu Jianping Wang Jianping Wang Jianping Wang Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array Frontiers in Plant Science polyploidy SNP SNP array genotype calling high throughput genotyping |
| title | Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array |
| title_full | Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array |
| title_fullStr | Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array |
| title_full_unstemmed | Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array |
| title_short | Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array |
| title_sort | development and applications of a high throughput genotyping tool for polyploid crops single nucleotide polymorphism snp array |
| topic | polyploidy SNP SNP array genotype calling high throughput genotyping |
| url | http://journal.frontiersin.org/article/10.3389/fpls.2018.00104/full |
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