Haplotypes-based genetic analysis: benefits and challenges
The increasing availability of Single Nucleotide Polymorphisms (SNPs) discovered by Next Generation Sequencing will enable a range of new genetic analyses in crops, which was not possible before. Concomitantly, researchers will face the challenge of handling large data sets at the whole-genome level...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2019-11-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/2331 |
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| author | D. Sehgal S. Dreisigacker |
| author_facet | D. Sehgal S. Dreisigacker |
| author_sort | D. Sehgal |
| collection | DOAJ |
| description | The increasing availability of Single Nucleotide Polymorphisms (SNPs) discovered by Next Generation Sequencing will enable a range of new genetic analyses in crops, which was not possible before. Concomitantly, researchers will face the challenge of handling large data sets at the whole-genome level. By grouping thousands of SNPs into a few hundred haplotype blocks, complexity of the data can be reduced with fewer statistical tests and a lower probability of spurious associations. Owing to the strong genome structure present in breeding lines of most crops, the deployment of haplotypes could be a powerful complement to improve efficiency of marker-assisted and genomic selection. This review describes in brief the commonly used approaches to construct haplotype blocks and some examples in animals and crops are cited where haplotype-based dissection of traits were proven beneficial. Some important considerations and facts while working with haplotypes in crops are reviewed at the end. |
| format | Article |
| id | doaj-art-85f5d808b3004d2c8b0c6540d268f9d0 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2019-11-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-85f5d808b3004d2c8b0c6540d268f9d02025-02-01T09:58:08ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592019-11-0123780380810.18699/VJ19.37-o976Haplotypes-based genetic analysis: benefits and challengesD. Sehgal0S. Dreisigacker1International Center for Maize and Wheat Improvement (CIMMYT)International Center for Maize and Wheat Improvement (CIMMYT)The increasing availability of Single Nucleotide Polymorphisms (SNPs) discovered by Next Generation Sequencing will enable a range of new genetic analyses in crops, which was not possible before. Concomitantly, researchers will face the challenge of handling large data sets at the whole-genome level. By grouping thousands of SNPs into a few hundred haplotype blocks, complexity of the data can be reduced with fewer statistical tests and a lower probability of spurious associations. Owing to the strong genome structure present in breeding lines of most crops, the deployment of haplotypes could be a powerful complement to improve efficiency of marker-assisted and genomic selection. This review describes in brief the commonly used approaches to construct haplotype blocks and some examples in animals and crops are cited where haplotype-based dissection of traits were proven beneficial. Some important considerations and facts while working with haplotypes in crops are reviewed at the end.https://vavilov.elpub.ru/jour/article/view/2331haplotypegwasgenomic selectionsnp |
| spellingShingle | D. Sehgal S. Dreisigacker Haplotypes-based genetic analysis: benefits and challenges Вавиловский журнал генетики и селекции haplotype gwas genomic selection snp |
| title | Haplotypes-based genetic analysis: benefits and challenges |
| title_full | Haplotypes-based genetic analysis: benefits and challenges |
| title_fullStr | Haplotypes-based genetic analysis: benefits and challenges |
| title_full_unstemmed | Haplotypes-based genetic analysis: benefits and challenges |
| title_short | Haplotypes-based genetic analysis: benefits and challenges |
| title_sort | haplotypes based genetic analysis benefits and challenges |
| topic | haplotype gwas genomic selection snp |
| url | https://vavilov.elpub.ru/jour/article/view/2331 |
| work_keys_str_mv | AT dsehgal haplotypesbasedgeneticanalysisbenefitsandchallenges AT sdreisigacker haplotypesbasedgeneticanalysisbenefitsandchallenges |