Haplotypes-based genetic analysis: benefits and challenges

• Main Authors: D. Sehgal, S. Dreisigacker
• Format: Article
• Language: English
• Published: Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences 2019-11-01
• Series: Vavilovskij Žurnal Genetiki i Selekcii
• Subjects: haplotype; gwas; genomic selection; snp
• Online Access: https://vavilov.elpub.ru/jour/article/view/2331

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.