Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations.

Autor: Warburton CL; Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia. c.warburton@uq.edu.au., Costilla R; Agresearch Limited, Ruakura Research Centre, Hamilton, 3214, New Zealand., Engle BN; Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia., Moore SS; Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia., Corbet NJ; Formerly Central Queensland University, School of Health, Medical and Applied Sciences, Rockhampton, QLD, Australia., Fordyce G; Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia., McGowan MR; The University of Queensland, School of Veterinary Science, St Lucia, QLD, Australia., Burns BM; Formerly Department of Agriculture and Fisheries, Rockhampton, QLD, Australia., Hayes BJ; Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia.
Jazyk: angličtina
Zdroj: Heredity [Heredity (Edinb)] 2023 Dec; Vol. 131 (5-6), pp. 350-360. Date of Electronic Publication: 2023 Oct 06.
DOI: 10.1038/s41437-023-00651-4
Abstrakt: Many of the world's agriculturally important plant and animal populations consist of hybrids of subspecies. Cattle in tropical and sub-tropical regions for example, originate from two subspecies, Bos taurus indicus (Bos indicus) and Bos taurus taurus (Bos taurus). Methods to derive the underlying genetic architecture for these two subspecies are essential to develop accurate genomic predictions in these hybrid populations. We propose a novel method to achieve this. First, we use haplotypes to assign SNP alleles to ancestral subspecies of origin in a multi-breed and multi-subspecies population. Then we use a BayesR framework to allow SNP alleles originating from the different subspecies differing effects. Applying this method in a composite population of B. indicus and B. taurus hybrids, our results show that there are underlying genomic differences between the two subspecies, and these effects are not identified in multi-breed genomic evaluations that do not account for subspecies of origin effects. The method slightly improved the accuracy of genomic prediction. More significantly, by allocating SNP alleles to ancestral subspecies of origin, we were able to identify four SNP with high posterior probabilities of inclusion that have not been previously associated with cattle fertility and were close to genes associated with fertility in other species. These results show that haplotypes can be used to trace subspecies of origin through the genome of this hybrid population and, in conjunction with our novel Bayesian analysis, subspecies SNP allele allocation can be used to increase the accuracy of QTL association mapping in genetically diverse populations.
(© 2023. The Author(s).)
Databáze: MEDLINE
Externí odkaz: