Abstract
BackgroundThe domestication of wild goats and subsequent intensive trait-driven crossing, inbreeding, and selection have led to dramatic phenotypic purification and intermediate breeds for the high-quality production of dairy, cashmere wool, and meat. Genomic resequencing provides a powerful means for the direct identification of trait-associated sequence variations that underlie molecular mechanisms of domestication.ResultsHere, we report our effort to define such variations based on data from domestic goat breeds (Capra aegagrus hircus; five each) selected for dairy, cashmere, and meat production in reference to their wild ancestors, the Sindh ibex (Capra aegagrus blythi; two) and the Markhor (Capra falconeri; two). Using ∼24 million high-quality single nucleotide polymorphisms (SNPs), ∼1.9 million insertions/deletions, and 2,317 copy number variations, we define SNP-desert-associated genes (SAGs), domestic-associated genes (DAGs), and trait-associated genes (TAGs) and attempt to associate them with quantitative trait loci (QTL), domestication, and agronomic traits. A greater majority of SAGs shared by all domestic breeds are classified into Gene Ontology categories of metabolism and cell cycle. DAGs, together with some SAGs, are most relevant to behavior, immunity, and trait specificity. Whereas, TAGs such as growth differentiation factor 5 and fibroblast growth factor 5 for bone and hair growth, respectively, appear to be directly involved in growth regulation.ConclusionsWhen investigating the divergence of Capra populations, the sequence variations and candidate function-associated genes we have identified provide valuable molecular markers for trait-driven genetic mapping and breeding.
Highlights
Reviewer Comments to Author: In this manuscript the authors have identified several polymorphisms in domestic goat breeds that could be linked to their domestication process
The authors have shown that these polymorphisms could be good molecular markers for genetic mapping and breeding
* Does the manuscript adhere to the journal's guidelines on minimum standards of reporting? No
Summary
Title: Genome-wide definition of selective sweeps reveals molecular evidence of trait-driven domestication among elite goat (Capra species) breeds for the production of dairy, cashmere, and meat. The authors have shown that these polymorphisms could be good molecular markers for genetic mapping and breeding These findings are interesting and the authors have presented some novel data. - Lines 168-170 "all results suggest that the domestication traits of dairy production may occur ahead of cashmere and meat in the domestication history of goats": There are already references suggesting the fact that goats could primarily have be domesticated for dairy purposes, so you should include them. - Section TAGs in the dairy breed: Various TAGs, the authors does not explain how and why this could be due to Why do you think the explanation of this SNP is due to the largest body of dairy goats when it is in this breed where the most frequent allele is T as in concordance with the rest of the species analyzed? Why do you think there is a SNP desert along the RSRC1 sequence (Fig.2))? What could this gene have as special? Could you take a look to the wild species or to other species to compare this phenomenon?
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