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

GigaScience
Bao ZhangShengbin Li

Abstract

The 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. Here, 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 releva...Continue Reading

Datasets Mentioned

BETA
SRP124668

Methods Mentioned

BETA
genotyping
PCA

Key Resources (RRID) Mentioned

SCR_010910
SCR_004965
SCR_006244

Software Mentioned

ANGSD
PHYLIP
lastz
BWA
Eigensoft
Control
Animal QTLdb
- FREEC
Eigensoft package
Dindel

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