Identification of Genes Targeted in South African Merino and Afrino Sheep Populations Under Long-Term Selection for Reproduction and Body Weight

Abstract

Background: Reproductive performance and body weight are of the utmost economic importance in determining the efficiency of sheep production. Simultaneous selection for increased reproductive performance and early growth traits is a common strategy in many flocks, but ambiguous results regarding the relationship between reproduction and body weight have been reported. The objective of this study was to perform a genome-wide association study (GWAS) in two South African Merino flocks and an Afrino sheep flock that were selected for both reproduction and body weight over decades. The GWAS aimed to identify SNPs associated with genes affecting the traits number of lambs born (NLB), number of lambs weaned (NLW), total weight of lamb weaned (TWW) and body weight (BW) and thus to ascertain which genes were targeted through directional selection.Results: In the GWAS, 16 SNP markers associated with reproductive traits were identified among the three populations, while 15 SNPs were associated with body weight. These SNPs were linked respectively to 26 and 21 documented genes in the sheep genome. Most of these genes were previously associated in literature with reproduction related, as well as with growth related traits in various farm animal species. This study, supported by results from previous studies performed on sheep and cattle, identified the following genes that warrant further investigation as to their functions and processes relating to growth and reproduction in sheep: MAP7D1, TRAPPC3, THRAP3, TRMP8, SPP2, HDAC9, ZFHX3, SIX6, C14orf39, TAF4B, TRSP1 EYA2, RBMS3, STL38L, BSPH1, LIG1, CABP5 and ELSPBP1. Conclusions: Long-term selection in the flocks for both body weight and reproductive traits, and especially on the composite trait TWW, have favoured genes with pleiotropic effects influencing both groups of traits. SNPs associated with these pleiotropic genes were detected in the association analyses for the various traits.

Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders

“…For AFR, FGF12, a candidate gene for hair follicle development ( Lv et al, 2020 ) and reproductive traits ( An et al, 2018 ), and ICA1 and NXPH1 , associated with metabolic pathways ( Akanno et al, 2018 ), were some of the key candidate genes identified. Although the AFR is predominantly selected or weighted for meat quality traits, the breed was established as a white-woolen breed for use as a terminal sire when crossed with Merino ewes ( Synman, 2014 ) in response to the presence of kemp (coloured fibre) in crosses of Merino ewes with mutton breeds. The signature for hair follicle development might be a reflection of this selection.…”

“…The signature for hair follicle development might be a reflection of this selection. ICA1 and NXPH1 , on the other hand, are signatures of the intensive selection weight put on the AFR for meat traits ( Synman, 2014 ).…”