Genomic analysis of the origins of extant casein variation in goats

Abstract

The variation in the casein genes has a major impact on the milk composition of goats. Even though many casein polymorphisms have been identified so far, we do not know yet whether they are evolutionarily ancient (i.e., they existed before domestication) or young (i.e., they emerged after domestication). Herewith, we identified casein polymorphisms in a data set of 106 caprine whole-genome sequences corresponding to bezoars (Capra aegagrus, the ancestor of domestic goats) and 4 domestic goat (Capra hircus) populations from Europe, Africa, the Far East, and the Near East. Domestic and wild goat populations shared a substantial number of casein SNP, from 36.1% (CSN2) to 55.1% (CSN1S2). The comparison of casein variation among bezoars and the 4 domestic goat populations demonstrated that more than 50% of the casein SNP are shared by 2 or more populations, and 18 to 44% are shared by all populations. Moreover, the majority of casein alleles reported in domestic goats also segregate in the bezoar, including several alleles displaying significant associations with milk composition (e.g., the A/B alleles of the CSN1S1 and CSN3 genes, the A allele of the CSN2 gene). We conclude that much of the current diversity of the caprine casein genes comes from ancient standing variation segregating in the ancestor of modern domestic goats.

Comparing the diversity of the casein genes in the Asian mouflon and domestic sheep

“…The π-values of each casein gene were estimated with VCFtools (Danecek et al 2011) as previously explained (Table S7). The π estimates obtained in the per-site analysis were consistent with those previously reported by Guan et al (2019) in goats and bezoars. Moreover, we observed higher π-values in the sheep CSN1S1, CSN1S2 and CSN3 genes when compared to those of mouflons.…”

“…The comparison of casein variation between sheep and mouflons revealed an extensive sharing of polymorphic sites (Figs, 2C and S9), a finding that agrees well with results reported by Guan et al (2019) in goats and bezoars. Consistently, Chessa et al (2017) showed the existence of a haplotype formed by 8 SNPs that segregates in 51% of the mouflons as well as in the majority of the domestic sheep breeds sampled in their study.…”

“…In a previous work (Guan et al 2019), we compared the variability of the casein genes in domestic goats (Capra hircus) and their ancestor, the bezoar (Capra aegagrus). By doing so, we demonstrated that a relevant proportion of casein variants are shared by bezoars and domestic goats, suggesting that these variants emerged before goat domestication (Guan et al 2019). The goal of the current work was to extend these studies to sheep.…”

Genetic Diversity in Casein Gene Cluster in a Dromedary Camel (C. dromedarius) Population from the United Arab Emirates

“…These genes have been characterized at the genomic [ 7 ], transcriptomic [ 8 ], and proteomic [ 9 ] levels. Furthermore, genetic polymorphisms and variants in casein genes have been reported in various animal species [ 10 ], including cattle [ 11 , 12 , 13 ], goats [ 14 ], and sheep [ 15 ], with goats and cows having the largest genetic variability. The identified variants have been associated with differential gene expression and rates of protein synthesis [ 14 , 15 ].…”

A hypomorphic mutation in the mouse Csn1s1 gene generated by CRISPR/Cas9 pronuclear microinjection

“…During breeding, casein genes acquired many sequence variations that can lead to altered gene expression and are characteristic of some goat and cow breeds (Yue et al, 2011;Fomichev et al, 2012;Guan et al, 2019). Many of these sequence variants could be used as markers for breeding.…”