Genomic Regions Associated With Skeletal Type Traits in Beef and Dairy Cattle Are Common to Regions Associated With Carcass Traits, Feed Intake and Calving Difficulty

Abstract

Linear type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlated with a range of other performance traits in cattle including feed intake, reproduction traits and carcass merit; thus, type traits could also provide useful insights into the morphological differences among animals underpinning phenotypic differences in these complex traits. The objective of the present study was to identify genomic regions associated with five subjectively scored skeletal linear traits, to determine if these associated regions are common in multiple beef and dairy breeds, and also to determine if these regions overlap with those proposed elsewhere to be associated with correlated performance traits. Analyses were carried out using linear mixed models on imputed whole genome sequence data separately in 1,444 Angus, 1,129 Hereford, 6,433 Charolais, 8,745 Limousin, 1,698 Simmental, and 4,494 Holstein-Friesian cattle, all scored for the linear type traits. There was, on average, 18 months difference in age at assessment of the beef versus the dairy animals. While the majority of the identified quantitative trait loci (QTL), and thus genes, were both trait-specific and breed-specific, a large-effect pleiotropic QTL on BTA6 containing the NCAPG and LCORL genes was associated with all skeletal traits in the Limousin population and with wither height in the Angus. Other than that, little overlap existed in detected QTLs for the skeletal type traits in the other breeds. Only two QTLs overlapped the beef and dairy breeds; both QTLs were located on BTA5 and were associated with height in both the Angus and the Holstein-Friesian, despite the difference in age at assessment. Several detected QTLs in the present study overlapped with QTLs documented elsewhere that are associated with carcass traits, feed intake, and calving difficulty. While most breeding programs select for the macro-traits like carcass weight, carcass conformation, and feed intake, the higher degree of granularity with selection on the individual linear type traits in a multi-trait index underpinning the macro-level goal traits, presents an opportunity to help resolve genetic antagonisms among morphological traits in the pursuit of the animal with optimum performance metrics.

Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs

“…CSRNP3 encodes a transcription factor, cysteine and serine rich nuclear protein 3, and the expression level of CSRNP3 was associated with pig residual feed intake and feed conversion ratio traits (Vincent et al, 2015;Messad et al, 2019). In cattle, SNPs located in CSRNP3 were significantly associated with chest width, hip width, or rump width (Doyle et al, 2020). We also compared these genotypes between European and Chinese pigs, and these showed obvious similarity to European commercial pigs (EUD) compared to Chinese wild pigs and other Chinese indigenous pigs (Figure 5).…”

Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle

“…No SNP genotypes located within 500 kb of an associated CNV in the present study associated with the trait of interest in the given breed; this, therefore, suggests that the CNVs and SNP genotypes in the present study had independent contributions to the carcass traits analysed. Nonetheless, the QTL regions of associated CNVs and associated SNP LRRs were compared to QTL regions reported in other genome-wide SNP genotype association analyses of carcass traits [ 7 ], muscularity traits [ 29 ], and skeletal traits [ 35 ]; each of these studies used imputed sequence data and similar cattle populations to the population used in the present study. The studies on muscularity and skeletal traits were also included in this comparison because muscularity and skeletal traits are strongly correlated with carcass traits in cattle [ 36 , 37 ].…”

“…The studies on muscularity and skeletal traits were also included in this comparison because muscularity and skeletal traits are strongly correlated with carcass traits in cattle [ 36 , 37 ]. A CNV associated with carcass conformation in the Holstein-Friesians, located on chromosome 7 between 28.81 Mb and 28.86 Mb, overlapped in genomic position with a QTL associated with stature in Holstein-Friesians [ 35 ]. None of the other associated CNVs overlapped in genomic position with QTLs reported by either Doyle et al [ 29 ], Doyle et al [ 35 ], or Purfield et al [ 7 ].…”

Single nucleotide polymorphisms affect miRNA target prediction in bovine

“…The LCORL gene is highly conserved among mammals and is related to skeletal height and size in humans [51][52][53], body size in horses [54][55][56][57], dogs [58] and pigs [59], body weight in chickens [60,61] and sheep [62]. Previous studies in cattle have linked the LCORL gene with body conformation indexes in Nordic red cattle [63], carcass weight [64] and organ weight [65] in Simmental cattle, growth in Quinchuan cattle [66] and stature in Limousin, Hereford and Angus [67], thus, suggesting that the acquisition of regulation of LCORL, caused by a SNP in bta-miR-1256, may affect overall size and therefore calving ease. In addition, Purfield et al [31] detected a SNP close to the IGFBP-2 gene in a QTL related to calving difficulty.…”