Genomic Approaches Reveal Pleiotropic Effects in Crossbred Beef Cattle

Abstract

Carcass and meat quality are two important attributes for the beef industry because they drive profitability and consumer demand. These traits are of even greater importance in crossbred cattle used in subtropical and tropical regions for their superior adaptability because they tend to underperform compared to their purebred counterparts. Many of these traits are challenging and expensive to measure and unavailable until late in life or after the animal is harvested, hence unrealistic to improve through traditional phenotypic selection, but perfect candidates for genomic selection. Before genomic selection can be implemented in crossbred populations, it is important to explore if pleiotropic effects exist between carcass and meat quality traits. Therefore, the objective of this study was to identify genomic regions with pleiotropic effects on carcass and meat quality traits in a multibreed Angus–Brahman population that included purebred and crossbred animals. Data included phenotypes for 10 carcass and meat quality traits from 2,384 steers, of which 1,038 were genotyped with the GGP Bovine F-250. Single-trait genome-wide association studies were first used to investigate the relevance of direct additive genetic effects on each carcass, sensory and visual meat quality traits. A second analysis for each trait included all other phenotypes as covariates to correct for direct causal effects from identified genomic regions with pure direct effects on the trait under analysis. Five genomic windows on chromosomes BTA5, BTA7, BTA18, and BTA29 explained more than 1% of additive genetic variance of two or more traits. Moreover, three suggestive pleiotropic regions were identified on BTA10 and BTA19. The 317 genes uncovered in pleiotropic regions included anchoring and cytoskeletal proteins, key players in cell growth, muscle development, lipid metabolism and fat deposition, and important factors in muscle proteolysis. A functional analysis of these genes revealed GO terms directly related to carcass quality, meat quality, and tenderness in beef cattle, including calcium-related processes, cell signaling, and modulation of cell–cell adhesion. These results contribute with novel information about the complex genetic architecture and pleiotropic effects of carcass and meat quality traits in crossbred beef cattle.

Impact of Brahman genetics on skin histology characteristics with implications for heat tolerance in cattle

“…Animals in this herd are raised as contemporaries and range from 0% to 100% Bos Taurus Indicus influence. Many economically important traits have been studied in this population to determine the optimum Brahman genetics composition producers interested in improving the thermotolerance in their herds while maximizing production traits ( Elzo and Wakeman, 1998 ; Elzo et al, 2012 ; Elzo et al, 2016 ; Dikmen et al, 2018 ; Rezende et al, 2021 ; Martins et al, 2022 ).…”

Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing

“…Those nine genes are located on BTA 4, 14, and 18. The region on BTA 4 has been reported for mastitis resistance ( Rupp and Boichard, 2003 ), growth ( Lu et al, 2013 ), fertility ( Grigoletto et al, 2020b ), and primarly milk ( Ibeagha-Awemu et al, 2016 ; Sanchez et al, 2017 , 2019 ; Van Den Berg et al, 2020 ), while the region on BTA 14 was primarly reported for meat ( Bolormaa et al, 2011 ; Neto et al, 2012 ; Saatchi et al, 2014 ; Sharma et al, 2014 ; Ali et al, 2015 ; Song et al, 2016 ; Kim et al, 2017 ; Akanno et al, 2018 ; Grigoletto et al, 2020a ; Srikanth et al, 2020 ; Wang et al, 2020 ; Rezende et al, 2021 ), production ( Snelling et al, 2010 ; Lu et al, 2013 ; Martínez et al, 2014 ; Saatchi et al, 2014 ; Akanno et al, 2018 ; Zhong et al, 2019 ; Zhang et al, 2020 ), and exterior traits ( Pryce et al, 2011 ; Pausch et al, 2016 ; Wu et al, 2016 ; Marete A. G. et al, 2018 ; Bouwman et al, 2018 ; Tribout et al, 2020 ). Within this region, for example, we find the gene XKR4 associated with subcutaneous rump fat thickness and growth ( Neto et al, 2012 ; Magalhã et al, 2016 ; An et al, 2019 ; Smith et al, 2019 ) .…”

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context

“…These findings support farmers’ perceptions about the good tolerance of Noticiana to summertime heat. Additionally, STAT6 and GPR182 are potential meat quality genes in livestock species ( 74 ). Noticiana shared with Comisana ( 58 ), and Barbaresca ( 75 ) the hotspot in OAR6:35.70–39.80 which is a region fairly fixed in sheep species ( 69 , 76 ), particularly in European breeds ( 77 – 79 ).…”