Genome-Wide Analyses Reveal the Genetic Architecture and Candidate Genes of Indicine, Taurine, Synthetic Crossbreds, and Locally Adapted Cattle in Brazil

Abstract

Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (Ne), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, Ne, ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among the evaluated breeds, different marker densities should be used to improve the genomic prediction accuracy and power of genome-wide association studies. Breeds showing low Ne values indicate a recent inbreeding, also reflected by the occurrence of longer ROH, which demand special attention in the matting schemes to avoid extensive inbreeding. Candidate genes (e.g., ABCA7, PENK, SPP1, IFNAR1, IFNAR2, SPEF2, PRLR, LRRTM1, and LRRTM4) located in the identified ROH islands were evaluated, highlighting biological processes involved with milk production, behavior, rusticity, and fertility. Furthermore, we were successful in obtaining the breed composition regarding the taurine and indicine composition using single-nucleotide polymorphism (SNP) data. Our results were able to observe in detail the genomic backgrounds that are present in each breed and allowed to better understand the various contributions of ancestor breeds to the modern breed composition to the Brazilian cattle.

Genome‐wide scan for signatures of selection in the Brangus cattle genome

“…Interestingly, a signature of selection in Brangus was previously reported by Goszczynski et al (2018) in this region. Some genes involved in dairy production traits, temperament and coat colour are also within candidate regions detected in both comparisons, such as HAL and CSF2RB and PPARGC1A, that influencing milk production (Kowalewska-Łuczak et al, 2010;Li et al, 2014;Lopdell et al, 2019;Wang et al, 2014), SNRPF (in BTA5) and PENK (in BTA14) previously reported to play a role in cattle temperament (Costilla et al, 2020;Verardo et al, 2021), and BLOC1S1, RAB5b, DCTN2 and MYO1A related to pigmentation (Gutiérrez-Gil et al, 2007). Finally, some heat shock proteins were found within the candidate regions, for example HSPA13, HSP90B1, HSPA6, HSPA4, HSPA5, HSPH1 and HSPBAP1 (Archana et al, 2017).…”

Detection and characterization of copy number variation in three differentially-selected Nellore cattle populations

“…Several genes associated with male and female reproductive traits were identified, including THEG ( Nayernia et al, 1999 ; Mannan et al, 2003 ), FGF22 ( Castilho et al, 2017 ; 2019 ), KISS1R ( D’Occhio et al, 2020 ; Singh et al, 2020 ), and ARID3A ( Yang et al, 2018 ). Furthermore, genes linked to the immune system such as AZU1 ( Xu et al, 2018 ; Verardo et al, 2021 ) and ELANE ( Cassatella et al, 2019 ; Verardo et al, 2021 ) were also identified. The CFD gene was also previously associated with fat accumulation ( Wang et al, 2023 ) and overlapped with the region cited above.…”

Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers

“…LRRTM4 is essential for excitatory synaptic transmission and was proven to be associated with human mental disease. Genome-wide analysis in Brazilian cattle breeds showed that this gene is involved in biological processes related to fertility [ 11 ]. The selection signature analysis and ROHs also revealed some genes previously reported to be associated with litter size and other female animal reproduction-related traits, e.g., TSHR (seasonality of reproduction in modern domesticated goats) [ 12 ], ANGPT4 (bovine ovarian antral follicle development) [ 13 ], CENPF (early embryonic development in mice and bovines) [ 14 , 15 ], CHST1 (goat and sheep prolificacy) [ 16 ], PIBF1 (embryos quality and development) [ 17 ], DACH1 and DIS3 (sheep litter size) [ 18 ], COL4A1 (sheep prolificacy) [ 19 ], PRKD1 (pig litter size) [ 20 ] and DNMT3B (first-born litter size in goats) [ 21 ].…”