Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores

Abstract

Ramo Grande is a local cattle breed raised in the archipelago of Azores, with a small and dispersed census, where inbreeding control is of utmost importance. A single nucleotide polymorphism (SNP) Beadchip array was used to assess inbreeding, by analysis of genomic regions harboring contiguous homozygous genotypes named runs of homozygosity (ROH), and to estimate past effective population size by analysis of linkage disequilibrium (LD). Genetic markers associated with production traits were also investigated, exploiting the unique genetic and adaptation features of this breed. A total of 639 ROH with length >4 Mb were identified, with mean length of 14.96 Mb. The mean genomic inbreeding was 0.09, and long segments of ROH were common, indicating recent inbred matings. The LD pattern indicates a large effective population size, suggesting the inflow of exotic germplasm in the past. The genome-wide association study identified novel markers significantly affecting longevity, age at first calving and direct genetic effects on calf weight. These results provide the first evidence of the association of longevity with genes related with DNA recognition and repair, and the association of age at first calving with aquaporin proteins, which are known to have a crucial role in reproduction.

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN)

“…This chip contains about 36.9 k SNPs informative in DSN after filtering for a SNP call rate > 95% and a minor allele frequency (MAF) > 5% [ 7 ]. The loss of up to 20 k SNPs due to filtering has also been reported in other studies on small-breeds [ 8 – 11 ]. The loss can be even more extreme, if a commercial SNP chip is used for distantly related species (for example, Capra ibex when analyzed using the commercially available Illumina GoatSNP50 chip [ 12 ]).…”

Evolution of inbreeding: a gaze into five Italian beef cattle breeds history

“…The PLINK software v1.9 (Chang et al, 2015) was used to update the names and positions of SNP markers. The SNPs that did not match the following criteria were removed before performing population diversity analyses: (i) SNPs with call rates less than 90%, (ii) SNPs with minor allele frequencies less than 5%, (iii) SNPs with more than 1% missing genotypes, and (iv) SNPs displaying highly significant deviations (P-value < 10 −3 ) from the Hardy-Weinberg equilibrium (Amaral, Pavão & Gama, 2020). Another pruning step was performed to remove SNPs with high linkage disequilibrium (LD) using the command -indep 50 5 2 (Manunza et al, 2016) of the PLINK v1.9 software (Chang et al, 2015) as recommended in a previous publication (Howrigan, Simonson & Keller, 2011).…”

Disequilibrium linkage (gametic disequilibrium) of structural genes in the bovine population

“…Их низкая устойчивость к некоторым природно-очаговым эпизоотиям и экологическим стрессам в новых районах разведения при недостаточной оптимизации условий кормления и содержания становится препятствием для эффективного использования зональных природных биоэнергетических ресурсов и производства экологически чистых продуктов питания. Поэтому с каждым годом возрастает актуальность инвентаризации и сохранения исчезающих аборигенных генофондов, а в метисных популяциях выявление и использование сохранившихся от них селективно выгодных комбинаций генов [15,16].…”