Spliced genes in muscle from Nelore Cattle and their association with carcass and meat quality

Silva, Danielly B S; Fonseca, Larissa Fernanda Simielli; Pinheiro, Daniel Guariz; Magalhães, Ana Fabrícia Braga; Muniz, Maria Malane Magalhães; Ferro, Jesus Aparecido; Baldi, Fernando; Chardulo, Luis Artur Loyola; Schnabel, Robert D.; Jf, Taylor; Albuquerque, Lúcia Galvão de

doi:10.1038/s41598-020-71783-4

Cited by 31 publications

(16 citation statements)

References 89 publications

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“…LFMM identified four SNPs significantly associated (FDR < 0.05) with three different climatic variables (Mean Diurnal Range, Mean Temperature Wettest Quarter, and SlopeP), two of which intercepting NBEA, a gene located within a region involved with wool production in sheep 40 and previously associated with continental goat group in the work of Bertolini et all 2018 9 , and the RHOBTB1 gene that is known to be associated to meat quality in cattle 41 (Supplementary Table 4 ).…”

Section: Resultsmentioning

confidence: 94%

The climatic and genetic heritage of Italian goat breeds with genomic SNP data

Cortellari

Barbato

Talenti

et al. 2021

Sci Rep

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Local adaptation of animals to the environment can abruptly become a burden when faced with rapid climatic changes such as those foreseen for the Italian peninsula over the next 70 years. Our study investigates the genetic structure of the Italian goat populations and links it with the environment and how genetics might evolve over the next 50 years. We used one of the largest national datasets including > 1000 goats from 33 populations across the Italian peninsula collected by the Italian Goat Consortium and genotyped with over 50 k markers. Our results showed that Italian goats can be discriminated in three groups reflective of the Italian geography and its geo-political situation preceding the country unification around two centuries ago. We leveraged the remarkable genetic and geographical diversity of the Italian goat populations and performed landscape genomics analysis to disentangle the relationship between genotype and environment, finding 64 SNPs intercepting genomic regions linked to growth, circadian rhythm, fertility, and inflammatory response. Lastly, we calculated the hypothetical future genotypic frequencies of the most relevant SNPs identified through landscape genomics to evaluate their long-term effect on the genetic structure of the Italian goat populations. Our results provide an insight into the past and the future of the Italian local goat populations, helping the institutions in defining new conservation strategy plans that could preserve their diversity and their link to local realities challenged by climate change.

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Section: Resultsmentioning

confidence: 94%

The climatic and genetic heritage of Italian goat breeds with genomic SNP data

Cortellari

Barbato

Talenti

et al. 2021

Sci Rep

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“…The RCAN1 gene was found in the ROH island, and it plays an important role in the proliferation of smooth muscle cells. This gene was previously reported to be associated with the ribeye area in Nellore [55] and Wagyu cattle [56]. The TRNA-CCC gene was reported to be associated with immune-response processes (somatic cell score) and membrane transport in dairy cows and buffalos [57,58].…”

Section: Selection Signaturesmentioning

confidence: 92%

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Hidalgo

Cesarani

Garcia

et al. 2021

Animals

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The ultimate goal of genetic selection is to improve genetic progress by increasing favorable alleles in the population. However, with selection, homozygosity, and potentially harmful recessive alleles can accumulate, deteriorating genetic variability and hampering continued genetic progress. Such potential adverse side effects of selection are of particular interest in populations with a small effective population size like the Romosinuano beef cattle in Mexico. The objective of this study was to evaluate the genetic background and inbreeding depression in Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH) of different length classes. Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals born between 1950 and 2019, of which 71 had genotypes. LD decreased with the increase in distance between markers, and Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne estimated using pedigree information was 86.44. The reduction in effective population size implies the existence of genetic bottlenecks and the decline of genetic diversity due to the intensive use of few individuals as parents of the next generations. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The shortest and longest segments were 1.0 and 36.0 Mb long, respectively, reflecting ancient and recent inbreeding. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for FPED, FGRM, and FROH, respectively. The correlation between FPED and FGRM was −0.25, and the correlations among FPED and FROH of different length classes were low (from 0.16 to 0.31). The correlations between FGRM and FROH of different length classes were moderate (from 0.44 to 0.58), indicating better agreement. A 1% increase in population inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to more sustainable breeding programs for the Mexican Romosinuano beef cattle breed.

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“…The LFMM analysis identified four SNPs associated with Mean Diurnal Range and Mean Temperature. These SNP were near NBEA, located within a region involved with wool production in sheep [215], and RHOBTB1, which is known to be associated with meat quality in cattle [216]. As observed before, methods implemented in Samβada and LFMM produce non-overlapping results.…”

Section: Landscape Genomicsmentioning

confidence: 69%

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

Passamonti

Somenzi

Barbato

et al. 2021

Animals

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Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.

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Spliced genes in muscle from Nelore Cattle and their association with carcass and meat quality

Cited by 31 publications

References 89 publications

The climatic and genetic heritage of Italian goat breeds with genomic SNP data

The climatic and genetic heritage of Italian goat breeds with genomic SNP data

Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

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