Genome-wide association study identified genomic regions and putative candidate genes affecting meat color traits in Nellore cattle

Marín-Garzón, N.A.; Magalhães, Ana Fabrícia Braga; Mota, Lúcio Flávio Macêdo; Fonseca, Larissa Fernanda Simielli; Chardulo, Luis Artur Loyola; Albuquerque, Lúcia Galvão de

doi:10.1016/j.meatsci.2020.108288

Cited by 23 publications

(16 citation statements)

References 56 publications

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“…The GABAergic synapse pathway has also recently been associated with live weight in Simmental cattle [ 53 ]. In addition, GABRB1 and GABRA4 were reported as candidate genes affecting meat color traits in Nellore cattle [ 54 ].…”

Section: Discussionmentioning

confidence: 99%

Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

et al. 2021

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Background Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle. Results We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher’s exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle. Conclusions Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.

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Section: Discussionmentioning

confidence: 99%

Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

et al. 2021

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“…It is well-established that DNA-based inheritance enables the transmission of selected phenotypes across generations either without changes in the DNA sequence through epigenetic inheritance [31] or through functional mutations involving changes in only one base pair (single nucleotide polymorphisms-SNP). Through next-generation sequencing, SNP are valuable for detecting genetic variability and genomic prediction in sheep breeding programs [32], developing breed-specific DNA markers for breed identification [33,34], animal productivity [35], parentage assignment [36,37], forensics [38], and prediction of meat quality traits [39][40][41].…”

Section: Discussionmentioning

confidence: 99%

Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb

Pewan

Otto

Huerlimann

et al. 2021

Foods

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Meat quality data can only be obtained after slaughter when selection decisions about the live animal are already too late. Carcass estimated breeding values present major precision problems due to low accuracy, and by the time an informed decision on the genetic merit for meat quality is made, the animal is already dead. We report for the first time, a targeted next-generation sequencing (NGS) of single nucleotide polymorphisms (SNP) of lipid metabolism genes in Tattykeel Australian White (TAW) sheep of the MARGRA lamb brand, utilizing an innovative and minimally invasive muscle biopsy sampling technique for directly quantifying the genetic worth of live lambs for health-beneficial omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA), intramuscular fat (IMF), and fat melting point (FMP). NGS of stearoyl-CoA desaturase (SCD), fatty acid binding protein-4 (FABP4), and fatty acid synthase (FASN) genes identified functional SNP with unique DNA marker signatures for TAW genetics. The SCD g.23881050T>C locus was significantly associated with IMF, C22:6n-3, and C22:5n-3; FASN g.12323864A>G locus with FMP, C18:3n-3, C18:1n-9, C18:0, C16:0, MUFA, and FABP4 g.62829478A>T locus with IMF. These add new knowledge, precision, and reliability in directly making early and informed decisions on live sheep selection and breeding for health-beneficial n-3 LC-PUFA, FMP, IMF and superior meat-eating quality at the farmgate level. The findings provide evidence that significant associations exist between SNP of lipid metabolism genes and n-3 LC-PUFA, IMF, and FMP, thus underpinning potential marker-assisted selection for meat-eating quality traits in TAW lambs.

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“…The second signal on chromosome was only a single significant SNP at 220.4 Mb. The genes around this SNP were: TMBIM1 and PNKD , connected to meat color in cattle [ 64 ]; USP37 , involved in regulation of reproduction in mice [ 65 ]; VIL1 , related to meat tenderness [ 66 ]; CTDSP1 , related to milk fatty acid synthesis in goats [ 67 ]; SLC11A1 , with significant disease resistance related effects, in particular paratuberculosis, tuberculosis and brucellosis in a number of livestock species [ 68 , 69 ].…”

Section: Resultsmentioning

confidence: 99%

Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep

Mészárosová

Mészáros

Moravčíková

et al. 2022

Animals

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This study explored the genomic diversity and selection signatures in two Slovakian national breeds, the Original Valachian and the Improved Valachian sheep. As they are an important animal genetic resource within the country, but with decreasing population size, our aim is to identify potentially valuable genomic regions. A total of 97 sheep (18 male and 79 female) from the Original Valachian, and 69 sheep (25 male and 44 female) from the Improved Valachian populations were genotyped using the GeneSeek GGP Ovine 50 K chip. The inbreeding levels were assessed with runs of homozygosity (ROH). The selection signatures within breeds were identified based on the top 1% of most homozygous regions within the breed, the so-called ROH islands. The selection signatures between breeds were assessed based on variance in linkage disequilibrium. Overall, we have identified selection signatures with quantitative trait loci (QTL) and genes pointing towards all three production purposes of the Valachian sheep, milk, meat, and wool, including their quality characteristics. Another group with apparent large importance was the various traits related to health and resistance to parasites, which is well in line with the sturdy nature of this breed.

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Genome-wide association study identified genomic regions and putative candidate genes affecting meat color traits in Nellore cattle

Cited by 23 publications

References 56 publications

Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb

Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep

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