Genome-wide association studies reveal novel loci associated with carcass and body measures in beef cattle

Raza, Sayed Haidar Abbas; Khan, Samiullah; Amjadi, Motahareh; Abdelnour, Sameh A.; Ohran, Hussien; Al-Anazi, Khalid Mashay; El‐Hack, Mohamed E. Abd; Taha, Ayman E.; Khan, Rajwali; Chen, Gong; Schreurs, Nicola M.; Zhao, Chunping; Wei, Dawei; Zan, Linsen

doi:10.1016/j.abb.2020.108543

Cited by 31 publications

(16 citation statements)

References 72 publications

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“…Function of natriuretic peptides particularly NPR2 in porcine oocyte meiotic resumption, which was associated with in vitro maturation of porcine oocytes were shown in literature (Blaha et al, 2015;Sun et al, 2017;Wang et al, 2020). On the other hand, only a genomewide association study (GWAS) was identified an association between NPR2 gene variant and growth traits in Chinese indigenous sheep breeds (Wei et al, 2015;Raza et al, 2020b).…”

Section: Discussionmentioning

confidence: 99%

“…Selective breeding and genetic improvement during domestication have led to several genomic changes over generations in various animal species including livestock and left genomic footprints, called selection signatures (Raza et al, 2019;Kijas et al, 2012;Andersson et al, 2012). The elucidation of such signatures could help identification of genes that are difficult to identify through laboratory experiments and may also be useful in corroborating quantitative trait loci (QTL) mapping experiments in livestock (de Simoni Gouveia et al, 2014;Raza et al, 2020b). Plenty of selection signature have been identified and continuing to be identified in different livestock species and breeds (de Simoni Gouveia et al, 2014).…”

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confidence: 99%

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Association Between Natriuretic Peptide Receptor 2 (NPR2) RS208158047 Polymorphism and Fattening Performance of Young Bulls

Kiyici

Şenöz

Çınar

2022

Annals of Animal Science

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The objective of this study was to determine fattening performance data for Charolais, Limousin and Blonde d’Aquitaine beef cattle and associate these data with NPR2 gene 8:g.59961937 T>C (rs208158047) mutation. Experiments were conducted with 176 beef cattle (77 Charolais, 66 Limousin and 33 Blonde d’Aquitaine) at nine months of age. Experiments lasted for 9 months and animals were slaughtered at the age of 18 months. Cattle body weights were determined at four different periods: beginning of fattening (d0), 60th day of fattening (d60), 120th day of fattening (d120) and at the end of fattening (sw). In terms of rs208158047 mutation of Charolais, Limousin and Blonde d’Aquitaine breeds, TT and CT genotypes were identified, and CC genotype was not encountered. The association of average daily gain (ADG) in d0-d60, d0-d120 and d0-sw periods with the genotypes of rs208158047 mutation was found to be significant (P<0.05). Greater ADGs were observed in rs208158047-CT genotypes compared to rs208158047-TT genotypes. These results indicate that the selection of bovine NPR2 gene could be used to ensure the breeding direction for growth related traits of the beef cattle.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Association Between Natriuretic Peptide Receptor 2 (NPR2) RS208158047 Polymorphism and Fattening Performance of Young Bulls

Kiyici

Şenöz

Çınar

2022

Annals of Animal Science

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“…SLIT2 play highly conserved roles in axon guidance and neuronal migration. A lot of genomewide studies have reported this gene to QTL for beef complex traits including organ weight [25,26], body weight [27], and fertility [28].…”

Section: Identification Of Qtl Using Gpnetmentioning

confidence: 99%

GpNet: Genomic Prediction Network Using Locally Connected Layers in Korean Native Cattle

Lee

Seo

Chung

et al. 2021

Preprint

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Background: The use of DNA marker information for the prediction of genetic merit in animal and plant breeding, and susceptibility to disease in human medicine has become widespread. Therefore, an increasing number of methods have been proposed for more accurate and efficient genomic prediction. However, most of the commonly used models for genomic prediction only account for additive effects since most of them are designed based on the linear model. Results: Here, we proposed a GpNet, a deep learning network for genomic prediction in Korean beef cattle. With a locally connected layer, GpNet can estimate LD-block effects of single nucleotide polymorphisms (SNP) with adjacent two or more SNPs closer to 3’-end. This operation is quite similar to how the DNA sequence is used in the translation process in which the RNA polymerase interprets DNA sequence by units of codons to downstream (3’ to 5’). GpNet archived a superior performance than previous state-of-arts methods for beef carcass weight with a predictive ability of 0.721%. GpNet also found two significant quantitative trait locus (QTL) on the regions (bta 6:38464203–39816133, bta 14:25307116–29987025) for carcass weight. However, GpNet showed less performance than linear methods in backfat thickness and eye-muscle area.Conclusions: GpNet outperformed the previous state-of-arts methods for beef carcass weight. However, GpNet cannot achieve superior performance in backfat thickness and eye-muscle area. We noticed that the lack of ability to estimate distant epistasis and dominance was the weakness of GpNet. Therefore, it remains a future research issue to expand GpNet to resolve these flaws and this further study will accelerate the new phase of the genomic prediction.

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“…More than 1,000 cattle breeds are living in the world, 1 making up a vital part of economic livestock by offering major sources (e.g., milk, meat, leather, and power) to humans. Modern cattle are stratified into two types according to the common usage, Bos taurus and Bos indicus, which have been differentiated from each other for >250,000 years [2][3][4][5][6] and independently domesticated in the Fertile Crescent $8,000-10,000 years ago and the Indus Valley $6,000-8,000 years ago. 7,8 China has broad and diverse bovine genetic resources, with 53 indigenous cattle breeds.…”

Section: Introductionmentioning

confidence: 99%

Insights into adaption and growth evolution: a comparative genomics study on two distinct cattle breeds from Northern and Southern China

Mei

Gui

Hong

et al. 2021

Molecular Therapy - Nucleic Acids

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Mongolian cattle (MG, Bos taurus) and Minnan cattle (MN, Bos indicus) are two different breeds of Chinese indigenous cattle, representing North type and South type, respectively. However, their value and potential have not yet been discovered at the genomic level. In this study, 26 individuals of MN and MG were sequenced for the first time at an average of 13.9-and 12.8-fold, respectively. Large numbers of different variations were identified. In addition, the analyses of phylogenetic and population structure showed that these two cattle breeds are distinct from each other, and results of linkage disequilibrium analysis revealed that these two cattle breeds have undergone various degrees of intense natural or artificial selection. Subsequently, 496 and 306 potential selected regions (PSRs) were obtained in MN and MG, containing 1,096 and 529 potential selected genes (PSGs), respectively. These PSGs, together with the analyzed copy number variation (CNV)-related genes, showed potential relations with their phenotypic characteristics, including environmental adaptability (e.g., DVL2, HSPA4, CDHR4), feed efficiency (e.g., R3HDM1, PLAG1, XKR4), and meat/milk production (e.g., PDHB, LEMD3, APOF). The results of this study help to gain new insights into the genetic characteristics of two distinct cattle breeds and will contribute to future cattle breeding.

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Genome-wide association studies reveal novel loci associated with carcass and body measures in beef cattle

Cited by 31 publications

References 72 publications

Association Between Natriuretic Peptide Receptor 2 (NPR2) RS208158047 Polymorphism and Fattening Performance of Young Bulls

Association Between Natriuretic Peptide Receptor 2 (NPR2) RS208158047 Polymorphism and Fattening Performance of Young Bulls

GpNet: Genomic Prediction Network Using Locally Connected Layers in Korean Native Cattle

Insights into adaption and growth evolution: a comparative genomics study on two distinct cattle breeds from Northern and Southern China

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