1
|
Alam MZ, Haque MA, Iqbal A, Lee YM, Ha JJ, Jin S, Park B, Kim NY, Won JI, Kim JJ. Genome-Wide Association Study to Identify QTL for Carcass Traits in Korean Hanwoo Cattle. Animals (Basel) 2023; 13:2737. [PMID: 37685003 PMCID: PMC10486602 DOI: 10.3390/ani13172737] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
This study aimed to identify genetic associations with carcass traits in Hanwoo cattle using a genome-wide association study. A total of 9302 phenotypes were analyzed, and all animals were genotyped using the Illumina Bovine 50K v.3 SNP chip. Heritabilities for carcass weight (CWT), eye muscle area (EMA), backfat thickness (BF), and marbling score (MS) were estimated as 0.42, 0.36, 0.36, and 0.47, respectively, using the GBLUP model, and 0.47, 0.37, 0.36, and 0.42, respectively, using the Bayes B model. We identified 129 common SNPs using DGEBV and 118 common SNPs using GEBV on BTA6, BTA13, and BTA14, suggesting their potential association with the traits of interest. No common SNPs were found between the GBLUP and Bayes B methods when using residuals as a response variable in GWAS. The most promising candidate genes for CWT included SLIT2, PACRGL, KCNIP4, RP1, XKR4, LYN, RPS20, MOS, FAM110B, UBXN2B, CYP7A1, SDCBP, NSMAF, TOX, CA8, LAP3, FAM184B, and NCAPG. For EMA, the genes IBSP, LAP3, FAM184B, LCORL, NCAPG, SLC30A9, and BEND4 demonstrated significance. Similarly, CYP7B1, ARMC1, PDE7A, and CRH were associated with BF, while CTSZ, GNAS, VAPB, and RAB22A were associated with MS. This finding offers valuable insights into genomic regions and molecular mechanisms influencing Hanwoo carcass traits, aiding efficient breeding strategies.
Collapse
Affiliation(s)
- Mohammad Zahangir Alam
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.Z.A.); (M.A.H.); (A.I.); (Y.-M.L.)
| | - Md Azizul Haque
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.Z.A.); (M.A.H.); (A.I.); (Y.-M.L.)
| | - Asif Iqbal
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.Z.A.); (M.A.H.); (A.I.); (Y.-M.L.)
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.Z.A.); (M.A.H.); (A.I.); (Y.-M.L.)
| | - Jae-Jung Ha
- Gyeongbuk Livestock Research Institute, Yeongju 36052, Republic of Korea;
| | - Shil Jin
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Byoungho Park
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Nam-Young Kim
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Jeong Il Won
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.Z.A.); (M.A.H.); (A.I.); (Y.-M.L.)
| |
Collapse
|
2
|
Ghoreishifar SM, Eriksson S, Johansson AM, Khansefid M, Moghaddaszadeh-Ahrabi S, Parna N, Davoudi P, Javanmard A. Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds. Genet Sel Evol 2020; 52:52. [PMID: 32887549 PMCID: PMC7487911 DOI: 10.1186/s12711-020-00571-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/21/2020] [Indexed: 02/01/2023] Open
Abstract
Background Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. Results Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8, PPP1R12A, SLC16A3, UCP2, UCP3, TIGAR), cold acclimation (AQP3, AQP7, HSPB8), body size and stature (PLAG1, KCNA6, NDUFA9, AKAP3, C5H12orf4, RAD51AP1, FGF6, TIGAR, CCND2, CSMD3), resistance to disease and bacterial infection (CHI3L2, GBP6, PPFIBP1, REP15, CYP4F2, TIGD2, PYURF, SLC10A2, FCHSD2, ARHGEF17, RELT, PRDM2, KDM5B), reproduction (PPP1R12A, ZFP36L2, CSPP1), milk yield and components (NPC1L1, NUDCD3, ACSS1, FCHSD2), growth and feed efficiency (TMEM68, TGS1, LYN, XKR4, FOXA2, GBP2, GBP5, FGD6), and polled phenotype (URB1, EVA1C). Conclusions We identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p-values of different statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses.
Collapse
Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden.
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Majid Khansefid
- AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia
| | - Sima Moghaddaszadeh-Ahrabi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Islamic Azad University, Tabriz Branch, Tabriz, Iran
| | - Nahid Parna
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N5E3, Canada
| | - Arash Javanmard
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| |
Collapse
|
3
|
Kowalewska-Łuczak I, Czerniawska-Piątkowska E, Kowalczyk A. Relationship between polymorphism in the CRH gene and the traits of body conformation of Salers cows. Anim Biotechnol 2019; 32:38-42. [PMID: 31328644 DOI: 10.1080/10495398.2019.1643357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The study analyzed three SNP polymorphisms located in exon 2 of the corticotropin-coding genes (rs110167397, rs381116984, rs109244394), later referred to as CRH1, CRH2, CRH3, respectively. The research was conducted in a Salers cattle herd. Identification of genotypes of individual animals was carried out using polymerase chain reaction - restriction fragments length polymorphism (PCR-RFLP). The heterozygous genotypes of all analyzed polymorphisms they determined the most extensive body mass of the analyzed animals. Other traits, such as cow size, muscularity, hip height and chest girth, were the most favorable for homozygous GG individuals concerning CRH1 polymorphism. Studying the relationship between CRH2 polymorphism and the animals with the genotype TT was preferred for traits such as muscularity and chest girth. It was shown that the CRH3 polymorphism significantly affected the muscularity and higher values of the zoometric measurement (hip height, chest girth) in the case of cows with the genotype CC. Significant differences were found in the study (p ≤ 0.01; p ≤ 0.05).
Collapse
Affiliation(s)
- Inga Kowalewska-Łuczak
- Department of Genetics and Animal Breeding, Faculty of Biotechnology and Animal Breeding, West Pomeranian University of Technology, Szczecin, Poland
| | - Ewa Czerniawska-Piątkowska
- Department of Ruminant Sciences, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology, Szczecin, Poland
| | - Alicja Kowalczyk
- Department of Environment, Animal Hygiene and Welfare, Wrocław University Of Environmental and Life Sciences, Wrocław, Poland
| |
Collapse
|
4
|
van der Kolk JH, Fouché N, Gross JJ, Gerber V, Bruckmaier RM. A comparison between the equine and bovine hypothalamus-pituitary-adrenocortical axis. Domest Anim Endocrinol 2016; 56 Suppl:S101-11. [PMID: 27345307 DOI: 10.1016/j.domaniend.2016.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 01/02/2023]
Abstract
In this review, we address the function of the hypothalamus-pituitary-adrenocortical (HPA) axis with special emphasis on the comparison between the bovine and equine species. The pars intermedia of the pituitary gland is particularly well developed in horses and cattle. However, its function is not well appreciated in cattle yet. The Wulzen's cone of the adenohypophysis is a special feature of ruminants. Total basal cortisol concentration is much higher in horses than that in cows with similar free cortisol fractions. Corticotropin-releasing factor (CRF) concentrations in equine pituitary venous blood are lower compared with other species, whereas plasma ACTH concentrations in cows are higher than those in horses. A CRF challenge test induced a more pronounced cortisol response in horses compared with cattle, whereas regarding ACTH challenge testing, the opposite seems true. Based on data from literature, the bovine species is characterized by relatively high basal blood CRF and ACTH and low cortisol and glucose concentrations. Obviously, further lowering of blood cortisol in cattle is easily prevented by the high sensitivity to ACTH, and as a consequence, subsequent increased gluconeogenesis prevents imminent hypoglycemia. Hypoglycemia is less likely in horses given their high muscle glycogen content and their relatively high cortisol concentration. When assessing HPA axis reactivity, response patterns to exogenous ACTH or CRH might be used as a reliable indicator of animal welfare status in cows and horses, respectively, although it is emphasized that considerable caution should be exercised in using measures of HPA activity solely to assess animal welfare.
Collapse
Affiliation(s)
- J H van der Kolk
- Department of Clinical Veterinary Medicine, Swiss Institute for Equine Medicine (ISME), Vetsuisse Faculty, University of Bern and Agroscope, Bern 3012, Switzerland.
| | - N Fouché
- Department of Clinical Veterinary Medicine, Swiss Institute for Equine Medicine (ISME), Vetsuisse Faculty, University of Bern and Agroscope, Bern 3012, Switzerland
| | - J J Gross
- Veterinary Physiology, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland
| | - V Gerber
- Department of Clinical Veterinary Medicine, Swiss Institute for Equine Medicine (ISME), Vetsuisse Faculty, University of Bern and Agroscope, Bern 3012, Switzerland
| | - R M Bruckmaier
- Veterinary Physiology, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland
| |
Collapse
|
5
|
Seong J, Yoon H, Kong HS. Identification of microRNA and target gene associated with marbling score in Korean cattle (Hanwoo). Genes Genomics 2016. [DOI: 10.1007/s13258-016-0401-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
6
|
Allais S, Levéziel H, Hocquette JF, Rousset S, Denoyelle C, Journaux L, Renand G. Fine mapping of quantitative trait loci underlying sensory meat quality traits in three French beef cattle breeds. J Anim Sci 2014; 92:4329-41. [PMID: 25149327 DOI: 10.2527/jas.2014-7868] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Improving the traits that underlie meat quality is a major challenge in the beef industry. The objective of this paper was to detect QTL linked to sensory meat quality traits in 3 French beef cattle breeds. We genotyped 1,059, 1,219, and 947 young bulls and their sires belonging to the Charolais, Limousin, and Blonde d'Aquitaine breeds, respectively, using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). After estimating relevant genetic parameters using VCE software, we performed a linkage disequilibrium and linkage analysis on 4 meat traits: intramuscular fat content, muscle lightness, shear force, and tenderness score. Heritability coefficients largely ranged between 0.10 and 0.24; however, they reached a maximum of 0.44 and 0.50 for intramuscular fat content and tenderness score, respectively, in the Charolais breed. The 2 meat texture traits, shear force and tenderness score, were strongly genetically correlated (-0.91 in the Charolais and Limousin breed and -0.86 in the Blonde d'Aquitaine breed), indicating that they are 2 different measures of approximately the same trait. The genetic correlation between tenderness and intramuscular fat content differed across breeds. Using a significance threshold of 5 × 10(-4) for QTL detection, we found more than 200 significant positions across the 29 autosomal chromosomes for the 4 traits in the Charolais and Blonde d'Aquitaine breeds; in contrast, there were only 78 significant positions in the Limousin breed. Few QTL were common across breeds. We detected QTL for intramuscular fat content located near the myostatin gene in the Charolais and Blonde d'Aquitaine breeds. No mutation in this gene has been reported for the Blonde d'Aquitaine breed; therefore, it suggests that an unknown mutation could be segregating in this breed. We confirmed that, in certain breeds, markers in the calpastatin and calpain 1 gene regions affect tenderness. We also found new QTL as several QTL on chromosome 3 that are significantly associated with meat tenderness in the Blonde d'Aquitaine breed. Overall, these results greatly contribute to the goal of building a panel of markers that can be used to select animals of high meat quality.
Collapse
Affiliation(s)
- S Allais
- INRA, AgroParisTech, UMR1313 Unité de Génétique Animale et Biologie Intégrative, F-78350 Jouy-en-Josas, France Union Nationale des Coopératives agricoles d'Elevage et d'Insémination Animale, F-75595 Paris Cedex 12, France
| | - H Levéziel
- INRA, Université de Limoges, UMR1061 Unité de Génétique Moléculaire Animale, F-87060 Limoges, France
| | - J F Hocquette
- INRA, VetAgro Sup, UMR1213, Recherches sur les Herbivores, F-63122 Saint Genès Champanelle, France
| | - S Rousset
- INRA, Clermont Université, UMR1019 Unité de Nutrition Humaine, Centre de Recherches en Nutrition Humaine d'Auvergne, F-63001 Clermont-Ferrand, France
| | - C Denoyelle
- Institut de l'Elevage, F-75595 Paris Cedex 12, France
| | - L Journaux
- Institut de l'Elevage, F-75595 Paris Cedex 12, France
| | - G Renand
- INRA, Clermont Université, UMR1019 Unité de Nutrition Humaine, Centre de Recherches en Nutrition Humaine d'Auvergne, F-63001 Clermont-Ferrand, France
| |
Collapse
|
7
|
Lim D, Lee SH, Kim NK, Cho YM, Chai HH, Seong HH, Kim H. Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:19-29. [PMID: 25049701 PMCID: PMC4093059 DOI: 10.5713/ajas.2012.12375] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/26/2012] [Accepted: 08/07/2012] [Indexed: 11/27/2022]
Abstract
Marbling (intramuscular fat) is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the 'marbling score' trait and systemically analyzed the network topology in Hanwoo (Korean cattle). As a result, we determined 3 modules (gene groups) that showed statistically significant results for marbling score. In particular, one module (denoted as red) has a statistically significant result for marbling score (p = 0.008) and intramuscular fat (p = 0.02) and water capacity (p = 0.006). From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA) have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.
Collapse
Affiliation(s)
- Dajeong Lim
- National Institute of Animal Science, RDA, Suwon, Korea ; Department of Food and Animal Biotechnology, Seoul National University, Seoul, Korea
| | | | - Nam-Kuk Kim
- National Agricultural products Quality management Service(NAQS), Seoul, Korea
| | - Yong-Min Cho
- National Institute of Animal Science, RDA, Suwon, Korea
| | - Han-Ha Chai
- National Institute of Animal Science, RDA, Suwon, Korea
| | | | - Heebal Kim
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Korea
| |
Collapse
|
8
|
Ribeca C, Bonfatti V, Cecchinato A, Albera A, Gallo L, Carnier P. Effect of polymorphisms in candidate genes on carcass and meat quality traits in double muscled Piemontese cattle. Meat Sci 2013; 96:1376-83. [PMID: 24361557 DOI: 10.1016/j.meatsci.2013.11.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/25/2013] [Accepted: 11/26/2013] [Indexed: 11/27/2022]
Abstract
The aim of this study was to investigate the association between 10 candidate genes and carcass weight and conformation, carcass daily gain, and meat quality (pH, color, cooking loss, drip loss and shear force) in 990 double-muscled Piemontese young bulls. Animals were genotyped at each of the following genes: growth hormone, growth hormone receptor, pro-opiomelanocortin, pro-opiomelanocortin class 1 homeobox 1, melanocortin-4 receptor, corticotrophin-releasing hormone, diacylglycerol O-acyltransferase-1, thyroglobulin, carboxypeptidase E and gamma-3 regulatory subunit of the AMP-activated protein kinase. All the investigated SNPs had additive effects which were relevant for at least one of the traits. Relevant associations between the investigated SNPs and carcass weight, carcass daily gain and carcass conformation were detected, whereas associations of SNPs with meat quality were moderate. Results confirmed some of previously reported associations, but diverged for others. Validation in other cattle breeds is required to use these SNPs in gene-assisted selection programs for enhancement of carcass traits and meat quality.
Collapse
Affiliation(s)
- C Ribeca
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - V Bonfatti
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy.
| | - A Cecchinato
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - A Albera
- Piemontese Cattle Breeders Association (ANABoRaPi), strada Trinità 32/a, Carrù, 12061, Italy
| | - L Gallo
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - P Carnier
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| |
Collapse
|
9
|
Wathes DC, Clempson AM, Pollott GE. Associations between lipid metabolism and fertility in the dairy cow. Reprod Fertil Dev 2013; 25:48-61. [PMID: 23244828 DOI: 10.1071/rd12272] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dairy cows mobilise body tissues to support milk production and, because glucose supplies are limited, lipids are used preferentially for energy production. Lipogenic activity is switched off and lipolytic mechanisms in adipose tissue increase through changes in the expression of several key enzymes. This results in a loss of body condition, together with high circulating concentrations of non-esterified fatty acids. Changes in the synthesis, secretion and signalling pathways of somatotrophic hormones (insulin, growth hormone, insulin-like growth factor 1) and adipokines (e.g. leptin) are central to the regulation of these processes. A high reliance on fatty acids as an energy source in the peripartum period causes oxidative damage to mitochondria in metabolically active tissues, including the liver and reproductive tract. The expression of genes involved in insulin resistance (PDK4, AHSG) is increased, together with expression of TIEG1, a transcription factor that can induce apoptosis via the mitochondrial pathway. Polymorphisms in TFAM and UCP2, two autosomal mitochondrial genes, have been associated with longevity in dairy cows. Polymorphisms in many other genes that affect lipid metabolism also show some associations with fertility traits. These include DGAT1, SCD1, DECR1, CRH, CBFA2T1, GH, LEP and NPY. Excess lipid accumulation in oocytes and the regenerating endometrium reduces fertility via reductions in embryo survival and increased inflammatory changes, respectively.
Collapse
Affiliation(s)
- D Claire Wathes
- Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Herts AL9 7TA, UK.
| | | | | |
Collapse
|
10
|
Tizioto P, Meirelles S, Veneroni G, Tullio R, Rosa A, Alencar M, Medeiros S, Siqueira F, Feijó G, Silva L, Torres R, Regitano L. A SNP in ASAP1 gene is associated with meat quality and production traits in Nelore breed. Meat Sci 2012; 92:855-7. [DOI: 10.1016/j.meatsci.2012.05.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 03/16/2012] [Accepted: 05/18/2012] [Indexed: 11/24/2022]
|
11
|
Zhang L, Michal JJ, O'Fallon JV, Pan Z, Gaskins CT, Reeves JJ, Busboom JR, Zhou X, Ding B, Dodson MV, Jiang Z. Quantitative genomics of 30 complex phenotypes in Wagyu x Angus F₁ progeny. Int J Biol Sci 2012; 8:838-58. [PMID: 22745575 PMCID: PMC3385007 DOI: 10.7150/ijbs.4403] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/04/2012] [Indexed: 12/25/2022] Open
Abstract
In the present study, a total of 91 genes involved in various pathways were investigated for their associations with six carcass traits and twenty-four fatty acid composition phenotypes in a Wagyu×Angus reference population, including 43 Wagyu bulls and their potential 791 F1 progeny. Of the 182 SNPs evaluated, 102 SNPs that were in Hardy-Weinberg equilibrium with minor allele frequencies (MAF>0.15) were selected for parentage assignment and association studies with these quantitative traits. The parentage assignment revealed that 40 of 43 Wagyu sires produced over 96.71% of the calves in the population. Linkage disequilibrium analysis identified 75 of 102 SNPs derived from 54 genes as tagged SNPs. After Bonferroni correction, single-marker analysis revealed a total of 113 significant associations between 44 genes and 29 phenotypes (adjusted P<0.05). Multiple-marker analysis confirmed single-gene associations for 10 traits, but revealed two-gene networks for 9 traits and three-gene networks for 8 traits. Particularly, we observed that TNF (tumor necrosis factor) gene is significantly associated with both beef marbling score (P=0.0016) and palmitic acid (C16:0) (P=0.0043), RCAN1 (regulator of calcineurin 1) with rib-eye area (P=0.0103), ASB3 (ankyrin repeat and SOCS box-containing 3) with backfat (P=0.0392), ABCA1 (ATP-binding cassette A1) with both palmitic acid (C16:0) (P=0.0025) and oleic acid (C18:1n9) (P=0.0114), SLC27A1(solute carrier family 27 A1) with oleic acid (C18:1n9) (P=0.0155), CRH (corticotropin releasing hormone) with both linolenic acid (OMEGA-3) (P=0.0200) and OMEGA 6:3 RATIO (P=0.0054), SLC27A2 (solute carrier family 27 A2) with both linoleic acid (OMEGA-6) (P=0.0121) and FAT (P=0.0333), GNG3 (guanine nucleotide binding protein gamma 3 with desaturase 9 (P=0.0115), and EFEMP1 (EGF containing fibulin-like extracellular matrix protein 1), PLTP (phospholipid transfer protein) and DSEL (dermatan sulfate epimerase-like) with conjugated linoleic acid (P=0.0042-0.0044), respectively, in the Wagyu x Angus F1 population. In addition, we observed an interesting phenomenon that crossbreeding of different breeds might change gene actions to dominant and overdominant modes, thus explaining the origin of heterosis. The present study confirmed that these important families or pathway-based genes are useful targets for improving meat quality traits and healthful beef products in cattle.
Collapse
Affiliation(s)
- Lifan Zhang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Kowalewska-Luczak I, Wachelko B, Kulig H. The study of the SNP in the corticotropin-releasing hormone gene (Exon 2) and milk production traits in cattle. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412020093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
13
|
Veneroni-Gouveia G, Meirelles SL, Grossi DA, Santiago AC, Sonstegard TS, Yamagishi MEB, Matukumalli LK, Coutinho LL, Alencar MM, Oliveira HN, Regitano LCA. Whole-genome analysis for backfat thickness in a tropically adapted, composite cattle breed from Brazil. Anim Genet 2012; 43:518-24. [PMID: 22497247 DOI: 10.1111/j.1365-2052.2011.02286.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Backfat thickness affects the preservation of the beef carcass after slaughter and confers organoleptic characteristics assessed by the consumer. One of the breeding goals for Canchim, a tropically adapted breed, is to comprehensively increase fat thickness. Our goals were to identify genomic regions associated with backfat in Canchim populations and validate the association of single nucleotide polymorphisms (SNPs) overlapping previously identified QTL regions known to affect fat deposition. Fifteen animals with lower and 15 animals with higher residues for backfat, according to a linear model using the SAS GLM procedure, were selected from a population of 1171 animals and genotyped using the BovineSNP50 BeadChip. Initial analysis revealed more than 100 SNPs that discriminated the tails of phenotypic distribution. One extended region of association included the centromeric region of chromosome (Chr) 14. Because this region overlapped with QTL from previous reports, we developed SNP assays to interrogate two linkage disequilibrium blocks, one in the centromeric region and another in the middle region of Chr 14 to confirm the association. The analysis validated the presence of specific haplotypes affecting fat thickness.
Collapse
Affiliation(s)
- G Veneroni-Gouveia
- Graduate Program on Genetics and Evolution, São Carlos Federal University, São Carlos, SP 13565-905, Brazil
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Marques E, Grant J, Wang Z, Kolbehdari D, Stothard P, Plastow G, Moore S. Identification of candidate markers on bovine chromosome 14 (BTA14) under milk production trait quantitative trait loci in Holstein. J Anim Breed Genet 2011; 128:305-13. [DOI: 10.1111/j.1439-0388.2010.00910.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
15
|
Dodson MV, Jiang Z, Chen J, Hausman GJ, Guan LL, Novakofski J, Thompson DP, Lorenzen CL, Fernyhough ME, Mir PS, Reecy JM. Allied industry approaches to alter intramuscular fat content and composition in beef animals. J Food Sci 2010; 75:R1-8. [PMID: 20492190 DOI: 10.1111/j.1750-3841.2009.01396.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biochemical and biophysical research tools are used to define the developmental dynamics of numerous cell lineages from a variety of tissues relevant to meat quality. With respect to the adipose cell lineage, much of our present understanding of adipogenesis and lipid metabolism was initially determined through the use of these methods, even though the in vitro or molecular environments are far removed from the tissues of meat animals. This concise review focuses on recent cellular and molecular biology-related research with adipocytes, and how the research might be extended to the endpoint of altering red meat quality. Moreover, economic and policy impacts of such in animal production regimens is discussed. These issues are important, not only with respect to palatability, but also to offer enhanced health benefits to the consumer by altering content of bioactive components in adipocytes.
Collapse
Affiliation(s)
- Michael V Dodson
- Dept. of Animal Science, Washington State Univ., Pullman, WA 99164, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Gill JL, Bishop SC, McCorquodale C, Williams JL, Wiener P. Associations between single nucleotide polymorphisms in multiple candidate genes and carcass and meat quality traits in a commercial Angus-cross population. Meat Sci 2010; 86:985-93. [PMID: 20826071 DOI: 10.1016/j.meatsci.2010.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 07/30/2010] [Accepted: 08/09/2010] [Indexed: 11/28/2022]
Abstract
The aim of this study was to evaluate the effects of 28 single nucleotide polymorphisms (SNP) in 10 candidate genes previously shown to be associated with quality traits in pigs and cattle. The data set comprised 28 traits recorded on a commercial population of 536 Aberdeen Angus-cross beef cattle. Among the traits, 20 were carcass and sirloin quality related, one mechanical measure of tenderness, and the remaining seven were taste panel assessed sensory traits. The candidate genes studied included growth hormone (GH) and pro-opiomelanocortin (POMC). Association analysis showed that 13 of the 28 SNPs were significantly associated with at least one of the traits. Some of these were novel (POMC and mechanical tenderness), whilst others confirmed previous results (GH and eye muscle length). Following validation in other populations and breeds, these markers could be incorporated into breeding programs to increase the rate of improvement in carcass and meat quality traits.
Collapse
Affiliation(s)
- Jennifer L Gill
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Roslin BioCentre, Roslin, Midlothian EH25 9PS, UK.
| | | | | | | | | |
Collapse
|
17
|
Jiang Z, Michal JJ, Chen J, Daniels TF, Kunej T, Garcia MD, Gaskins CT, Busboom JR, Alexander LJ, Wright RW, Macneil MD. Discovery of novel genetic networks associated with 19 economically important traits in beef cattle. Int J Biol Sci 2009; 5:528-42. [PMID: 19727437 PMCID: PMC2726579 DOI: 10.7150/ijbs.5.528] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 07/16/2009] [Indexed: 11/20/2022] Open
Abstract
Quantitative or complex traits are determined by the combined effects of many loci, and are
affected by genetic networks or molecular pathways. In the present study, we genotyped a total
of 138 mutations, mainly single nucleotide polymorphisms derived from 71 functional genes on a
Wagyu x Limousin reference population. Two hundred forty six F2 animals were
measured for 5 carcass, 6 eating quality and 8 fatty acid composition traits. A total of 2,280
single marker-trait association runs with 120 tagged mutations selected based on the HAPLOVIEW
analysis revealed 144 significant associations (P < 0.05), but 50 of them were removed
from the analysis due to the small number of animals (≤ 9) in one genotype group or
absence of one genotype among three genotypes. The remaining 94 single-trait associations were
then placed into three groups of quantitative trait modes (QTMs) with additive, dominant and
overdominant effects. All significant markers and their QTMs associated with each of these 19
traits were involved in a linear regression model analysis, which confirmed single-gene
associations for 4 traits, but revealed two-gene networks for 8 traits and three-gene networks
for 5 traits. Such genetic networks involving both genotypes and QTMs resulted in high
correlations between predicted and actual values of performance, thus providing evidence that
the classical Mendelian principles of inheritance can be applied in understanding genetic
complexity of complex phenotypes. Our present study also indicated that carcass, eating quality
and fatty acid composition traits rarely share genetic networks. Therefore, marker-assisted
selection for improvement of one category of these traits would not interfere with improvement
of another.
Collapse
Affiliation(s)
- Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Southey BR, Rodriguez-Zas SL, Sweedler JV. Characterization of the prohormone complement in cattle using genomic libraries and cleavage prediction approaches. BMC Genomics 2009; 10:228. [PMID: 19445702 PMCID: PMC2698874 DOI: 10.1186/1471-2164-10-228] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 05/16/2009] [Indexed: 12/30/2022] Open
Abstract
Background Neuropeptides are cell to cell signalling molecules that regulate many critical biological processes including development, growth and reproduction. These peptides result from the complex processing of prohormone proteins, making their characterization both challenging and resource demanding. In fact, only 42 neuropeptide genes have been empirically confirmed in cattle. Neuropeptide research using high-throughput technologies such as microarray and mass spectrometry require accurate annotation of prohormone genes and products. However, the annotation and associated prediction efforts, when based solely on sequence homology to species with known neuropeptides, can be problematic. Results Complementary bioinformatic resources were integrated in the first survey of the cattle neuropeptide complement. Functional neuropeptide characterization was based on gene expression profiles from microarray experiments. Once a gene is identified, knowledge of the enzymatic processing allows determination of the final products. Prohormone cleavage sites were predicted using several complementary cleavage prediction models and validated against known cleavage sites in cattle and other species. Our bioinformatics approach identified 92 cattle prohormone genes, with 84 of these supported by expressed sequence tags. Notable findings included an absence of evidence for a cattle relaxin 1 gene and evidence for a cattle galanin-like peptide pseudogene. The prohormone processing predictions are likely accurate as the mammalian proprotein convertase enzymes, except for proprotein convertase subtilisin/kexin type 9, were also identified. Microarray analysis revealed the differential expression of 21 prohormone genes in the liver associated with nutritional status and 8 prohormone genes in the placentome of embryos generated using different reproductive techniques. The neuropeptide cleavage prediction models had an exceptional performance, correctly predicting cleavage in more than 86% of the prohormone sequence positions. Conclusion A substantial increase in the number of cattle prohormone genes identified and insights into the expression profiles of neuropeptide genes were obtained from the integration of bioinformatics tools and database resources and gene expression information. Approximately 20 prohormones with no empirical evidence were detected and the prohormone cleavage sites were predicted with high accuracy. Most prohormones were supported by expressed sequence tag data and many were differentially expressed across nutritional and reproductive conditions. The complete set of cattle prohormone sequences identified and the cleavage prediction approaches are available at .
Collapse
Affiliation(s)
- Bruce R Southey
- Department of Chemistry, University of Illinois, Urbana, IL, USA.
| | | | | |
Collapse
|
19
|
Wibowo TA, Gaskins CT, Newberry RC, Thorgaard GH, Michal JJ, Jiang Z. Genome assembly anchored QTL map of bovine chromosome 14. Int J Biol Sci 2008; 4:406-14. [PMID: 19043607 PMCID: PMC2586679 DOI: 10.7150/ijbs.4.406] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2008] [Accepted: 11/11/2008] [Indexed: 11/07/2022] Open
Abstract
Bovine chromosome 14 (BTA14) has been widely explored for quantitative trait loci (QTL) and genes related to economically important traits in both dairy and beef cattle. We reviewed more than 40 investigations and anchored 126 QTL to the current genome assembly (Btau 4_0). Using this anchored QTL map, we observed that, in dairy cattle, the region spanning 0 – 10 Mb on BTA14 has the highest density QTL map with a total of 56 QTL, mainly for milk production traits. It is very likely that both somatic cell score (SCS) and clinical mastitis share some common QTL in two regions: 61.48 Mb - 73.84 Mb and 7.86 Mb – 39.55 Mb, respectively. As well, both ovulation rate and twinning rate might share a common QTL region from 34.16 Mb to 65.38 Mb. However, there are no common QTL locations in three pregnancy related phenotypes: non-return rate, pregnancy rate and daughter pregnancy rate. In beef cattle, the majority of QTL are located in a broad region of 15 Mb – 45 Mb on the chromosome. Functional genes, such as CRH, CYP11B1, DGAT1, FABP4 and TG, as potential candidates for some of these QTL, were also reviewed. Therefore, our review provides a standardized QTL map anchored within the current genome assembly, which would enhance the process of selecting positional and physiological candidate genes for many important traits in cattle.
Collapse
Affiliation(s)
- Tito A Wibowo
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
| | | | | | | | | | | |
Collapse
|
20
|
Abe T, Saburi J, Hasebe H, Nakagawa T, Kawamura T, Saito K, Nade T, Misumi S, Okumura T, Kuchida K, Hayashi T, Nakane S, Mitsuhasi T, Nirasawa K, Sugimoto Y, Kobayashi E. Bovine quantitative trait loci analysis for growth, carcass, and meat quality traits in an F2 population from a cross between Japanese Black and Limousin. J Anim Sci 2008; 86:2821-32. [PMID: 18599673 DOI: 10.2527/jas.2007-0676] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- T Abe
- National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Hausman GJ, Dodson MV, Ajuwon K, Azain M, Barnes KM, Guan LL, Jiang Z, Poulos SP, Sainz RD, Smith S, Spurlock M, Novakofski J, Fernyhough ME, Bergen WG. Board-invited review: the biology and regulation of preadipocytes and adipocytes in meat animals. J Anim Sci 2008; 87:1218-46. [PMID: 18849378 DOI: 10.2527/jas.2008-1427] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The quality and value of the carcass in domestic meat animals are reflected in its protein and fat content. Preadipocytes and adipocytes are important in establishing the overall fatness of a carcass, as well as being the main contributors to the marbling component needed for consumer preference of meat products. Although some fat accumulation is essential, any excess fat that is deposited into adipose depots other than the marbling fraction is energetically unfavorable and reduces efficiency of production. Hence, this review is focused on current knowledge about the biology and regulation of the important cells of adipose tissue: preadipocytes and adipocytes.
Collapse
Affiliation(s)
- G J Hausman
- USDA-ARS, Richard B. Russell Agricultural Research Station, Athens, GA 30604, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|