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Dubon MAC, Pedrosa VB, Feitosa FLB, Costa RB, de Camargo GMF, Silva MR, Pinto LFB. Identification of novel candidate genes for age at first calving in Nellore cows using a SNP chip specifically developed for Bos taurus indicus cattle. Theriogenology 2021; 173:156-162. [PMID: 34392169 DOI: 10.1016/j.theriogenology.2021.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 01/08/2023]
Abstract
The age at first calving has a great economic impact on the beef cattle system and calving at 24 months is an objective of selection for a more efficient herd. However, an age at first calving around 36 months has been observed for Nellore cattle in Brazil. Thus, a genome-wide association study (GWAS) was carried out with 8376 records of age at first calving and 3239 animals genotyped with the GGP-Indicus 35K, which has been developed specifically for Bos taurus indicus. The weighted single-step genomic best linear unbiased prediction method was used, with adjacent SNPs (single nucleotide polymorphisms) in genomic windows of 1.0 Mb. After quality control, 3239 (2161 males and 1078 females) animals genotyped for 30,519 SNPs were used in GWAS analysis. The average and standard deviation of age at first calving were 1041.7 and 140.6 days, respectively. The heritability estimate was 0.10 ± 0.02. The GWAS analysis found seven genomic regions in BTA1, 2, 5, 12, 18, 21, and 24, which explained a total of 11.24% of the additive genetic variance of age at first calving. In these regions were found 62 protein coding genes, and the genes HSD17B2, SERPINA14, SERPINA1, SERPINA5, STAT1, NFATC1, ATP9B, CTDP1, THPO, ECE2, PSMD2, EIF4G1, EIF2B2, DVL3, POLR2H, TMTC2, and GPC6 are possible candidates for age at first birth due their function. Moreover, two molecular functions ("serine-type endopeptidase inhibitor activity" and "negative regulation of endopeptidase activity") were significant, which depend on several serpin genes. The use of a SNP chip developed especially for Bos taurus indicus allowed to find genomic regions for age at first calving, which are close to QTLs previously reported for other reproduction-related traits. Future studies can reveal the causal variants and their effects on reproductive precocity of Nellore cows.
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Affiliation(s)
| | - Victor Breno Pedrosa
- State University of Ponta Grossa, 4748, Av. General Carlos Cavalcanti, Ponta Grossa, PR, 84030900, Brazil.
| | | | - Raphael Bermal Costa
- Federal University of Bahia, 500, Av. Adhemar de Barros, Salvador, BA, 40170110, Brazil.
| | | | - Marcio Ribeiro Silva
- Melhore Animal and Katayama Agropecuaria Lda, Guararapes, SP, 16700-000, Brazil.
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Tiezzi F, Arceo ME, Cole JB, Maltecca C. Including gene networks to predict calving difficulty in Holstein, Brown Swiss and Jersey cattle. BMC Genet 2018; 19:20. [PMID: 29609562 PMCID: PMC5880070 DOI: 10.1186/s12863-018-0606-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/15/2018] [Indexed: 11/10/2022] Open
Abstract
Background Calving difficulty or dystocia has a great economic impact in the US dairy industry. Reported risk factors associated with calving difficulty are feto-pelvic disproportion, gestation length and conformation. Different dairy cattle breeds have different incidence of calving difficulty, with Holstein having the highest dystocia rates and Jersey the lowest. Genomic selection becomes important especially for complex traits with low heritability, where the accuracy of conventional selection is lower. However, for complex traits where a large number of genes influence the phenotype, genome-wide association studies showed limitations. Biological networks could overcome some of these limitations and better capture the genetic architecture of complex traits. In this paper, we characterize Holstein, Brown Swiss and Jersey breed-specific dystocia networks and employ them in genomic predictions. Results Marker association analysis identified single nucleotide polymorphisms explaining the largest average proportion of genetic variance on BTA18 in Holstein, BTA25 in Brown Swiss, and BTA15 in Jersey. Gene networks derived from the genome-wide association included 1272 genes in Holstein, 1454 genes in Brown Swiss, and 1455 genes in Jersey. Furthermore, 256 genes in Holstein network, 275 genes in the Brown Swiss network, and 253 genes in the Jersey network were within previously reported dystocia quantitative trait loci. The across-breed network included 80 genes, with 9 genes being within previously reported dystocia quantitative trait loci. The gene-gene interactions in this network differed in the different breeds. Gene ontology enrichment analysis of genes in the networks showed Regulation of ARF GTPase was very significant (FDR ≤ 0.0098) on Holstein. Neuron morphogenesis and differentiation was the term most enriched (FDR ≤ 0.0539) on the across-breed network. Genomic prediction models enriched with network-derived relationship matrices did not outperform regular GBLUP models. Conclusions Regions identified in the genome were in the proximity of previously described quantitative trait loci that would most likely affect calving difficulty by altering the feto-pelvic proportion. Inclusion of identified networks did not increase prediction accuracy. The approach used in this paper could be extended to any instance with asymmetric distribution of phenotypes, for example, resistance to disease data. Electronic supplementary material The online version of this article (10.1186/s12863-018-0606-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Maria E Arceo
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD, 27705, USA
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA.
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Polymorphisms and genes associated with puberty in heifers. Theriogenology 2016; 86:333-9. [PMID: 27238439 DOI: 10.1016/j.theriogenology.2016.04.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 02/10/2016] [Accepted: 03/14/2016] [Indexed: 01/02/2023]
Abstract
Puberty onset is a multifactorial process influenced by genetic determinants and environmental conditions, especially nutritional status. Genes, genetic variations, and regulatory networks compose the molecular basis of achieving puberty. In this article, we reviewed the discovery of multiple polymorphisms and genes associated with heifer puberty phenotypes and discuss the opportunities to use this evolving knowledge of genetic determinants for breeding early pubertal Bos indicus-influenced cattle. The discovery of polymorphisms and genes was mainly achieved through candidate gene studies, quantitative trait loci analyses, genome-wide association studies, and recently, global gene expression studies (transcriptome). These studies are recapitulated and summarized in the current review.
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Li Y, Kim JJ. Multiple Linkage Disequilibrium Mapping Methods to Validate Additive Quantitative Trait Loci in Korean Native Cattle (Hanwoo). ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:926-35. [PMID: 26104396 PMCID: PMC4478501 DOI: 10.5713/ajas.15.0077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/23/2015] [Accepted: 04/25/2015] [Indexed: 01/11/2023]
Abstract
The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium analysis (LDLA) and a BayesCπ approach. The phenotypes of 486 steers were collected for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area, and marbling score (Marb). Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP) chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA) 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX]) may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.
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Affiliation(s)
- Yi Li
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea
| | - Jong-Joo Kim
- School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Korea
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Fernández ME, Lirón JP, Prando A, Rogberg-Muñoz A, Peral-García P, Baldo A, Giovambattista G. Evidence of association of a BTA20 region peaked in ISL1 with puberty in Angus bulls. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Chang LY, Pitchford WS, Bottema CDK. Modeling tenderness for genetic and quantitative trait loci analyses. J Anim Sci 2013; 92:39-47. [PMID: 24249798 DOI: 10.2527/jas.2013-6696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tenderness is the one of the most important attributes of beef with regards to the intent of consumers to repurchase. Beef tenderness is frequently measured objectively as Warner-Bratzler shear force. However, to better understand the genetics underlying tenderness, better descriptors were derived herein. Two traits, adjusted shear force and aging rate, were calculated to incorporate measures of Warner-Bratzler shear force repeated over aging time of 2 muscles, longissimus dorsi (LD) and semitendinosus (ST). Analysis of these traits indicated that the shear forces of the 2 muscles are lowly correlated and aging rate, as calculated, was not correlated with adjusted shear force. Breed, SNP, and QTL effects were analyzed for the 4 traits (2 traits × 2 muscles). For adjusted shear force, the QTL were located on cattle chromosomes BTA 5, 18, 25, and 29. With the exception of the QTL on BTA 5, the adjusted shear force QTL were observed for either the LD or the ST but not both muscles. The QTL for aging rate were located on BTA 1, 4, 7, 11, 13, 19, and 20.
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Affiliation(s)
- L Y Chang
- Cooperative Research Centre for Beef Genetic Technologies, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy Campus, South Australia, 5371 Australia
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Fortes MR, DeAtley KL, Lehnert SA, Burns BM, Reverter A, Hawken RJ, Boe-Hansen G, Moore SS, Thomas MG. Genomic regions associated with fertility traits in male and female cattle: Advances from microsatellites to high-density chips and beyond. Anim Reprod Sci 2013; 141:1-19. [DOI: 10.1016/j.anireprosci.2013.07.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 07/03/2013] [Accepted: 07/07/2013] [Indexed: 01/08/2023]
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Raadsma HW, Jonas E, Fleet MR, Fullard K, Gongora J, Cavanagh CR, Tammen I, Thomson PC. QTL and association analysis for skin and fibre pigmentation in sheep provides evidence of a major causative mutation and epistatic effects. Anim Genet 2013; 44:547-59. [PMID: 23451726 DOI: 10.1111/age.12033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2013] [Indexed: 11/30/2022]
Abstract
The pursuits of white features and white fleeces free of pigmented fibre have been important selection objectives for many sheep breeds. The cause and inheritance of non-white colour patterns in sheep has been studied since the early 19th century. Discovery of genetic causes, especially those which predispose pigmentation in white sheep, may lead to more accurate selection tools for improved apparel wool. This article describes an extended QTL study for 13 skin and fibre pigmentation traits in sheep. A total of 19 highly significant, 10 significant and seven suggestive QTL were identified in a QTL mapping experiment using an Awassi × Merino × Merino backcross sheep population. All QTL on chromosome 2 exceeded a LOD score of greater than 4 (range 4.4-30.1), giving very strong support for a major gene for pigmentation on this chromosome. Evidence of epistatic interactions was found for QTL for four traits on chromosomes 2 and 19. The ovine TYRP1 gene on OAR 2 was sequenced as a strong positional candidate gene. A highly significant association (P < 0.01) of grandparental haplotypes across nine segregating SNP/microsatellite markers including one non-synonymous SNP with pigmentation traits could be shown. Up to 47% of the observed variation in pigmentation was accounted for by models using TYRP1 haplotypes and 83% for models with interactions between two QTL probabilities, offering scope for marker-assisted selection for these traits.
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Affiliation(s)
- H W Raadsma
- ReproGen-Animal Bioscience Group, Faculty of Veterinary Science, University of Sydney, Camden, NSW 2570, Australia.
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Morris CA, Bottema CDK, Cullen NG, Hickey SM, Knowles SO, S. Pitchford W. Effects of quantitative trait loci and themyostatinlocus on trace and macro elements (minerals) in bovine liver, muscle and kidney. Anim Genet 2012; 44:361-8. [DOI: 10.1111/age.12012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2012] [Indexed: 11/29/2022]
Affiliation(s)
- C. A. Morris
- Ruakura Research Centre; AgResearch; Private Bag 3123; Hamilton; 3240; New Zealand
| | - C. D. K. Bottema
- School of Animal and Veterinary Sciences; University of Adelaide; Roseworthy Campus; Roseworthy; SA; 5371; Australia
| | - N. G. Cullen
- Ruakura Research Centre; AgResearch; Private Bag 3123; Hamilton; 3240; New Zealand
| | - S. M. Hickey
- Ruakura Research Centre; AgResearch; Private Bag 3123; Hamilton; 3240; New Zealand
| | - S. O. Knowles
- Grasslands Research Centre; AgResearch; Private Bag 11008; Palmerston North; 4442; New Zealand
| | - W. S. Pitchford
- School of Animal and Veterinary Sciences; University of Adelaide; Roseworthy Campus; Roseworthy; SA; 5371; Australia
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A chromosome-wide QTL study on BTA29 affecting temperament traits in German Angus beef cattle and mapping of DRD4. Animal 2012; 5:195-7. [PMID: 22440763 DOI: 10.1017/s1751731110001801] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The behaviour of beef cattle is important for the safety and welfare of stockmen and animals. Ten microsatellites spanning BTA29 and, in addition, the candidate gene, dopamine receptor D4 gene, were analysed in 545 German Angus calves of six sires and included in a quantitative trait locus (QTL) study on the basis of three different behaviour tests. A putative QTL for the score while entering the scale (ScE) was detected at BMS764. The DRD4 fragment was mapped in the distal region of BTA29 15.3 cM distal of ILSTS081. The results clearly indicate that BTA29 with a putative QTL in the proximal part and the candidate gene, DRD4, in the distal part plays an important role in the regulation of temperament. During the study one of the sires was detected to be a blood chimera.
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Lirón JP, Prando AJ, Fernández ME, Ripoli MV, Rogberg-Muñoz A, Goszczynski DE, Posik DM, Peral-García P, Baldo A, Giovambattista G. Association between GNRHR, LHR and IGF1 polymorphisms and timing of puberty in male Angus cattle. BMC Genet 2012; 13:26. [PMID: 22480211 PMCID: PMC3344682 DOI: 10.1186/1471-2156-13-26] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 04/05/2012] [Indexed: 11/14/2022] Open
Abstract
Background In bovines, there are significant differences within and among beef breeds in the time when bulls reach puberty. Although the timing of puberty is likely to be a multigenic trait, previous studies indicate that there may also be single genes that exert major effects on the timing of puberty within the general population. Despite its economic importance, there are not many SNPs or genetic markers associated with the age of puberty in male cattle. In the present work, we selected three candidate genes, GNRHR, LHR and IGF1, and associated their polymorphisms with the age of puberty in Angus male cattle. Results After weaning, 276 Angus males were measured every month for weight (W), scrotal circumference (SC), sperm concentration (C) and percentage of motility (M). A total of 4 SNPs, two within GNRHR, one in LHR and one in IGF1 were genotyped using the pyrosequencing technique. IGF1-SnaBI SNP was significant associated (P < 0.01) with age at SC 28 cm, but it were not associated with age at M 10% and C 50 million. Genotype CC exhibited an average age at SC 28 cm of 7 and 11 days higher than CT (p = 0.037) and TT (p = 0.012), respectively. This SNP explained 1.5% of the genetic variance of age of puberty at SC28. LHR-I499L, GNRHR-SNP5 and GNRHR-SNP6 were not associated with any of the measurements. However, GNRHR haplotypes showed a suggestive association with age at SC 28 cm. Conclusions The findings presented here could support the hypothesis that IGF1 is a regulator of the arrival to puberty in male calves and is involved in the events that precede and initiate puberty in bull calves. Given that most studies in cattle, as well as in other mammals, were done in female, the present results are the first evidence of markers associated with age at puberty in male cattle.
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Affiliation(s)
- Juan P Lirón
- Instituto de Genética Veterinaria, CCT La Plata - CONICET - Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Argentina
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Tian R, Cullen NG, Morris CA, Fisher PJ, Pitchford WS, Bottema CDK. Major effect of retinal short-chain dehydrogenase reductase (RDHE2) on bovine fat colour. Mamm Genome 2012; 23:378-86. [DOI: 10.1007/s00335-012-9396-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
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Morris CA, Bottema CDK, Cullen NG, Hickey SM, Esmailizadeh AK, Siebert BD, Pitchford WS. Quantitative trait loci for organ weights and adipose fat composition in Jersey and Limousin back-cross cattle finished on pasture or feedlot. Anim Genet 2011; 41:589-96. [PMID: 20477785 DOI: 10.1111/j.1365-2052.2010.02058.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A QTL study of live animal and carcass traits in beef cattle was carried out in New Zealand and Australia. Back-cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. This paper reports on weights of eight organs (heart, liver, lungs, kidneys, spleen, gastro-intestinal tract, fat, and rumen contents) and 12 fat composition traits (fatty acid (FA) percentages, saturated and monounsaturated FA subtotals, and fat melting point). The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. For organ weights and fat composition traits, 10 and 12 significant QTL locations (P<0.05), respectively, were detected on a genome-wide basis, in combined-sire or within-sire analyses. Seven QTL significant for organ weights were found at the proximal end of chromosome 2. This chromosome carries a variant myostatin allele (F94L), segregating from the Limousin ancestry, and this is a positional candidate for the QTL. Ten significant QTL for fat composition were found on chromosomes 19 and 26. Fatty acid synthase and stearoyl-CoA desaturase (SCD1), respectively, are positional candidate genes for these QTL. Two FA QTL found to be common to sire groups in both populations were for percentages of C14:0 and C14:1 (relative to all FAs) on chromosome 26, near the SCD1 candidate gene.
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Affiliation(s)
- C A Morris
- AgResearch, Ruakura Research Centre, Hamilton 3240, New Zealand.
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Esmailizadeh AK, Morris CA, Cullen NG, Kruk ZA, Lines DS, Hickey SM, Dobbie PM, Bottema CDK, Pitchford WS. Genetic mapping of quantitative trait loci for meat quality and muscle metabolic traits in cattle. Anim Genet 2011; 42:592-9. [PMID: 22035000 DOI: 10.1111/j.1365-2052.2011.02197.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A whole-genome scan was carried out in New Zealand and Australia to detect quantitative trait loci (QTL) for live animal and carcass composition traits and meat quality attributes in cattle. Backcross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. This paper reports on meat quality traits (tenderness measured as shear force at 4-5 ages on two muscles as well as associated traits of meat colour, pH and cooking loss) and a number of metabolic traits. For meat quality traits, 18 significant QTL (P < 0.05), located in nine linkage groups, were detected on a genome-wise basis, in combined-sire (seven QTL) or within-sire analyses (11 QTL). For metabolic traits, 11 significant QTL (P < 0.05), located in eight linkage groups, were detected on a genome-wise basis, in combined-sire (five QTL) or within-sire analyses (six QTL). BTA2 and BTA3 had QTL for both metabolic traits and meat quality traits. Six significant QTL for meat quality and metabolic traits were found at the proximal end of chromosome 2. BTA2 and BTA29 were the most common chromosomes harbouring QTL for meat quality traits; QTL for improved tenderness were associated with Limousin-derived and Jersey-derived alleles on these two chromosomes, respectively.
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Affiliation(s)
- A K Esmailizadeh
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy Campus, Roseworthy, SA 5371, Australia.
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Rogberg-Muñoz A, Melucci L, Prando A, Villegas-Castagnasso E, Ripoli M, Peral-García P, Baldo A, Añon M, Giovambattista G. Association of bovine chromosome 5 markers with birth and weaning weight in Hereford cattle raised under extensive conditions. Livest Sci 2011. [DOI: 10.1016/j.livsci.2010.06.160] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Weikard R, Altmaier E, Suhre K, Weinberger KM, Hammon HM, Albrecht E, Setoguchi K, Takasuga A, Kühn C. Metabolomic profiles indicate distinct physiological pathways affected by two loci with major divergent effect on Bos taurus growth and lipid deposition. Physiol Genomics 2010; 42A:79-88. [DOI: 10.1152/physiolgenomics.00120.2010] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Identifying trait-associated genetic variation offers new prospects to reveal novel physiological pathways modulating complex traits. Taking advantage of a unique animal model, we identified the I442M mutation in the non-SMC condensin I complex, subunit G ( NCAPG) gene and the Q204X mutation in the growth differentiation factor 8 ( GDF8) gene as substantial modulators of pre- and/or postnatal growth in cattle. In a combined metabolomic and genotype association approach, which is the first respective study in livestock, we surveyed the specific physiological background of the effects of both loci on body-mass gain and lipid deposition. Our data provided confirming evidence from two historically and geographically distant cattle populations that the onset of puberty is the key interval of divergent growth. The locus-specific metabolic patterns obtained from monitoring 201 plasma metabolites at puberty mirror the particular NCAPG I442M and GDF8 Q204X effects and represent biosignatures of divergent physiological pathways potentially modulating effects on proportional and disproportional growth, respectively. While the NCAPG I442M mutation affected the arginine metabolism, the 204X allele in the GDF8 gene predominantly raised the carnitine level and had concordant effects on glycerophosphatidylcholines and sphingomyelins. Our study provides a conclusive link between the well-described growth-regulating functions of arginine metabolism and the previously unknown specific physiological role of the NCAPG protein in mammalian metabolism. Owing to the confirmed effect of the NCAPG/LCORL locus on human height in genome-wide association studies, the results obtained for bovine NCAPG might add valuable, comparative information on the physiological background of genetically determined divergent mammalian growth.
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Affiliation(s)
- Rosemarie Weikard
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf
| | - Elisabeth Altmaier
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Karsten Suhre
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Klaus M. Weinberger
- Biocrates Life Sciences Aktiengesellschaft, Innsbruck, Austria; Research Units
| | | | - Elke Albrecht
- Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Kouji Setoguchi
- Cattle Breeding Development Institute of Kagoshima Prefecture, Osumi, So, Kagoshima; and
| | - Akiko Takasuga
- Shirikawa Institute of Animal Genetics, Japan Livestock Technology Association, Odakura, Nishigo, Fukushima, Japan
| | - Christa Kühn
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf
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Cavanagh CR, Jonas E, Hobbs M, Thomson PC, Tammen I, Raadsma HW. Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL. Genet Sel Evol 2010; 42:36. [PMID: 20846385 PMCID: PMC2949606 DOI: 10.1186/1297-9686-42-36] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 09/16/2010] [Indexed: 11/10/2022] Open
Abstract
An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.
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Affiliation(s)
- Colin R Cavanagh
- ReproGen - Animal Bioscience Group, Faculty of Veterinary Science, University of Sydney, 425 Werombi Road, Camden NSW 2570, Australia
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Rogberg-Muñoz A, Prando A, Melucci L, Villegas-Castagnaso E, Ripoli M, Peral-García P, Baldo A, Añon M, Givambattista G. Possible association of bovine chromosome 5 markers with growth and fat traits in Hereford cattle raised under extensive conditions. Livest Sci 2010. [DOI: 10.1016/j.livsci.2010.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Tian R, Pitchford WS, Morris CA, Cullen NG, Bottema CDK. Genetic variation in the beta, beta-carotene-9', 10'-dioxygenase gene and association with fat colour in bovine adipose tissue and milk. Anim Genet 2009; 41:253-9. [PMID: 19968649 DOI: 10.1111/j.1365-2052.2009.01990.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
beta, beta-carotene-9', 10'-dioxygenase (BCO2) plays a role in cleaving beta-carotene eccentrically, and may be involved in the control of adipose and milk colour in cattle. The bovine BCO2 gene was sequenced as a potential candidate gene for a beef fat colour QTL on chromosome (BTA) 15. A single nucleotide base change located in exon 3 causes the substitution of a stop codon (encoded by the A allele) for tryptophan(80) (encoded by the G allele) (c. 240G>A, p.Trp80stop, referred to herein as SNP W80X). Association analysis showed significant differences in subcutaneous fat colour and beta-carotene concentration amongst cattle with different BCO2 genotypes. Animals with the BCO2 AA genotype had more yellow beef fat and a higher beta-carotene concentration in adipose tissues than those with the GA or GG genotype. QTL mapping analysis with the BCO2 SNP W80X fitted as a fixed effect confirmed that this SNP is likely to represent the quantitative trait nucleotide (QTN) for the fat colour-related traits on BTA 15. Moreover, animals with the AA genotype had yellower milk colour and a higher concentration of beta-carotene in the milk.
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Affiliation(s)
- R Tian
- School of Agriculture, Food and Wine, University of Adelaide, Roseworthy SA 5371 Australia
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