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Wang T, Shi X, Liu Z, Ren W, Wang X, Huang B, Kou X, Liang H, Wang C, Chai W. A Novel A > G Polymorphism in the Intron 1 of LCORL Gene Is Significantly Associated with Hide Weight and Body Size in Dezhou Donkey. Animals (Basel) 2022; 12:ani12192581. [PMID: 36230323 PMCID: PMC9559650 DOI: 10.3390/ani12192581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/12/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022] Open
Abstract
Several studies have shown the association between the ligand-dependent nuclear receptor compression-like protein (LCORL) gene and body size in horses, pigs and donkeys. Based on previous studies, the LCORL gene was hypothesized to be associated with growth traits and hide weight in Dezhou donkeys. In this study, we aimed to reveal the variation of the LCORL gene in the Dezhou donkey and explore whether the gene is associated with hide weight and body size. In this study, genetic polymorphisms in the LCORL gene of the Dezhou donkey were studied using targeted sequencing technology, and single nucleotide polymorphisms (SNPs) of the LCORL gene were analyzed for association with hide weight and body size in Dezhou donkeys. The results showed that there was an SNP locus situated in intron 1 of the LCORL gene. Association analysis revealed that individuals with the GG genotype had significantly higher body height, body length, chest circumference and hide weight than those with the AA genotype (p < 0.05). Therefore, the g.112558859 A > G locus can be used as a potential candidate marker affecting body size and hide weight. This study provides the foundation for breeding high-quality donkeys with high hide yield.
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Guo S, Wu X, Pei J, Wang X, Bao P, Xiong L, Chu M, Liang C, Yan P, Guo X. Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Rafter P, Gormley IC, Purfield D, Parnell AC, Naderi S, Berry DP. Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle. BMC Genomics 2021; 22:757. [PMID: 34688258 PMCID: PMC8542340 DOI: 10.1186/s12864-021-08075-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/07/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understanding of the genetic variants that contribute to carcass merit is useful to maximize the efficiency of breeding for improved carcass merit. The objectives of the present study were two-fold: firstly, to perform genome-wide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). The LRR value of a SNP is a measure of the signal intensity of the SNP generated during the genotyping process. RESULTS A total of 13,969, 3,954, and 2,805 detected CNVs were tested for association with the three carcass traits for the Holstein-Friesian, Charolais, and Limousin, respectively. The copy number of 16 CNVs and the LRR of 34 SNPs were associated with at least one of the three carcass traits in at least one of the three cattle breeds. With the exception of three SNPs, none of the quantitative trait loci detected in the CNV association analyses or the SNP LRR association analyses were also detected using traditional association analyses based on SNP allele counts. Many of the CNVs and SNPs associated with the carcass traits were located near genes related to the structure and function of the spliceosome and the ribosome; in particular, U6 which encodes a spliceosomal subunit and 5S rRNA which encodes a ribosomal subunit. CONCLUSIONS The present study demonstrates that CNV data and SNP LRR data can be used to detect genomic regions associated with carcass traits in cattle providing information on quantitative trait loci over and above those detected using just SNP allele counts, as is the approach typically employed in genome-wide association analyses.
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Affiliation(s)
- Pierce Rafter
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Cork, Fermoy, Ireland
- School of Mathematics and Statistics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Isobel Claire Gormley
- School of Mathematics and Statistics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Deirdre Purfield
- Department of Biological Sciences, Munster Technological University Institute, Cork, Bishopstown, Ireland
| | - Andrew C Parnell
- Hamilton Institute, Insight Centre for Data Analytics, Maynooth University, Kildare, Ireland
| | - Saeid Naderi
- Irish Cattle Breeding Federation, Cork, Bandon, Ireland
| | - Donagh P Berry
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Cork, Fermoy, Ireland.
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Martinez-Castillero M, Then C, Altarriba J, Srihi H, López-Carbonell D, Díaz C, Martinez P, Hermida M, Varona L. Detection of Genomic Regions with Pleiotropic Effects for Growth and Carcass Quality Traits in the Rubia Gallega Cattle Breed. Animals (Basel) 2021; 11:ani11061682. [PMID: 34200089 PMCID: PMC8227173 DOI: 10.3390/ani11061682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/25/2021] [Accepted: 06/02/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. We have developed a ssGWAS by backsolving the SNP effects after implementing a ssGBLUP. The results showed an apparent heterogeneity of the additive genetic variance across the genome. Some of the genomic regions explaining the most of this additive variance were shared across traits, indicating the presence of pleiotropic effects, which were reflected in their genetic correlations. Abstract The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. In recent years, genomic evaluation has been implemented by using a ssGBLUP (single-step Genomic Best Linear Unbiased Prediction). This procedure can reparameterized to perform ssGWAS (single-step Genome Wide Association Studies) by backsolving the SNP (single nucleotide polymorphisms) effects. Therefore, the objective of this study was to identify genomic regions associated with the genetic variability in growth and carcass quality traits. We implemented a ssGBLUP by using a database that included records for Birth Weight (BW-327,350 records-), Weaning Weight (WW-83,818-), Cold Carcass Weight (CCW-91,621-), Fatness (FAT-91,475-) and Conformation (CON-91,609-). The pedigree included 464,373 individuals, 2449 of which were genotyped. After a process of filtering, we ended up using 43,211 SNP markers. We used the GBLUP and SNPBLUP model equivalences to obtain the effects of the SNPs and then calculated the percentage of variance explained by the regions of the genome between 1 Mb. We identified 7 regions of the genome for CCW; 8 regions for BW, WW, FAT and 9 regions for CON, which explained the percentage of variance above 0.5%. Furthermore, a number of the genome regions had pleiotropic effects, located at: BTA1 (131–132 Mb), BTA2 (1–11 Mb), BTA3 (32–33 Mb), BTA6 (36–38 Mb), BTA16 (24–26 Mb), and BTA 21 (56–57 Mb). These regions contain, amongst others, the following candidate genes: NCK1, MSTN, KCNA3, LCORL, NCAPG, and RIN3.
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Affiliation(s)
- Maria Martinez-Castillero
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
- Correspondence:
| | - Carlos Then
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
| | - Juan Altarriba
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
| | - Houssemeddine Srihi
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
| | - David López-Carbonell
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
| | - Clara Díaz
- Instituto Nacional de Investigación y Tecnología Agraria (INIA), 28040 Madrid, Spain;
| | - Paulino Martinez
- Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002 Lugo, Spain; (P.M.); (M.H.)
| | - Miguel Hermida
- Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002 Lugo, Spain; (P.M.); (M.H.)
| | - Luis Varona
- Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain; (C.T.); (J.A.); (H.S.); (D.L.-C.); (L.V.)
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de Sousa MAP, de Athayde FRF, Maldonado MBC, de Lima AO, Fortes MRS, Lopes FL. Single nucleotide polymorphisms affect miRNA target prediction in bovine. PLoS One 2021; 16:e0249406. [PMID: 33882076 PMCID: PMC8059806 DOI: 10.1371/journal.pone.0249406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/17/2021] [Indexed: 02/06/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) can have significant effects on phenotypic characteristics in cattle. MicroRNAs (miRNAs) are small, non-coding RNAs that act as post-transcriptional regulators by binding them to target mRNAs. In the present study, we scanned ~56 million SNPs against 1,064 bovine miRNA sequences and analyzed, in silico, their possible effects on target binding prediction, primary miRNA formation, association with QTL regions and the evolutionary conservation for each SNP locus. Following target prediction, we show that 71.6% of miRNA predicted targets were altered as a consequence of SNPs located within the seed region of the mature miRNAs. Next, we identified variations in the Minimum Free Energy (MFE), which represents the capacity to alter molecule stability and, consequently, miRNA maturation. A total of 48.6% of the sequences analyzed showed values within those previously reported as sufficient to alter miRNA maturation. We have also found 131 SNPs in 46 miRNAs, with altered target prediction, occurring in QTL regions. Lastly, analysis of evolutionary conservation scores for each SNP locus suggested that they have a conserved biological function through the evolutionary process. Our results suggest that SNPs in microRNAs have the potential to affect bovine phenotypes and could be of great value for genetic improvement studies, as well as production.
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Affiliation(s)
- Marco Antônio Perpétuo de Sousa
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Flavia Regina Florêncio de Athayde
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | | | - Andressa Oliveira de Lima
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Marina Rufino S. Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Flavia Lombardi Lopes
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
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Salek Ardestani S, Aminafshar M, Zandi Baghche Maryam MB, Banabazi MH, Sargolzaei M, Miar Y. Signatures of selection analysis using whole-genome sequence data reveals novel candidate genes for pony and light horse types. Genome 2020; 63:387-396. [PMID: 32407640 DOI: 10.1139/gen-2020-0001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural selection and domestication have shaped modern horse populations, resulting in a vast range of phenotypically diverse breeds. Horse breeds are classified into three types (pony, light, and draft) generally based on their body type. Understanding the genetic basis of horse type variation and selective pressures related to the evolutionary trend can be particularly important for current selection strategies. Whole-genome sequences were generated for 14 pony and 32 light horses to investigate the genetic signatures of selection of the horse type in pony and light horses. In the overlapping extremes of the fixation index and nucleotide diversity results, we found novel genomic signatures of selective sweeps near key genes previously implicated in body measurements including C4ORF33, CRB1, CPN1, FAM13A, and FGF12 that may influence variation in pony and light horse types. This study contributes to a better understanding of the genetic background of differences between pony and light horse types.
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Affiliation(s)
- Siavash Salek Ardestani
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | - Mehdi Aminafshar
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | | | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of Iran, Agricultural Research, Education & Extension Organization, Karaj 3146618361, Iran
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON NIG 2W1, Canada.,Select Sires Inc., Plain City, OH 43064, USA
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
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Doyle JL, Berry DP, Veerkamp RF, Carthy TR, Walsh SW, Evans RD, Purfield DC. Genomic Regions Associated With Skeletal Type Traits in Beef and Dairy Cattle Are Common to Regions Associated With Carcass Traits, Feed Intake and Calving Difficulty. Front Genet 2020; 11:20. [PMID: 32117439 PMCID: PMC7010604 DOI: 10.3389/fgene.2020.00020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/07/2020] [Indexed: 12/22/2022] Open
Abstract
Linear type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlated with a range of other performance traits in cattle including feed intake, reproduction traits and carcass merit; thus, type traits could also provide useful insights into the morphological differences among animals underpinning phenotypic differences in these complex traits. The objective of the present study was to identify genomic regions associated with five subjectively scored skeletal linear traits, to determine if these associated regions are common in multiple beef and dairy breeds, and also to determine if these regions overlap with those proposed elsewhere to be associated with correlated performance traits. Analyses were carried out using linear mixed models on imputed whole genome sequence data separately in 1,444 Angus, 1,129 Hereford, 6,433 Charolais, 8,745 Limousin, 1,698 Simmental, and 4,494 Holstein-Friesian cattle, all scored for the linear type traits. There was, on average, 18 months difference in age at assessment of the beef versus the dairy animals. While the majority of the identified quantitative trait loci (QTL), and thus genes, were both trait-specific and breed-specific, a large-effect pleiotropic QTL on BTA6 containing the NCAPG and LCORL genes was associated with all skeletal traits in the Limousin population and with wither height in the Angus. Other than that, little overlap existed in detected QTLs for the skeletal type traits in the other breeds. Only two QTLs overlapped the beef and dairy breeds; both QTLs were located on BTA5 and were associated with height in both the Angus and the Holstein-Friesian, despite the difference in age at assessment. Several detected QTLs in the present study overlapped with QTLs documented elsewhere that are associated with carcass traits, feed intake, and calving difficulty. While most breeding programs select for the macro-traits like carcass weight, carcass conformation, and feed intake, the higher degree of granularity with selection on the individual linear type traits in a multi-trait index underpinning the macro-level goal traits, presents an opportunity to help resolve genetic antagonisms among morphological traits in the pursuit of the animal with optimum performance metrics.
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Affiliation(s)
- Jennifer L Doyle
- Animal and Grassland Research and Innovation Centre, Moorepark, Teagasc, Fermoy, Ireland.,Department of Science, Waterford Institute of Technology, Waterford, Ireland
| | - Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Moorepark, Teagasc, Fermoy, Ireland
| | - Roel F Veerkamp
- Animal Breeding and Genomics Centre, Wageningen Livestock Research, Wageningen University & Research, Wageningen, Netherlands
| | - Tara R Carthy
- Animal and Grassland Research and Innovation Centre, Moorepark, Teagasc, Fermoy, Ireland
| | - Siobhan W Walsh
- Department of Science, Waterford Institute of Technology, Waterford, Ireland
| | - Ross D Evans
- Animal Breeding and Genomics Centre, Wageningen Livestock Research, Wageningen University & Research, Wageningen, Netherlands.,Irish Cattle Breeding Federation, Bandon, Ireland
| | - Deirdre C Purfield
- Animal and Grassland Research and Innovation Centre, Moorepark, Teagasc, Fermoy, Ireland
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Smith JL, Wilson ML, Nilson SM, Rowan TN, Oldeschulte DL, Schnabel RD, Decker JE, Seabury CM. Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle. BMC Genomics 2019; 20:926. [PMID: 31801456 PMCID: PMC6892214 DOI: 10.1186/s12864-019-6231-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 10/28/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Genotype-by-environment (GxE) interactions were also investigated. RESULTS GEMMA and EMMAX produced moderate marker-based heritability estimates that were similar for BW (0.36-0.37, SE = 0.02-0.06), WW (0.27-0.29, SE = 0.01), and YW (0.39-0.41, SE = 0.01-0.02). GWAA using 856K imputed SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL for Gelbvieh growth traits on BTA6, BTA7, BTA14, and BTA20. The estimated proportion of phenotypic variance explained (PVE) by the lead SNP defining these QTL (EMMAX) was larger and most similar for BW and YW, and smaller for WW. Collectively, GWAAs (GEMMA; EMMAX) produced a highly concordant set of BW, WW, and YW QTL that met a nominal significance level (P ≤ 1e-05), with prioritization of common positional candidate genes; including genes previously associated with stature, feed efficiency, and growth traits (i.e., PLAG1, NCAPG, LCORL, ARRDC3, STC2). Genotype-by-environment QTL were not consistent among traits at the nominal significance threshold (P ≤ 1e-05); although some shared QTL were apparent at less stringent significance thresholds (i.e., P ≤ 2e-05). CONCLUSIONS Pleiotropic QTL for growth traits were detected on BTA6, BTA7, BTA14, and BTA20 for U.S. Gelbvieh beef cattle. Seven QTL detected for Gelbvieh growth traits were also recently detected for feed efficiency and growth traits in U.S. Angus, SimAngus, and Hereford cattle. Marker-based heritability estimates and the detection of pleiotropic QTL segregating in multiple breeds support the implementation of multiple-breed genomic selection.
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Affiliation(s)
- Johanna L Smith
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA
| | - Miranda L Wilson
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA
| | - Sara M Nilson
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA
| | - Troy N Rowan
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA
- Genetics Area Program, University of Missouri, Columbia, 65211, USA
| | - David L Oldeschulte
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA
- Genetics Area Program, University of Missouri, Columbia, 65211, USA
- Informatics Institute, University of Missouri, Columbia, 65211, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA
- Genetics Area Program, University of Missouri, Columbia, 65211, USA
- Informatics Institute, University of Missouri, Columbia, 65211, USA
| | - Christopher M Seabury
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA.
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Mostafavi A, Fozi MA, Koshkooieh AE, Mohammadabadi M, Babenko OI, Klopenko NI. Effect of LCORL gene polymorphism on body size traits in horse populations. ACTA SCIENTIARUM: ANIMAL SCIENCES 2019. [DOI: 10.4025/actascianimsci.v42i1.47483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The aim of this study was to determine polymorphism of LCORL gene in horse breeds and its association with body size. PCR-RFLP technique was performed using AluI for genotyping of 306 horses. Results showed that C is the rare allele in Iranian Breeds, because these horses have been used since ancient times as a courier and for war and archery, hence selection has done to benefit of spiky horses with medium body that need less food and are tireless. While, for foreign breeds; frequency of C allele was high that can be concluded these breeds used in fields, forests, and mines. A UPGMA dendrogram based on the Nei's standard genetic distance among studied breeds showed separate clusters for Iranian native and exotic breeds. Statistical association analysis of three observed genotypes with body size showed that there is an association between this polymorphism and body size criteria (p < 0.01). Overall, it can be concluded that studied mutation in LCORL gene can be used as candidate marker for improving body weight in horse.
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Iung LHDS, Mulder HA, Neves HHDR, Carvalheiro R. Genomic regions underlying uniformity of yearling weight in Nellore cattle evaluated under different response variables. BMC Genomics 2018; 19:619. [PMID: 30115034 PMCID: PMC6097312 DOI: 10.1186/s12864-018-5003-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/08/2018] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND In livestock, residual variance has been studied because of the interest to improve uniformity of production. Several studies have provided evidence that residual variance is partially under genetic control; however, few investigations have elucidated genes that control it. The aim of this study was to identify genomic regions associated with within-family residual variance of yearling weight (YW; N = 423) in Nellore bulls with high density SNP data, using different response variables. For this, solutions from double hierarchical generalized linear models (DHGLM) were used to provide the response variables, as follows: a DGHLM assuming non-null genetic correlation between mean and residual variance (rmv ≠ 0) to obtain deregressed EBV for mean (dEBVm) and residual variance (dEBVv); and a DHGLM assuming rmv = 0 to obtain two alternative response variables for residual variance, dEBVv_r0 and log-transformed variance of estimated residuals (ln_[Formula: see text]). RESULTS The dEBVm and dEBVv were highly correlated, resulting in common regions associated with mean and residual variance of YW. However, higher effects on variance than the mean showed that these regions had effects on the variance beyond scale effects. More independent association results between mean and residual variance were obtained when null rmv was assumed. While 13 and 4 single nucleotide polymorphisms (SNPs) showed a strong association (Bayes Factor > 20) with dEBVv and ln_[Formula: see text], respectively, only suggestive signals were found for dEBVv_r0. All overlapping 1-Mb windows among top 20 between dEBVm and dEBVv were previously associated with growth traits. The potential candidate genes for uniformity are involved in metabolism, stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation. CONCLUSIONS It is necessary to use a strategy like assuming null rmv to obtain genomic regions associated with uniformity that are not associated with the mean. Genes involved not only in metabolism, but also stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation were the most promising biological candidates for uniformity of YW. Although no clear evidence of using a specific response variable was found, we recommend consider different response variables to study uniformity to increase evidence on candidate regions and biological mechanisms behind it.
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Affiliation(s)
- Laiza Helena de Souza Iung
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Via de Acesso Prof. Paulo Donato Castelane, S/N, Vila Industrial, FCAV/UNESP, Jaboticabal, São Paulo, 14884-900 Brazil
| | - Herman Arend Mulder
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH Wageningen, The Netherlands
| | | | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Via de Acesso Prof. Paulo Donato Castelane, S/N, Vila Industrial, FCAV/UNESP, Jaboticabal, São Paulo, 14884-900 Brazil
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An B, Xia J, Chang T, Wang X, Miao J, Xu L, Zhang L, Gao X, Chen Y, Li J, Gao H. Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle. Physiol Genomics 2018; 50:523-531. [DOI: 10.1152/physiolgenomics.00022.2018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are of economic interest to breeders, but they are intrinsically linked to many valuable traits, such as growth, health, and productivity. Using the Illumina Bovine HD 770K SNP array, we performed a genome-wide association study for heart weight, liver weight, spleen weight, lung weight, and kidney weight in 1,217 Simmental cattle. In our research, 38 significant single nucleotide polymorphisms (SNPs) ( P < 1.49 × 10−6) were identified for five internal organ weight traits. These SNPs are within or near 13 genes, and some of them have been reported previously, including NDUFAF4, LCORL, BT.94996, SLIT2, FAM184B, LAP3, BBS12, MECOM, CD300LF, HSD17B3, TLR4, MXI1, and MB21D2. In addition, we detected four haplotype blocks on BTA6 containing 18 significant SNPs associated with spleen weight. Our results offer worthy insights into understanding the genetic mechanisms of internal organs' development, with potential application in breeding programs of Simmental beef cattle.
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Affiliation(s)
- Bingxing An
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Jiangwei Xia
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Xiaoqiao Wang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Jian Miao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, People’s Republic of China
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Wang X, Miao J, Xia J, Chang T, E G, Bao J, Jin S, Xu L, Zhang L, Zhu B, Gao X, Chen Y, Li J, Gao H. Identifying novel genes for carcass traits by testing G × E interaction through genome-wide meta-analysis in Chinese Simmental beef cattle. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Zhao H, Wu M, Wang S, Yu X, Li Z, Dang R, Sun X. Identification of a novel 24 bp insertion–deletion (indel) of the androgen receptor gene and its association with growth traits in four indigenous cattle breeds. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-71-2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. During the past decades, insertions and deletions (indels) have become
increasingly popular in animal breeding for understanding the relationship
between genotypes and phenotypes. The androgen receptor (AR) plays the
vital role of a bridge on the function of the androgen and has sexual size
dimorphism. For this reason, the objective of this study was to explore the
novel indel variants within the cattle AR gene and to detect their
effects on growth traits in four breeds of Chinese yellow cattle. Herein, we
first confirmed a novel 24 bp indel (AC_000187.1g.4187270-4187293delAATTTATTGGGAGATTATTGAATT) within the intron of
the cattle AR gene. This is consistent with the results predicted
from the NCBI SNP database. The distribution of the indel genotypes of four
Chinese yellow cattle were significantly different from each other
(P < 0.01). After significant correlation analysis, many remarkable
phenotypic differences among the three genotypes were found (P < 0.05).
In conclusion, a novel 24 bp indel within the AR gene
significantly affected growth traits, suggesting that this indel may be a
useful DNA marker for the elimination or selection of excellent individuals for
cattle breeding.
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