1
|
|
2
|
Abstract
There are genetic conditions that influence production in dairy and beef cattle. The objective of this review was to describe relevant genetic conditions that have been associated with productivity and health in cattle. Genes or genomic regions that have been identified as a candidate for the condition will be included, and the genetic basis of the condition will be defined. Genes and genetic conditions included in this review are bovine leukocyte adhesion deficiency, deficiency of the uridine monophosphate synthase, bovine chronic interstitial nephritis, horn development, myostatin, complex vertebral malformation, leptin, osteopetrosis, apoptosis peptide activating factor 1, chondrodysplastic dwarfism, caseins, calpastatin, umbilical hernia, lactoglobulin, citrullinemia, cholesterol deficiency, prions, thyroglobulin, diacylglycerol acyltransferase, syndactyly, maple syrup urine disease, slick hair, Factor XI deficiency, and μ-Calpain. This review is not meant to be comprehensive, and relevant information is provided to ascertain genetic markers associated with the conditions.
Collapse
Affiliation(s)
- Eduardo Casas
- National Animal Disease Center, USDA, ARS , Ames, IA , USA
| | | |
Collapse
|
3
|
Liang C, Wang L, Wu X, Wang K, Ding X, Wang M, Chu M, Xie X, Qiu Q, Yan P. Genome-wide Association Study Identifies Loci for the Polled Phenotype in Yak. PLoS One 2016; 11:e0158642. [PMID: 27389700 PMCID: PMC4936749 DOI: 10.1371/journal.pone.0158642] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/20/2016] [Indexed: 12/17/2022] Open
Abstract
The absence of horns, known as the polled phenotype, is an economically important trait in modern yak husbandry, but the genomic structure and genetic basis of this phenotype have yet to be discovered. Here, we conducted a genome-wide association study with a panel of 10 horned and 10 polled yaks using whole genome sequencing. We mapped the POLLED locus to a 200-kb interval, which comprises three protein-coding genes. Further characterization of the candidate region showed recent artificial selection signals resulting from the breeding process. We suggest that expressional variations rather than structural variations in protein probably contribute to the polled phenotype. Our results not only represent the first and important step in establishing the genomic structure of the polled region in yak, but also add to our understanding of the polled trait in bovid species.
Collapse
Affiliation(s)
- Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Lizhong Wang
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Kun Wang
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, China
| | - Xuezhi Ding
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, China
| | - Mingcheng Wang
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Xiuyue Xie
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, China
| | - Qiang Qiu
- State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, China
- * E-mail: (QQ); (PY)
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Science, Lanzhou, China
- * E-mail: (QQ); (PY)
| |
Collapse
|
4
|
Yang BC, Lee SH, Hwang S, Lee HC, Im GS, Kim DH, Lee DK, Lee KT, Jeon IS, Oh SJ, Park SB. Phenotypic characterization of Hanwoo (native Korean cattle) cloned from somatic cells of a single adult. BMB Rep 2012; 45:38-43. [PMID: 22281011 DOI: 10.5483/bmbrep.2012.45.1.38] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated phenotypic differences in Hanwoo cattle cloned from somatic cells of a single adult. Ten genetically identical Hanwoo were generated by somatic cell nuclear transfer from a single adult. Weights at birth, growing pattern, horn and noseprint patterns were characterized to investigate phenotypic differences. The weights of clones at 6 and 12 months were slightly heavier than that of the donor. A horn pattern analysis revealed that seven clones had exactly the same horn pattern as the donor cow, whereas three were different. Although similarities such as general appearance can often be used to identify individual cloned animals, no study has characterized noseprint patterns for this end. A noseprint pattern analysis of all surviving clones showed that all eight animals had distinct noseprints. Four were similar to the donor, and the remaining four had more secondary-like characteristics.
Collapse
Affiliation(s)
- Byoung-Chul Yang
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Suwon, Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Flori L, Gonzatti MI, Thevenon S, Chantal I, Pinto J, Berthier D, Aso PM, Gautier M. A quasi-exclusive European ancestry in the Senepol tropical cattle breed highlights the importance of the slick locus in tropical adaptation. PLoS One 2012; 7:e36133. [PMID: 22675421 PMCID: PMC3366548 DOI: 10.1371/journal.pone.0036133] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Accepted: 03/26/2012] [Indexed: 01/12/2023] Open
Abstract
Background The Senepol cattle breed (SEN) was created in the early XXth century from a presumed cross between a European (EUT) breed (Red Poll) and a West African taurine (AFT) breed (N’Dama). Well adapted to tropical conditions, it is also believed trypanotolerant according to its putative AFT ancestry. However, such origins needed to be verified to define relevant husbandry practices and the genetic background underlying such adaptation needed to be characterized. Methodology/Principal Findings We genotyped 153 SEN individuals on 47,365 SNPs and combined the resulting data with those available on 18 other populations representative of EUT, AFT and Zebu (ZEB) cattle. We found on average 89% EUT, 10.4% ZEB and 0.6% AFT ancestries in the SEN genome. We further looked for footprints of recent selection using standard tests based on the extent of haplotype homozygosity. We underlined i) three footprints on chromosome (BTA) 01, two of which are within or close to the polled locus underlying the absence of horns and ii) one footprint on BTA20 within the slick hair coat locus, involved in thermotolerance. Annotation of these regions allowed us to propose three candidate genes to explain the observed signals (TIAM1, GRIK1 and RAI14). Conclusions/Significance Our results do not support the accepted concept about the AFT origin of SEN breed. Initial AFT ancestry (if any) might have been counter-selected in early generations due to breeding objectives oriented in particular toward meat production and hornless phenotype. Therefore, SEN animals are likely susceptible to African trypanosomes which questions the importation of SEN within the West African tsetse belt, as promoted by some breeding societies. Besides, our results revealed that SEN breed is predominantly a EUT breed well adapted to tropical conditions and confirmed the importance in thermotolerance of the slick locus.
Collapse
|
6
|
Mariasegaram M, Harrison BE, Bolton JA, Tier B, Henshall JM, Barendse W, Prayaga KC. Fine-mapping thePOLLlocus in Brahman cattle yields the diagnostic markerCSAFG29. Anim Genet 2012; 43:683-8. [DOI: 10.1111/j.1365-2052.2012.02336.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2011] [Indexed: 11/30/2022]
Affiliation(s)
- Maxy Mariasegaram
- Cooperative Research Centre for Beef Genetic Technologies; CSIRO Livestock Industries; Queensland Bioscience Precinct; St. Lucia; QLD; 4067; Australia
| | - Blair E. Harrison
- Cooperative Research Centre for Beef Genetic Technologies; CSIRO Livestock Industries; Queensland Bioscience Precinct; St. Lucia; QLD; 4067; Australia
| | - Jennifer A. Bolton
- Cooperative Research Centre for Beef Genetic Technologies; CSIRO Livestock Industries; Queensland Bioscience Precinct; St. Lucia; QLD; 4067; Australia
| | - Bruce Tier
- Animal Genetics and Breeding Unit; University of New England; Armidale; NSW; 2351; Australia
| | - John M. Henshall
- CSIRO Livestock Industries; FD McMaster Laboratory; Armidale; NSW; 2350; Australia
| | - William Barendse
- Cooperative Research Centre for Beef Genetic Technologies; CSIRO Livestock Industries; Queensland Bioscience Precinct; St. Lucia; QLD; 4067; Australia
| | - Kishore C. Prayaga
- Cooperative Research Centre for Beef Genetic Technologies; CSIRO Livestock Industries; Queensland Bioscience Precinct; St. Lucia; QLD; 4067; Australia
| |
Collapse
|
7
|
Johnston SE, McEwan JC, Pickering NK, Kijas JW, Beraldi D, Pilkington JG, Pemberton JM, Slate J. Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population. Mol Ecol 2011; 20:2555-66. [PMID: 21651634 DOI: 10.1111/j.1365-294x.2011.05076.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Understanding the genetic architecture of phenotypic variation in natural populations is a fundamental goal of evolutionary genetics. Wild Soay sheep (Ovis aries) have an inherited polymorphism for horn morphology in both sexes, controlled by a single autosomal locus, Horns. The majority of males have large normal horns, but a small number have vestigial, deformed horns, known as scurs; females have either normal horns, scurs or no horns (polled). Given that scurred males and polled females have reduced fitness within each sex, it is counterintuitive that the polymorphism persists within the population. Therefore, identifying the genetic basis of horn type will provide a vital foundation for understanding why the different morphs are maintained in the face of natural selection. We conducted a genome-wide association study using ∼36000 single nucleotide polymorphisms (SNPs) and determined the main candidate for Horns as RXFP2, an autosomal gene with a known involvement in determining primary sex characters in humans and mice. Evidence from additional SNPs in and around RXFP2 supports a new model of horn-type inheritance in Soay sheep, and for the first time, sheep with the same horn phenotype but different underlying genotypes can be identified. In addition, RXFP2 was shown to be an additive quantitative trait locus (QTL) for horn size in normal-horned males, accounting for up to 76% of additive genetic variation in this trait. This finding contrasts markedly from genome-wide association studies of quantitative traits in humans and some model species, where it is often observed that mapped loci only explain a modest proportion of the overall genetic variation.
Collapse
Affiliation(s)
- Susan E Johnston
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
| | | | | | | | | | | | | | | |
Collapse
|
8
|
Mariasegaram M, Reverter A, Barris W, Lehnert SA, Dalrymple B, Prayaga K. Transcription profiling provides insights into gene pathways involved in horn and scurs development in cattle. BMC Genomics 2010; 11:370. [PMID: 20537189 PMCID: PMC3017764 DOI: 10.1186/1471-2164-11-370] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 06/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Two types of horns are evident in cattle - fixed horns attached to the skull and a variation called scurs, which refers to small loosely attached horns. Cattle lacking horns are referred to as polled. Although both the Poll and Scurs loci have been mapped to BTA1 and 19 respectively, the underlying genetic basis of these phenotypes is unknown, and so far, no candidate genes regulating these developmental processes have been described. This study is the first reported attempt at transcript profiling to identify genes and pathways contributing to horn and scurs development in Brahman cattle, relative to polled counterparts. RESULTS Expression patterns in polled, horned and scurs tissues were obtained using the Agilent 44 k bovine array. The most notable feature when comparing transcriptional profiles of developing horn tissues against polled was the down regulation of genes coding for elements of the cadherin junction as well as those involved in epidermal development. We hypothesize this as a key event involved in keratinocyte migration and subsequent horn development. In the polled-scurs comparison, the most prevalent differentially expressed transcripts code for genes involved in extracellular matrix remodelling, which were up regulated in scurs tissues relative to polled. CONCLUSION For this first time we describe networks of genes involved in horn and scurs development. Interestingly, we did not observe differential expression in any of the genes present on the fine mapped region of BTA1 known to contain the Poll locus.
Collapse
Affiliation(s)
- Maxy Mariasegaram
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia 4067, Queensland, Australia
| | - Antonio Reverter
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia 4067, Queensland, Australia
| | - Wes Barris
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia 4067, Queensland, Australia
| | - Sigrid A Lehnert
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia 4067, Queensland, Australia
| | - Brian Dalrymple
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia 4067, Queensland, Australia
| | - Kishore Prayaga
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia 4067, Queensland, Australia
- Cooperative Research Centre for Beef Genetic Technologies, Armidale, NSW, 2351 Australia
| |
Collapse
|
9
|
Ratnakumar A, Barris W, McWilliam S, Brauning R, McEwan JC, Snelling WM, Dalrymple BP. A multiway analysis for identifying high integrity bovine BACs. BMC Genomics 2009; 10:46. [PMID: 19166603 PMCID: PMC2660975 DOI: 10.1186/1471-2164-10-46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 01/23/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In large genomics projects involving many different types of analyses of bacterial artificial chromosomes (BACs), such as fingerprinting, end sequencing (BES) and full BAC sequencing there are many opportunities for the identities of BACs to become confused. However, by comparing the results from the different analyses, inconsistencies can be identified and a set of high integrity BACs preferred for future research can be defined. RESULTS The location of each bovine BAC in the BAC fingerprint-based genome map and in the genome assembly were compared based on the reported BESs, and for a smaller number of BACs the full sequence. BACs with consistent positions in all three datasets, or if the full sequence was not available, for both the fingerprint map and BES-based alignments, were deemed to be correctly positioned. BACs with consistent BES-based and fingerprint-based locations, but with conflicting locations based on the fully sequenced BAC, appeared to have been misidentified during sequencing, and included a number of apparently swapped BACs. Inconsistencies between BES-based and fingerprint map positions identified thirty one plates from the CHORI-240 library that appear to have suffered substantial systematic problems during the end-sequencing of the BACs. No systematic problems were identified in the fingerprinting of the BACs. Analysis of BACs overlapping in the assembly identified a small overrepresentation of clones with substantial overlap in the library and a substantial enrichment of highly overlapping BACs on the same plate in the CHORI-240 library. More than half of these BACs appear to have been present as duplicates on the original BAC-library plates and thus should be avoided in subsequent projects. CONCLUSION Our analysis shows that approximately 95% of the bovine CHORI-240 library clones with both a BAC fingerprint and two BESs mapping to the genome in the expected orientations (approximately 27% of all BACs) have consistent locations in the BAC fingerprint map and the genome assembly. We have developed a broadly applicable methodology for checking the integrity of BAC-based datasets even where only incomplete and partially assembled genomic sequence is available.
Collapse
Affiliation(s)
- Abhirami Ratnakumar
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, QLD 4067, Australia.
| | | | | | | | | | | | | |
Collapse
|
10
|
Cargill EJ, Nissing NJ, Grosz MD. Single nucleotide polymorphisms concordant with the horned/polled trait in Holsteins. BMC Res Notes 2008; 1:128. [PMID: 19063733 PMCID: PMC2615027 DOI: 10.1186/1756-0500-1-128] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Accepted: 12/08/2008] [Indexed: 11/10/2022] Open
Abstract
Background Cattle that naturally do not grow horns are referred to as polled, a trait inherited in a dominant Mendelian fashion. Previous studies have localized the polled mutation (which is unknown) to the proximal end of bovine chromosome 1 in a region approximately 3 Mb in size. While a polled genetic test, Tru-Polled™, is commercially available from MetaMorphix Inc., Holsteins are not a validated breed for this test. Findings Approximately 160 kb were sequenced within the known polled region from 12 polled and 12 horned Holsteins. Analysis of the polymorphisms identified 13 novel single nucleotide polymorphisms (SNPs) that are concordant with the horned/polled trait. Three of the 13 SNPs are located in gene coding or regulatory regions (e.g., the untranslated region, or UTR) where one is located in the 3'UTR of a gene and the other two are located in the 5'UTR and coding region (synonymous SNP) of another gene. The 3'UTR of genes have been shown to be targets of microRNAs regulating gene expression. In silico analysis indicates the 3'UTR SNP may disrupt a microRNA target site. Conclusion These 13 novel SNPs concordant with the horned/polled trait in Holsteins represent a test panel for the breed and this is the first report to the authors' knowledge of SNPs within gene coding or regulatory regions concordant with the horned/polled trait in cattle. These SNPs will require further testing for verification and further study to determine if the 3'UTR SNP may have a functional effect on the polled trait in Holsteins.
Collapse
Affiliation(s)
- Edward J Cargill
- Monsanto Company, 800 N, Lindbergh Blvd, St Louis, MO 63167, USA.
| | | | | |
Collapse
|
11
|
Croxford AE, Rogers T, Caligari PDS, Wilkinson MJ. High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar. New Phytol 2008; 180:594-607. [PMID: 18684160 DOI: 10.1111/j.1469-8137.2008.02588.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
* The provision of sequence-tagged site (STS) anchor points allows meaningful comparisons between mapping studies but can be a time-consuming process for nonmodel species or orphan crops. * Here, the first use of high-resolution melt analysis (HRM) to generate STS markers for use in linkage mapping is described. This strategy is rapid and low-cost, and circumvents the need for labelled primers or amplicon fractionation. * Using white lupin (Lupinus albus, x = 25) as a case study, HRM analysis was applied to identify 91 polymorphic markers from expressed sequence tag (EST)-derived and genomic libraries. Of these, 77 generated STS anchor points in the first fully resolved linkage map of the species. The map also included 230 amplified fragment length polymorphisms (AFLP) loci, spanned 1916 cM (84.2% coverage) and divided into the expected 25 linkage groups. * Quantitative trait loci (QTL) analyses performed on the population revealed genomic regions associated with several traits, including the agronomically important time to flowering (tf), alkaloid synthesis and stem height (Ph). Use of HRM-STS markers also allowed us to make direct comparisons between our map and that of the related crop, Lupinus angustifolius, based on the conversion of RFLP, microsatellite and single nucleotide polymorphism (SNP) markers into HRM markers.
Collapse
Affiliation(s)
- Adam E Croxford
- Institute of Biological, Environmental and Rural Sciences, Edward Llwyd Building, Aberystwyth University, SY23 3DA, UK
| | - Tom Rogers
- KG Fruits Ltd, Tatlingbury Oast, Five Oak Green, Tonbridge, Kent TN12 6RG, UK
| | - Peter D S Caligari
- Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, 2 Norte 685 Talca, Chile
| | - Michael J Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Edward Llwyd Building, Aberystwyth University, SY23 3DA, UK
| |
Collapse
|
12
|
Miziara MN, Goldammer T, Stafuzza NB, Ianella P, Agarwala R, Schaffer AA, Elliott JS, Riggs PK, Womack JE, Amaral MEJ. A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome 1 (BBU1). Cytogenet Genome Res 2007; 119:100-4. [PMID: 18160788 DOI: 10.1159/000109625] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Accepted: 04/27/2007] [Indexed: 11/19/2022] Open
Abstract
The largest chromosome in the river buffalo karyotype, BBU1, is a submetacentric chromosome with reported homology between BBU1q and bovine chromosome 1 and between BBU1p and BTA27. We present the first radiation hybrid map of this chromosome containing 69 cattle derived markers including 48 coding genes, 17 microsatellites and four ESTs distributed in two linkage groups spanning a total length of 1330.1 cR(5000). The RH map was constructed based on analysis of a recently developed river buffalo-hamster whole genome radiation hybrid (BBURH(5000)) panel. The retention frequency of individual markers across the panel ranged from 17.8 to 52.2%. With few exceptions, the order of markers within linkage groups is identical to the order established for corresponding cattle RH maps. The BBU1 map provides a starting point for comparison of gene order rearrangements between river buffalo chromosome 1 and its bovine homologs.
Collapse
Affiliation(s)
- M N Miziara
- Departamento Biologia, UNESP - São Paulo State University, IBILCE, São Jose Rio Preto, Brazil
| | | | | | | | | | | | | | | | | | | |
Collapse
|