A genetic linkage map of the bovine genome

Barendse, W.; Armitage, S. M.; Kossarek, L. M.; Shalom, A.; Kirkpatrick, Brian; Ryan, Anne; Clayton, D; Li, Li; Neibergs, Holly L.; Zhang, N.; Grosse, WM; Weiss, Judith; Creighton, P.; McCarthy, Fiona M.; Maymon, Ron; Teale, A.J.; Fries, R.; McGraw, RA; Moore, S. S.; Georges, Michel; Soller, M.; Womack, James E.; Hetzel, David J.

doi:10.1038/ng0394-227

Cited by 470 publications

(221 citation statements)

References 65 publications

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“…These were : INRA005, INRA023, INRA032, INRA035, INRA037, INRA063, CHIAE54, CSSM66, HEL9, ILST005, ETH10, ETH152, ETH225. Primer identification, PCR conditions and amplification profiles for each microsatellite locus are described elsewhere (Brezinsky et al, 1993;Kaukinen and Varvio, 1993;Steffen et al, 1993;Toldo et al, 1993;Barendse et al, 1994;Vaiman et al, 1994;Amills et al, 1996b). Fluorescent genotyping was performed in an ABI Prism 310 automated DNA sequencing system (Perkin Elmer Biosystems, Foster City, CA 94404, USA).…”

Section: Amills Et Almentioning

confidence: 99%

Low diversity in the major histocompatibility complex class II DRB1 gene of the Spanish ibex, Capra pyrenaica

et al. 2004

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During the last two centuries, the Spanish ibex (Capra pyrenaica) has shown a significant demographic decline as a result of the progressive destruction of its natural habitat, disease epidemics, and uncontrolled hunting. Partial sequencing of the class II MHC DRB1 gene revealed that the Spanish ibex has remarkably low levels of genetic variation at this locus, with only six different DRB1 alleles and an observed heterozygosity of 0.429-0.579. The rates of nonsynonymous vs synonymous substitutions were significantly different in the peptide-binding region (d N /d S ¼ 5.347, P ¼ 0.002), a feature that indicates that the DRB1 gene is under positive selection. A phylogenetic analysis of the Spanish ibex and a set of domestic goat DRB1 alleles revealed that the reported sequences represent four major allelic lineages. The limited allelic repertoire of the DRB1 gene in the Spanish ibex is likely the direct result of the recent history of population bottlenecks and marked demographic decline of this species. A genetic survey of 13 microsatellite loci was consistent with this idea. The Spanish ibex subspecies C. p. hispanica and C. p. victoriae consistently showed considerably lower levels of microsatellite heterozygosity (H o ¼ 0.184-0.231) and allelic diversity (mean number of alleles per locus ¼ 2-2.4) than those reported in other wild ruminants. This study demonstrates the significance of both natural selection and the demographic history of populations in determining patterns of genetic variation at MHC loci. In addition, our results emphasize the importance of locally adapted populations for the preservation of genetic diversity.

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Section: Amills Et Almentioning

confidence: 99%

Low diversity in the major histocompatibility complex class II DRB1 gene of the Spanish ibex, Capra pyrenaica

et al. 2004

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“…A previous attempt to integrate bovine maps combined the linkage maps of Bishop et al (1994) and Barendse et al (1994) by visually aligning the final results (Eggen and Fries 1995). A more accurate method of merging maps combines and reanalyzes genotypic data de novo (Matise et al 1994).…”

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confidence: 99%

A comprehensive map of the porcine genome.

Rohrer¹,

Alexander²,

Hu³

et al. 1996

Genome Res.

448

382

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We report the highest density genetic linkage map for a livestock species produced to date. Three published maps for Sus scrofa were merged by genotyping virtually every publicly available microsatellite across a single reference population to yield 1042 linked loci, 536 of which are novel assignments, spanning 2286.2 cM (average interval 2.23 cM) in 19 linkage groups 08 autosomal and X chromosomes, n = 19). Linkage groups were constructed de novo and mapped by locus content to avoid propagation of errors in older genotypes. The physical and genetic maps were integrated with 123 informative loci assigned previously by fluorescence in situ hybridization {FISH). Fourteen linkage groups span the entire length of each chromosome. Coverage of chromosomes 11, 12, 15, and 18 will be evaluated as more markers are physically assigned. Marker-deficient regions were identified only on Ilql.7-qter and 14 cen-ql.2. Recombination rates [cM/Mbp) varied between and within chromosomes. Short chromosomal arms recombined at higher rates than long arms, and recombination was more frequent in telomeric regions than in pericentric regions. The high-resolution comprehensive map has the marker density needed to identify quantitative trait loci [QTL), implement marker-assisted selection or introgression and YAC contig construction or chromosomal microdissection.

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“…They can also be used to trace the meat through the production chain (Vázquez et al, 2004), to study genetic diversity in cattle (Radko et al, 2005), and to select animals in breeding programs. Currently, more than 1000 microsatellite markers have been evaluated for cattle (e.g., Barendse et al, 1994;Kappes et al, 1997). Although many of these studies were conducted using European cattle (MacHugh et al, 1998), the Sicilian cattle population has not been studied.…”

Section: Introductionmentioning

confidence: 99%

“…In the last two decades, this approach has become the most reliable molecular marker for forensic analysis. Microsatellites are recognized as genetic markers because of their random distribution (Tautz and Renz, 1984), co-dominant mode of inheritance (Barbarà et al, 2007), discriminant power (e.g., Barendse et al, 1994), and overall ability for simultaneous analysis (Cañón et al, 2001). Microsatellite markers represent the gold standard for unequivocal determination of the genetic identity and/or parentage, even with limited sample quantities (Taberlet et al, 1996) or when DNA is degraded.…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, allele frequency studies to evaluate microsatellite informativeness and their efficiency are lacking. In 2006, the International Society for Animal Genetics (ISAG) recommended a panel of nine microsatellite loci for cattle genetic analysis: TGLA227 (Georges and Massey, 1992), BM2113 (Sunden et al, 1993), ETH10 (Toldo et al, 1993), SPS115 (Baylor College of Medicine Human Genome Sequencing Center, 2006), TGLA126 (Georges and Massey, 1992), TGLA122 (Georges and Massey, 1992), INRA023 (Vaiman et al, 1994), ETH225 , and BM1824 (Barendse et al, 1994). In 2008, the ISAG added three additional microsatellite loci: BM1818 (Bishop et al, 1994), ETH3 (Toldo et al, 1993), and TGLA53 (Georges and Massey, 1992).…”

Section: Introductionmentioning

confidence: 99%

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Allele frequencies of microsatellite loci for genetic characterization of a Sicilian bovine population

Cosenza¹,

Reale²,

Lupo³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Short tandem repeats are used as an effective method to trace DNA markers in genotyping. Using a standardized kit, we tested 11 microsatellite markers recommended by the International Society for Animal Genetics (ISAG) in a sample of 495 Sicilian cattle. The aim of this study was to investigate the allele frequencies in the Sicilian cattle population to provide a reference database and at the same time to assess the use of the ISAG microsatellite panel for pedigree analysis. DNA samples were collected from blood and amplified in an 11-plex polymerase chain reaction (PCR); PCR products were injected in a 3130 Genetic Analyzer. All loci showed high mean polymorphism information content (0.768), and the observed mean heterozygosity was less than the expected value (0.732 vs 0.794, respectively). The exact test for Hardy-Weinberg proportions, allele number, and inbreeding coefficient were calculated. Our results indicated that equilibrium was not always maintained. The observed mean homozygote value exceeded the expected value (132.81 vs 102.14), but no evidence for allele dropout was found. These results could be explained by a nonrandom mating; further studies using a larger number of animals could confirm or invalidate this hypothesis. The probability of identity and exclusion of a locus were also estimated and proved to be useful in paternity testing. The ISAG microsatellite panel is useful to screen the Sicilian bovine kinship. Currently, an allele frequency database is being constructed.

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A genetic linkage map of the bovine genome

Cited by 470 publications

References 65 publications

Low diversity in the major histocompatibility complex class II DRB1 gene of the Spanish ibex, Capra pyrenaica

Low diversity in the major histocompatibility complex class II DRB1 gene of the Spanish ibex, Capra pyrenaica

A comprehensive map of the porcine genome.

Allele frequencies of microsatellite loci for genetic characterization of a Sicilian bovine population

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