A Comprehensive Genetic Map of the Cattle Genome Based on 3802 Microsatellites

Ihara, Naoya; Takasuga, Akiko; Mizoshita, Kazunori; Takeda, Hitoshi; Sugimoto, Mayumi; Mizoguchi, Yasushi; Hirano, Takashi; Itoh, Tomomichi; Watanabe, Toshio; Reed, Kent M.; Snelling, W. M.; Kappes, S. M.; Beattie, Craig W.; Bennett, G. L.; Sugimoto, Yoshikazu

doi:10.1101/gr.2741704

Cited by 243 publications

(237 citation statements)

References 23 publications

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“…It may also indicate that the effect on YW attributed to this candidate gene reflects a segregating QTL or even a linked polymorphism in this gene rather than a direct effect of a GH AluI polymorphism. Bovine GH has been mapped to position 65.7 cM on chromosome 19 (Ihara et al, 2004). The hypothesis of a segregating QTL close to the bovine GH is not supported by the results reported in the literature, since the QTLs for growth or meat production traits where mapped to intervals that do not include bGH, as discussed in Casas et al (2003).…”

Section: Discussionmentioning

confidence: 71%

Association of GH and IGF-1 polymorphisms with growth traits in a synthetic beef cattle breed

et al. 2005

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The Canchim beef cattle (5/8 Charolais + 3/8 Zebu) has been selected for meat production in Brazil since late 1950. In the present work the effects of growth hormone (GH) and insulin-like growth factor 1 (IGF-1) polymorphisms were investigated in 688 animals born between 1998 and 2000. These animals belonged to two genetic groups, i.e., traditional and new lineages. Genotype effects on expected breeding values for birth weight (BW), weaning weight (WW) and yearling weight (YW) were investigated by the least square method. Significant effects were found for GH genotype on YW (p ≤ 0.05), with positive effects associated with the LV (leucine/valine) genotype. For IGF-1 genotypes, significant effects were found on BW (p ≤ 0.01) and YW (p ≤ 0.01). Average substitution effects for IGF-1 alleles estimated by regression analysis suggested a positive effect of the IGF-1 225 bp allele on BW and of the 229 bp allele on YW.

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Section: Discussionmentioning

confidence: 71%

Association of GH and IGF-1 polymorphisms with growth traits in a synthetic beef cattle breed

et al. 2005

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“…Inaccurate estimates of distances in the genetic maps are mainly because of the limited recombination events available in the resource population used for linkage mapping. This fact can be noted in the substantial changes recently in the genetic distances in MARC maps after incorporation of new map information [20]. From the mapping perspective, it is important to know the extent of LD over physical distances, so that marker density on the physical map can be determined.…”

Section: Discussionmentioning

confidence: 99%

Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

Khatkar¹,

Thomson²,

Tammen³

et al. 2006

Genet. Sel. Evol.

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-We analysed linkage disequilibrium (LD) in Australian Holstein-Friesian cattle by genotyping a sample of 45 bulls for 15 closely-spaced microsatellites on two regions of BTA6 reported to carry important QTL for dairy traits. The order and distance of markers were based on the USDA-MARC linkage map. Frequencies of haplotypes were estimated using the E-M approach and a more computationally-intensive Bayesian approach as implemented in PHASE. LD was then estimated using the Hedrick multiallelic extension of Lewontin normalised coefficient D . Estimates of D from the two approaches were in close agreement (r = 0.91). The mean estimates of D for marker pairs with an inter-marker distance of less than 5 cM (n = 13) are 0.57 and 0.51, and for distances more than 20 cM (n = 44) are 0.29 and 0.17, estimated from the E-M and Bayesian approaches, respectively. The Malecot model was fitted for the exponential decline of LD with map distance between markers. The swept radii (the distance at which LD has declined to 1/e (∼37%) of its initial value) are 11.6 and 13.7 cM for the above two methods, respectively. The Malecot model was also fitted using map distance in Mb from the bovine integrated map (bovine location database, bLDB) in addition to cM from the MARC map. Overall, the results indicate a high level of LD on chromosome 6 in Australian dairy cattle.linkage disequilibrium / dairy cattle / markers / chromosome 6

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“…In mammals, the gene order in the X chromosomes has been conserved across such distantly related species as human, cat, horse, cattle, and elephant, with the exception of mouse (22)(23)(24)(25)(26). In the human X and chicken Z, gene trafficking and sequence expansion have been detected, using comparisons with orthologous autosomal segments of other species (12)(13)(14).…”

Section: Discussionmentioning

confidence: 99%

Rapid divergence and expansion of the X chromosome in papaya

Gschwend

Tong

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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X chromosomes have long been thought to conserve the structure and gene content of the ancestral autosome from which the sex chromosomes evolved. We compared the recently evolved papaya sex chromosomes with a homologous autosome of a close relative, the monoecious Vasconcellea monoica, to infer changes since recombination stopped between the papaya sex chromosomes. We sequenced 12 V. monoica bacterial artificial chromosomes, 11 corresponding to the papaya X-specific region, and 1 to a papaya autosomal region. The combined V. monoica X-orthologous sequences are much shorter (1.10 Mb) than the corresponding papaya region (2.56 Mb). Given that the V. monoica genome is 41% larger than that of papaya, this finding suggests considerable expansion of the papaya X; expansion is supported by a higher repetitive sequence content of the X compared with the papaya autosomal sequence. The alignable regions include 27 transcriptencoding sequences, only 6 of which are functional X/V. monoica gene pairs. Sequence divergence from the V. monoica orthologs is almost identical for papaya X and Y alleles; the Carica-Vasconcellea split therefore occurred before the papaya sex chromosomes stopped recombining, making V. monoica a suitable outgroup for inferring changes in papaya sex chromosomes. The papaya X and the hermaphrodite-specific region of the Y h chromosome and V. monoica have all gained and lost genes, including a surprising amount of changes in the X.Carica papaya | gene gains and losses | sex chromosome evolution | suppression of recombination | centromere of X chromosome P apaya (Carica papaya L.) is a trioecious tropical fruit crop that has a nascent XY sex chromosome system, in which the sex determining region occupies a small fraction of the X/Y chromosome pair (1-3). Papaya has two slightly different Y chromosomes that diverged about 73,000 y ago, Y in males and Y h in hermaphrodites (4). All genotypes without X chromosomes (YY, YY h , and Y h Y h ) are lethal in early development, resulting in 25% aborted seeds in selfed hermaphrodites and in crosses between hermaphrodites and males (5), indicating that both Y types have lost at least one gene essential for development.Papaya belongs to the family Caricaceae, with six genera and 35 species, 32 of which are dioecious, two are trioecious (with male, female, and hermaphrodite individuals) and one, Vasconcellea monoica, is monoecious (with male and female flowers on a single plant). The predominance of dioecious species suggests that dioecy is ancestral in this family and that the trioecious and monoecious species evolved recently. V. monoica has no sex chromosomes, because there is no sexual dimorphism among individuals, and there is a single sequence corresponding to each of the several papaya X/Y h gene pairs tested, whereas distinct X and Y alleles were detected in several dioecious Vasconcellea species (6), which indicates that the sex chromosomes in these species are homologous with those in papaya.V. monoica therefore provides an opportunity to compare the recentl...

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A Comprehensive Genetic Map of the Cattle Genome Based on 3802 Microsatellites

Cited by 243 publications

References 23 publications

Association of GH and IGF-1 polymorphisms with growth traits in a synthetic beef cattle breed

Association of GH and IGF-1 polymorphisms with growth traits in a synthetic beef cattle breed

Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

Rapid divergence and expansion of the X chromosome in papaya

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