A physical map of the bovine genome

Snelling, W. M.; Chiu, Readman; Schein, Jacqueline E.; Hobbs, Matthew; Abbey, Colette A.; Adelson, David L.; Aerts, Jan; Bennett, G. L.; Bosdet, Ian; Boussaha, Mekki; Bräuning, Rüdiger; Caetano, Alexandre Rodrigues; Costa, Marcos Mota do Carmo; Crawford, A. M.; Dalrymple, Brian P.; Eggen, Andre A.; Wind, Annelie Everts-van der; Floriot, Sandrine; Gautier, Mathieu; Gill, C. A.; Green, Ronnie D.; Holt, Robert A.; Jann, O.; Jones, Steven J.M.; Kappes, S. M.; Keele, J. W.; Jong, Pieter J. de; Larkin, Denis M.; Lewin, Harris A.; McEwan, John C.; McKay, Stephanie; Marra, Marco A.; Mathewson, Carrie; Matukumalli, Lakshmi K.; Moore, S. S.; Murdoch, Brenda M.; Nicholas, F. W.; Osoegawa, Kazutoyo; Roy, Alice C.; Salih, Hanni; Schibler, Laurent; Schnabel, Robert D.; Silveri, Licia; Skow, Loren C.; Smith, Timothy P. L.; Sonstegard, Tad S.; Taylor, Jeremy F.; Tellam, Ross L.; Tassell, Curtis P. Van; Williams, J. L.; Womack, James E.; Wye, Natasja; Yang, George; Zhao, Shaying

doi:10.1186/gb-2007-8-8-r165

Cited by 74 publications

(67 citation statements)

References 69 publications

(76 reference statements)

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“…Thus, after divergence of human and chimpanzee, the human lineage has had a surprisingly stable genome compared with chimpanzee. With the use of high-quality physical maps of the cattle (Snelling et al 2007) and pig (Humphray et al 2007) chromosomes, we were able to identify twice as many Cetartiodactyla-specific EBRs than previously (Murphy et al 2005). This was largely due to the increased number of pig-specific EBRs identified using the integrated physical map versus the RH map alone.…”

Section: Discussionmentioning

confidence: 65%

Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories

Larkin¹,

Pape²,

Donthu³

et al. 2009

Genome Res.

167

219

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The persistence of large blocks of homologous synteny and a high frequency of breakpoint reuse are distinctive features of mammalian chromosomes that are not well understood in evolutionary terms. To gain a better understanding of the evolutionary forces that affect genome architecture, synteny relationships among 10 amniotes (human, chimp, macaque, rat, mouse, pig, cattle, dog, opossum, and chicken) were compared at <1 human-Mbp resolution. Homologous synteny blocks (HSBs; N = 2233) and chromosome evolutionary breakpoint regions (EBRs; N = 1064) were identified from pairwise comparisons of all genomes. Analysis of the size distribution of HSBs shared in all 10 species' chromosomes (msHSBs) identified three (>20 Mbp) that are larger than expected by chance. Gene network analysis of msHSBs >3 human-Mbp and EBRs <1 Mbp demonstrated that msHSBs are significantly enriched for genes involved in development of the central nervous and other organ systems, whereas EBRs are enriched for genes associated with adaptive functions. In addition, we found EBRs are significantly enriched for structural variations (segmental duplications, copy number variants, and indels), retrotransposed and zinc finger genes, and single nucleotide polymorphisms. These results demonstrate that chromosome breakage in evolution is nonrandom and that HSBs and EBRs are evolving in distinctly different ways. We suggest that natural selection acts on the genome to maintain combinations of genes and their regulatory elements that are essential to fundamental processes of amniote development and biological organization. Furthermore, EBRs may be used extensively to generate new genetic variation and novel combinations of genes and regulatory elements that contribute to adaptive phenotypes.

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Section: Discussionmentioning

confidence: 65%

Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories

Larkin¹,

Pape²,

Donthu³

et al. 2009

Genome Res.

167

219

View full text Add to dashboard Cite

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“…The simulated genome consisted of 29 autosomes with a total genome length of 2333cM. Chromosomes were given the same length as observed in cattle data by Snelling et al (2007). Initially, 46660 markers and 7250 QTL were evenly spaced across the genome with equal allele frequencies for both alleles.…”

Section: Datamentioning

confidence: 99%

Updating the reference population to achieve constant genomic prediction reliability across generations

Pszczoła

Calus

2016

Animal

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The reliability of genomic breeding values (DGV) decays over generations. To keep the DGV reliability at a constant level, the reference population (RP) has to be continuously updated with animals from new generations. Updating RP may be challenging due to economic reasons, especially for novel traits involving expensive phenotyping. Therefore, the goal of this study was to investigate a minimal RP update size to keep the reliability at a constant level across generations. We used a simulated dataset resembling a dairy cattle population. The trait of interest was not included itself in the selection index, but it was affected by selection pressure by being correlated with an index trait that represented the overall breeding goal. The heritability of the index trait was assumed to be 0.25 and for the novel trait the heritability equalled 0.2. The genetic correlation between the two traits was 0.25. The initial RP ( n = 2000) was composed of cows only with a single observation per animal. Reliability of DGV using the initial RP was computed by evaluating contemporary animals. Thereafter, the RP was used to evaluate animals which were one generation younger from the reference individuals. The drop in the reliability when evaluating younger animals was then assessed and the RP was updated to re-gain the initial reliability. The update animals were contemporaries of evaluated animals (EVA). The RP was updated in batches of 100 animals/update. First, the animals most closely related to the EVA were chosen to update RP. The results showed that, approximately, 600 animals were needed every generation to maintain the DGV reliability at a constant level across generations. The sum of squared relationships between RP and EVA and the sum of off-diagonal coefficients of the inverse of the genomic relationship matrix for RP, separately explained 31% and 34%, respectively, of the variation in the reliability across generations. Combined, these parameters explained 53% of the variation in the reliability across generations. Thus, for an optimal RP update an algorithm considering both relationships between reference and evaluated animals, as well as relationships among reference animals, is required.

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“…We extended the region to the end of scaffold chr3.49 and added 4.2 Mbp of assembled sequence upstream of marker BL41 to examine differences in haplotype structure beyond but proximal to the QTL interval mapped by Heyen et al (26). Microsatellites BL41 and TGLA263 were also found to be located within the mapped and sequenced cattle BAC clones CH240-514H13 and CH240-176P18, respectively (54).…”

Section: Selection Of a 163 Mbp Qtl Region On Bta3 For High-density mentioning

confidence: 99%

Multisite haplotype on cattle chromosome 3 is associated with quantitative trait locus effects on lactation traits

Cohen

Donthu

Larkin

et al. 2011

Physiological Genomics

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Multisite haplotype on cattle chromosome 3 is associated with quantitative trait locus effects on lactation traits. Physiol Genomics 43: 1185-1197, 2011. First published September 6, 2011 doi:10.1152/physiolgenomics.00253.2010.-The goal of this study was to identify candidate genes and DNA polymorphisms for quantitative trait loci (QTL) affecting milk yield (MY), fat yield (FY), and protein yield (PY) previously mapped to bovine chromosome 3 (BTA3). To accomplish this, 373 half-siblings sired by three bulls previously shown to be segregating for lactation trait QTL, and 263 additional sires in the U.S. Dairy Bull DNA Repository (DBDR) were genotyped for 2,500 SNPs within a 16.3 Mbp QTL critical region on BTA3. Targeted resequencing of ϳ1.8 Mbp within the QTL critical region of one of the QTL heterozygous sires identified additional polymorphisms useful for association studies. Twentythree single nucleotide polymorphisms (SNPs) within a fine-mapped region were associated with effects on breeding values for MY, FY, or PY in DBDR sires, of which five SNPs were in strong linkage disequilibrium in the population. This multisite haplotype included SNPs located within exons or promoters of four tightly linked genes: RAP1A, ADORA3, OVGP1, and C3H1orf88. An SNP within RAP1A showed strong evidence of a recent selective sweep based on integrated haplotype score and was also associated with breeding value for PY. Because of its known function in alveolar lumen formation in the mammary gland, RAP1A is thus a strong candidate gene for QTL effects on lactation traits. Our results provide a detailed assessment of a QTL region that will be a useful guide for complex traits analysis in humans and other noninbred species.genes; single nucleotide polymorphisms; RAP1A; milk ONE OF THE GRAND CHALLENGES in modern genetics is to identify the molecular genetic basis for complex traits (20). In cattle, the low-to-moderate heritability of quantitative traits under selection and limited sizes of resource populations are largely responsible for mapping most quantitative trait loci (QTL) to large intervals of Ͼ10 cM (http://www.genome.iastate.edu/ cgi-bin/QTLdb/BT/index). The poor genomic resolution of mapped cattle QTL makes identification of the genes and polymorphisms underlying their effects a difficult and expensive endeavor. Despite these limitations, two QTL with large effects on milk, milk fat, and protein yields were resolved at the gene level with high probability (12, 23), thereby demonstrating the strength of available cattle resource populations and genomic tools for complex traits analysis. These findings have been rapidly implemented by the dairy industry for genetic improvement in milk production traits (24). Moreover, these studies have illuminated our general understanding of the genetic control of complex traits and have provided two new model systems for lactation biology. Therefore, genetic dissection of QTL affecting lactation traits is important both as a biomedical model system and for applications in animal breeding...

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A physical map of the bovine genome

Abstract: A new physical map of the bovine genome has been constructed by integrating data from genetic and radiation hybrid maps, and a new bovine BAC map, with the bovine genome draft assembly.

Cited by 74 publications

References 69 publications

Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories

Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories

Updating the reference population to achieve constant genomic prediction reliability across generations

Multisite haplotype on cattle chromosome 3 is associated with quantitative trait locus effects on lactation traits

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