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      Polymorphic Regions Affecting Human Height Also Control Stature in Cattle

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      Journal: Genetics
      Publisher: Genetics Society of America

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          Abstract

          Orthologous positions of 55 genes associated with height in four human populations were located on the bovine genome. Single nucleotide polymorphisms close to eight of these genes were significantly associated with stature in cattle (Bos taurus and Bos indicus). This suggests that these genes may contribute to controlling stature across mammalian species. © 2011 by the Genetics Society of America

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          Development and Characterization of a High Density SNP Genotyping Assay for Cattle

          Lakshmi Matukumalli, Cynthia Lawley, Robert Schnabel … (2009)
          The success of genome-wide association (GWA) studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP) genotyping for the identification of quantitative trait loci (QTL) and for marker-assisted selection in model and agricultural species. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF) ranging from 0.24 to 0.27). The assay also identified 79 putative copy number variants in cattle. Utility for GWA was demonstrated by localizing known variation for coat color and the presence/absence of horns to their correct genomic locations. The combination of SNP selection and the novel spacing algorithm allows an efficient approach for the development of high-density genotyping platforms in species having full or even moderate quality draft sequence. Aspects of the approach can be exploited in species which lack an available genome sequence. The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle.
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            Many sequence variants affecting diversity of adult human height.

            Daniel Gudbjartsson, G Walters, Gudmar Thorleifsson … (2008)
            Adult human height is one of the classical complex human traits. We searched for sequence variants that affect height by scanning the genomes of 25,174 Icelanders, 2,876 Dutch, 1,770 European Americans and 1,148 African Americans. We then combined these results with previously published results from the Diabetes Genetics Initiative on 3,024 Scandinavians and tested a selected subset of SNPs in 5,517 Danes. We identified 27 regions of the genome with one or more sequence variants showing significant association with height. The estimated effects per allele of these variants ranged between 0.3 and 0.6 cm and, taken together, they explain around 3.7% of the population variation in height. The genes neighboring the identified loci cluster in biological processes related to skeletal development and mitosis. Association to three previously reported loci are replicated in our analyses, and the strongest association was with SNPs in the ZBTB38 gene.
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              Efficient mapping of mendelian traits in dogs through genome-wide association.

              Elinor K Karlsson, Izabella Baranowska, Claire Wade … (2007)
              With several hundred genetic diseases and an advantageous genome structure, dogs are ideal for mapping genes that cause disease. Here we report the development of a genotyping array with approximately 27,000 SNPs and show that genome-wide association mapping of mendelian traits in dog breeds can be achieved with only approximately 20 dogs. Specifically, we map two traits with mendelian inheritance: the major white spotting (S) locus and the hair ridge in Rhodesian ridgebacks. For both traits, we map the loci to discrete regions of <1 Mb. Fine-mapping of the S locus in two breeds refines the localization to a region of approximately 100 kb contained within the pigmentation-related gene MITF. Complete sequencing of the white and solid haplotypes identifies candidate regulatory mutations in the melanocyte-specific promoter of MITF. Our results show that genome-wide association mapping within dog breeds, followed by fine-mapping across multiple breeds, will be highly efficient and generally applicable to trait mapping, providing insights into canine and human health.
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                Author and article information

                Journal
                Title: Genetics
                Abbreviated Title: Genetics
                Publisher: Genetics Society of America
                ISSN (Print): 0016-6731
                ISSN (Electronic): 1943-2631
                Publication date Created: March 16 2011
                Publication date Created: March 2011
                Publication date (Print): March 2011
                Publication date (Electronic): January 06 2011
                Volume: 187
                Issue: 3
                Pages: 981-984
                Article
                DOI: 10.1534/genetics.110.123943
                PMC ID: 3048786
                PubMed ID: 21212230
                SO-VID: a3e23f63-7fe6-474f-b197-9b618e379f21
                Copyright © © 2011
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