Mapping of the SDHA Locus to Bovine Chromosome 20

Source/description Primer sequences PCR and PCR-RFLP conditions Polymorphism Linkage analysis and chromosomal location Acknowledgements Reference

An integrated genetic and physical map of the bovine X Chromosome

Genotypic data for 56 microsatellites (ms) generated from maternal full sib families nested within paternal half sib pedigrees were used to construct a linkage map of the bovine X Chromosome (Chr) (BTX) that spans 150 cM (ave. interval 2.7 cM). The linkage map contains 36 previously unlinked ms; seven generated from a BTXp library. Genotypic data from these 36 ms was merged into an existing linkage map to more than double the number of informative BTX markers. A male specific linkage map of the pseudoautosomal region was also constructed from five ms at the distal end of BTXq. Four informative probes physically assigned by fluorescence in situ hybridization defined the extent of coverage, confirmed the position of the pseudoautosomal region on the q-arm, and identified a 4.1-cM marker interval containing the centromere of BTX

Genetic variability of a Bos taurus x Bos indicus cross population and validation of genomic regions influencing nematode resistance.

SIRGEALC. Resumo 305

Genomic data as the “hitchhiker's guide” to cattle adaptation: tracking the milestones of past selection in the bovine genome

The bovine species have witnessed and played a major role in the drastic socio-economical changes that shaped our culture over the last 10,000 years. During this journey, cattle hitchhiked on human development and colonized the world, facing strong selective pressures such as dramatic environmental changes and disease challenge. Consequently, hundreds of specialized cattle breeds emerged and spread around the globe, making up a rich spectrum of genomic resources. Their DNA still carry the scars left from adapting to this wide range of conditions, and we are now empowered with data and analytical tools to track the milestones of past selection in their genomes. In this review paper, we provide a summary of the reconstructed demographic events that shaped cattle diversity, offer a critical synthesis of popular methodologies applied to the search for signatures of selection (SS) in genomic data, and give examples of recent SS studies in cattle. Then, we outline the potential and challenges of the application of SS analysis in cattle, and discuss the future directions in this field

Identification and characterization of microRNAs expressed in chicken skeletal muscle.

MicroRNAs (miRNAs, miRs) encompass a class of small non-coding RNAs that often negatively regulate gene expression. miRNAs play an essential role in skeletal muscle, determining the proper development and maintenance of this tissue. In comparison to other organs and tissues, the full set of muscle miRNAs and its expression patterns are still poorly understood. In this report, a chicken skeletal muscle miRNA library was constructed, and the expression of selected miRNAs was further characterized during muscle development in chicken lines with distinct muscling phenotypes. Clone library sequence analysis revealed 40 small RNAs with similarities to previously described chicken miRNAs, seven miRNAs that were never identified before in chicken, and some sequence clusters representing other possible novel miRNAs. Temporal expression profiles of three miRNAs associated with cell proliferation and differentiation (miR-125b, miR-221, and miR-206) in two chicken lines (broiler and layer) revealed the differential steady-state levels of these miRs during skeletal muscle growth and suggests that miR-206 is involved in the muscling phenotype that is observed in growth-selected chicken lines

MicroRNA transcriptome profiles during swine skeletal muscle development

<p>Abstract</p> <p>Background</p> <p>MicroRNA (miR) are a class of small RNAs that regulate gene expression by inhibiting translation of protein encoding transcripts. To evaluate the role of miR in skeletal muscle of swine, global microRNA abundance was measured at specific developmental stages including proliferating satellite cells, three stages of fetal growth, day-old neonate, and the adult.</p> <p>Results</p> <p>Twelve potential novel miR were detected that did not match previously reported sequences. In addition, a number of miR previously reported to be expressed in mammalian muscle were detected, having a variety of abundance patterns through muscle development. Muscle-specific miR-206 was nearly absent in proliferating satellite cells in culture, but was the highest abundant miR at other time points evaluated. In addition, miR-1 was moderately abundant throughout developmental stages with highest abundance in the adult. In contrast, miR-133 was moderately abundant in adult muscle and either not detectable or lowly abundant throughout fetal and neonate development. Changes in abundance of ubiquitously expressed miR were also observed. MiR-432 abundance was highest at the earliest stage of fetal development tested (60 day-old fetus) and decreased throughout development to the adult. Conversely, miR-24 and miR-27 exhibited greatest abundance in proliferating satellite cells and the adult, while abundance of miR-368, miR-376, and miR-423-5p was greatest in the neonate.</p> <p>Conclusion</p> <p>These data present a complete set of transcriptome profiles to evaluate miR abundance at specific stages of skeletal muscle growth in swine. Identification of these miR provides an initial group of miR that may play a vital role in muscle development and growth.</p

Caracterização genética de uma população experimental F2 usando marcadores moleculares no cromossomo 14 ( BTA 14) de bovinos.

No presente trabalho foi usada uma população experimental resultante do cruzamento de 28 fêmeas da raça Gir com quatro touros da ral¥a Holandesa, resultando ern 150 anirnais Fl , que posterior mente foram acasalados entre si, totalizando 382 animais F2. As arnostras de DNA dos anirnais foram extrafdas a partir do sangue e do semen, e os dados genotfpicos foram obtidos at raves do seqlienciador ABI Prism 3100 Avant (Applied Biosysterns). As analises das freqüências alélicas dos marcadores moleculares (CSSM066, ILSTS011, BMC1207, BMS2055, BL1036, BMS740 e BMS1899) foram realizadas através do software Cervus v.2.0 (Marshall et at. , 1998), onde foi calculado o número de alemos dos marcadores, com um total de 46 alelos nos sete loci estudados, com média de 6,57 alelos por locus. Dos sete loci, apenas dois estavam em equilíbrio de Hardy-Weinberg, possivelmente devido as duas populações parentais possuírem frequências alélicas semelhantes, o que permitiria a manutenção do equilíbrio mesmo após o cruzamento. A heterozigosidade esperada e definida como a probabilidade de um indivíduo ser heterozigoto para o locus em uma população. Para um marcador genético, um locus com heterozigosidade maior do que 70% e comumente considerado um marcador altamente polimorfico (Ott, 1992). As maiores e menores heterozigosidades esperadas foram dos rnarcadores " , CSSM066 e ILSTSO 11, com valores de 0,864 e 0,668, respectivamente, com media de heterozigosidade de 0,765, indicando que, os marcadores utilizados neste trabalho são altamente polirn6rficos. O valor do PIC (conteúdo de informação de polimorfismo), que e comente usado como uma medida do polimorfismo para um locus marcador na analise de ligação, foi calculado para cada marcador, obtendo- se nos marcadores CSSM066 e ILSTS011, os valores 0,847 e 0,594, respectivamente. A media dos valores de PIC na população foi de 0, 726. O maior e o menor valor de PIC correspondem ao maior e menor valor de heterozigosidade esperada, refletindo o número de alemos de cada marcador. Trabalhos futuros complementares incluem a construção de um mapa de ligação para estes marcadores e a comparação com um mapa consenso.

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

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

Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes.

201