genotypes affects milk production in slick and normal ... been given to Holsteins that inherit a novel slick coat ... 186 Holstein cows (107 slick and 79 normal coat).
35th INTERNATIONAL SOCIETY FOR ANIMAL GENETICS CONFERENCE 7 . 2 3 . 16 – 7 . 2 7 . 2016
Salt L ake C ity, Utah
ABSTRACT BOOK
https://www.asas.org/meetings/isag2016
distribution with multiple domestication centers. This study analyzed 485 boars belonging to 16 breeds (7 commercial: Berkshire, Duroc, Hampshire, Landrace, Yorkshire, Chester White, Spotted; 6 rare: Guinea Hog, Hereford, Large Black, Mangalista, Ossabaw Island, Tamworth; 3 from China: Fengjing, Meishan, Minzhu) and 3 feral populations (Pacific islands of Guam, Kauai and Hawaii) by 14 SNP markers on the Y chromosome in a commercial 70K chip. After quality control (SNP call rate, heterozygosity and absence of polymorphism), 6 of the 14 markers remained in the analysis. Five different haplotypes were found among the animals sampled. The H3 was present in 278 samples (57%). Except for Large Black and Mangalista, this haplotype was observed in all breeds that came to the US via the Atlantic. H3 was also the only haplotype observed in Duroc, Yorkshire, Tamworth, Hampshire and Guinea Hog breeds. The haplotypes H1 and H2 were present in pigs from the Hawaiian Islands, China, and the US mainland. If this represents admixture between Asian and European populations it would seem to have taken place a relatively long ago. The H4 haplotype was exclusive to animals from China and the Pacific islands. Pigs from Guam and Kauai islands were the only populations exhibiting the H5 haplotype. Median joining network analysis has shown that haplotypes H4 and H5 (China and Pacific islands) are closer than the remaining three haplotypes. However, there seems to have been no human migration between Guam and Kauai Islands but there may have been exchange between Guam and Polynesia. We find it interesting that 10 of the populations sampled only exhibited one haplotype and this lack of variation was inclusive of both rare, commercially important, and Chinese breeds. Key Words: animal genetics resources, molecular markers, conservation genetics, gene banks, phylogeography
genotypes affects milk production in slick and normal coat Holsteins. B. Velez, J. Patino (University of Puerto Rico, Mayaguez, Puerto Rico), Y. R. Velez (University of Puerto Rico, Mayagüez Campus, Mayagüez, Puerto Rico), T. S. Sonstegard (USDA, ARS, BFGL, Beltsville, MD), and M. Pagán-Morales (Department of Animal Science, University of Puerto Rico, Mayaguez Campus, Mayaguez, Puerto Rico)
Candidate genes polymorphisms (SNPs) interactions can unveil functional relationships between genes and production traits. Recently, special attention has been given to Holsteins that inherit a novel slick coat
mutation that provides adaptation to high temperature and humidity conditions characteristic of the tropics. DNA and phenotypic records (DHIP) from 186 Holstein cows (107 slick and 79 normal coat) were collected. Animals were genotyped for SNPs at the progesterone receptor (PGR) and signal transducer and activator of transcription 1 (STAT1) using restriction fragment length polymorphism (RFLP). It has been documented that a AdeI-RFLP in PGR (at least one copy of allele G) increased fertilization rate and embryo survival in vitro. On the other hand, PagI-RFLP in STAT1 (at least one copy of allele C) gene had been associated with significant increases in milk, fat, and protein yields. Both SNPs, found in PGR and STAT1, were used for an association study with milk production, somatic cell count, and calving interval. These genes showed a significant interaction (P < .0011) for 305 d adjusted milk. Favorable genotype combinations for that trait (CC for PGR; CT for STAT1) in both types of cattle (slick and normal coat) were observed and phenotipically validated. Meanwhile, slick resulted in higher milk yields than normal coat even when the same genotype combination was observed (GC-PGR/CT-STAT1). The percentage of favorable genotypic combination for milk production (CC for PGR, CT for STAT1) seemed to be greater in slick (70%) than normal coat cattle (30%; P < .0001)). Conversely, the percentage of the reproductive favorable genotype (GG for PGR) was greater in normal coat cattle (78.95%) than slick (21.05%; P < .0001). This marvel may be due to mutations associated with slick coated cattle’s adaptation to high temperatures. Studying gene interaction with production traits could provide a better understanding of molecular markers and their importance in dairy herd improvement particularly in slick and non-slick cows. Key Words: PGR, STAT1, slick P4069 Genetic differences in a Colombian Paso horse breed by gait selection. M. A. Novoa (Genetica Animal de Colombia Ltda., Bogota, Colombia; Universidad Nacional de Colombia, Bogota, Colombia) and L. F. García (Universidad Nacional de Colombia, Bogota, Colombia)
The Colombian Paso breed CCC is the main horse breed in the country, with more than a half million animals, and includes three different subpopulations defined by gaits. It descended from some horse populations which Columbus brought to the Americas in the XVI century. These populations were selected by local breeders for different farming activities considering the variety of Colombian topographic landscapes; therefore, for centuries those breeders were looking
113
for animals with particular movements that were able to correctly perform on those places. We tested the hypothesis whether or not there is a genetic structure based on gait selection. This approach was made through an exhaustive analysis of genetic information including 14–16 autosomal microsatellite markers (140,000 genotypes), X chromosome microsatellites (1000 genotypes), mitochondrial d-loop sequences (200 animals), genealogical information (226,000 records approx.), and phenotypic data (morphometric and gait information). All data were analyzed by using statistical tools, population genetics approaches and phylogenetic reconstruction. The analyses show a single breed with a genetic structure based on the selection of different gaits through the history of this population. That is supported by significant phenotypic differences among the populations defined by gaits. Genetic differences have been increasing in the last 20 yr, so it is possible that if artificial selection provides the reproductive barriers among gaits, it could be possible in the near future that the CCC breed would become two or more different breeds. Finally, the phylogenetic and genealogical reconstructions show a single common origin of these subpopulation which demonstrates a single substructured breed. Key Words: horse gait substructured P4070 SNP discovery and allele frequency estimation in indigenous breeds of South Africa. A. Zwane (Agricultural Research Council, Pretoria, South Africa), A. A. Maiwashe (ARC-Animal Production Institute, Irene, South Africa), and E. van Marle-Koster (University of Pretoria, Pretoria, South Africa)
Indigenous breeds generally perform poorly as compared to other commercial breeds. This is because there have not been in-depth studies that focus on determining the important production traits at a genome-wide level that will help to improve them. This is due to lack of genomic data that allows these breeds to be thoroughly investigated. SNP arrays have revolutionized the ability of genome-wide studies to detect regions harboring sequence variants that affect complex traits. Extensive numbers of validated SNPs with known allele frequencies have rather mainly focused on breeds other than South African breeds, and were essential to construct genotyping assays with broad utility. This biasness makes the use of existing assays in local breeds less efficient in studies such as genome-wide association studies due to lower minor allele frequencies exhibited by these breeds as described in previous studies. The aim of this project was to discover SNPs in Afrikaner, Drakensberger and Nguni indigenous
114
breeds and estimate their allele frequencies. 90 cattle representing these three populations were used to identify more than 30 000 putative SNPs and predicted their allele frequencies. The data from 90 individuals validated about 90% of 10 000 SNPs selected genomewide with a genotypic and allele frequency correlation of r = 0.42. Analysis included mapping of the sequence to the available Bos taurus reference genome. Identification of high frequency markers in indigenous breeds suggests the utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets and functional allelic variants adaptive to diverse climatic regions, for genetic enhancement of the gene-pools. Key Words: SNP discovery, allele frequency, indigenous breeds P4071 Extensive functional class I MHC diversity in sheep. K. Ballingall (Moredun Research Institute, Edinburgh, United Kingdom), S. Goh (Royal Veterinary College, Hatfield, United Kingdom), J. M. Pemberton, and K. Dicks (The University of Edinburgh, Edinburgh, United Kingdom)
We have previously described functional class I MHC allelic and haplotype diversity associated with four MHC haplotypes from a Scottish blackface sheep flock. This provided reference sequences representing at up to three classical class I and up to six other class I loci. However, only limited information is available on the extent of MHC class I allelic diversity at these loci in sheep. To begin to explore the relationship between class I diversity and immune function we need to be able to genotype animals across the range of different class I loci. To do so we first need to understand the level of diversity at each of the previously identified class I loci in sheep. Using a set of pan-class I specific primers designed to amplify a 500 bp fragment representing the polymorphic second and third exons from all transcribed class I loci, we amplified, cloned and sequenced the range of class I alleles from 38 sheep of 9 different breeds from the UK and continental Europe. From these 38 animals, 104 different class I transcripts were sequenced. Phylogenetic analysis of these sequences with the previously described locus specific reference sequences identified clusters which are likely to represent alleles at each locus. Unlike diversity at the highly polymorphic class II MHC DRB1 locus where a substantial proportion of alleles are shared between breeds, only two of the 104 class I sequences was shared between animals of different breeds. This suggests that substantial breed-specific diversity remains to be identified at the class I loci and that diversity at class I loci
