Assessment of OvineSNP50 in Nigerian and Kenyan sheep populations

Deciphering genomic information requires markers that are polymorphic and sufficient enough to capture its vast array of genetic data. Polymorphic loci can differ greatly between breeds of the same species and the exclusion of the Nigerian and some African sheep breeds during the development of the OvineSNP50 chip necessitated the validation of SNPs included on the chip to allow for genomic applications of the excluded breeds. A total of sixty sheep samples were genotyped [10 each of the Balami, Uda, West African Dwarf and Yankasa from Nigeria, Dorper and Red Maasai from Kenya (East Africa)] using the Ovine 50k Illumina SNP bead chip. Results revealed that 33,994 SNPs (97.47%) of the called 34,876 SNPs were validated for downstream analysis. Mean heterozygosity values of 0.154 and 0.153 were obtained for polymorphic SNPs on sex and autosomal chromosomes respectively, while the values of 0.662 and 0.054 were obtained on the sex and autosomal chromosomes respectively for the mean identity-bystate (IBS). Six and three individuals violated the per ID and identity-by-state (IBS) thresholds, respectively. It was observed that the Ovine 50k Illumina SNP bead chip wasinformative in the Nigerian and East African sheep that were studied, and should be useful in examining the underlying genetic variation.Keywords: Sheep, OvineSNP50, genome-wide, call rate, minor allele frequenc

The SLICK hair locus derived from Senepol cattle confers thermotolerance to intensively managed lactating Holstein cows

AbstractThe SLICK haplotype (http://omia.angis.org.au/OMIA001372/9913/) in cattle confers animals with a short and sleek hair coat. Originally identified in Senepol cattle, the gene has been introduced into Holsteins. The objectives of the current study were to determine (1) whether lactating Holsteins with the slick hair phenotype have superior ability for thermoregulation compared with wild-type cows or relatives not inheriting the SLICK haplotype, and (2) whether seasonal depression in milk yield would be reduced in SLICK cows. In experiment 1, diurnal variation in vaginal temperature in the summer was monitored for cows housed in a freestall barn with fans and sprinklers. Vaginal temperatures were lower in slick-haired cows than in relatives and wild-type cows. In experiment 2, acute responses to heat stress were monitored after cows were moved to a dry lot in which the only heat abatement was shade cloth. The increases in rectal temperature and respiration rate caused by heat stress during the day were lower for slick cows than for relatives or wild-type cows. Moreover, sweating rate was higher for slick cows than for cows of the other 2 types. In experiment 3, effects of season of calving (summer vs. winter) on milk yield and composition were determined. Compared with milk yield of cows calving in winter, milk yield during the first 90 d in milk was lower for cows calving in the summer. However, this reduction was less pronounced for slick cows than for wild-type cows. In conclusion, Holsteins with slick hair have superior thermoregulatory ability compared with non-slick animals and experience a less drastic depression in milk yield during the summer

Genetic and phenotypic characterization of African goat populations to prioritize conservation and production efforts for small-holder farmers in sub-Saharan Africa

Food production systems in Africa depend heavily on the use of locally adapted animals. Goats are critical to small-holder farmers being easier to acquire, maintain, and act as scavengers in sparse pasture. Indigenous goats have undergone generations of adaptation and genetic isolation that have led to great phenotypic variation. These indigenous goats serve as a genetic reservoir for the identification of genes important to environmental adaptation, disease resistance, and improved productivity under local conditions. The immediate goal is to characterize African goat populations to prioritize conservation and production efforts and to develop genomic tools for use in selective breeding programs. We have established a standardized phenotypic scoring system to characterize goats including geographical information data, body measurements, photo characterization, and DNA. To date, 2,443 goats from 12 countries, representing 46 breeds have been sampled. Using the 50K goat beadchip, we report parameters of population structure of 620 African goats

Copy number variation of individual cattle genomes using next-generation sequencing

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome - wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising ∼55.6-Mbp sequence-476 of which (~38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (∼52%, χ 2 test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome. © 2012 by Cold Spring Harbor Laboratory Press

Whole genome study of linkage disequilibrium in Sahiwal cattle

The linkage disequilibrium (LD) is an important tool to study quantitative trait locus (QTL) mapping and genetic selection. In this study, we identified the extent of linkage disequilibrium (LD) in Sahiwal (n = 14) cattle using the bovine high density single-nucleotide polymorphisms (SNPs) BeadChip. After data filtering, 500,968 SNPs comprising 2518.1 Mb of the genome, were used for the LD estimation. The minior allele frequency (MAF) was 0.21 in a substantial proportion of SNPs and mean distance between adjacent markers was 4.77 ± 2.83 kb. The overall mean LD between adjacent markers was 0.18 (r2) and 0.55 (|D'|), respectively. The LD (r2) values reduced with the increase in distance between adjacent markers from 1 kb (0.35) to 100 kb (0.12) and |D'| specified distinct decay of the LD. Chromosomes 1, 27, 28 and 29 presented the LD at some distance between markers. The extent of LD was higher, except these four chromosomes, for markers separated by 20 kb. At < 3 kb distance, the upper value of the linkage disequilibrium (LD) was observed at 0.30. High level of the linkage disequilibrium (LD) between markers was observed at high minor allele frequency (MAF) threshold (0.15), at the short distance between markers. The results of this study revealed that the Bovine high density SNPs BeadChip will be informative for the estimation of breeding value in Sahiwal cattle.Keywords: Breeding value, linkage disequilibrium, minor allele frequency, molecular marke

Quantitative trait loci for resistance to Haemonchus contortus artificial challenge in Red Maasai and Dorper sheep of East Africa

A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to the gastrointestinal nematode Haemonchus contortus in a double backcross population of Red Maasai and Dorper sheep. The mapping population comprised six sire families, with 1026 lambs in total. The lambs were artificially challenged with H. contortus at about 6.5 months of age, and nine phenotypes were measured: fecal egg count, packed cell volume decline, two weight traits and five worm traits. A subset of the population (342 lambs) was selectively genotyped for 172 microsatellite loci covering 25 of the 26 autosomes. QTL mapping was performed for models which assumed that the QTL alleles were either fixed or segregating within each breed, combined with models with only an additive QTL effect fitted or both additive and dominance QTL effects fitted. Overall, QTL significant at the 1% chromosome-wide level were identified for 22 combinations of trait and chromosome. Of particular interest are a region of chromosome 26 with putative QTL for all nine traits and a region of chromosome 2 with putative QTL for three traits. Favorable QTL alleles for disease resistance originated in both the Red Maasai and Dorper breeds, were not always fixed within breed and had significant dominance effects in some cases. We anticipate that this study, in combination with follow-up work and other relevant studies, will help elucidate the biology of disease resistance

Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium

Effective population size is an important parameter for the assessment of genetic diversity within a livestock population and its development over time. If pedigree information is not available, linkage disequilibrium (LD) analysis might offer an alternative perspective for the estimation of effective population size. In this study, 128 individuals of the Swiss Eringer breed were genotyped using the Illumina BovineSNP50 beadchip. We set bin size at 50 kb for LD analysis, assuming that LD for proximal single nucleotide polymorphism (SNP)-pairs reflects distant breeding history while LD from distal SNP-pairs would reflect near history. Recombination rates varied among different regions of the genome. The use of physical distances as an approximation of genetic distances (e.g. setting 1 Mb = 0.01 Morgan) led to an upward bias in LD-based estimates of effective population size for generations beyond 50, while estimates for recent history were unaffected. Correction for restricted sample size did not substantially affect these results. LD-based actual effective population size was estimated in the range of 87–149, whereas pedigree-based effective population size resulted in 321 individuals. For conservation purposes, requiring knowledge of recent history (<50 generations), approximation assuming constant recombination rate seemed adequate

Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo)

Background The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Results Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. Conclusion The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turke