We present results from a genomewide association study (GWAS) and a single-marker association study. The GWAS was performed with the Illumina PorcineSNP60 BeadChip from which 5 markers were selected for a validation analysis. Genetic effects were estimated for feed intake, weight gain, and traits of fat and muscle tissue in German Landrace boars kept on performance test stations. The GWAS was performed in a population of 288 boars and the validation study for another 432 boars. No statistically significant effect was found in the GWAS after adjusting for multiple testing. Effects of 2 markers, which were significant genomewide before correction for multiple testing (P < 0.00005), could be confirmed in the validation study. The major allele of marker ALGA0056781 on SSC1 was positively associated with both higher weight gain and fat deposition. The effect on live-weight gain was 2.25 g/d in the GWAS (P=0.0003) and 3.73 g/d in the validation study (P=0.01) and for back fat thickness was 0.15 mm in the GWAS (P < 0.0001) and 0.20 mm in the validation study (P=0.02). The marker had similar effects on test-day weight gain (GWAS: 3.85 g/d, P=0.001; validation study: 6.80 g/d, P=0.003) and back fat area (GWAS: 0.27 ㎠ , P < 0.0001; validation study: 0.35 ㎠ , P=0.03). Marker ASGA0056782 on SSC13 was associated with live-weight gain. The major allele had negative effects in both studies (GWAS: -4.88 g/d, P < 0.0001; validation study: -3.75 g/d, P=0.02). The effects of these 2 markers would have been excluded based on the GWAS alone but were shown to be significantly trait associated in the validation study indicating a false-negative result. The G protein-coupled receptor 126 (GPR126) gene approximately 200 kb downstream of marker ALGA0001781 was shown to be associated with human height and therefore might explain the association with weight gain in pigs. Several traits were affected in an economically desired direction by the minor allele of the markers, pointing to the possibility of improvement through further selection.

Background: This study focused on the dynamics of genome-wide effects on five milk production and eight fertility traits as well as genetic correlations between the traits. For 2,405 Holstein Friesian bulls, estimated breeding values (EBVs) were used. The production traits were additionally assessed in 10-day intervals over the first 60 lactation days, as this stage is physiologically the most crucial time in milk production. Results: SNPs significantly affecting the EBVs of the production traits could be separated into three groups according to the development of the size of allele effects over time: 1) increasing effects for all traits; 2) decreasing effects for all traits; and 3) increasing effects for all traits except fat yield. Most of the significant markers were found within 22 haplotypes spanning on average 135,338 bp. The DGAT1 region showed high density of significant markers, and thus, haplotype blocks. Further functional candidate genes are proposed for haplotype blocks of significant SNPs (KLHL8, SICLEC12, AGPAT6 and NID1). Negative genetic correlations were found between yield and fertility traits, whilst content traits showed positive correlations with some fertility traits. Genetic correlations became stronger with progressing lactation. When correlations were estimated within genotype classes, correlations were on average 0.1 units weaker between production and fertility traits when the yield increasing allele was present in the genotype. Conclusions: This study provides insight into the expression of genetic effects during early lactation and suggests possible biological explanations for the presented time-dependent effects. Even though only three markers were found with effects on fertility, the direction of genetic correlations within genotype classes between production and fertility traits suggests that alleles increasing the milk production do not affect fertility in a more negative way compared to the decreasing allele.

Iranian cattle breeds are currently under-represented in studies regarding genetic variability and conservation effort even though they are settled in a region that is believed to be one of two ancient cattle domestication centres. This study provides first population genetic parameters for eight Iranian cattle breeds collected from across the entire country to highlight the necessity for conservation programs. High density genome-wide SNP chips were used. None of the Iranian breeds showed a decreased heterozygosity compared to outgroup breeds (Holstein, Jersey, and Brahman) and inbreeding coefficients were low. Nevertheless, estimated effective population sizes were <10 for the Mazandarani, Sarabi, and Kermani breeds and it is predicted that most of the genetic variability will be lost within 20-30 generations if no intervention measures are taken. Effective population size estimates varied between chromosomes with occasional extremely high values, especially for Najdi, Pars, and Kermani which have high proportions of indicine ancestry as represented by the Brahman outgroup.

Genetic diversity and breed proportions of Indian stud cattle India is the world's leading milk producer, however, average milk yield per animal is low. Most of India's cattle milk is produced by indigenous breeds, followed by crossbred cows. Crossbreeding intensified in the 1960s and 70s with a large influx of Holstein Friesian and Jersey bulls, and an increased use of artificial insemination. Based on genotypes generated from the 50K v2 BovineHD BeadChip assay, we analysed the genetic diversity and breed composition of 242 breeding cattle sampled from the BAIF breed herds, including indigenous, exotic dairy, and crossbred animals. We compared these animals to indigenous and animals used in smallholder systems in East Africa. Key findings were: confirmation that Indian Zebu breeds are pure Bos indicus in contrast to African Zebu and Sanga breeds, which are admixtures of Bos indicus and African Bos taurus; as found elsewhere, many apparently pure animals contain some admixture from imported breeds; crossbred animals exhibit a wider range of breed composition than intended, reflecting the lack of pedigree when sampling bull mothers from smallholder farms; breed composition of purebred and crossbred animals can in future be tested using SNP data, and only those meeting the desired composition retained for breeding.

Korean Hanwoo cattle have been subjected to intensive artificial selection over the past four decades to improve meat production traits. Another three cattle varieties very closely related to Hanwoo reside in Korea (Jeju Black and Brindle) and in China (Yanbian). These breeds have not been part of a breeding scheme to improve production traits. Here, we compare the selected Hanwoo against these similar but presumed to be unselected populations to identify genomic regions that have been under recent selection pressure due to the breeding program. Rsb statistics were used to contrast the genomes of Hanwoo versus a pooled sample of the three unselected population (UN). We identified 37 significant SNPs (FDR corrected) in the HW/UN comparison and 21 known protein coding genes were within 1 MB to the identified SNPs. These genes were previously reported to affect traits important for meat production (14 genes), reproduction including mammary gland development (3 genes), coat color (2 genes), and genes affecting behavioral traits in a broader sense (2 genes). We subsequently sequenced (Illumina HiSeq 2000 platform) 10 individuals of the brown Hanwoo and the Chinese Yanbian to identify SNPs within the candidate genomic regions. Based on allele frequency differences, haplotype structures, and literature research, we singled out one non-synonymous SNP in the APP gene (APP: c.569C>T, Ala199Val) and predicted the mutational effect on the protein structure. We found that protein-protein interactions might be impaired due to increased exposed hydrophobic surfaces of the mutated protein. The APP gene has also been reported to affect meat tenderness in pigs and obesity in humans. Meat tenderness has been linked to intramuscular fat content, which is one of the main breeding goals for brown Hanwoo, potentially supporting a causal influence of the herein described nsSNP in the APP gene.

Background: Two separate domestication events gave rise to humped zebu cattle in India and humpless taurine cattle in the Fertile Crescent of the Near and Middle East. Iran covers the Eastern side of the Fertile Crescent and exhibits a variety of native cattle breeds, however, only little is known about the admixture patterns of Iranian cattle and their contribution to the formation of modern cattle breeds. Results: Genome-wide data (700k chip) of eight Iranian cattle breeds (Sarabi N = 19, Kurdi N = 7, Taleshi N = 7, Mazandarani N = 10, Najdi N = 7, Pars N = 7, Kermani N = 9, and Sistani N = 9) were collected from across Iran. For a local assessment, taurine (Holstein and Jersey) and indicine (Brahman) outgroup samples were used. For the global perspective, 134 world-wide cattle breeds were included. Between breed variation amongst Iranian cattle explained 60% (p < 0.001) of the total molecular variation and 82.88% (p < 0.001) when outgroups were included. Several migration edges were observed within the Iranian cattle breeds. The highest indicine proportion was found in Sistani. All Iranian breeds with higher indicine ancestry were more admixed with a complex migration pattern. Nineteen founder populations most accurately explained the admixture of 44 selected representative cattle breeds (standard error 0.4617). Low levels of African ancestry were identified in Iranian cattle breeds (on average 7.5%); however, the signal did not persist through all analyses. Admixture and migration analyses revealed minimal introgression from Iranian cattle into other taurine cattle (Holstein, Hanwoo, Anatolian breeds). Conclusion: The eight Iranian cattle breeds feature a discrete genetic composition which should be considered in conservation programs aimed at preserving unique species and genetic diversity. Despite a complex admixture pattern among Iranian cattle breeds, there was no strong introgression from other world-wide cattle breeds into Iranian cattle and vice versa. Considering Iran's central location of cattle domestication, Iranian cattle might represent a local domestication event that remained contained and did not contribute to the formation of modern breeds, or genetics of the ancestral population that gave rise to modern cattle is too diluted to be linked directly to any current cattle breeds.

Genotypic data of 700k markers for five beef cattle breeds were analyzed in regards to their allele frequencies based on their fixation index (FST). The two breeds of interest were the Korean Hanwoo and the Australian Wagyu which are known to have high intramuscular fat content. FST values were compared to Angus, Holstein, and Chinese Yeonbyun. We found 27 and 24 breed specific genome regions for the Hanwoo and Wagyu, respectively. These regions differed significantly between the five breeds, indicating selection pressure on these regions. We narrowed down 18 and 14 regions that were unique to the Hanwoo and Wagyu, respectively. Of these, six regions in the Hanwoo and three regions in the Wagyu harbor potential candidate genes involved either directly in fat metabolism and synthesis or indirectly in blood vessel development.

The selection of small numbers of SNPs to analyse population features is an important task in the livestock industry. Populations differ in their genetic architecture, which often requires the selection of population specific SNPs. Different tasks, such as breed proportion prediction or parentage testing, also require specific panels. We tested which selection methods are best for breed proportion estimation and parentage testing in a crossbred dairy population from East Africa. We selected SNPs from a 735k SNP panel (Illumina) based on several methods:a) high minor allele frequencies; b) high allele frequency differences between ancestral populations; c) at random; d) with a differential evolution algorithm. Estimates of breed proportions in the subsets were tested against true breed proportions based on all 770k SNP obtained from ADMIXTURE. Parentage assignments was based on opposing homozygotes. Panels selected for largest allele frequency differences in ancestral populations gave best results for breed proportion predictions and panels selected for highest minor allele frequency gave best parentage resolution.