Four Korean native cattle (KNC) breeds—Hanwoo, Chikso, Heugu, and Jeju black—are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO). The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120) and exotic breeds (Holstein and Charolais, n = 56). Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources.

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (FIT) in native chicken was 0.234±0.025. Over 30.7% of FIT was contributed by within-population deficiency (FIS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds

ObjectiveIn Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping array.MethodsSample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). The single-nucleotide polymorphism (SNP) genotyping was performed using the Illumina BovineHD SNP 777K Bead chip.ResultsHeterozygosity, used as a measure of within-breed genetic diversity, was higher in BH (0.293) and BRH (0.296) than in JB (0.266). Linkage disequilibrium decay was more rapid in BH and BRH than in JB, reaching an average r2 value of 0.2 before 26 kb in BH and BRH, whereas the corresponding value was reached before 32 kb in JB. Intra-population, inter-population, and Fst analyses were used to identify candidate signatures of positive selection in the genome of a domestic Korean cattle population and 48, 11, and 11 loci were detected in the genomic region of the BRH breed, respectively. A Neighbor-Joining phylogenetic tree showed two main groups: a group comprising BH and BRH on one side and a group containing JB on the other. The runs of homozygosity analysis between Korean breeds indicated that the BRH and JB breeds have high inbreeding within breeds compared with BH. An analysis of differentiation based on a high-density SNP chip showed differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic regions where they are evolving.ConclusionOur results indicate that although the Korean cattle breeds have common features, they also show reliable breed diversity.

ABSTRACT. Genetic characterization of the Jeju horse (JH) was performed to construct a correct pedigree of the JH family. A total of 111 horses including 79 JH were genotyped using 20 microsatellite loci. The number of alleles varied from 5 to 11 (mean 7.45) in the JH. The observed heterozygosity and expected heterozygosity ranged from 0.293 to 0.891 and from 0.357 to 0.841, respectively. The polymorphic information contents (PIC) ranged from 0.335 to 0.816. AHT4, ASB2, ASB17, ASB23, CA425, HMS2, HMS3, HTG10, LEX3 and VHL20 loci had relatively high PIC values (> 0.7). The total exclusion probability (PE) of the 20 microsatellite loci was 0.9999 in the JH. These results provide basic information for developing an accurate pedigree and will be useful in making decisions regarding conservation of the JH.

BackgroundEAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data.ResultsAn average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31−6), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05).ConclusionsOur results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1954-x) contains supplementary material, which is available to authorized users.

A c c e p t e d A r t i c l e 2 ABSTRACT 52Objectives: Estimating the genetic diversity and structures, both within and among chicken 53 breeds, is critical for the identification and conservation of valuable genetic resources. In 54 chickens, microsatellite (MS) marker polymorphisms have previously been widely used to 55 evaluate these distinctions. Our objective was to analyze the genetic diversity and 56 relationships among 22 chicken breeds in Asia based on allelic frequencies. 57 Methods: We used 469 genomic DNA samples from 22 chicken breeds from eight Asian 58 countries (South Korea: KNG, KNB, KNR, KNW, KNY, KNO, Laos: LYO, LCH, LBB, 59 LOU, Indonesia: INK, INS, ING, Vietnam: VTN, VNH, Mongolia: MGN, Kyrgyzstan: 60 KGPS, Nepal: NPS, Sri Lanka: SBC) and three imported breeds (RIR: Rhode Island Red, 61 WLG: White Leghorn, CON: Cornish). Their genetic diversity and phylogenetic relationships 62 were analyzed using 20 MS markers. 63Results: In total, 193 alleles were observed across all 20 MS markers, and the number of 64 alleles ranged from 3 (MCW0103) to 20 (LEI0192) with a mean of 9.7 overall. The NPS 65 breed had the highest expected heterozygosity (H exp , 0.718 ± 0.027) and polymorphism 66 information content (PIC, 0.663 ± 0.030). Additionally, the observed heterozygosity (H obs ) 67 was highest in LCH (0.690 ± 0.039), whereas WLG showed the lowest H exp (0.372 ± 0.055), 68 H obs (0.384 ± 0.019), and PIC (0.325 ± 0.049). Nei's D A genetic distance was the closest 69 between VTN and VNH (0.086), and farthest between KNG and MGN (0.503). Principal 70 coordinate analysis showed similar results to the phylogenetic analysis, and three axes 71 explained 56.2 % of the variance (axis 1: 19.17 %; 2: 18.92 %; 3: 18.11 %). STRUCTURE 72 analysis revealed that the 22 chicken breeds should be divided into 20 clusters, based on the 73 highest △K value (46.92). 74 Conclusion: This study provides a basis for future genetic variation studies and the 75 development of conservation strategies for 22 chicken breeds in Asia. 76 77

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