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.

Winter wheat (Triticum aestivum L.), harvested at late milk, early dough, and hard dough stages of maturity was ensiled for nutritive comparisons. Diets were adjusted to 13% CP with a soy protein concentrate and fed to six ruminally fistulated growing steers and nine adult wethers in a repeated 3 x 3 Latin square design to study the effects of maintenance and ad libitum intakes on digestibility of different feed fractions. At both intakes, digestion values for the steers were greater than or equal to those for the sheep for all feed fractions except CP. Wethers achieved greater intake per unit of BW than steers during ad libitum intake. Voluntary OM intakes of steers only differed between the milk stage diet and the dough stage diets. At low intake, the diets containing the more mature silage were more digestible. At high intake, the OM of diet containing the early dough stage silage ws most digestible. Increased intake caused a depression in digestibility of different feed fractions. The magnitude of the depression varied among diets and fractions. Data indicated that the nutritive value of diets based on whole crop wheat silage is affected by stage of maturity, animal species, and amount of intake. The assessment of the nutritive value of diets based on whole crop wheat silage should therefore be made with the animal species and at the amount of intake for which the diets are intended.

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

A number of Korean native chicken(KNC) populations were registered in FAO (Food and Agriculture Organization) DAD-IS (Domestic Animal Diversity Information Systems, http://www.fao.org/dad-is). But there is a lack of scientific basis to prove that they are unique population of Korea. For this reason, this study was conducted to prove KNC's uniqueness using 25 Microsatellite markers. A total of 548 chickens from 11 KNC populations (KNG, KNB, KNR, KNW, KNY, KNO, HIC, HYD, HBC, JJC, LTC) and 7 introduced populations (ARA: Araucana, RRC and RRD: Rhode Island Red C and D, LGF and LGK: White Leghorn F and K, COS and COH: Cornish brown and Cornish black) were used. Allele size per locus was decided using GeneMapper Software (v 5.0). A total of 195 alleles were observed and the range was 3 to 14 per locus. The MNA, H exp , H obs , PIC value within population were the highest in KNY (4.60, 0.627, 0.648, 0.563 respectively) and the lowest in HYD (1.84, 0.297, 0.286, 0.236 respectively). The results of genetic uniformity analysis suggested 15 cluster (ΔK = 66.22). Excluding JJC, the others were grouped in certain cluster with high genetic uniformity. JJC was not grouped in certain cluster but grouped in cluster 2 (44.3%), cluster 3 (17.7%) and cluster8 (19.1%). As a results of this study, we can secure a scientific basis about KNC's uniqueness and these results can be use to basic data for the genetic evaluation and management of KNC breeds.(

The aim of this study was to evaluate the genetic diversity and relationships of Ogye populations in Korea. A total of 243 genomic DNA samples from 6 Ogye population (Yeonsan Ogye; YSO, Animal Genetic Resources Research Center Ogye; ARO, Chungbuk Ogye; CBO, Chungnam Ogye; CNO, Gyeongbuk Ogye; GBO, Seoul National University Ogye; SUO) and 3 introduced chicken breeds (Rhode Island Red; RIR, White Leghorn; LG, Cornish; CN) were used. Sizes of 25 microsatellite markers were decided using GeneMapper Software(v 5.0) after analyzing ABI 3130XL. A total of 153 alleles were observed and the range was 2 to 10 per each locus. The mean of expected and observed heterozygosity and PIC (Polymorphism Information Content) value was 0.53, 0.50, 0.46 respectively. The lowest genetic distance (0.073) was observed between YSO and SUO, and the highest distance (0.937) between the RIR and CBO. The results of clustering analysis suggested 3 clusters (ΔK=7.96). Excluding GBO population, 5 Ogye populations (YSO, ARO, CBO, CNO, SUO) were grouped in same cluster with high genetic uniformity (0.990, 0.979, 0.989, 0.994, 0.985 respectively). But GBO population was grouped in cluster 1 with low genetic uniformity (0.340). The results of this study can be use to basic data for the genetic evaluation and management of Ogye populations in Korea.

Objective: A genomic region associated with a particular phenotype is called QTL. To detect the optimal F 2 population size associated with QTLs in native chicken, we performed a simulation study on F 2 population derived from crosses between two different breeds.Methods: A total of 15 males and 150 females were randomly selected from the last generation of each F 1 population which was composed of different breed to create two different F 2 populations.The progenies produced from these selected individuals were simulated for six more generations.Their marker genotypes were simulated with a density of 50K at three different heritability levels for the traits such as 0.1, 0.3 and 0.5. Our study is that to compare 100, 500, 1000 TPreference population (RP) groups to each other with three different heritability levels. And a total of 35 QTLs were used, and their locations were randomly created.Results: With a TPRP size of 100, no QTL was detected to satisfy Bonferroni value at three different heritability levels. In a TPRP size of 500, two QTLs were detected when the heritability was 0.5. With a TPRP size of 1,000, 0.1 heritability was detected only one QTL, and 0.5 heritability shows that five QTLs were detected. To sum up, TPRP size and heritability are playing a key role to detect QTLs in QTL study. The larger TPRP size and greater heritability value, the higher the probability of detection of QTLs.With a TPRP size of 100, some QTLs were found, even though the number of QTLs were somewhat similar for h 2 = 0.1, 0.3, and 0.5, respectively. This result indicates an increased in h 2 did not improve number of QTLs at TPRP size of 100. With a TPRP size of 1000, many QTLs were detected at different h 2 levels of traits, even at the h 2 value of 0.1 Conclusion:Our study suggests that the use of a large TPRP and heritability can improve QTL detection in an F 2 chicken population.

Application of genomic big data to analyze the genetic diversity and population structure of Korean domestic chickens Running Title (within 10 words) Genetic diversity and population structure of Korean domestic chickens Author

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