RESEARCH : A whole genomic scan to detect selection signatures between Berkshire and Korean native pig breeds

( Zewdu Edea ),( Kwan Suk Kim ) 한국동물자원과학회(구 한국축산학회) 2014 한국축산학회지 Vol.56 No.23

Background: Scanning of the genome for selection signatures between breeds may play important role in understanding the underlie causes for observable phenotypic variations. The discovery of high density single nucleotide polymorphisms (SNPs) provide a useful starting point to perform genome?wide scan in pig populations in order to identify loci/candidate genes underlie phenotypic variation in pig breeds and facilitate genetic improvement programs. However, prior to this study genomic region under selection in commercially selected Berkshire and Korean native pig breeds has never been detected using high density SNP markers. To this end, we have genotyped 45 animals using Porcine SNP60 chip to detect selection signatures in the genome of the two breeds by using the FST approach. Results: In the comparison of Berkshire and KNP breeds using the FDIST approach, a total of 1108 outlier loci (3.48%) were significantly different from zero at 99% confidence level with 870 of the outlier SNPs displaying high level of genetic differentiation (FST ≥0.490). The identified candidate genes were involved in a wide array of biological processes and molecular functions. Results revealed that 19 candidate genes were enriched in phosphate metabolism (GO: 0006796; ADCK1, ACYP1, CAMK2D, CDK13, CDK13, ERN1, GALK2, INPP1; MAK, MAP2K5, MAP3K1, MAPK14, P14KB, PIK3C3, PRKC1, PTPRK, RNASEL, THBS1, BRAF, VRK1). We have identified a set of candidate genes under selection and have known to be involved in growth, size and pork quality (CART, AGL, CF7L2, MAP2K5, DLK1, GLI3, CA3 and MC3R), ear morphology and size (HMGA2 and SOX5) stress response (ATF2, MSRB3, TMTC3 and SCAF8) and immune response ( HCST and RYR1). Conclusions: Some of the genes may be used to facilitate genetic improvement programs. Our results also provide insights for better understanding of the process and influence of breed development on the pattern of genetic variations.

Signatures of positive selection underlying beef production traits in Korean cattle breeds

( Zewdu Edea ),( Kyoung Sub Jung ),( Sung-sub Shin ),( Song-won Yoo ),( Jae Won Choi ),( Kwan-suk Kim ) 한국축산학회(구 한국동물자원과학회) 2020 한국축산학회지 Vol.62 No.3

The difference in the breeding programs and population history may have diversely shaped the genomes of Korean native cattle breeds. In the absence of phenotypic data, comparisons of breeds that have been subjected to different selective pressures can aid to identify genomic regions and genes controlling qualitative and complex traits. In this study to decipher genetic variation and identify evidence of divergent selection, 3 Korean cattle breeds were genotyped using the recently developed high-density GeneSeek Genomic Profiler F250 (GGP-F250) array. The three Korean cattle breeds clustered according to their coat color phenotypes and breeding programs. The Heugu breed reliably showed smaller effective population size at all generations considered. Across the autosomal chromosomes, 113 and 83 annotated genes were identified from Hanwoo-Chikso and Hanwoo-Heugu comparisons, respectively of which 16 genes were shared between the two pairwise comparisons. The most important signals of selection were detected on bovine chromosomes 14 (24.39–25.13 Mb) and 18 (13.34–15.07 Mb), containing genes related to body size, and coat color (XKR4, LYN, PLAG1, SDR16C5, TMEM68, CDH15, MC1R, and GALNS). Some of the candidate genes are also associated with meat quality traits (ACSF3, EIF2B1, BANP, APCDD1, and GALM) and harbor quantitative trait locus (QTL) for beef production traits. Further functional analysis revealed that the candidate genes (DBI, ACSF3, HINT2, GBA2, AGPAT5, SCAP, ELP6, APOB, and RBL1) were involved in gene ontology (GO) terms relevant to meat quality including fatty acid oxidation, biosynthesis, and lipid storage. Candidate genes previously known to affect beef production and quality traits could be used in the beef cattle selection strategies.

Comparison of SNP Variation and Distribution in Indigenous Ethiopian and Korean Cattle (Hanwoo) Populations

Edea, Zewdu,Dadi, Hailu,Kim, Sang-Wook,Dessie, Tadelle,Kim, Kwan-Suk Korea Genome Organization 2012 Genomics & informatics Vol.10 No.3

Although a large number of single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project, few of these have been validated at large in Bos indicus breeds. We have genotyped 192 animals, representing 5 cattle populations of Ethiopia, with the Illumina Bovine 8K SNP BeadChip. These include 1 Sanga (Danakil), 3 zebu (Borana, Arsi and Ambo), and 1 zebu ${\times}$ Sanga intermediate (Horro) breeds. The Hanwoo (Bos taurus) was included for comparison purposes. Analysis of 7,045 SNP markers revealed that the mean minor allele frequency (MAF) was 0.23, 0.22, 0.21, 0.21, 0.23, and 0.29 for Ambo, Arsi, Borana, Danakil, Horro, and Hanwoo, respectively. Significant differences of MAF were observed between the indigenous Ethiopian cattle populations and Hanwoo breed (p < 0.001). Across the Ethiopian cattle populations, a common variant MAF (${\geq}0.10$ and ${\leq}0.5$) accounted for an overall estimated 73.79% of the 7,045 SNPs. The Hanwoo displayed a higher proportion of common variant SNPs (90%). Investigation within Ethiopian cattle populations showed that on average, 16.64% of the markers were monomorphic, but in the Hanwoo breed, only 6% of the markers were monomorphic. Across the sampled Ethiopian cattle populations, the mean observed and expected heterozygosities were 0.314 and 0.313, respectively. The level of SNP variation identified in this particular study highlights that these markers can be potentially used for genetic studies in African cattle breeds.

Genome–wide association study of carcass weight in commercial Hanwoo cattle

Zewdu Edea,Yeong Ho Jeoung,신성섭,Jaeul Ku,Sungbo Seo,Il-Hoi Kim,김상욱,김관석 아세아·태평양축산학회 2018 Animal Bioscience Vol.31 No.3

Objective: The objective of the present study was to validate genes and genomic regions associated with carcass weight using a low-density single nucleotide polymorphism (SNP) Chip in Hanwoo cattle breed. Methods: Commercial Hanwoo steers (n = 220) were genotyped with 20K GeneSeek genomic profiler BeadChip. After applying the quality control of criteria of a call rate ≥90% and minor allele frequency (MAF) ≥0.01, a total of 15,235 autosomal SNPs were left for genome-wide association (GWA) analysis. The GWA tests were performed using single-locus mixed linear model. Age at slaughter was fitted as fixed effect and sire included as a covariate. The level of genome-wide significance was set at 3.28×10–6 (0.05/15,235), corresponding to Bonferroni correction for 15,235 multiple independent tests. Results: By employing EMMAX approach which is based on a mixed linear model and accounts for population stratification and relatedness, we identified 17 and 16 loci significantly (p<0.001) associated with carcass weight for the additive and dominant models, respectively. The second most significant (p = 0.000049) SNP (ARS-BFGL-NGS-28234) on bovine chromosome 4 (BTA4) at 21 Mb had an allele substitution effect of 43.45 kg. Some of the identified regions on BTA2, 6, 14, 22, and 24 were previously reported to be associated with quantitative trait loci for carcass weight in several beef cattle breeds. Conclusion: This is the first genome-wide association study using SNP chips on commercial Hanwoo steers, and some of the loci newly identified in this study may help to better DNA markers that determine increased beef production in commercial Hanwoo cattle. Further studies using a larger sample size will allow confirmation of the candidates identified in this study.

Genetic Structure of and Evidence for Admixture between Western and Korean Native Pig Breeds Revealed by Single Nucleotide Polymorphisms

Edea, Zewdu,Kim, Sang-Wook,Lee, Kyung-Tai,Kim, Tae Hun,Kim, Kwan-Suk Asian Australasian Association of Animal Productio 2014 Animal Bioscience Vol.27 No.9

Comprehensive information on genetic diversity and introgression is desirable for the design of rational breed improvement and conservation programs. Despite the concerns regarding the genetic introgression of Western pig breeds into the gene pool of the Korean native pig (KNP), the level of this admixture has not yet been quantified. In the present study, we genotyped 93 animals, representing four Western pig breeds and KNP, using the porcine SNP 60K BeadChip to assess their genetic diversity and to estimate the level of admixture among the breeds. Expected heterozygosity was the lowest in Berkshire (0.31) and highest in Landrace (0.42). Population differentiation ($F_{ST}$) estimates were significantly different (p<0.000), accounting for 27% of the variability among the breeds. The evidence of inbreeding observed in KNP (0.029) and Yorkshire (0.031) may result in deficient heterozygosity. Principal components one (PC1) and two (PC2) explained approximately 35.06% and 25.20% of the variation, respectively, and placed KNP somewhat proximal to the Western pig breeds (Berkshire and Landrace). When K = 2, KNP shared a substantial proportion of ancestry with Western breeds. Similarly, when K = 3, over 86% of the KNP individuals were in the same cluster with Berkshire and Landrace. The linkage disquilbrium (LD) values at $r^2_{0.3}$, the physical distance at which LD decays below a threshold of 0.3, ranged from 72.40 kb in Landrace to 85.86 kb in Yorkshire. Based on our structure analysis, a substantial level of admixture between Western and Korean native pig breeds was observed.

Comparison of SNP Variation and Distribution in Indigenous Ethiopian and Korean Cattle (Hanwoo) Populations

Zewdu Edea,김관석,Hailu Dadi,김상욱,Tadelle Dessie 한국유전체학회 2012 Genomics & informatics Vol.10 No.3

Although a large number of single nucleotide polymorphisms (SNPs) have been identified from the bovine genomesequencing project, few of these have been validated at large in Bos indicus breeds. We have genotyped 192 animals,representing 5 cattle populations of Ethiopia, with the Illumina Bovine 8K SNP BeadChip. These include 1 Sanga (Danakil), 3zebu (Borana, Arsi and Ambo), and 1 zebu × Sanga intermediate (Horro) breeds. The Hanwoo (Bos taurus) was included for comparison purposes. Analysis of 7,045 SNP markers revealed that the mean minor allele frequency (MAF) was 0.23, 0.22,0.21, 0.21, 0.23, and 0.29 for Ambo, Arsi, Borana, Danakil, Horro, and Hanwoo, respectively. Significant differences of MAF were observed between the indigenous Ethiopian cattle populations and Hanwoo breed (p < 0.001). Across the Ethiopian cattle populations, a common variant MAF (≥0.10 and ≤0.5) accounted for an overall estimated 73.79% of the 7,045 SNPs. The Hanwoo displayed a higher proportion of common variant SNPs (90%). Investigation within Ethiopian cattle populations showed that on average, 16.64% of the markers were monomorphic, but in the Hanwoo breed, only 6% of the markers were monomorphic. Across the sampled Ethiopian cattle populations, the mean observed and expected heterozygosities were 0.314 and 0.313, respectively. The level of SNP variation identified in this particular study highlights that these markers can be potentially used for genetic studies in African cattle breeds.

Genome-wide linkage disequilibrium analysis of indigenous cattle breeds of Ethiopia and Korea using different SNP genotyping BeadChips

Edea, Zewdu,Dadi, Hailu,Dessie, Tadelle,Lee, Seung-Hwan,Kim, Kwan-Suk Springer-Verlag 2015 Genes & Genomics Vol.37 No.9

A whole genomic scan to detect selection signatures between Berkshire and Korean native pig breeds

Edea, Zewdu,Kim, Kwan-Suk Korean Society of Animal Sciences and Technology 2014 한국축산학회지 Vol.56 No.7

Background: Scanning of the genome for selection signatures between breeds may play important role in understanding the underlie causes for observable phenotypic variations. The discovery of high density single nucleotide polymorphisms (SNPs) provide a useful starting point to perform genome-wide scan in pig populations in order to identify loci/candidate genes underlie phenotypic variation in pig breeds and facilitate genetic improvement programs. However, prior to this study genomic region under selection in commercially selected Berkshire and Korean native pig breeds has never been detected using high density SNP markers. To this end, we have genotyped 45 animals using Porcine SNP60 chip to detect selection signatures in the genome of the two breeds by using the $F_{ST}$ approach. Results: In the comparison of Berkshire and KNP breeds using the FDIST approach, a total of 1108 outlier loci (3.48%) were significantly different from zero at 99% confidence level with 870 of the outlier SNPs displaying high level of genetic differentiation ($F_{ST}{\geq}0.490$). The identified candidate genes were involved in a wide array of biological processes and molecular functions. Results revealed that 19 candidate genes were enriched in phosphate metabolism (GO: 0006796; ADCK1, ACYP1, CAMK2D, CDK13, CDK13, ERN1, GALK2, INPP1; MAK, MAP2K5, MAP3K1, MAPK14, P14KB, PIK3C3, PRKC1, PTPRK, RNASEL, THBS1, BRAF, VRK1). We have identified a set of candidate genes under selection and have known to be involved in growth, size and pork quality (CART, AGL, CF7L2, MAP2K5, DLK1, GLI3, CA3 and MC3R), ear morphology and size (HMGA2 and SOX5) stress response (ATF2, MSRB3, TMTC3 and SCAF8) and immune response (HCST and RYR1). Conclusions: Some of the genes may be used to facilitate genetic improvement programs. Our results also provide insights for better understanding of the process and influence of breed development on the pattern of genetic variations.

Association of MITF loci with coat color spotting patterns in Ethiopian cattle

Edea, Zewdu,Dadi, Hailu,Dessie, Tadelle,Kim, Il-Hoi,Kim, Kwan-Suk Springer-Verlag 2017 Genes & Genomics Vol.39 No.3

<P>The genetics of coat color have been the focus of investigation for decades because beyond its aesthetic values, coat color is associated with thermo-tolerance, production and health traits. Despite the fascinating coat color phenotypes observed in Ethiopian cattle populations, up to now, there are no studies performed to identify and characterize polymorphisms associated with such variation at the genome level. In an attempt to identify and map the genetic basis of coat color variation in Ethiopian cattle, a genome-wide association study (GWAS), selection signatures test and network analysis were performed in 187 cattle populations genotyped on Illumina high-density chip. Loci significant at the genome-wide level (P ae<currency> 8.29 x 10(-7)) and show selection signals (F (ST) - 5SNP window = 0.13) were mainly localized on BTA22 (31.53-31.99) within the MITF gene. Network and functional annotation clustering analyses revealed that the candidate genes are involved in important pathways including melanogenesis. The results of the present study suggest a role of the MITF gene and its interaction with other genes in determining the spotting patterns observed in the Begait and Fogera cattle populations.</P>

Genomic signatures of high‑altitude adaptation in Ethiopian sheep populations

Zewdu Edea,Hailu Dadi,Tadelle Dessie,김관석 한국유전학회 2019 Genes & Genomics Vol.41 No.8

Background Ethiopian sheep populations such as Arsi-Bale, Horro and Adilo (long fat-tailed, LFT) inhabit mid to highaltitude areas; and Menz sheep (MZ, short fat-tailed) are adapted to cool sub-alpine environments. In contrast, Blackhead Somali sheep (BHS, fat-rumped) thrive well in arid and semi-arid areas characterized by high temperature and low precipitation. The genomic investigation of Ethiopian sheep populations may help to identify genes and biological pathways enable to adapt to the different ecological conditions. Objective To uncover genomic regions and genes showing evidence of positive selection for altitude adaptation in Ethiopian sheep populations. Methods A total of 72 animals inhabiting high-versus low-altitude environments were genotyped on an Ovine Infinium HD array (~ 600 K). Pairwise genetic differentiation (Fst) was calculated in sliding windows of 20 SNPs and the upper 1% smoothed Fst values were considered to represent positive selection signatures. Genes within < 25 kb of the most differentiated SNPs were considered as selection candidates. Results Signatures of selection were detected in genes known to be associated high with altitude adaptation in MZ–BHS pair comparison (PPP1R12A, RELN, PARP2, and DNAH9) and in LFT–BHS pair comparison (VAV3, MSRB3, EIF2AK4, MET, and TACR1). The candidate genes (MITF, FGF5, MTOR, TRHDE, and TUBB3) associated with altitude adaptation and shared between the MZ–BHS and LTF–BHS pair comparisons were also detected as under selection. Further functional analyses reveal that the candidate genes were involved in biological processes and pathways relevant to adaptation under extreme altitudes, including respiratory system development and smoothened signaling pathway. Conclusion The results of the present study could aid in-depth understanding and exploitation of the underlying genetic mechanisms for sheep and other livestock species adaptation to high-altitude environments.