Edea, Zewdu
(Department of Animal Science, Chungbuk National University)
,
Jung, Kyoung Sub
(Institute of Livestock and Veterinary Research)
,
Shin, Sung-Sub
(Korea Institute for Animal Products Quality Evaluation)
,
Yoo, Song-Won
(Korea Institute for Animal Products Quality Evaluation)
,
Choi, Jae Won
(Institute of Livestock and Veterinary Research)
,
Kim, Kwan-Suk
(Department of Animal Science, Chungbuk National University)
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 contro...
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.
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.
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제안 방법
BANP is associated with preadipocyte proliferation [47]. Following the association of several of our candidate genes with meat quality traits, further functional analysis of the divergently selected genes (DBI, ACSF3, HINT2, GBA2, AGPAT5, SCAP, ELP6, APOB, and RBL1) was associated with relevant gene ontology (GO) terms including fatty oxidation, metabolism, biosynthesis, and storage.
To assess the consequences of artificial selection and demographic events in shaping the genetic constitution of Korean native cattle breeds, level of within breed genetic variability was assessed based on observed and expected heterozygosity. Results show that a deficiency of heterozygosity was detected in the three cattle populations.
대상 데이터
1 genome assembly. QTL regions that overlapped with the identified candidate regions were searched from the cattle QTLdb (http://www.animalgenome.org/cgibin/QTLdb/BT/index).
The SNP windows that display high genetic differentiations (ZFst ≥5) were considered as candidates.
성능/효과
The percentage of SNPs with MAF > 5% was 44%, 41%, and 44% in Hanwoo, Heugu, and Chikso, respectively.
To portray population structure, a principal component was carried out and results showed that the three breeds were clustered based on their coat color phenotypes and breeding histories. As well depicted in Fig.
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