Analysis of extended haplotype in Korean cattle (Hanwoo) population

Lim, Dajeong; Choi, Bong Hwan; Cho, Yong Min; Chai, Han Ha; Jang, Gul Won; Gondro, Cedric; Jeoung, Yeoung Ho; Lee, Seung H.

doi:10.5483/bmbrep.2016.49.9.074

Cited by 9 publications

(4 citation statements)

References 24 publications

(21 reference statements)

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“…Korean cattle (Hanwoo) are categorized into three sub-groups based on coat color: brown, brindle, and black. The Brown Hanwoo is the largest and most common subgroup, and intensive selection has occurred to improve meat quality and quantity traits (Lee et al, 2014; Lim et al, 2016; Sharma et al, 2016). Korean beef consumers prefer Hanwoo beef compared to the imported beef from the US or Australia, mainly due to high intramuscular fat content and excellent flavor of Hanwoo cattle meat (Bulik-Sullivan et al, 2015; Strucken et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study of Meat Quality Traits in Hanwoo Beef Cattle Using Imputed Whole-Genome Sequence Data

et al. 2019

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The discovery of single nucleotide polymorphisms (SNP) and the subsequent genotyping of large numbers of animals have enabled large-scale analyses to begin to understand the biological processes that underpin variation in animal populations. In beef cattle, genome-wide association studies using genotype arrays have revealed many quantitative trait loci (QTL) for various production traits such as growth, efficiency and meat quality. Most studies regarding meat quality have focused on marbling, which is a key trait associated with meat eating quality. However, other important traits like meat color, texture and fat color have not commonly been studied. Developments in genome sequencing technologies provide new opportunities to identify regions associated with these traits more precisely. The objective of this study was to estimate variance components and identify significant variants underpinning variation in meat quality traits using imputed whole genome sequence data. Phenotypic and genomic data from 2,110 Hanwoo cattle were used. The estimated heritabilities for the studied traits were 0.01, 0.16, 0.31, and 0.49 for fat color, meat color, meat texture and marbling score, respectively. Marbling score and meat texture were highly correlated. The genome-wide association study revealed 107 significant SNPs located on 14 selected chromosomes (one QTL region per selected chromosome). Four QTL regions were identified on BTA2, 12, 16, and 24 for marbling score and two QTL regions were found for meat texture trait on BTA12 and 29. Similarly, three QTL regions were identified for meat color on BTA2, 14 and 24 and five QTL regions for fat color on BTA7, 10, 12, 16, and 21. Candidate genes were identified for all traits, and their potential influence on the given trait was discussed. The significant SNP will be an important inclusion into commercial genotyping arrays to select new breeding animals more accurately.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study of Meat Quality Traits in Hanwoo Beef Cattle Using Imputed Whole-Genome Sequence Data

et al. 2019

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“…Strong artificial selection increases the frequency of favorable alleles at the loci that affect meat quality traits in meat production breeds. In this process, a small region of the genome surrounding mutations is also selected, resulting in a small genomic region that shows reduced variation [ 14 ]. This region of reduced variation is referred to as a selection signature, which is identified by nucleotide distributions around favorable mutations that differ statistically from those expected purely by chance [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and divergence among Korean cattle breeds assessed using a BovineHD single-nucleotide polymorphism chip

Kim

Cheong

Shin

et al. 2018

Asian-Australas J Anim Sci

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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.

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“…Functioning as an essential homotetrameric enzyme, ADSL plays a pivotal role in two key reactions: 1) the conversion of succinylaminoimidazolecarboxamide (SAICA)-ribotide (SAICAR) into AICA-ribotide (AICAR) through the de novo purine synthesis pathway, and 2) the generation of AMP by converting adenylo-succinate into adenosine monophosphate as part of the purine nucleotide cycle [ 54 ]. Potential modifications to the purine nucleotide degradation pathway resulting from non-synonymous SNPs in the ADSL gene could lead to structural or functional alterations in its associated protein [ 55 ]. Available evidence suggests that point mutations within the ADSL gene can result in significant variations in IMP content [ 56 , 57 ].…”

Section: Discussionmentioning

confidence: 99%

The prevalence of ADSL (rs3788579) and CYP1A2 (rs17861162) polymorphisms in female breast cancer patients in North-West Iran

Valizadeh Osalo,

Hosseini,

Charkhian

et al. 2024

Discov Onc

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Introduction Breast cancer is a prevalent and significant contributor to cancer-related mortality among women worldwide. Its increasing incidence, especially in regions like North-West Iran, necessitates a deeper understanding of genetic factors contributing to its development. Genetic alterations, particularly single nucleotide polymorphisms (SNPs), are implicated in breast cancer susceptibility, making investigation in this context crucial. This study explores the role of CYP1A2-rs17861162 and ADSL-rs3788579 SNPs in breast cancer risk among Iranian women. Methods This study involved 200 female breast cancer patients and 200 healthy controls in North-West Iran. DNA was extracted from blood samples, and PCR–RFLP was used for genotyping the CYP1A2 and ADSL genes. Results The CYP1A2-rs17861162 SNP exhibited a shift from the C allele to the G allele in breast cancer patients, resulting in a 21.7% decrease in CC genotype frequency and a 21.6% and 77.8% increase in CG and GG genotypes, respectively, compared to controls. In ADSL-rs3788579 SNP, breast cancer patients had a significantly higher prevalence of the T allele, with a 28.5% increase compared to controls. In healthy participants, CC was most common, while in the breast cancer group, TT was most common. Conclusion This study highlights significant genetic alterations in CYP1A2-rs17861162 and ADSL-rs3788579 SNPs among breast cancer patients in North-West Iran, suggesting their potential as diagnostic and prognostic biomarkers. Further research is warranted to elucidate the precise mechanisms underlying their contributions to breast cancer susceptibility in this population.

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Analysis of extended haplotype in Korean cattle (Hanwoo) population

Cited by 9 publications

References 24 publications

Genome-Wide Association Study of Meat Quality Traits in Hanwoo Beef Cattle Using Imputed Whole-Genome Sequence Data

Genome-Wide Association Study of Meat Quality Traits in Hanwoo Beef Cattle Using Imputed Whole-Genome Sequence Data

Genetic diversity and divergence among Korean cattle breeds assessed using a BovineHD single-nucleotide polymorphism chip

The prevalence of ADSL (rs3788579) and CYP1A2 (rs17861162) polymorphisms in female breast cancer patients in North-West Iran

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