Genome Wide Association Study to Identity QTL for Growth Taits in Hanwoo

Lee, Seung Hwan; Lim, Dajeong; Jang, Gul Won; Cho, Yong Min; Choi, Bong Hwan; Kim, Si Dong; Oh, Sung Jong; Lee, Jun Heon; Yoon, Duhak; Park, Eung Woo; Lee, Hak Kyo; Hong, Sung Kee; Yang, Boh Suk

doi:10.5187/jast.2012.54.5.323

Cited by 3 publications

(1 citation statement)

References 18 publications

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“…In particular, while producing Korean beef, meat has important traits, such as marbling (Lee et al, 2010), longissimus muscle area (Lee and Kim, 2009), backfat thickness (Seong et al, 2014), carcass weight (Lee et al, 2013), and the corresponding genes. Studies on SNPs in Hanwoo have been conducted and have undergone many improvements using molecular genetics (Lee et al, 2012). In addition, there have been studies on CNV in Hanwoo using NGS (Choi et al, 2013) or SNP chips (Bae et al, 2010), but an analysis of the relationship between CNV in Hanwoo and the meat traits is lacking.…”

Section: Identification Of Cnvs and Their Association With The Meat T...mentioning

confidence: 99%

Identification of CNVs and their association with the meat traits of Hanwoo

Bang,

Tseveen,

Lee

et al. 2023

J Anim Reprod Biotechnol

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Background: Copy number variation (CNV) can be identified using next-generation sequencing and microarray technologies, the research on the analysis of its association with meat traits in livestock breeding has significantly increased in recent years. Hanwoo is an inherent species raised in the Republic of Korea. It is now considered one of the most economically important species and a major food source mainly used for meat (Hanwoo beef). Methods: In this study, CNVs and the relationship between the obtained CNV regions (CNVRs) can be identified in the Hanwoo steer samples (n = 473) using Illumina Hanwoo SNP 50K bead chip and bioinformatic tools, which were used to locate the required data and meat traits were investigated. The PennCNV software was used for the identification of CNVs, followed by the use of the CNV Ruler software for locating the different CNVRs. Furthermore, bioinformatics analysis was performed. Results: We found a total of 2,575 autosomal CNVs (933 losses, 1,642 gains) and 416 CNVRs (289 gains, 111 losses, and 16 mixed), which were established with ranged in size from 2,183 bp to 983,333 bp and 10,004 bp to 381,836 bp, respectively. Upon analyzing the restriction of minor alleles frequency > 0.05 for meat traits association, 6 CNVRs in the carcass weight, 2 CNVRs in the marbling score, 3 CNVRs in the backfat thickness, and 2 CNVRs in the longissimus muscle area were related to the meat traits. In addition, we identified an overlap of 347 CNVRs. Moreover, 3 CNVRs were determined to have a gene that affects meat quality. Conclusions: Our results confirmed the relationship between Hanwoo CNVR and meat traits, and the possibility of overlapping candidate genes, annotations, and quantitative trait loci that results depended on to contribute to the greater understanding of CNVs in Hanwoo and its role in genetic variation among cattle livestock.

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Section: Identification Of Cnvs and Their Association With The Meat T...mentioning

confidence: 99%

Identification of CNVs and their association with the meat traits of Hanwoo

Bang,

Tseveen,

Lee

et al. 2023

J Anim Reprod Biotechnol

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Estimation of the Accuracy of Genomic Breeding Value in Hanwoo (Korean Cattle)

Lee¹,

Lee²,

Choi³

et al. 2013

Journal of Animal Science and Technology

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This study was conducted to estimate the Genomic Estimated Breeding Value (GEBV) using Genomic Best Linear Unbiased Prediction (GBLUP) method in Hanwoo (Korean native cattle) population. The result is expected to adapt genomic selection onto the national Hanwoo evaluation system. Carcass weight (CW), eye muscle area (EMA), backfat thickness (BT), and marbling score (MS) were investigated in 552 Hanwoo progeny-tested steers at Livestock Improvement Main Center. Animals were genotyped with Illumina BovineHD BeadChip (777K SNPs). For statistical analysis, Genetic Relationship Matrix (GRM) was formulated on the basis of genotypes and the accuracy of GEBV was estimated with 10-fold Cross-validation method. The accuracies estimated with cross-validation method were between 0.915~0.957. In 534 progeny-tested steers, the maximum difference of GEBV accuracy compared to conventional EBV for CW, EMA, BT, and MS traits were 9.56%, 5.78%, 5.78%, and 4.18% respectively. In 3,674 pedigree traced bulls, maximum increased difference of GEBV for CW, EMA, BT, and MS traits were increased as 13.54%, 6.50%, 6.50%, and 4.31% respectively. This showed that the implementation of genomic pre-selection for candidate calves to test on meat production traits could improve the genetic gain by increasing accuracy and reducing generation interval in Hanwoo genetic evaluation system to select proven bulls.

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Genome-wide association analysis to identify QTL for carcass traits in Hanwoo (Korean native cattle)

Hong

Choi

Singh

et al. 2019

Indian J of Anim Sci

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A genome-wide association study (GWAS) was performed to investigate the genetic markers associated with carcass traits of Hanwoo (Bos taurus coreanae) steer in the Gangwon region of Korea. Hanwoo steer (139) from the Gangwon region were genotyped with Bovine SNP50K BeadChip, and 35,769 SNPs were analyzed for five specific carcass traits after applying several filters. A total of seven quantitative trait loci were detected, of which four, one, and 2 SNPs were detected on various B. taurus autosomal chromosomes (BTA) by the respective model. The four significant SNPs associated with backfat thickness were ARS-BFGL-NGSâ€“41475 on BTA 5, ARS-BFGLNGS- 36359 on BTA 19, ARS-BFGL-NGS-56813 on BTA 22, and Hapmap25048-BTA-138242 on BTA 25. Among the detected SNPs, one and two SNPs were associated with marbling score (ARS-BFGL-NGS-110066 on BTA 23) and meat colour (BTB-01920239 on BTA 15 and ARS-BFGL-NGS-24934 on BTA 18). In this GWAS, we identified three positional candidate genes for carcass traits, backfat thickness (Fibulin-2, FBLN2; Sorting nexin 29, SNX29) and meat colour (WW domain containing oxidoreductase, WWOX). Our results suggest that the candidate SNP markers do affect the genomic selection of associated carcass traits for Hanwoo in the Gangwon region.

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Genome Wide Association Study to Identity QTL for Growth Taits in Hanwoo

Cited by 3 publications

References 18 publications

Identification of CNVs and their association with the meat traits of Hanwoo

Identification of CNVs and their association with the meat traits of Hanwoo

Estimation of the Accuracy of Genomic Breeding Value in Hanwoo (Korean Cattle)

Genome-wide association analysis to identify QTL for carcass traits in Hanwoo (Korean native cattle)

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