Journal of Animal Breeding and Genomics (J Anim Breed Genom)
Eun Ho Kim1, Du Won Sun2, Ho Chan Kang3, Dae Yong Yang4, Cheol Hyun Myung1, Ji Yeong Kim1, Hyun Tae Lim1*
1Department of Animal Science, Gyeongsang National University, Jinju 52828, Korea
2Gyeongnam Animal Science & Technology, Gyeongsang National University, Jinju 52828, Korea
3Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea
4Korea Institute for Animal Product Quality Evaluation, Sejong 30100, Korea
Correspondence to Hyun Tae Lim, E-mail: s_htim@gnu.ac.kr
Volume 6, Number 4, Pages 155-161, December 2022.
Journal of Animal Breeding and Genomics 2022, 6(4), 155-161. https://doi.org/10.12972/jabng.20220017
Received on November 09, 2022, Revised on December 15, 2022, Accepted on December 16, 2021, Published on December 31, 2022.
Copyright © 2022 Korean Society of Animal Breeding and Genetics.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0).
Reproductive trait of cows are important factors affecting pregnancy and calving cycle, and a short calving cycle leads to increase productivity of livestock, so improvement is essential. However, the improvement standards for reproductive traits and studies on causative genes are insufficient. Therefore, in this study, GWAS (Genome-Wide Association Study) analysis was conducted on Hanwoo cow in the Gyeongsan provice. Heifer traits were FS (Age at 1st service), FCO (Age at 1st conception), FCA (Age at 1st calving) and 874 animals were used for analysis, and cow traits were GL (Gestation length), DO (Day open), CI (Calving interval), NS (Number of service) and 741 animals were used for analysis. Hanwoo 50K SNP (Single Nucleotide Polymorphism) BeadChiop was used for the genotype, and 37,903 SNP markers were used for the heifer trait and 38,011 SNP markers were used for the cow trait through the quality control option of less than 1% minor allele frequency, more than10% missing genotype, less than 10-6 HWE (Hardy-Weinberg Equilibrium) on the PLINK 1.9. Thereafter, the genome-wide threshold level was determined using the Bonferroni method, and SNP marker were identified according to each trait. As a result, three SNP markers on chromosomes 12, 13, 24 in FS (ARS-BFGL-BAC-830, BTB-00532606, ARS-BFGL-NGS-33785), and two SNP markers on chromosomes 3, 20 in GL (BTA-94162-no-rs, Hapmap47647-BTA-50780), and two SNP marker on chromosomes 27, 28 in NS (ARS-BFGL-NGS-58109, BTB-00973399) were identified. Then, the seven candidate genes with the closest significant SNP markers were identified. Among them, PCK1 in FS is a gene that affects the promotion of progesterone activity, and it has been reported that it is helpful for reproductive efficiency by affecting follicle development and pregnancy rate. In the future, if additional research is conducted by setting up suitable models for reproductive traits and continuously increasing the test population, it is judged that it will be possible to clearly identify causative genes for each trait.
cow, genotype, genome-wide association study, reproductive trait, single nucleotide polymorphism
농촌진흥청(Rural Development Administration) 공동연구사업(과제번호: PJ0162182021)의 지원에 의해 이루어진 것이며, 연구비 지원에 감사드립니다.
No potential conflict of interest relevant to this article was reported.
Bland JM, Altman DG. 1995. Multiple significance tests: The Bonferroni method. British Medical Journal 310:170.
[DOI][PubMed][PMC]
Bedford A, Beckett L, Hardin K, Dias NW, Davis T, Mercadante VRG, Ealy AD, White RR. 2018. Propionate affects insulin signaling and progesterone profiles in dairy Heifers. Scientific Reports 8:17629.
[DOI][PubMed][PMC]
Choe CY, Son DS, Choi GC, Song SH, Choe CY, Kim HJ, Cho SR, Hur CG, Kang DW. 2006. Survey on the incidence of reproductive disorder in Hanwoo. Journal of Embryo Transfer 21(4):331-338. [in Korean]
Cho JS, Do CH, Choi IC. 2016. Reproductive performance of Korean native cattle (Hanwoo) focusing on calving interval and parity. Journal of Embryo transfer 31(3):273-279. [in Korean]
[DOI]
Cochran SD, Cole JB, Null DJ, Hansen PJ. 2013. Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle. BMC Genetics 14:49.
[DOI][PubMed][PMC]
Han KJ. 2002. Effects of environmental factors on reproductive traits in Korean cattle. Journal of Animal Science and Technology 44(2):191-200. [in Korean]
[DOI]
Hudson NJ, Porto-Neto L, Naval-Sanchez M, Lyons RE, Reverter A. A conserved haplotype in Wagyu cattle contains RAB4A whose encoded protein regulates glucose trafficking in muscle and fat cells. Animal Genetics 52(3):275-283.
[DOI][PubMed]
Jeong CS, Jang SS, Lee SS, Moon YH. 2016. Effects of Concentrate Feeding Level after Sexual Maturity on the Growth and Breeding Performances, Blood Composition, and Ultrasonic Carcass Traits in Hanwoo Cows. Journal of Agriculture & Life Science 50(4):113-125. [in Korean]
[DOI]
Kim EH, Kim HK, Sun DW, Kang HC, Lee DH, Lee SH, Lee JB, Lim HT. 2020. The study on estimated breeding value and accuracy for economic traits in Gyoungnam Hanwoo cow (Korean cattle). Journal of Animal Science and Technology 62(4):429-437
[DOI][PubMed][PMC]
KIAPQE (Korea Institute for Animal Products Quality Evaluation). 2021. 2020 animal products garding statistical yearbook. KIAPQE, Sejong, Korea. [in Korean]
Kim HJ, Heras-Saldana SDL, Moghaddar N, Lee SH, Lim DJ, Werf JVD. 2022. Genome-wide association study for carcass trait in Hanwoo cattle using additional relatives’ information of non-genotyped animals. Animal Genetics 53(6):863-866.
[DOI][PubMed]
Kwon DJ, Lee SM, Kim DH, Oh JD. 2019. Analysis and evaluation of reproductive performance of Korean native cattle (Hanwoo) in Jeonbuk province. Jouranl of Agricultural & Life Science 53(3):113-121. [in Korean]
[DOI]
Mahnani A, Sadeghi-Sefidmazgi A, Ansari-Mahyari S, Ghiasi H, Toghiani S. 2022. Genetic analysis of retained placenta and its association with reproductive disorder, production, and fertility traits of Iranian Holstein dairy cows. Theriogenology 189:59.63.
[DOI][PubMed]
Penagaricano F, Weigel KA, Khatib H. 2012. Genome-wide association study identifies candidate markers for bull fertility in Holstein dairy cattle. Animal Genetics 43(s1):65-71.
[DOI][PubMed]
Song CW. 2017. Assessment of inbreeding effects and estimation of genetic parameters for economic traits in Hanwoo cattle. Ph.D. dissertation. Sunchon National Univ., Jeonnam, Korean. [in Korean]
Utrera AR, Van Vleck LD. 2004. Heritability estimates for carcass traits of cattle: a review. Genetics and Molecular Research 3(3):380-394.
Yang BC, Kang SS, Kim UH, Jang SS, Yang BS, Lee SD, Cho SR. 2017. Surveys on reproduction status and calf production of Hanwoo farmers. Journal of Embryo Transfer 32(3):171-176. [in Korean]
[DOI]
Zhou X, Stephens M. 2012. Genome-wide efficient mixed-model analysis for association studies. Nature Geneics 44:821-824.
[DOI][PubMed][PMC]
Zhang Q, Koser SL, Donkin SS. 2021. Identification of promoter response elements that mediate propionate induction of bovine cytosolic phosphoenolpyruvate carboxykinase (PCK1) gene transcription. Journal of Dairy Science 104(6):7252-7261.
[DOI][PubMed]