제주흑돈 산육형질의 후보유전자 탐색을 위한 전장유전체 분석 및 유전체 육종가 정확도 평가
Evaluation of the Accuracy of Genomic Breeding Value and Genome-wide Association Study to Identity Candidate Genes for Productive Traits in Jeju Black Pigs
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초록
본 연구는 제주지역에서 사육되고 있는 제주 재래돼지기반의 제주흑돈(제주재래돼지 합성돈)에 대하여 산육형질인 등지방 두께, 일당증체량, 90 kg 도달일령에 대한 후보유전자 탐색을 위해 전장유전체 분석을 실시하였고, 유전체 육종가의 정확도 비교를 위해 베이지안 방법(BayesB, BayesC), (0.00, 0.50, 0.90, 0.99)값과 개체 자신과 후대의 정보만 포함하고 조상의 정보에 대해 정보를 보정한 DEBVexcPA (Deregressed EBV exlude parents average)와 부모 평균을 포함한 DEBVincPA (Deregressed EBV include parents average)의 반응변수를 이용하였다. 산육형질에 대한 전장유전체 분석을 실시한 결과 등지방두께는 KIAA1549 유전자(SSC18 at 11Mb region), 일당증체량과 90 kg 도달일령에서POLD3(SSC9 at 9Mb region), STX6(SSC9 at 134Mb region) 유전자가 공통적으로 탐색되었다. 유전체의 정확도 범위는 일당증체량 BayesB의경우 DEBVexcPA와 DEBVincPA에서 각각 0.285~0.305와 0.497~0.510과 BayesC에서 0.287~0.296와 0.499~0.511으로 추정되었다. 90 kg 도달일령은 BayesB에서 DEBVexcPA와 DEBVincPA는 각각 0.284~0.305와 0.497~0.510, BayesC에서는 0.284~0.296와 0.498-0.511로 추정되었다. 특히, 등지방두께의 유전체 정확도가 BayesB방법론의 DEBVincPA에서 0.625로 가장 높게 추정되었다. 제주흑돈의 산육형질에 대한 유전적인개량 속도를 가속화하기 위해 유전체 선발법을 적용하는데 있어 부모 평균을 포함한 DEBVincPA (Deregressed EBV include parents average)의반응변수를 이용하는 것이 바람직하다고 판단된다.
Abstract
This study investigated the genomic prediction accuracy for backfat thickness (BF), average daily gain (ADG) and days to 90 kg (DAYS) of Jeju Black pigs. The genome-wide association study (GWAS) was performed by using Illumina porcine80Kv1. The BayesB and BayesC methods with various π(0.00, 0.50, 0.90, 0.99) and weighted response variables (DEBVincPA and DEBVexcPA) were used to estimate SNP effects. In GWAS, KIAA1549 gene (SSC18 at 11Mb region) was found at backfat thickness, and POLD3 (SSC9 at 9Mb region) and STX6 genes (SSC9 at 134Mb region) were commonly identified at the DAYS and ADG. The genomic prediction accuracy for BF using BayesB ranges from 0.479 to 0.495 for DEBVexcPA, and 0.617 to 0.625 for DEBVincPA, whereas the BayesC based ranges were 0.471 to 0.490, 0.615 to 0.623, respectively. In the ADG, using BayesB ranges from 0.285 to 0.305 for DEBVexcPA, and 0.568 to 0.613 for DEBVincPA, whereas the BayesC based ranges were 0.287 to 0.296, 0.499 to 0.511, respectively. The traits of DAYS using BayesB ranges from 0.284 to 0.305 for DEBVexcPA, and 0.497 to 0.510 for DEBVincPA, whereas the BayesC based ranges were 0.284 to 0.296, 0.498 to 0.511, respectively. In particular, the genomic prediction accuracy of BF was estimated to be 0.625 in the DEBVincPA of BayesB method, and it was found that the genetic improvement rate for BF, which is the most important issue in Jeju black pigs, can be accelerated by adding genomic information to the traditional BLUP methods.
참고문헌 (14)
- Bergamaschi M, "Gut microbiome composition differences among breeds impact feed efficiency in swine", Microbiome, 8, pp.1~15 (2020)
- Dashab GR, "Comparison of linear mixed model analysis and genealogy-based haplotype clustering with a Bayesian approach for association mapping in a pedigreed population", BMC Proceedings, 6, pp.1~5 (2012)
- 가천흥, "개량종 돼지와 재래 흑돼지에서 도체중과 등지방 두께간의 상관 관계", 동물자원연구, 18, pp.111~121 (2007), 동물생명과학연구소
- Garrick DJ, "Implementing a QTL detection study (GWAS) using genomic prediction methodology", pp.275~298 (2013), Humana Press
- Garrick DJ, "Deregressing estimated breeding values and weighting information for genomic regression analyses", Genetics Selection Evolution, 41, pp.1~8 (2009)
- Gilmour A, "ASReml user guide release 4.1 structural specification" (2015), VSN International Ltd
- Habier D, "Extension of the bayesian alphabet for genomic selection", BMC Bioinformatics, 12, pp.186~ (2011)
- Jin SK, "Physicochemical characteristics of longissimus muscle between the Korean native pig and Landrace", Korean J Food Sci Anim Resour, 21, pp.142~148 (2001)
- Kizilkaya K, "Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes", J. of Animal Science, 88, pp.544~551 (2010)
- Meuwissen THE, "Prediction of total genetic value using genome-wide dense marker maps", Genetics, 157, pp.1819~1829 (2001)
- 문윤희, "제주도 개량 흑돼지 고기의 이화학적 및 관능적 품질 특성", 한국축산식품학회지, 24(3), pp.238~245 (2004), 한국축산식품학회
- Saatchi M, "Accuracy of direct genomic breeding values for nationally evaluated traits in US Limousin and Simmental beef cattle", Genetics Selection Evolution, 44, pp.1~10 (2012)
- Sargolzaei M, "A new approach for efficient genotype imputation using information from relatives", BMC Genomics, 15, pp.1~12 (2014)
- Amino acid contents and meat quality properties on the loin from crossbred black and crossbred black and crossbred pigs reared in Jejudo, "Yang SJ", Food Science of Animal, ~ (2005)