A genome-wide association study of reproduction traits in four pig populations with different genetic backgrounds

Jiang Yao,Tang Shaoqing,Xiao Wei,Yun Peng,Ding Xiangdong 아세아·태평양축산학회 2020 Animal Bioscience Vol.33 No.9

Objective: Genome-wide association study and two meta-analysis based on GWAS performed to explore the genetic mechanism underlying variation in pig number born alive (NBA) and total number born (TNB). Methods: Single trait GWAS and two meta-analysis (single-trait meta analysis and multi-trait meta analysis) were used in our study for NBA and TNB on 3,121 Yorkshires from 4 populations, including three different American Yorkshire populations (n = 2,247) and one British Yorkshire populations (n = 874). Results: The result of single trait GWAS showed that no significant associated single nucleotide polymorphisms (SNPs) were identified. Using single-trait meta analysis and multi-trait meta analysis within populations, 11 significant loci were identified associated with target traits. Spindlin 1, vascular endothelial growth factor A, forkhead box Q1, msh homeobox 1, and LHFPL tetraspan submily member 3 are five functionally plausible candidate genes for NBA and TNB. Compared to the single population GWAS, single-trait Meta analysis can improve the detection power to identify SNPs by integrating information of multiple populations. The multiple-trait analysis reduced the power to detect trait-specific loci but enhanced the power to identify the common loci across traits. Conclusion: In total, our findings identified novel genes to be validated as candidates for NBA and TNB in pigs. Also, it enabled us to enlarge population size by including multiple populations with different genetic backgrounds and increase the power of GWAS by using meta analysis.

국내 품종 재래돼지 산자수에 대한 근친퇴화 효과

김영신(Young-Sin Kim),조규호(Kyu-Ho Cho),이미진(Mi-Jin Lee),김정아(Jeong-A Kim),조은석(Eun-Seok Cho),홍준기(Joon-Ki Hong) 한국산학기술학회 2019 한국산학기술학회논문지 Vol.20 No.6

근친에 따른 개체의 능력저하 현상은 다양한 식물과 동물에서 밝혀져 왔다. 재래돼지는 국내 유일 품종이며 소규모 집단으로 유지되고 있어 국가차원에서 중요한 유전자원이다. 본 연구의 목적은 총산자수와 생존산자수에 대한 근교계수, 유전모수 및 근친퇴화 효과를 분석하는 것이다. 국립축산과학원에서 보유한 재래돼지 혈통 2,806두와 483개(1~5산차)의 번식성적을 보유한 모돈 303두의 자료를 활용하였다. 각 형질에 대한 유전모수 추정 후 혼합모형으로 근교계수에 대한 근친퇴화 효과를 분석하였다. 유전모수 추정결과, 총산자수와 생존산자수는 고도의 유전력을 유지하였다. 근교계수는 1998년에서 2017~2018년까지 꾸준히 증가하였으나, 각 형질에 대해 1998년 대비 2017~2018년의 능력감소는 확인되지 않았다. 근교계수 증가에 따라 총산자수의 유의적인 근친퇴화(p=0.03)가 확인되었지만, 생존산자수에서는 유의적인 근친퇴화가 없었다(p=0.41). 또한 두 형질 모두 근교계수와 육종가의 긍정적 상호작용이 확인되었다(p<0.05). 본 연구 결과, 재래돼지 산자수에 대한 근친퇴화 효과가 일부 확인되었지만, 세대가 지남에 따라 명확한 표현형 감소는 확인되지 않았다. 이는 현재까지 높은 유전효과로 근친퇴화를 극복할 수 있음을 시사한다. The reduction in performance due to inbreeding (i.e. inbreeding depression) has long been documented in plant and animal populations. The population of Korean native pigs are small and this breed is valuable in Korea.. This study was aimed to investigate effects of inbreeding depression on total number of piglets born (TNB) and number of piglets born alive (NBA) in Korean native pigs. We used 2,806 pedigree and 303 sows’s data with 483 phenotypic records. After estimating genetic parameters for each traits, inbreeding depression was estimated using a mixed model in which the inbreeding coefficient was included as a covariate. Korean native pigs had high heritability for each traits. Inbreeding coefficient constantly increased from 1998 to 2017~2018 but there is no reduction for each traits in 2017~2018 in compared with those in 1998. Significant inbreeding depression was detected for TNB (p=0.03) but not for NBA (p=0.41). In addition there are significantly positive interactions between inbreeding coefficient and breeding value for both traits (p<0.05). These results suggest that Korean native pigs are still having genetic variation for TNB and NBA, which could overcome reproductive risks from inbreeding coefficient increase.

Connectedness rating among commercial pig breeding herds in Korea

Wonseok Lee,Jong Hyun Jung,오상현 한국축산학회 2024 한국축산학회지 Vol.66 No.2

This study aims to estimate the connectedness rating (CR) of Korean swine breeding herds. Using 104,380 performance and 83,200 reproduction records from three swine breeds (Yorkshire, Landrace and Duroc), the CR was estimated for two traits: average daily gain (ADG) and number born alive (NBA) in eight breeding herds in the Republic of Korea (hereafter, Korea). The average CR for ADG in the Yorkshire breed ranges from 1.32% to 28.5% depending on the farm. The average CR for NBA in the Yorkshire herd ranges from 0% to 12.79%. A total of 60% of Yorkshire and Duroc herds satisfied the preconditions suggested for genetic evaluation among the herds. The precondition for the genetic evaluation of CR for ADG, as a productive trait, was higher than 3% and that of NBA, as a reproductive trait, was higher than 1.5%. The ADG in the Yorkshire herds showed the highest average CR. However, the average CR of ADG in the Landrace herds was lower than the criterion of the precondition. The prediction error variance of the difference (PEVD) was employed to assess the validation of the CR, as PEVDs exhibit fluctuations that are coupled with the CR across the herds. A certain degree of connectedness is essential to estimate breeding value comparisons between pig herds. This study suggests that it is possible to evaluate the genetic performance together for ADG and NBA in the Yorkshire herds since the preconditions were satisfied for these four herds. It is also possible to perform a joint genetic analysis of the ADG records of all Duroc herds since the preconditions were also satisfied. This study provides new insight into understanding the genetic connectedness of Korean pig breeding herds. CR could be utilized to accelerate the genetic progress of Korean pig breeding herds.

요크셔종의 산자수에 대한 통합평가모형에서 농장과 산차간 상호작용 효과

박준,나종삼 경상대학교 농업생명과학연구원 2020 농업생명과학연구 Vol.54 No.2

본 연구는 3개의 종돈회사가 보유하고 있는 6곳의 GGP 농장에서 분만한 Yorkshire종의 번식기록을 이용하여 농장과 산차간의 상호작용효과를 구명하는데 있다. 총산자수와 생존산자수의 평균은 각각 13.4±3.6두와 12.5±3.4두였으며, LSO와 LDO의 평균 세대간격은 각각 17.5개월과 22.0개월로 추정되었다. 산차별 총산자수 기록의 분포는 A(10), B(21), C(30) 그룹과 B(20), B(22), C(31) 그룹에서 뚜렷한 차이를 나타내었으며, 농장×산차의 상호작용효과는 고도의 유의차(P < 0.01)가 인정되었다. Model Ⅱ에서 추정된 유전력과 반복력은 총산자수에서 각각 0.13과 0.21, 생존산자수에서 각각 0.11과 0.19로 나타났다. 총산자수의 육종가를 이용하여 선발된 분만 기록이 있는 개체의 top 1% 비율은 ModelⅠ에서 A(10)농장이 67.4%로 가장 높았고 B(20), C(30), B(21)순이었으나, ModelⅡ에서 B(22)농장이 35.8%로 가장 높았고, B(20) 34.7%, B(21) 12.6%순이었다. 총산자수의 육종가를 이용하여 선발된 자손의 기록이 있는 씨수퇘지들의 top 1% 비율은 ModelⅠ에서 A(10)농장이 55.6%로 가장 높았으나 ModelⅡ에서 C(31)농장이 33.3%로 가장 높았고 B(20)과 B(21) 22.2%순이었다. This study was conducted to investigate the interaction effect between farms and parity using the reproductive records of Yorkshire pig from six GGP farms owned by three breeding companies. The means of the TNB and NBA were 13.4±3.6 and 12.5±3.4 heads, respectively. Average generation intervals of the LSO and LDO were estimated to be 17.5 and 22.0 months, respectively. The distribution of TNB records by parity showed distinct differences in two groups as farm code A(10), B(21), C(30) and farm code B(20), B(22), C(31). The interaction effect between parity and farm was found to be highly significant (p < 0.01). The estimates of heritability and repeatability in Model II which additionally considered the interaction effect of parity and farm for TNB were 0.13 & 0.21 and for NBA were 0.11 & 0.19, respectively. The proportion of sows with delivery records that were selected in the top 1% according to the breeding value of TNB estimated in Model I was the highest at 67.4%, in A(10) farms, followed by B(20), C(30) and B(21). However, the proportion was highest in B(22), 35.8%, followed by B(20), 34.7% and B(21), 12.6% in Model II. The proportion of boars with progeny records that were selected in the top 1% according to the breeding value of TNB estimated in Model I was the highest at 55.6% in A(10) farms, however, the proportion was highest in C(31), 33.3%, followed by B(20) & B(21), both 22.2% in Model II.