Identification of new semen trait-related candidate genes in Duroc boars through genome-wide association and weighted gene co-expression network analyses

Semen traits are crucial in commercial pig production since semen from boars is widely used in artificial insemination for both purebred and crossbred pig production. Revealing the genetic architecture of semen traits potentially promotes the efficiencies of improving semen traits through artificial selection. This study is aimed to identify candidate genes related to the semen traits in Duroc boars. First, we identified the genes that were significantly associated with three semen traits, including sperm motility (MO), sperm concentration (CON), and semen volume (VOL) in a Duroc boar population through a genome-wide association study (GWAS). Second, we performed a weighted gene co-expression network analysis (WGCNA). A total of 2, 3, and 20 single-nucleotide polymorphisms were found to be significantly associated with MO, CON, and VOL, respectively. Based on the haplotype block analysis, we identified one genetic region associated with MO, which explained 6.15% of the genetic trait variance. ENSSSCG00000018823 located within this region was considered as the candidate gene for regulating MO. Another genetic region explaining 1.95% of CON genetic variance was identified, and, in this region, B9D2, PAFAH1B3, TMEM145, and CIC were detected as the CON-related candidate genes. Two genetic regions that accounted for 2.23% and 2.48% of VOL genetic variance were identified, and, in these two regions, WWC2, CDKN2AIP, ING2, TRAPPC11, STOX2, and PELO were identified as VOL-related candidate genes. WGCNA analysis showed that, among these candidate genes, B9D2, TMEM145, WWC2, CDKN2AIP, TRAPPC11, and PELO were located within the most significant module eigengenes, confirming these candidate genes’ role in regulating semen traits in Duroc boars. The identification of these candidate genes can help to better understand the genetic architecture of semen traits in boars. Our findings can be applied for semen traits improvement in Duroc boars.     

Comparison of genetic improvement for litter size at birth by direct and indirect selection in swine herd

Responses to selection for number of piglets born alive (NBA) by the total number of piglets born (TNB), the NBA, and the NBA plus number of piglets born dead (NBD) were compared using the accuracy of selection and expected genetic gain calculated from the selection index with family information and the real response to selection, using data generated by Monte Carlo computer simulation. The accuracy of selection for NBA selected by TNB was higher than that by NBA only if the genetic correlation between TNB and NBA was close to 1.0, or the value of heritability for the TNB was much larger than that for the NBA. The accuracy of selection for the NBA selected by the combination of the TNB and the NBA was generally highest in the three selection methods in each family structure. Selection by the TNB resulted in the greatest expected genetic gain for the TNB among the selection methods. In the best linear unbiased prediction (BLUP) selection, the genetic gain for the NBA accumulated by the NBA tended to be similar to that accumulated by the combination of the NBA and the NBD, and both genetic gains at generation 10 were significantly larger than that by the TNB (P < 0.001). The accumulated responses selected by the two‐trait animal model BLUP estimated from genetic parameters with errors were similar to those estimated from the true parameters, and there was no significant difference between them. These results indicate that selection by the NBA or by the NBA and the NBD gives more genetic improvement in the NBA than that by the TNB.     

军牧1号白猪6号染色体抗病基因FUT1和RYR1的合并选择

FUT1和RYR1是猪6q11～12区段的抗病侯选基因,为探讨军牧1号白猪群体中2基因的关联度,随机选取177头军牧1号白猪,采用PCR-RFLP法检测2对等位基因频率和基因型频率、计算连锁不平衡参数。结果表明,军牧1号白猪群体中优势基因FUT1A的频率为0.395,RYR1T的频率为0.765,两者的连锁不平衡参数LD=0.010 7和相关系数r=0.093 6均接近于零,可判定两者不存在连锁关系。研究结果支持在军牧1号白猪群体中同时进行抗病基因FUT1和RYR1的合并选择。     

An evaluation of alternative selection indexes for a non‐linear profit trait approaching its economic optimum

This study used simulation to evaluate the performance of alternative selection index configurations in the context of a breeding programme where a trait with a non‐linear economic value is approaching an economic optimum. The simulation used a simple population structure that approximately mimics selection in dual purpose sheep flocks in New Zealand (NZ). In the NZ dual purpose sheep population, number of lambs born is a genetic trait that is approaching an economic optimum, while genetically correlated growth traits have linear economic values and are not approaching any optimum. The predominant view among theoretical livestock geneticists is that the optimal approach to select for nonlinear profit traits is to use a linear selection index and to update it regularly. However, there are some nonlinear index approaches that have not been evaluated. This study assessed the efficiency of the following four alternative selection index approaches in terms of genetic progress relative to each other: (i) a linear index, (ii) a linear index updated regularly, (iii) a nonlinear (quadratic) index, and (iv) a NLF index (nonlinear index below the optimum and then flat). The NLF approach does not reward or penalize animals for additional genetic merit beyond the trait optimum. It was found to be at least comparable in efficiency to the approach of regularly updating the linear index with short (15 year) and long (30 year) time frames. The relative efficiency of this approach was slightly reduced when the current average value of the nonlinear trait was close to the optimum. Finally, practical issues of industry application of indexes are considered and some potential practical benefits of efficient deployment of a NLF index in highly heterogeneous industries (breeds, flocks and production environments) such as in the NZ dual purpose sheep population are discussed.     

PRKAG3基因在不同品种猪不同生长阶段骨骼肌中的表达差异及其表达量与肉质的关系

本试验中旨在比较PRKAG3基因在不同品种猪不同生长阶段骨骼肌中的表达差异,并探讨PRKAG3基因与肉质的关系。挑选15 kg左右的汉普夏阉公猪17头和长撒阉公猪16头,饲喂相同饲粮,当体重分别达到20和50 kg时,2个品种的猪分别屠宰5头,体重达到100 kg时分别屠宰7和6头。各生长阶段屠宰后均测定骨骼肌pH、肌糖原含量以及PRKAG3基因表达量,且在100 kg阶段屠宰后同时测定肉质性状。结果表明:1)在不同生长阶段长撒猪骨骼肌中PRKAG3基因的表达量均高于汉普夏猪,特别是在100 kg阶段,长撒猪骨骼肌中PRKAG3基因的表达量是汉普夏猪的6.81倍(P0.05)。长撒猪与汉普夏猪骨骼肌中PRKAG3基因的表达量均随体重的增加而增加,但汉普夏猪不同生长阶段PRKAG3基因的表达量差异不显著(P0.05),而长撒猪PRKAG3基因的表达量在100 kg阶段时显著高于20和50 kg阶段时(P0.05)。2)汉普夏猪和长撒猪的肉质存在差异。汉普夏猪的滴水损失和失水率显著高于长撒猪(P0.05),而熟肉率、黄度(b)值极显著低于长撒猪(P0.01),剪切力和pH2(屠宰后24 h的pH)显著低于长撒猪(P0.05)。与长撒猪相比,汉普夏猪具有较高的肌糖原含量(P0.05)。3)猪骨骼肌中PRKAG3基因的表达量与肉质的相关性存在品种效应。汉普夏猪骨骼肌中PRKAG3基因表达量与滴水损失呈正相关,与熟肉率呈负相关,与pH2呈显著负相关(P0.05)。长撒猪骨骼肌中PRKAG3基因表达量与滴水损失和失水率呈正相关,与pH2呈负相关。上述结果表明,猪骨骼肌中PRKAG3基因具有品种和生长阶段表达差异;猪骨骼肌中PRKAG3基因的表达量与肉质性状相关,特别是与pH2,二者呈显著负相关。     

Quantitative genetic changes in reproductive performance of giant freshwater prawn after 10 years of selection for increased growth rate

Effect of long‐term selection for improved growth on reproductive performance of giant freshwater prawn (GFP) Macrobrachium rosenbergii has not been reported in the literature. The present study aimed to measure correlated responses in reproductive traits and to estimate genetic parameters for these characters in a GFP population selected for high growth over ten generations from 2007 to 2016. A total of 959 breeding females (offspring of 515 sires and 810 dams) had measurements for seven reproductive traits (weight before spawn WBS; weight after spawn WAS; Fecundity FEC or number of larvae per female at hatching; first age to reach post‐larvae PLAGE; zoea (e) weight ZOEAWT; larval survival during hatchery phase SURV1 and survival from PL to tagging SURV2. The restricted maximum likelihood (REML) and mixed model analysis were used to estimate genetic parameters and evaluate selection responses for the seven traits studied. Our REML analysis showed that heritability for these traits ranged from 0.04 to 0.42 (SE: 0.19–0.28). Female body weight either before or after spawning had strong positive phenotypic correlations with fecundity (0.52–0.98). By contrast, the phenotypic correlations of WBS/WAS with larval and fry survivals were not significant (?0.08–0.05). Genetic correlations among fecundity‐related traits studied were not different from zero due to their high standard errors. Correlated responses in reproductive traits were measured by comparing least squares means of the selection line and control group. Females of the selected line for high growth had significantly greater weight before or after spawning than that of the control group. There were, however, no statistical differences between the two lines in the other traits. It is concluded that selection for high growth did not have detrimental impact on reproductive performance of breeding females in the present population of GFP.     

Genome‐wide association study for carcass traits,fatty acid composition,chemical composition,sugar, and the effects of related candidate genes in Japanese Black cattle

We performed a genome‐wide association study (GWAS) and candidate gene analysis to: (i) evaluate the effectiveness of the GWAS in our small population by performing GWAS for carcass weight (CW) and fatty acid composition; (ii) detect novel candidate regions affecting non‐CW carcass traits, chemical composition and sugar; and (iii) evaluate the association of the candidate genes previously detected in CW and fatty acid composition with other economically important traits. A total of 574 Japanese Black cattle and 40 657 Single nucleotide polymorphisms were used. In addition, candidate gene analyses were performed to evaluate the association of three CW‐related genes and two fatty acid‐related genes with carcass traits, fatty acid composition, chemical composition and sugar. The significant regions with the candidate genes were detected for CW and fatty acid composition, and these results showed that a significant region would be detectable despite the small sample size. The novel candidate regions were detected on BTA23 for crude protein and on BTA19 for fructose. CW‐related genes associated with the rib‐eye area and fatty acid composition were identified, and fatty acid‐related genes had no relationship with other traits. Moreover, the favorable allele of CW‐related genes had an unfavorable effect on fatty acid composition.