Arachnomelia syndrome (AS) is an autosomal recessive hereditary disorder in cattle, and affected calves are usually stillborn and characterized by complex anomalies. Therefore, identification of the carrier animals based on genetic tests is important for the control and elimination of this defect. The aim of this study was to build an effective workflow to routinely screen the AS mutations in bovine MOSC1 and SUOX genes and determine individuals carrying the AS mutations in four Chinese cattle populations.

本研究通过选择难产率低的蒙贝利亚公牛与荷斯坦母牛杂交,比较蒙×荷杂种牛和纯种荷斯坦牛早期生长发育性状.结果表明杂种牛在初生～3月龄期间与荷斯坦牛各项指标差异不显著(P≥0.05);4月龄后,杂种牛体重、胸围、体高等性状都极显著高于同期的荷斯坦牛(P<0.01).相关性分析显示发育早期阶段,体重与胸围、体斜长、十字部高、尻长和腰角宽相关程度最高,相关系数为0.91以上(P<0.05).结果表明,选种难产率低的蒙贝利亚公牛与荷斯坦牛杂交,犊牛出生时体重与体尺与荷斯坦牛无差异,但杂种牛表现出更优的增长趋势,杂交效果明显.

Utilization of feed in livestock species consists of a wide range of biological processes, and therefore, its efficiency can be expressed in various ways, including direct measurement, such as daily feed intake, as well as indicator measures, such as feeding behavior. Measuring feed efficiency is important to the swine industry, and its accuracy can be enhanced by using automated feeding systems, which record feed intake and associated feeding behavior of individual animals. Each automated feeder space is often shared among several pigs and therefore raises concerns about social interactions among pen mates with regard to feeding behavior. The study herein used a data set of 14,901 Duroc boars with individual records on feed intake, feeding behavior, and other off-test traits. These traits were modeled with and without the random spatial effect of Pen_Room, a concatenation of room and pen, or random social interaction among pen mates. The nonheritable spatial effect of common Pen-Room was observed for traits directly measuring feed intake and accounted for up to 13% of the total phenotypic variance in the average daily feeding rate. The social interaction effect explained larger proportions of phenotypic variation in all the traits studied, with the highest being 59% for ADFI in the group of feeding behaviors, 73% for residual feed intake (RFI; RFI4 and RFI6) in the feed efficiency traits, and 69% for intramuscular fat percentage in the off-test traits. After accounting for the social interaction effect, residual BW gain and RFI and BW gain (RIG) were found to have the heritability of 0.38 and 0.18, respectively, and had strong genetic correlations with growth and off-test traits. Feeding behavior traits were found to be moderately heritable, ranging from 0.14 (ADFI) to 0.52 (average daily occupation time), and some of them were strongly correlated with feed efficiency measures; for example, there was a genetic correlation of 0.88 between ADFI and RFI6. Our work suggested that accounting for the social common pen effect was important for estimating genetic parameters of traits recorded by the automated feeding system. Residual BW gain and RIG appeared to be two robust measures of feed efficiency. Feeding behavior measures are worth further investigation as indicators of feed efficiency.

Obtaining accurate individual feed intake records is the key first step in achieving genetic progress toward more efficient nutrient utilization in pigs. Feed intake records collected by electronic feeding systems contain errors (erroneous and abnormal values exceeding certain cutoff criteria), which are due to feeder malfunction or animal-feeder interaction. In this study, we examined the use of a novel data-editing strategy involving multiple imputation to minimize the impact of errors and missing values on the quality of feed intake data collected by an electronic feeding system. Accuracy of feed intake data adjustment obtained from the conventional linear mixed model (LMM) approach was compared with 2 alternative implementations of multiple imputation by chained equation, denoted as MI (multiple imputation) and MICE (multiple imputation by chained equation). The 3 methods were compared under 3 scenarios, where 5, 10, and 20% feed intake error rates were simulated. Each of the scenarios was replicated 5 times. Accuracy of the alternative error adjustment was measured as the correlation between the true daily feed intake (DFI; daily feed intake in the testing period) or true ADFI (the mean DFI across testing period) and the adjusted DFI or adjusted ADFI. In the editing process, error cutoff criteria are used to define if a feed intake visit contains errors. To investigate the possibility that the error cutoff criteria may affect any of the 3 methods, the simulation was repeated with 2 alternative error cutoff values. Multiple imputation methods outperformed the LMM approach in all scenarios with mean accuracies of 96.7, 93.5, and 90.2% obtained with MI and 96.8, 94.4, and 90.1% obtained with MICE compared with 91.0, 82.6, and 68.7% using LMM for DFI. Similar results were obtained for ADFI. Furthermore, multiple imputation methods consistently performed better than LMM regardless of the cutoff criteria applied to define errors. In conclusion, multiple imputation is proposed as a more accurate and flexible method for error adjustments in feed intake data collected by electronic feeders.

Background: Feed intake and growth are economically important traits in swine production. Previous genome wide association studies (GWAS) have utilized average daily gain or daily feed intake to identify regions that impact growth and feed intake across time. The use of longitudinal models in GWAS studies, such as random regression, allows for SNPs having a heterogeneous effect across the trajectory to be characterized. The objective of this study is therefore to conduct a single step GWAS (ssGWAS) on the animal polynomial coefficients for feed intake and growth.Results: Corrected daily feed intake (DFIAdj) and average daily weight measurements (DBWAvg) on 8981 (n = 525,240 observations) and 5643 (n = 283,607 observations) animals were utilized in a random regression model using Legendre polynomials (order = 2) and a relationship matrix that included genotyped and un-genotyped animals. A ssGWAS was conducted on the animal polynomials coefficients (intercept, linear and quadratic) for animals with genotypes (DFIAdj: n = 855; DBWAvg: n = 590). Regions were characterized based on the variance of 10-SNP sliding windows GEBV (WGEBV). A bootstrap analysis (n = 1000) was conducted to declare significance. Heritability estimates for the traits trajectory ranged from 0.34-0.52 to 0.07-0.23 for DBWAvg and DFIAdj, respectively. Genetic correlations across age classes were large and positive for both DBWAvg and DFIAdj, albeit age classes at the beginning had a small to moderate genetic correlation with age classes towards the end of the trajectory for both traits. The WGEBV variance explained by significant regions (P < 0.001) for each polynomial coefficient ranged from 0.2-0.9 to 0.3-1.01 % for DBWAvg and DFIAdj, respectively. The WGEBV variance explained by significant regions for the trajectory was 1.54 and 1.95 % for DBWAvg and DFIAdj. Both traits identified candidate genes with functions related to metabolite and energy homeostasis, glucose and insulin signaling and behavior.Conclusions: We have identified regions of the genome that have an impact on the intercept, linear and quadratic terms for DBWAvg and DFIAdj. These results provide preliminary evidence that individual growth and feed intake trajectories are impacted by different regions of the genome at different times.

Efficient use of feed resources has become a clear challenge for the U.S. pork industry as feed costs continue to be the largest variable expense. The availability of the Illumina Porcine60K BeadChip has greatly facilitated whole-genome association studies to identify chromosomal regions harboring genes influencing those traits. The current study aimed at identifying genomic regions associated with variation in feed efficiency and several production traits in a Duroc terminal sire population, including ADFI, ADG, feed conversion ratio, residual feed intake (RFI), real-time ultrasound back fat thickness (BF), ultrasound muscle depth, intramuscular fat content (IMF), birth weight (BW at birth), and weaning weight (BW at weaning). Single trait association analyses were performed using Bayes B models with 35,140 SNP on 18 autosomes after quality control. Significance of nonoverlapping 1-Mb length windows (n = 2,380) were tested across 3 QTL inference methods: posterior distribution of windows variances from Monte Carlo Markov Chain, naive Bayes factor, and nonparametric bootstrapping. Genes within the informative QTL regions for the traits were annotated. A region ranging from166 to 140 Mb (4-Mb length) on SSC 1, approximately 8 Mb upstream of the MC4R gene, was significantly associated with ADFI, ADG, and BF, where SOCS6 and DOK6 are proposed as the most likely candidate genes. Another region affecting BW at weaning was identified on SSC 4 (84-85 Mb), harboring genes previously found to influence both human and cattle height: PLAG1, CHCHD7, RDHE2 (or SDR16C5), MOS, RPS20, LYN, and PENK. No QTL were identified for RFI, IMF, and BW at birth. In conclusion, we have identified several genomic regions associated with traits affecting nutrient utilization that could be considered for future genomic prediction to improve feed utilization.

The efficiency of producing salable products in the pork industry is largely determined by costs associated with feed and by the amount and quality of lean meat produced. The objectives of this paper were 1) to explore heritability and genetic correlations for growth, feed efficiency, and real-time ultrasound traits using both pedigree and marker information and 2) to assess accuracy of genomic prediction for those traits using Bayes A prediction models in a Duroc terminal sire population. Body weight at birth (BW at birth) and weaning (BW at weaning) and real-time ultrasound traits, including back fat thickness (BF), muscle depth (MD), and intramuscular fat content (IMF), were collected on the basis of farm protocol. Individual feed intake and serial BW records of 1,563 boars obtained from feed intake recording equipment (FIRE; Osborne Industries Inc., Osborne, KS) were edited to obtain growth, feed intake, and feed efficiency traits, including ADG, ADFI, feed conversion ratio (FCR), and residual feed intake (RFI). Correspondingly, 1,047 boars were genotyped using the Illumina PorcineSNP60 BeadChip. The remaining 516 boars, as an independent sample, were genotyped with a low-density GGP-Porcine BeadChip and imputed to 60K. Magnitudes of heritability from pedigree analysis were moderate for growth, feed intake, and ultrasound traits (ranging from 0.44 ± 0.11 for ADG to 0.58 ± 0.09 for BF); heritability estimates were 0.32 ± 0.09 for FCR but only 0.10 ± 0.05 for RFI. Comparatively, heritability estimates using marker information by Bayes A models were about half of those from pedigree analysis, suggesting "missing heritability." Moderate positive genetic correlations between growth and feed intake (0.32 ± 0.05) and back fat (0.22 ± 0.04), as well as negative genetic correlations between growth and feed efficiency traits (-0.21 ± 0.08, -0.05 ± 0.07), indicate selection solely on growth traits may lead to an undesirable increase in feed intake, back fat, and reduced feed efficiency. Genetic correlations among growth, feed intake, and FCR assessed by a multiple-trait Bayes A model resulted in increased genetic correlation between ADG and ADFI, a negative correlation between ADFI and FCR, and a positive correlation between ADG and FCR. Accuracies of genomic prediction for the traits investigated, ranging from 9.4% for RFI to 36.5% for BF, were reported that might provide new insight into pig breeding and future selection programs using genomic information.

牛蜘蛛腿综合征(Arachnomelia syndrome,AS)是一种隐性遗传疾病,虽然在瑞士褐牛和西门塔尔牛中症 状相同,然而却是由两个不同的基因突变引起的,分别是SUOX 基因c.363-364insG 突变和MOCS1 基因 c.1224_1225delCA 突变.文章利用51 头西门塔尔牛及80 头与配母牛和106 头杂交后代,以及55 头新疆褐牛 公牛为研究群体,通过荧光标记引物PCR 扩增结合毛细管电泳技术,建立了一种荧光自动化检测方法,能够快 速、准确、一次性实现对引起牛AS 疾病的两个突变位点的同时检测,为今后我国牛群中AS 致病位点的筛查 工作奠定了基础.

Arachnomelia syndrome (AS), mainly found in Brown Swiss and Simmental cattle, is a congenital lethal genetic malformation of the skeletal system. In this study, a network-based disease gene prioritization approach was implemented to rank genes in the previously reported ∼7 Mb region on chromosome 23 associated with AS in Simmental cattle. The top 6 ranked candidate genes were sequenced in four German Simmental bulls, one known AS-carrier ROMEL and a pooled sample of three known non-carriers (BOSSAG, RIFURT and HIRMER). Two suspicious mutations located in coding regions, a mis-sense mutation c.1303G>A in the bystin-like (BYSL) gene and a 2-bp deletion mutation c.1224_1225delCA in the molybdenum cofactor synthesis step 1 (MOCS1) gene were detected. Bioinformatic analysis revealed that the mutation in MOCS1 was more likely to be the causative mutation. Screening the c.1224_1225delCA site in 383 individuals from 12 cattle breeds/lines, we found that only the bull ROMEL and his 12 confirmed progeny carried the mutation. Thus, our results confirm the conclusion of Buitkamp et al. that the 2-bp deletion mutation c.1224_1225delCA in exon 11 of the MOCS1 gene is causative for AS in Simmental cattle. Furthermore, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was developed to detect the causative mutation.

The objective of this research was to develop genomic strategies for improving nutrient utilization by identifying genomic regions affecting feed intake, growth rate, and ultrasound traits in a Duroc terminal sire population. Individual feed intake, growth rate, and ultrasound data were available on 1022 Duroc boars. Boars were genotyped at GENESEEK using the Illumina Porcine SNP60 BeadChip. The criteria for screening the genomic data was a call rate per animal of 0.9, call rate per SNP marker of 0.9, Hardy Weinberg equation test with P < 0.001, and minor allele frequency >0.01. After editing, 40,008 SNPs were retained for genome wide association analysis. The Bayes B and C options in GenSel 4.0.1 were used with pen and contemporary group included as fixed effects for all traits. A preliminary analysis of average daily feed intake, intramuscular fat, and muscle depth was completed. Regions on chromosomes 1, 6, 9, 10, 12, 15, and X were identified affecting average daily feed intake, intramuscular fat, and muscle depth. Additional regions affecting average daily feed intake were found on chromosomes 3, 4, 5, 7, 8, 11, 13, and 17. The markers explained 16% of the total variance for average daily feed intake, 44% for intramuscular fat, and 49% for muscle depth. Analyses of ADG and feeding behavior are currently in progress. Markers identified on chromosome 1 effecting average daily feed intake were in the general region of MC4R. Several other markers were also located in regions where QTL have previously been reported. It was concluded that opportunities exist to use genomic markers to increase accuracy of selection in a Duroc terminal sire population.

蜘蛛腿综合征(Arachnomelia syndrome,AS)是一种牛的先天性致死性骨骼畸形遗传病.在瑞士褐牛群体中该病是由位于BTA5上编码亚硫酸盐氧化酶的SUOX基因外显子4上的一个G碱基的插入所致,插入突变c.363-364insG会导致SUOX蛋白编码提前终止,从而导致犊牛患病.鉴于我国新疆褐牛含有瑞士褐牛血液,本研究对我国新疆地区广泛使用的55头褐牛公牛AS致病位点c.363-364insG进行了筛查.结果显示被检的55头公牛在SUOX基因该突变位点全部为纯合子,不含G碱基插入位点,表明目前经常使用的褐牛公牛不含有致病位点,不存在传播AS疾病的风险,但未来仍需要对其他褐牛公牛及母牛群体开展检测工作,进而排除AS在中国牛群中的传播.

Arachnomelia syndrome (AS) is a lethal congenital malformation of skeleton in cattle, which proved to be an autosomal recessive inherited defect. This disease was mainly observed in European Brown Swiss and German Fleckvieh populations. This review focused on the discovery history, pathologic characteristics, mode of inheritance, and progresses on molecular mechanism of AS in both European Brown Swiss and German Fleckvieh populations. Moreover, through analyzing candidate genes in the mapping region related to bone development and using the methods of comparative genomics, this paper provides a starting point of identifying the causal gene(s) of AS and establishing detection method of the mutations.