Model averaging for genome‐enabled prediction with reproducing kernel Hilbert spaces: a case study with pig litter size and wheat yield

Predictive ability of yet‐to‐be observed litter size (pig) grain yield (wheat) records of several reproducing kernel Hilbert spaces (RKHS) regression models combining different number of Gaussian or t kernels was evaluated. Predictive performance was assessed as the average (over 50 replicates) predictive correlation in the testing set. Predictions from these models were combined using three different types of model averaging: (i) mean of predicted phenotypes obtained in each model, (ii) weighted average using mean squared error as weight or (iii) using the marginal likelihood as weight. (ii) and (iii) were obtained in a validation set with 5% of the data. Phenotypes consisted of 2598, 1604 and 1879 average litter size records from three commercial pig lines and wheat grain yield of 599 lines evaluated in four macro‐environments. SNPs from the PorcineSNP60 BeadChip and 1447 DArT markers were used as predictors for the pig and wheat data analyses, respectively. Gaussian and univariate t kernels led to same predictive performance. Multikernel RKHS regression models overcame shortcomings of single kernel models (increasing the predictive correlation of RKHS models by 0.05 where 3 Gaussian or t kernels were fitted in the RKHS models simultaneously). None of the proposed averaging strategies improved the predictive correlations attained with single models using multiple kernel fitting.     

Whole genome sequence analysis to detect signatures of positive selection for high fecundity in sheep

Ovulation rate and prolificacy are the most important reproductive traits that have major impact on the efficiency of lamb meat production. Here, we compared the whole genomes of the Romanov sheep, known as one of the high prolific breeds, and four other sheep breeds namely Assaf, Awassi, Cambridge and British du cher, to identify genetic mechanisms underlying prolificacy in sheep. Selection signature analysis revealed 637 and 477 protein‐coding genes under positive selection from F_ST and nucleotide diversity (Pi) statistics, respectively. Further analysis showed that several candidate genes including LEPR, PDGFRL and KLF5 genes are involved in sheep prolificacy. The identified candidate genes in the selected regions are novel and provide new insights into the genetic mechanisms underlying prolificacy in sheep and can be useful in sheep breeding programmes to develop improved breeds for high reproductive efficiency.     

Evaluation of Breeding Value and Selection of Bull Dams in the Danish Dairy Breeds: I. Studies on Realized Efficiency of Bull Dam and Bull Sire Selection

Abstract

The relationship between twice the adjusted daughter yield deviation (DYD) of the son and the average of the estimated breeding values (EBV) of his parents was investigated for milk and fat yield. Deviations from expectations of DYD minus the pedigree index and the regression of DYD on the EBV for each of the parents were estimated. The EBV of each bull dam was calculated in several ways using different combinations of pedigree information and their own records. In all, 1693 bulls (880 Black and White (BW), 418 Red Danish (RD) and 395 Danish Jersey (DJ)) with Direct Updating indices for milk and fat yield were included in the investigation. Mean discrepancies between estimated and observed genetic merit for kg of milk yield were ?348 for BW, ?213 for RD and ?228 for DJ, when all of the bull dams' individual records were utilized in breeding value estimation. The corresponding mean discrepancies for kg of fat yield were ?14.7, ?11.5 and ?11.9, respectively. The discrepancies were positively correlated with the number of lactation records included in the dams' EBVs. Regression coefficients of bull DYDs on bull dam breeding values were significantly lower than expected for RD and BW regardless of the number of individual lactation records included in the dams' indexes for milk and fat yield. For all three breeds, the regression coefficients were lowest for fat yield. The most probable cause of overestimation in bull dam EBVs is preferential treatment, particularly in second and later lactations. To avoid this bias, estimation of a bull dam's breeding value should be based on pedigree information and on records from only her first lactation.     

Fattening performance and feed source preference of native Awassi lambs fed individually in a cafeteria feeding system

This experiment was conducted to investigate the effect of cafeteria (CF) and conventional (CN) feeding systems on feed intake, feed preferences with respect to voluntary feed source intake, feed conversion rate (FCR) and fattening performance of native Awassi lambs. Sixteen, 3 month old male lambs were used and kept individually for 70 days. Lambs in CF (n = 8) were offered to consume the main ingredients of barley, soybean meal (SBM), sunflower seed meal (SFM) and alfalfa straw, separately, while lambs in CN (n = 8) were fed with a concentrate feed containing 11.34 MJ/kg ME, 17.53% crude protein with the mixture of the same feed sources and alfalfa straw. The initial and final live weights of lambs were similar among groups (P > 0.05). Daily voluntary intake of ash, fat and neutral detergent fiber (NDF) consumptions among groups were quite different during the experiment (P < 0.001). Neither biweekly nor total results of voluntary protein intake between groups were not found statistically significant (P > 0.05). From beginning to the end of the study, the proportional barley intake increased 34 to 43% but reduced for SBM intake from 37 to 23% for the lambs in CF. On the other hand, the SFM intake of lambs did not changed significantly during the experiment and ranged between 2–5%. Lambs in CF did not consume SFM to meet their protein requirement and had 12.5% better total FCR result than the lambs in CN (6.86 and 7.84, respectively) (P > 0.05). The difference of average DWG, total live weight gain, final live weight of lambs in groups were similar (P > 0.05). In conclusion, Awassi lambs in CF can select a diet matching their nutritional requirements from a group of feed sources in response to their growth period when compared to CN system and better FCR result might help to decrease the feed expenses for fattening of native Awassi lambs.     

Phenotypic and genotypic background underlying variations in fatty acid composition and sensory parameters in European bovine breeds

Background： Consuming moderate amounts of lean red meat as part of a balanced diet valuably contributes to intakes of essential nutrients, in this study, we merged phenotypic and genotypic information to characterize the variation in lipid profile and sensory parameters and to represent the diversity among 15 cattle populations. Correlations between fat content, organoleptic characteristics and lipid profiles were also investigated. Methods： A sample of 436 largely unrelated purebred bulls belonging to 15 breeds and reared under comparable management conditions was analyzed. Phenotypic data -including fatness score, fat percentage, individual fatty acids （FA） profiles and sensory panel tests- and genotypic information from 11 polymorphisms was used. Results： The correlation coefficients between muscle total lipid measurements and absolute vs. relative amounts of polyunsaturated FA （PUFA） were in opposite directions. Increasing carcass fat leads to an increasing amount of FAs in triglycerides, but at the same time the relative amount of PUFAs is decreasing, which is in concordance with the negative correlation obtained here between the percentage of PUFA and fat measurements, as well as the weaker correlation between total phospholipids and total lipid muscle content compared with neutral lipids. Concerning organoleptic characteristics, a negative correlation between fiavour scores and the percentage of total PUFA, particularly to n-6 fraction, was found. The correlation between juiciness and texture is higher than with flavour scores. The distribution of SNPs plotted by principal components analysis （PCA） mainly reflects their known trait associations, although influenced by their specific breed allele frequencies. Conclusions： The results presented here help to understand the phenotypic and genotypic background underlying variations in FA composition and sensory parameters between breeds. The wide range of traits and breeds studied, along with the genotypic information on polymorphisms previo     

五常市杂种落叶松幼龄期变异分析

以5年生36个杂种落叶松家系为材料,测定其树高、胸径生长性状,估算变异系数、遗传力和遗传增益,筛选出优良家系。结果表明:各家系的树高、胸径存在较丰富变异,树高变异系数小于胸径,树高、胸径极显著相关(P<0.01),家系间树高、胸径差异均达极显著差异水平(P<0.01)。以10%的入选率,初选出家系1317、1324、1318、和1327为优良家系,树高平均增益为15.98%,胸径平均增益为29.46%。     

国外生猪育种体系简析及对我国生猪育种的几点思考

选择是生猪育种的核心,而准确地选择和选种依赖于完善和成熟的育种体系。国际养猪发达国家(国际育种企业)对育种体系不断完善,长期进行生长、繁殖和肉品质等各类性状的表型测定,运用多场联合评估和基因组选择等方法不断提高遗传评估的准确性,不断挖掘新的育种性状,并进行测定、评估和选育,实现了种猪群体持续的遗传改良和综合性能的不断提升。本文对欧美发达国家(国际育种企业)的生猪育种技术体系进行了综述,以期为我国的生猪育种工作提供参考,并促进我国生猪种业的创新发展。     

大丰麇鹿国家级自然保护区鸟类多样性

2010年1～12月,采用样线法对江苏大丰麋鹿国家级自然保护区内7种不同生境的鸟类进行了调查。结果如下:共记录到鸟类150种,分属16目43科,其中水鸟56种,分属7目12科。以密度划分鸟类优势种类,优势种21种,常见种53种,稀有种76种。鸟类的区系以广布种为主,占鸟类总数的48.67%,其次为古北界鸟类45种,占30%,东洋界鸟类32种,占21.33%。国家Ⅰ、Ⅱ级保护鸟类14种,占鸟类总数的9.33%。5月和9月鸟类的种类和数量分别出现峰值,为鸟类迁徙的重要时期。不同生境鸟类多样性比较:阔叶林生境最高,为3.488,其次为荒地、狼尾草、白茅、农田、互花米草,多样性分别为3.293、3.185、3.184、3.030和2.857,鱼塘生境最低为2.679。不同季节鸟类多样性比较:春季最高,为3.711,其次为秋季、夏季,多样性分别为3.538和3.381,冬季最低为3.043。     

Foraging behavior of heifers with or without social models in an unfamiliar site containing high plant diversity

Grazing behavior, diet selection and weight gain of heifers (with or without social models) were assessed in an unfamiliar site containing high plant diversity. The study was performed within a tropical forest ecosystem containing a mixture of grass forb/herb, shrub and tree species. Ten inexperienced crossbred Bos taurus × Bos indicus heifers (7 ± 1 months old) were randomly assigned to one of two groups: naive or naive + social model (sm) and two experienced heifers (16 months old) were assigned to the second group. Naive heifers were bottle-nursed from days 2 to 90 after birth and began grazing at 1 month of age in tropical grass monocultures, while experienced animals had been foraging in sites containing a high diversity of plant species for 3 months prior to the study. Each group grazed in separate paddocks for a 12-week period during the rainy season, and animals were observed using focal sampling from 7:00 to 19:30 h to assess diet composition based on bite counts. Weight gain was assessed every 14 days. Paddocks contained from 1481 to 1789 kg/ha of herbaceous dry matter, enough to support the heifers throughout the study without affecting diet selection. Shrub and tree cover ranged from 55.2 to 58.4% across treatments. Bites per minute were adjusted to a log-scaled quadratic-plateau model and the curves showed no differences between treatments (P = 0.756). However, diet composition differed between groups (P < 0.001), with naive + sm heifers ingesting a greater proportion of trees (P < 0.001) and shrubs (P = 0.02), while naive heifers ingested more forb/herbs (P = 0.02); no difference in grass consumption was observed (P = 0.92). Heifers in both treatments consumed the same plant species (50 from 26 families). Over time, utilization of several plant species increased or decreased (P < 0.05), eventually leveling off for the remainder of the study. Although differences in diet composition were observed, they did not affect overall weight gain (117 and 113 g/day in the naive and naive + sm groups, respectively; P = 0.913). However, initial post-weaning weight loss was avoided in the naive + sm group. Social learning facilitates a higher use of shrubs and trees in tropical pastures containing a high diversity of plant species with different growth habits. As many plant species have high potential as forage, more effort should be placed on developing mechanisms to increase their dietary inclusion by cattle.     

正交设计优化草地早熟禾SRAP-PCR反应体系及引物筛选

采用L9(34)正交试验设计方法,对草地早熟禾(Poa pratensis)基因组DNA SRAP PCR反应体系中的Taq DNA聚合酶、Mg2+、引物及dNTP四因素的用量进行优化,并比较不同模板DNA用量对扩增的影响,建立草地早熟禾SRAP PCR最佳反应体系,同时,利用该体系对SRAP引物进行筛选。结果表明,草地早熟禾SRAP PCR最佳反应体系为Taq DNA聚合酶1.0 U、Mg2+ 1.75 mmol·L-1、引物0.25 μmol·L-1、dNTP 220 μmol·L-1、40 ng模板DNA、2 μL 10×PCR buffer,总体积20 μL。运用该体系从100对SRAP引物中筛选出43对引物能够产生清晰稳定的扩增条带且多态性丰富。优化体系的建立及引物的筛选可为今后利用SRAP标记技术对草地早熟禾进行遗传多样性分析、图谱构建、种质资源鉴定奠定技术基础。