Prediction of response to marker-assisted and genomic selection using selection index theory

Selection index methods can be used for deterministic assessment of the potential benefit of including marker information in genetic improvement programmes using marker-assisted selection (MAS). By specifying estimates of breeding values derived from marker information (M-EBV) as a correlated trait with heritability equal to 1, it was demonstrated that marker information can be incorporated in standard software for selection index predictions of response and rates of inbreeding, which requires specifying phenotypic traits and their genetic parameters. Path coefficient methods were used to derive genetic and phenotypic correlations between M-EBV and the phenotypic data. Methods were extended to multi-trait selection and to the case when M-EBV are based on high-density marker genotype data, as in genomic selection. Methods were applied to several example scenarios, which confirmed previous results that MAS substantially increases response to selection but also demonstrated that MAS can result in substantial reductions in the rates of inbreeding. Although further validation by stochastic simulation is required, the developed methodology provides an easy means of deterministically evaluating the potential benefits of MAS and to optimize selection strategies with availability of marker data.     

Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters

Accuracy of prediction of estimated breeding values based on genome-wide markers (GEBV) and selection based on GEBV as compared with traditional Best Linear Unbiased Prediction (BLUP) was examined for a number of alternatives, including low heritability, number of generations of training, marker density, initial distributions, and effective population size (Ne). Results show that the more the generations of data in which both genotypes and phenotypes were collected, termed training generations (TG), the better the accuracy and persistency of accuracy based on GEBV. GEBV excelled for traits of low heritability regardless of initial equilibrium conditions, as opposed to traditional marker-assisted selection, which is not useful for traits of low heritability. Effective population size is critical for populations starting in Hardy-Weinberg equilibrium but not for populations started from mutation-drift equilibrium. In comparison with traditional BLUP, GEBV can exceed the accuracy of BLUP provided enough TG are included. Unfortunately selection rapidly reduces the accuracy of GEBV. In all cases examined, classic BLUP selection exceeds what was possible for GEBV selection. Even still, GEBV could have an advantage over traditional BLUP in cases such as sex-limited traits, traits that are expensive to measure, or can only be measured on relatives. A combined approach, utilizing a mixed model with a second random effect to account for quantitative trait loci in linkage equilibrium (the polygenic effect) was suggested as a way to capitalize on both methodologies.     

Effect of polymorphisms linked to LEP gene on its expression on adipose tissues in beef cattle

In cattle, genetic markers at the leptin (LEP) gene and at those linked to the gene have been described as affecting calving interval (markers LEPSau3AI and IDVGA51), or daily weight gain (BMS1074 and BM1500). This work investigated the effect of these alleles on LEP mRNA levels in cattle subcutaneous and omental adipose tissues. A sample of 137 females of a Brangus‐Ibage beef cattle herd was analysed to evaluate the distribution of the polymorphisms; then, animals having at least one of the IDVGA51*181 (allele 181 at marker IDVGA51; six animals), LEPSau3AI*2 (four), BMS1074*151 (13), BM1500*135 (six) alleles and a control group composed of animals without any of these alleles (four animals) were submitted to surgery to obtain omental and subcutaneous adipose tissues. Leptin mRNA expression was quantified by TaqMan RT‐PCR, using 18S rRNA as internal control and adjusted for the effect of body condition score, through regression analysis. Omental fat had LEP gene expression 33% lower than the subcutaneous tissue. Carriers of IDVGA*181 and BMS1074*151 showed subcutaneous fat leptin mRNA levels higher than the controls. Leptin controls feed intake and coordinates reproduction; therefore, animals with higher LEP gene expression will probably have lower daily weight gain than others with similar forage offer and nutritional condition and probably will also have longer calving interval.     

Comparison of grazing behaviour, dietary overlap and performance in non-lactating domestic ruminants grazing on marginal heathland areas

During the years 2000–2001, 7 non-lactating beef cows, 40 ewes and 40 does were managed in mixed grazing on a natural heathland vegetation plot (22 ha) with 20% improved pasture (perennial ryegrass) on a hill (1000 m a.s.l.) experimental farm located in the NW of Spain. Samples of faeces and vegetation components were collected monthly to estimate diet selection, using the alkane markers, and diet overlapping level. Animals were weighed monthly to quantify live weight changes and performance of the three livestock species during different periods (spring, summer, autumn, winter) of the grazing season.

The percentage of shrubs in the diet was significantly higher in the small ruminants (ranging between 36% and 85%) than in cows (less than 25%) in any period. Gorse (Ulex gallii) and heather (Erica spp., Calluna) percentages were always significantly higher in does than in ewes, except in autumn for heather. Herbaceous component (namely grasses) was higher in cattle (75–99%) than in small ruminants (15–64%). The lowest mean dietary overlap was found between cattle and goats (50.4%), with large differences during the grazing season, ranging between 20% and 70%.

The three animal species increased their live weight in the first grazing period (spring), when the mean sward height on the improved area was higher than 6.0 cm. However, when the sward height was lower than 3.5 cm (summer–winter), cows lost weight (− 437 g/day) while ewes and goats were still able to increase their weight (29 and 5 g/day, respectively).

Therefore, it seems that small ruminants, mainly sheep, are more suitable than cattle from the vegetation utilization and animal performance points of view, as cows were unable to maintain live weight when the preferred grass availability decreases. Goats were the species that included the highest proportion of heathland vegetation components in the diet, especially gorse, although their performance was significantly lower than in sheep. In consequence, small ruminant production systems could be more sustainable than cattle. The results indicate that mixed grazing of sheep and goats could be appropriate in these vegetation communities, allowing the development of sustainable systems, in which animal performance and the efficiency of resource use are maximized.     

表达新城疫病毒F基因重组鸡痘病毒的筛选

将转移载体P11SF和PN11SF分别与282E4株鸡痘病毒（282E4 strain fowlpox virus，282E4FPV）和大空斑株鸡疽病毒（large plaque strain fowlpox virus，LP FPV）共转染鸡胚成纤维细胞，通过蓝斑筛选，得到4株重组鸡痘病毒rFPV282E4-SFA、rFPVLP，-SFA、rFPV282E4-SFB和rFPVLP-SFB，通过PCR和间接免疫荧光鉴定均为阳性，另外将各重组病毒分别传20代，测其遗传稳定性，结果显示均具有良好的稳定性。对SPF鸡进行免疫效力试验，攻毒后均100％保护，而对于商品鸡，保护率分别为64％、60％、52％和88％。     

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.     

利用CAPS标记辅助辣椒PVY抗性基因PVr4转育的研究

利用国外报道的与PVr4基因紧密连锁的CAPS标记,对辣椒抗PVY基因PVr4的转育进行了研究和探讨。采用与报道的相同抗源材料CdM334为回交的供体亲本,与5个自交系77013、75-7-3-1、83077、83078、83-163进行回交,在BC1代进行了分子标记的选择。从5个BC1群体75-7-3-1×(CdM334×75-7-3-1)、77013×(CdM334×77013)、83077×(CdM334×83077)、83078×(CdM334×83078)、83-163×(CdM334×83-163)中,分别检测出含有抗病连锁标记的单株21株、15株、10株、11株、12株。     

优质高产绿豇豆绿豇1号的选育与应用研究

绿豇1号是从宁波绿豇豆品种宁波绿带中经系统选育而育成的。其生育期48～61d,嫩荚绿色,长圆棍形,平均荚长58.1cm、宽0.72cm,单荚重18.6g,质地脆嫩,风味好,品质优,商品性佳。抗白粉病、煤霉病能力均较强。平均产量2000kg/667m2,较宁波绿带增产10%左右。绿豇1号已在浙江、上海、福建、江苏等省市示范推广应用。     

李新品种—秦红李的选育

秦红李是从国外李品种幸运(Fortune)实生苗中选育出的优良新品种。果实圆形至长圆形,平均单果质量125g,最大果质量215g,果面鲜红至玫瑰红,果肉淡黄色,贮藏后紫红色。肉质松脆,汁多,味甜,有香气,纤维少而细,品质佳,无苦涩味,可溶性固形物15%￣16%。果实7月中下旬果实成熟,果实生育期110d左右。较抗细菌性穿孔病,无裂果或落果现象,丰产性强,耐贮运。     

苹果芽变选种鉴定及应用研究

芽变选种具有育种周期短、育种进程快的特点,是种质资源创新的重要途径。从形态学、解剖学、同工酶、孢粉学、染色体观察、生理生化特性及分子标记等方面对芽变鉴定的常规方法进行了综述,认为叶片栅栏组织比例、气孔密度、孢粉形态等是芽变品种鉴定的重要指标,同工酶技术及分子标记技术是芽变品种鉴定的重要手段。进一步对芽变发生的遗传类别及分子机理进行了初步探讨,对芽变选种的应用前景进行了展望。