Milk protein polymorphism in Danish dairy cattle and the influence of genetic variants on milk yield

In milk samples from 549 cows of the breeds Danish Jersey, Red Danish Dairy Cattle (RDM), and Black and White Danish Dairy Cattle (SDM) the genetic polymorphisms of the alpha-s1, beta and k-casein and beta=lactoglobulin (beta-Lg) loci were determined by isoelectric focusing in agarose gels. The results of the screening were compared with results obtained by Larsen and Thymann. In addition, the genetic linkage of the three casein loci was studied , and the association between milk protein genotypes and yields in first and second lactations of milk, fat and protein were investigated. The distribution of genotypes of all four milk protein systems was different from breed to breed. For Jersey cows, significant differences in the gene frequencies from the results of the 1966 investigation were found for alpha-s1 and k-casein and beta-Lg. For SDM cows a change in the k-casein frequency had occurred whereas for RDM cows no changes were found. Linkage between some of the casein loci was found within all three breeds. For the RDM breed the possible linkage between alpha-s1-casein and the other caseins could not be tested because nearly all the cows were homozygous for the alpha-s1-casein-B genotypes. beta-Casein genotypes were associated with yield parameters in all breeds. The A2A2 genotype of this protein gave higher yields of milk, fat, and protein in the second lactation than the A1A1 genotype.     

Influence of prion protein genotypes on milk production traits in Spanish Churra sheep

The aim of this work was to analyze the possible relationships between milk production traits and prion protein genotypes in Spanish Churra sheep. For this purpose, 2 analyses were carried out. First, an association study was performed of the prion protein genotypes of 12,533 Churra ewes and their milk yield, protein percentage, fat percentage, and somatic cell score as phenotypes, followed by a quantitative trait loci screening on the chromosome where the prion protein gene was located in this population. The latter analysis was carried out using 8 genetic markers (7 microsatellites and the prion protein genotypes) spanning ovine chromosome 13 using a daughter design. Regarding genotype frequencies, the most frequent allele was ARQ (75.90%), which linked with a high susceptibility to scrapie, followed by the resistant haplotype, ARR (18.16%). The frequency of the most susceptible allele, VRQ, was around 1%. No evidence of association or linkage between prion protein genotypes and milk traits has been detected in Churra sheep. These results indicate that increasing the ARR frequency in Churra population will not have an adverse effect on selection for milk traits included in the breeding objectives. However, the low allele frequencies for ARR should be considered in the initial stages to prevent possible bottlenecks in future genetic progress.     

开发TRAP标记的新策略

烟草作为重要的经济作物和生物工程研究领域的模式植物,由于基因组庞大、结构复杂、重复序列较多以及缺少理想的分子标记,致使大量重要农艺、品质性状缺少分子水平上的遗传研究.因此开发适合烟草的分子标记对其遗传研究具有重要意义.本研究在以往TRAP标记开发经验的基础上,探索了一种直接利用EST-SSR引物作为固定引物开发TRAP标记的新方法,降低了TRAP标记的开发难度和成本,在短期内能开发出丰富的TRAP标记组合.本研究开发了首套烟草TRAP标记,结果显示其扩增带型理想,多态性较高,并在普通烟草品种中筛选到一条类香料烟特殊高香气基因型特征带,显示出良好的应用前景.     

Growth,carcass traits and palatability: Can the influence of the feeding regimes explain the variability found on those attributes in different Uruguayan genotypes?

It is well known what genetic and nutritional factors affect growth and meat quality, but there is less information related to interactive importance of them during the productive process. These systems are mainly based on rangelands affecting animal growth in early stages of life thus producing smaller cattle and reduced retail yield comparing with well grown calves. During the last ten years, Uruguayan livestock production systems have been intensified using improved pastures, concentrates and better genetic. The main breeds in Uruguay are Hereford, Angus and their crosses. These British breeds are under genetic evaluation programs which consider carcass trait parameters. It is important for beef industry to know if interactions between genotype and nutrition during growth and fattening phases are influencing production, efficiency, carcass weight and meat quality attributes. The aim of this article is to present information obtained under different feeding strategies during the post weaning and fattening and their influence on those attributes.     

Drug-induced phenotypes provide a tool for the functional analysis of yeast genes

The post-genome sequencing era of Saccharomyces cerevisiae is defined by the analysis of newly discovered open reading frames of unknown function. In this report, we describe a genetic method for the rapid identification and characterisation of genes involved in a given phenotype. This approach is based on the ability of overexpressed genomic DNA fragments to cure an induced phenotype in yeast. To validate this concept, yeast cells carrying a yeast DNA library present on multicopy plasmid vectors were screened for resistance to the antifungal drug ketoconazole. Among 1·2 million colonies 13 clones tested positive, including those expressing the lanosterol C-14 demethylase, known to be a cellular target for azole drugs, and the cytochrome-c oxidase of mitochondria, regulating the respiratory chain electron transport. Several other resistant clones were identified, which code for yeast proteins of so far unknown function. These genes may represent potential candidates for antifungal drug effects. Together with the availability of the entire yeast genome sequence, the described genetic screening method is a powerful tool for the effective functional analysis of yeast genes. © 1998 John Wiley & Sons, Ltd.     

Short communication: The combined use of linkage disequilibrium–based haploblocks and allele frequency–based haplotype selection methods enhances genomic evaluation accuracy in dairy cattle

The construction and use of haploblocks [adjacent single nucleotide polymorphisms (SNP) in strong linkage disequilibrium] for genomic evaluation is advantageous, because the number of effects to be estimated can be reduced without discarding relevant genomic information. Furthermore, haplotypes (the combination of 2 or more SNP) can increase the probability of capturing the quantitative trait loci effect compared with individual SNP markers. With regards to haplotypes, the allele frequency parameter is also of interest, because as a selection criterion, it allows the number of rare alleles to be reduced, and the effects of those alleles are usually difficult to estimate. We have proposed a simple pipeline that simultaneously incorporates linkage disequilibrium and allele frequency information in genomic evaluation, and here we present the first results obtained with this procedure. We used a population of 2,235 progeny-tested bulls from the Montbéliarde breed for the tests. Phenotype data were available in the form of daughter yield deviations on 5 production traits, and genotype data were available from the 50K SNP chip. We conducted a classical validation study by splitting the population into training (80% oldest animals) and validation (20% youngest animals) sets to emulate a real-life scenario in which the selection candidates had no available phenotype data. We measured all reported parameters for the validation set. Our results proved that the proposed method was indeed advantageous, and that the accuracy of genomic evaluation could be improved. Compared with results from a genomic BLUP analysis, correlations between daughter yield deviations (a proxy for true) and genomic estimated breeding values increased by an average of 2.7 percentage points for the 5 traits. Inflation of the genomic evaluation of the selection candidates was also significantly reduced. The proposed method outperformed the other SNP and haplotype-based tests we had evaluated in a previous study. The combination of linkage disequilibrium–based haploblocks and allele frequency–based haplotype selection methods is a promising way to improve the efficiency of genomic evaluation. Further work is needed to optimize each step in the proposed analysis pipeline.     

Associations of bovine blood and milk polymorphisms with lactation traits: Guernseys

First lactation milk yield and percentages of fat, solids-not-fat, and protein were analyzed in Guernsey cows to determine relationships of production traits to genetic markers at 16 polymorphic loci. The polymorphic systems examined were blood groups A, B, C, F, J, L, M, S, and Z; blood proteins transferrin, hemoglobin, and alkaline phosphatase; and milk proteins beta-lactoglobulin, alpha s1-casein, beta-casein, and kappa-casein. Different statistical models were utilized to evaluate direct genetic marker effects, linkage group effects, and heterozygosity effects. There were many indications of relationship with milk composition traits but for milk yield only for A system direct effects and for F system linkage effects. Pronounced associations between markers and component percentages were noted for the J, Z, and beta-lactoglobulin systems with fat percentage, for the M system with fat and solids-not-fat percentages, for the alkaline phosphatase system with solids-not-fat percentage and protein percentages, and for L and alpha s1-casein systems with protein percentage. Additionally, the interaction of beta-lactoglobulin and alpha s1-casein markers was significant for deviations of percent fat and percent solids-not-fat.     

噬菌体展示技术定位主要食物过敏原表位的研究进展

噬菌体展示技术是一项可以在噬菌体颗粒的表面展示外源多肽的体外筛选技术。由于该技术实现了基因和蛋白质的体外统一,现已被广泛应用于生命科学和医学等领域。目前噬菌体展示系统主要有丝状噬菌体展示系统、λ噬菌体展示系统、T4噬菌体展示系统和T7噬菌体展示系统。本文主要介绍了噬菌体展示技术以及该技术在八类食物抗原表位分析的应用。      

Genetic diversity and background linkage disequilibrium in the North American Holstein cattle population

The objectives of this study were to 1) identify highly heterozygous Holstein bulls that are as unrelated as possible and widely used in the US dairy industry; 2) quantify the level of genetic diversity in US Holsteins; and 3) determine the extent of background linkage disequilibrium (BLD) and disease trait associated linkage disequilibrium (DLD) in the US Holstein population. Twenty-three Holstein bulls that are not closely related but were widely used in the US dairy industry were genotyped for 54 microsatellite loci. The genotyping was performed on automated DNA sequencers (PE Applied Biosystems, CA), following polymerase chain reaction amplification with fluorescent dye-labeled primers. The heterozygosity for the sampled population ranged from 0.43 to 0.80. This wide range of heterozygosity allows selection of the most heterozygous bulls to develop informative families for gene mapping studies. The degree of genetic diversity in this population is significant and allows selection for traits of economic importance. As expected, there is extensive linkage disequilibrium (LD) in the US Holstein population. About half of the syntenic marker pairs presented a typical pattern of LD produced by DLD. Most of the nonsyntenic marker pairs had a typical pattern of LD arising from BLD. These results suggest that the observed LD is not purely due to genetic drift and migration and that a portion might be due to DLD. This raises our hopes of successful fine-localization of genes for complex traits using LD mapping.     

Selection for the direct and maternal genetic effects for dystocia in Holsteins

The effects of selection for the direct and maternal components of dystocia were estimated for first, second and later, and all parities. The effect of restricting maternal change to zero and the effect of selection for only the direct component were also examined. Gene flow procedure was used to compute economic weights as 1 and .347 for the direct and maternal effects, respectively. Genetic gain in aggregate genotype was the largest for first parity. For all parities all the gain in the aggregate genotype was accounted for by the direct effects. At the same time, a slight decrease in the genetic maternal effects was observed. For all cases, selection for both traits had almost no loss in aggregate genotype or accuracy compared with when maternal changes were restricted to zero. Total genetic gain and genetic gain for the direct effect of dystocia were greater and accuracy of selection was lower when selection was for the genetic direct effect only versus the index that included both direct and maternal effects. Selection for only the direct effects is not likely to produce any significant change in dystocia as a maternal trait.     

Associations between leptin gene polymorphisms and production,live weight,energy balance,feed intake,and fertility in Holstein heifers

Leptin is a 16-kDa protein synthesized by adipose tissue and is involved in regulation of feed intake, energy balance, fertility, and immune functions. Since evidence of a genetic correlation between start of luteal activity and energy balance, milk yield, and live weights is present, we investigated the association of genetic differences in the bovine leptin gene with these traits. Between 1990 and 1997, a total of 613 Holstein-Friesian heifers of two genetic groups with known pedigree were followed from parturition until d 105 of lactation. During the first 15 wk of lactation live weight, feed intake, and milk yield were measured for 565 cows. The start of luteal activity was set at the first day with a progesterone concentration higher than 3 ng/ml. In addition to the interval between calving and start of luteal activity, analyses were performed for average milk yield, percentage fat, protein, and lactose in milk, dry matter intake, feed intake, energy balance, and live weight over the first 15 wk of lactation. All 613 cows were genotyped for two restricted fragment length polymorphisms and for the BM1500 microsatellite, all located at the leptin gene locus. Significances of the genotype effects were estimated using the approximated F-statistic provided by ASREML. Fixed effects were year-season, genetic group, and a quadratic polynomial for age at calving. Animal was fitted as a random effect including the additive relationship between animals to account for background genes. Firstly, each genotype effect was fitted in turn, and secondly the other restriction fragment length polymorphisms were fitted as a cofactor to take into account effects of linkage disequilibrium. Thirdly, sire x genotype interaction was investigated. Heifers with the RFLP1-AB genotype produce 1.32 kg/d more milk and consume 0.73 kg/d more food compared with the RFLP1-AA genotype. No effects were found for start of luteal activity. When linkage disequilibrium with the other markers was taken into account and DMI was included as fixed effect in the model a 0.96 kg/d higher milk yield was still found. Assuming that no pleiotropic effects on traits such as immunity and milk production in later lactations exist, future breeding programs favoring the RFLP1 B-allele can yield a higher milk production without negatively affecting energy balance and fertility. The prospects are good because in this study the frequency of the RFLP1 AB- and BB-genotypes were only 18.5 and 0.2%, respectively.     

Breeding value estimation for fat percentage using dense markers on Bos taurus autosome 14

Prediction of breeding values using whole-genome dense marker maps for genomic selection has become feasible with the advances in DNA chip technology and the discovery of thousands of single nucleotide polymorphisms in genome-sequencing projects. The objective of this study was to compare the accuracy of predicted breeding values from genomic selection (GS), selection without genetic marker information (BLUP), and gene-assisted selection (GEN) on real dairy cattle data for 1 chromosome. Estimated breeding values of 1,300 bulls for fat percentage, based on daughter performance records, were obtained from the national genetic evaluation and used as phenotypic data. All bulls were genotyped for 32 genetic markers on chromosome 14, of which 1 marker was the causative mutation in a gene with a large effect on fat percentage. In GS, the data were analyzed with a multiple quantitative trait loci (QTL) model with haplotype effects for each marker bracket and a polygenic effect. Identical-by-descent probabilities based on linkage and linkage disequilibrium information were used to model the covariances between haplotypes. A Bayesian method using Gibbs sampling was used to predict the presence of a putative QTL and the effects of the haplotypes in each marker bracket. In BLUP, the haplotype effects were removed from the model, whereas in GEN, the haplotype effects were replaced by the effect of the genotype at the known causative mutation. The breeding values from the national genetic evaluation were treated as true breeding values because of their high accuracy and were used to compute the accuracy of prediction for GS, BLUP, and GEN. The allele substitution effect for the causative mutation, obtained from GEN, was 0.35% fat. The accuracy of the predicted breeding values for GS (0.75) was as high as for GEN (0.75) and higher than for BLUP (0.51). When some markers close to the QTL were omitted from the model, the accuracy of prediction was only slightly lower, around 0.72. The removal of all markers within 8 cM from the QTL reduced the accuracy to 0.64, which was still much higher than BLUP. It is concluded that, when applied to 1 chromosome and if genetic markers close to the QTL are available, the presented model for GS is as accurate as GEN.     

Studies of yeast Kluyveromyces lactis mutations conferring super-secretion of recombinant proteins

We have isolated mutants responsible for a super-secretion phenotype in Kluyveromyces lactis using the gene coding for a Bacillus amyloliquefaciens alpha-amylase as a marker for secretion. These mutations defined two groups, dominant and recessive. The recessive mutant strain, which secreted the heterologous protein in five-fold excess compared to the wild-type strain, was used for the cloning of genes, restraining the super-secreting phenotype. In screening for genes affecting super-secreting phenotype, we found that multiple copies of 10 different independently isolated DNA sequences suppressed the super-secreting phenotype. The first among the genes characterized, named KlSEL1 ('secretion lowering') showed homology to Saccharomyces cerevisiae ORF YML013w. The KlSEL1 gene is predicted to encode a polypeptide of 620 amino acid residues containing a putative transmembrane domain and UBX domain, characteristic for the ubiquitin-regulatory proteins. We demonstrated that the disruption of the SEL1 orthologues in K. lactis and S. cerevisiae conferred the super-secreting phenotype. SEL1 isolated from S. cerevisiae suppressed the super-secretion phenotype in K. lactis klsel1 strain, likewise homologous KlSEL1. No other phenotypic features for strains lacking the SEL1 gene were noticed except for the S. cerevisiae mutant growth being notably slower than in a wt strain. No growth changes were observed in the K. lactis klsel1 mutant. The set of genes (suppressors of over-secreting phenotype) could be attractive for further analysis of gene functions, super-secreting mechanisms and construction of new strains. This collection could be useful for the expedient construction of reduced yeast genomes, optimized for heterologous protein secretion.     

Long-term selection strategies for complex traits using high-density genetic markers

Selection of animals for breeding ranked on estimated breeding value maximizes genetic gain in the next generation but does not necessarily maximize long-term response. An alternative method, as practiced by plant breeders, is to build a desired genotype by selection on specific loci. Maximal long-term response in animal breeding requires selection on estimated breeding values with constraints on coancestry. In this paper, we compared long-term genetic response using either a genotype building or a genomic estimated breeding value (GEBV) strategy for the Australian Selection Index (ASI), a measure of profit. First, we used real marker effects from the Australian Dairy Herd Improvement Scheme to estimate breeding values for chromosome segments (approximately 25 cM long) for 2,650 Holstein bulls. Second, we selected 16 animals to be founders for a simulated breeding program where, between them, founders contain the best possible combination of 2 segments from 2 animals at each position in the genome. Third, we mated founder animals and their descendants over 30 generations with 2 breeding objectives: (1) to create a population with the "ideal genotype," where the best 2 segments from the founders segregate at each position, or (2) obtain the highest possible response in ASI with coancestry lower than that achieved under breeding objective 1. Results show that genotype building achieved the ideal genotype for breeding objective 1 and obtained a large gain in ASI over the current population (+A$864.99). However, selection on overall GEBV had greater short-term response and almost as much long-term gain (+A$820.42). When coancestry was lowered under breeding objective 2, selection on overall GEBV achieved a higher response in ASI than the genotype building strategy. Selection on overall GEBV seems more flexible in its selection decisions and was therefore better able to precisely control coancestry while maximizing ASI. We conclude that selection on overall GEBV while minimizing average coancestry is the more practical strategy for dairy cattle where selection is for highly polygenic traits, the reproductive rate is relatively low, and there is low tolerance of coancestry. The outcome may be different for traits controlled by few loci of relatively large effects or for different species. In contrast to other simulations, our results indicate that response to selection on overall GEBV may continue for several generations. This is because long-term genetic change in complex traits requires favorable changes to allele frequencies for many loci located throughout the genome.     

Gene–gene and gene–environment interactions in complex traits in yeast

One of the fundamental questions in biology is how the genotype regulates the phenotype. An increasing number of studies indicate that, in most cases, the effect of a genetic locus on the phenotype is context‐dependent, i.e. it is influenced by the genetic background and the environment in which the phenotype is measured. Still, the majority of the studies, in both model organisms and humans, that map the genetic regulation of phenotypic variation in complex traits primarily identify additive loci with independent effects. This does not reflect an absence of the contribution of genetic interactions to phenotypic variation, but instead is a consequence of the technical limitations in mapping gene–gene interactions (GGI) and gene–environment interactions (GEI). Yeast, with its detailed molecular understanding, diverse population genomics and ease of genetic manipulation, is a unique and powerful resource to study the contributions of GGI and GEI in the regulation of phenotypic variation. Here we review studies in yeast that have identified GGI and GEI that regulate phenotypic variation, and discuss the contribution of these findings in explaining missing heritability of complex traits, and how observations from these GGI and GEI studies enhance our understanding of the mechanisms underlying genetic robustness and adaptability that shape the architecture of the genotype–phenotype map.     

利用DH群体构建烤烟分子标记遗传连锁图

以烤烟品种SpeightG-28和NC2326杂交得到的137个DH系为作图群体材料,通过ISSR和RAPD标记的遗传连锁分析,构建了包括27个连锁群、由10个ISSR标记和147个RAPD标记组成的烤烟分子标记遗传连锁图。该图谱覆盖长度1838.2cM,平均图距14.1cM。连锁群上有22个分子标记表现偏分离,其中10个集中在连锁群LG9上,其余分散在不同连锁群。这是国内外构建的第一张烤烟分子标记遗传连锁图,为烤烟性状的基因定位及分子标记辅助选择奠定了良好基础。      

Genetic methods of improving dairy cattle for the south: a review and prospects from Regional Project S-49

Objectives of Southern Regional Research Project S-49, comprising eight contributing experiment stations, are to determine direct response to selection in milk and the resultant correlated responses in nonyield traits, to define and evaluate selection criteria for total economic merit or profit, to quantify genetic and environmental components of underlying physiological characters responsible for genetic gains in economically important traits, to determine interactions of genotype by environment, and to estimate genetic values for males and females. More than 150 scientific articles from S-49 have been published in journals from 1975 to 1985. These results have contributed in a major way in identifying issues and understanding the genetic control of cow performance and economics of genetic improvement programs.     

大豆生育期性状QTL定位

选用中豆31×B13杂交组合的182个F2单株构成的群体,构建了一张包含155个SSR标记的简单遗传图谱。利用构建的遗传图谱采用区间作图法对在田间自然条件下大豆的出苗至初花日数、初花至完熟日数和全生育期进行QTL定位,以研究大豆生育期性状的遗传规律。结果发现在C1连锁群上有1个QTL与出苗至初花日数有关,可解释66.40%的遗传变异;发现7个QTL与初花至完熟日数有关,分别位于A2、B2、C1、L、M 5个不同的连锁群上,可解释6.70%~18.00%的遗传变异;2个QTL与全生育期有关,均在C1连锁群上,可分别解释31.90%和36.70%的遗传变异。这些QTL的发现可以为大豆生育期QTL的发掘和利用以及分子辅助育种提供参考。     

Marker-assisted selection can reduce true as well as pedigree-estimated inbreeding

This study investigated whether selection using genotype information reduced the rate and level of true inbreeding, that is, identity by descent, at a selectively neutral locus as well as a locus under selection compared with traditional BLUP selection. In addition, the founder representation at these loci and the within-family selection at the nonneutral locus were studied. The study was carried out using stochastic simulation of a population resembling the breeding nucleus of a dairy cattle population for 25 yr. Each year, 10 proven bulls were selected across herds along with 100 dams from within each of 40 herds. Selection was performed using BLUP, marker-assisted, or gene-assisted selection for a trait with low heritability (h² = 0.04) only expressed in females, mimicking a health trait. The simulated genome consisted of 2 chromosomes. One biallelic quantitative trait loci (QTL) with an initial frequency of the favorable allele of 0.1, and initially explaining 25% of the genetic variance as well as 4 markers were simulated in linkage disequilibrium, all positioned at chromosome 1. Chromosome 2 was selectively neutral, and consisted of a single neutral locus. The results showed that in addition to reducing pedigree-estimated inbreeding, the incorporation of genotype information in the selection criteria also reduced the level and rate of true inbreeding. In general, true inbreeding in the QTL was greater than pedigree-estimated inbreeding with respect to both the level and rate of inbreeding, as expected. Also as expected, true and pedigree-estimated inbreeding in the neutral locus were the same. Furthermore, after 25 yr, or approximately 5 generations, the pedigree-estimated level of inbreeding was reduced by 11 and 24% compared with BLUP in gene- and marker-assisted selection, respectively, and the level of true inbreeding in the QTL was reduced by 22 and 13%, respectively. The difference between selection scenarios was found to be caused by a larger number of founders being represented at the QTL when using genotype information in the selection criteria. This in turn was caused by an increased selection of individuals sharing the favorable QTL allele rather than individuals sharing genes on average, which was shown by a higher Mendelian selection differential in the QTL. Hence, even though the selection pressure was increased at the QTL, more variation was retained. The results suggest that marker-assisted selection is a useful selection strategy.