Genome-wide association and genomic selection in animal breeding

Results from genome-wide association studies in livestock, and humans, has lead to the conclusion that the effect of individual quantitative trait loci (QTL) on complex traits, such as yield, are likely to be small; therefore, a large number of QTL are necessary to explain genetic variation in these traits. Given this genetic architecture, gains from marker-assisted selection (MAS) programs using only a small number of DNA markers to trace a limited number of QTL is likely to be small. This has lead to the development of alternative technology for using the available dense single nucleotide polymorphism (SNP) information, called genomic selection. Genomic selection uses a genome-wide panel of dense markers so that all QTL are likely to be in linkage disequilibrium with at least one SNP. The genomic breeding values are predicted to be the sum of the effect of these SNPs across the entire genome. In dairy cattle breeding, the accuracy of genomic estimated breeding values (GEBV) that can be achieved and the fact that these are available early in life have lead to rapid adoption of the technology. Here, we discuss the design of experiments necessary to achieve accurate prediction of GEBV in future generations in terms of the number of markers necessary and the size of the reference population where marker effects are estimated. We also present a simple method for implementing genomic selection using a genomic relationship matrix. Future challenges discussed include using whole genome sequence data to improve the accuracy of genomic selection and management of inbreeding through genomic relationships.     

基因组选择技术在农业动物育种中的应用

基因组选择(genomic selection, GS)是畜禽经济性状遗传改良的重要方法。随着高密度SNP芯片和二代测序价格的下降,GS技术越来越多被应用于奶牛、猪、鸡等农业动物育种中。然而,降低全基因组SNP分型成本、提高基因组育种值(genomic estimated breeding value,GEBV)估计准确性仍然是GS研究的主要难题。本文从全基因组SNP分型策略和GEBV估计模型两个方面进行了综述,并对目前GS技术在主要畜禽品种中的应用现状进行了介绍,以期为GS在农业动物育种中的深入开展提供借鉴和参考。     

Optimising two-stage independent culling selection in tree and animal breeding

Summary Theory is given for a simple practical method of predicting gain from two-stage independent culling, where stage 1 of selection is for individual performance and stage 2 is for either progeny performance only, or an index combining individual and progeny performance. Expected gain is determined as a direct function of heritabilities, genetic correlations, selection intensities and progeny-testing capacity. Results show the effect these parameters can have on proportions selected at each stage and, if multiple selection criteria are used, traits selected for first. Methods are discussed in the context of tree and animal breeding, with an example taken from forestry.     

Congruence between selection on breeding values and farmers' selection criteria in sheep breeding under conventional nucleus breeding schemes

Designing breeding schemes suitable for smallholder livestock production systems in developing regions has hitherto been a challenge. The suggested schemes either do not address farmers' breeding goals (centralized station-based nucleus schemes) or yield slow genetic progress (village-based schemes). A new breeding scheme that integrates the merits of previously suggested schemes has been designed for Menz sheep improvement in Ethiopia. It involves selection based on breeding values in nucleus flocks to produce elite rams, a one-time only provision of improved rams to villagers and a follow-up village-based selection to sustain genetic progress in village flocks. Here, we assessed whether conventional selection of breeding rams based on breeding values for production traits, which is the practice in station-based nucleus flocks, meets farmers' breeding objectives. We also elicited determinants of farmers' ram choice. Low but significant correlations were found between rankings of rams based on farmers' selection criteria, estimated breeding values (EBV) and body weight (BW). Appearance traits (such as color and horn) and meat production traits (BW and linear size traits) significantly determined farmers' breeding ram choice. The results imply that conventional selection criteria based solely on EBV for production traits do not address farmers' trait preferences fully, but only partially. Thus, a two-stage selection procedure involving selection on breeding values in nucleus centers followed by farmers' selection among top- ranking candidate rams is recommended. This approach accommodates farmers' preferences and speeds up genetic progress in village-based selection. The Menz sheep scheme could be applied elsewhere with similar situations to transform conventional station-based nucleus breeding activities into participatory breeding programs.     

Piezophilic adaptation: a genomic point of view

Two-thirds of Earth's surface is covered by oceans, yet the study of this massive integrated living system is still in its infancy. Various environmental variables, such as high salinity, low and changeable nutrient availability and depth-correlated gradients of light, temperature, nutrients and pressure shape the diversity, physiology and ecology of marine species. As oceans present an average depth of 3800 m, deep-sea ecosystems represent the most common marine ecological niche. One of the key environment variables that influences the life and evolution of deep-sea organisms is high pressure. This extreme widespread condition requires specific adaptations, the nature of which remains largely unknown. Recent advances in genomic approaches, such as in sequencing technologies and global expression profiling, are rapidly increasing the data available to understand microbial evolution, biochemistry, physiology and diversity. This review summarises the analysis of the results published so far about microbial high pressure adaptation from a genomic point of view. Understanding high pressure adaptation mechanisms is not just a scientific exercise but has important biotechnological implications. For example, hydrostatic pressure is a reality for food science and technology, both for food preparation and preservation. An understanding of the effects of pressure on biomolecules will expand its use in the medical, industrial and biotechnological fields.     

Plant hormones: a fungal point of view

Most classical plant hormones are also produced by pathogenic and symbiotic fungi. The way in which these molecules favour the invasion of plant tissues and the development of fungi inside plant tissues is still largely unknown. In this review, we examine the different roles of such hormone production by pathogenic fungi. Converging evidence suggests that these fungal‐derived molecules have potentially two modes of action: (i) they may perturb plant processes, either positively or negatively, to favour invasion and nutrient uptake; and (ii) they may also act as signals for the fungi themselves to engage appropriate developmental and physiological processes adapted to their environment. Indirect evidence suggests that abscisic acid, gibberellic acid and ethylene produced by fungi participate in pathogenicity. There is now evidence that auxin and cytokinins could be positive regulators required for virulence. Further research should establish whether or not fungal‐derived hormones act like other fungal effectors.     

Scientific animal breeding in Moravia before and after the rediscovery of Mendel's theory

Leading Moravian sheep breeders, who joined with university professors and other educated citizens to form a Sheep Breeders' Society in 1814, looked to science to provide a reliable basis for breeding. Their activities reached a climax in the 1830s, when they defined and focused on heredity as the central research goal. Among the members taking part was Abbot Cyrill F Napp, who in 1843 would accept Mendel into the monastery. The contributions of Abbot Napp to the sheep breeders' view of heredity are here described. After 1900, when Moravian animal breeding sought to embrace Mendelism, in competition with other theories, a major influence was exerted by Jaroslav Krízenecky (1896-1964). In 1963, Krízenecky accepted responsibility for establishing the Mendel Museum (Mendelianum) in Brno as a vehicle for historical research into the origin and essence of Mendel's discovery.     

Oral lichen planus: a microbiologist point of view

International Microbiology - Oral lichen planus (OLP) is a chronic disease of uncertain etiology, although it is generally considered as an immune-mediated disease that affects the mucous membranes...     

The LAP family: a phylogenetic point of view

Recently, the LAP (for 'LRR and PDZ') family of adaptor proteins was described in vertebrates and invertebrates. The proteins are involved in cell polarity and receptor targeting, and they contain both LRR and PDZ domains in the same molecule, a combination that is specifically bilaterian. A search of available genome sequences reveals a limited number of lap genes, which we have classified by phylogenetic analysis. We propose a functional hypothesis for the origin of this protein family in bilaterians, and give a phylogenetic interpretation of their diversity.     

The human embryo: a scientist's point of view

...Thus, my judgement is that a human embryo is not a human person, and so we may do experiments on it which involve killing it. But my judgement is also that a human embryo has the potential to become a human being. The consequence of this attribute is that it imposes limits on the kinds of experiments which may be performed on human embryos. It is this which sets the boundaries. Experiments which may harm the embryo while still allowing it subsequently to realise its potential, and become a person, should not be permitted. It is the potentiality of the human embryo which governs our behaviour towards it. Its potential makes it special, and radically different from any other human tissue. This potential which the early embryo has means that great respect must always be accorded it, and great thought and care must surround any dealings with it....     

血管生成素样蛋白家族表达调控及其在动物分子育种领域的现状分析

血管生成素样蛋白(Angiopoietin-like proteins,Angptls)是与脂类、葡萄糖、能量代谢和血管生成密切相关的蛋白质家族,现已发现8个成员,因其在代谢调控和动物辅助选育方面发挥有重要作用而备受研究人员的关注。以下综述了该蛋白家族的结构、介导的信号通路、上游调控基因及代谢网络等方面,并结合课题组研究工作对其应用于动物育种领域的现状和问题进行了分析,对前景作了展望。     

Myostatin and its implications on animal breeding: a review

Myostatin, or growth and differentiation factor 8 (GDF8), has been identified as the factor causing a phenotype known as double muscling, in which a series of mutations render the gene inactive, and therefore, unable to regulate muscle fibre deposition. This phenotype occurs at a high frequency in some breeds of cattle such as Belgian Blue and Peidmontese. Phylogenetic analysis has shown that there has been positive selection pressure for non-synonymous mutations within the myostatin gene family, around the time of the divergence of cattle, sheep and goats, and these positive selective pressures on non-ancestral myostatin are relatively recent. To date, there have been reports of nine mutations in coding regions of myostatin that cause non-synonymous changes, of which three cause missense mutations, including two in exon 1 and one in exon 2. The remaining six mutations, located in exons 2 and 3, result in premature stop codons, which are the mutations responsible for the double-muscling phenotype. Unfortunately, breed management problems exist for double-muscled cattle, such as birthing difficulties, which can be overcome through genetically controlled breeding programmes, as shown in this review.     

Plant and animal rhabdovirus host range: a bug's view

Rhabdoviruses affect human health, terrestrial and aquatic livestock and crops. Most rhabdoviruses are transmitted by insects to their vertebrate or plant hosts. For insect transmission to occur, rhabdoviruses must negotiate barriers to acquisition, replication, movement, escape and inoculation. A better understanding of the molecular interactions of rhabdoviruses with insects will clarify the complexities of rhabdovirus infection processes and epidemiology. A unique opportunity for studying how insects become hosts and vectors of rhabdoviruses is provided by five maize-infecting rhabdoviruses that are differentially transmitted by one or more related species of two divergent homopteran families.     

Intensive rehabilitation in children with cerebral palsy: our view on the neuronal group selection theory

Cerebral palsy (CP) is one of the major forms of developmental disorders. There are different approaches and controversies in rehabilitation treatment. The Neuronal Group Selection theory could provide theoretical explanation for Stojcevi? Polovina rehabilitation method. The aim of the study was to evaluate long-term impact of intensive and continuously performed rehabilitation on the motor autonomy level children with CR Motor autonomy levels, defined according to the Gross Motor Function Classification System (GMFCS) and Gross Motor Function Measure (GMFM), were analyzed in 24 children with CP at the beginning of the study and at the last visit. During rehabilitation, GMFM scores increased above the expected value of initial GMFCS level in the majority of patients. Intensive rehabilitation had significant influence on motor improvement in children with CP.     

The controversial nuclear matrix: a balanced point of view

The nuclear matrix is defined as the residual framework after the removal of the nuclear envelope, chromatin, and soluble components by sequential extractions. According to several investigators the nuclear matrix provides the structural basis for intranuclear order. However, the existence itself and the nature of this structure is still uncertain. Although the techniques used for the visualization of the nuclear matrix have improved over the years, it is still unclear to what extent the isolated nuclear matrix corresponds to an in vivo existing structure. Therefore, considerable skepticism continues to surround the nuclear matrix fraction as an accurate representation of the situation in living cells. Here, we summarize the experimental evidence in favor of, or against, the presence of a diffuse nucleoskeleton as a facilitating organizational nonchromatin structure of the nucleus.