微卫星标记及其在动物遗传育种中的应用

微卫星标记技术一出现,就以其独特的优点引起了动物遗传育种学家的广泛关注,显示出较好的应用前景。本文就微卫星标记的特点及其在动物遗传育种中的应用作以综述。     

Simulation study on the efficiencies of MOET nucleus breeding schemes applying marker assisted selection in dairy cattle

Advantages of breeding schemes using genetic marker information and/or multiple ovulation and embryo transfer (MOET) technology over the traditional approach were extensively evaluated through simulation. Milk yield was the trait of interest and QTL was the genetic marker utilized. Eight dairy cattle breeding scenarios were considered, i.e., traditional progeny testing breeding scheme (denoted as STANPT), GASPT scheme including a pre-selection of young bulls entering progeny testing based on their own QTL information, MOETPT scheme using MOET technology to generate young bulls and a selection of young bulls limited within the full-sib family, GAMOPT scheme adopting both QTL pre-selection and MOET technology, COMBPT scheme using a mixed linear model which considered QTL genotype instead of the BLUP model in GAMOPT, and three non-progeny testing schemes, i.e. the MOET, GAMO and COMB schemes, corresponding to MOETPT, GAMOPT and COMBPT with progeny testing being part of the system. Animals were selected based on their breeding value which was estimated under an animal model framework. Sequential selection over 17 years was performed in the simulations and 30 replicates were designed for each scenario. The influences of using QTL information and MOET technology on favorable QTL allele frequency, true breeding values, polygenetic breeding values and the accumulated genetic superiority were extensively evaluated, for five different populations including active sires, lactating cows, bull dams, bull sires, and young bulls. The results showed that the combined schemes significantly outperformed other approaches wherein accumulated true breeding value progressed. The difference between schemes exclusively using QTL information or MOET technology was not significant. The STANPT scheme was the least efficient among the 8 schemes. The schemes using MOET technology had a higher polygenetic response than others in the 17th year. The increases of frequency of the favorable QTL allele varied more greatly across the 3 male groups than in the lactating cows group. The accumulated genetic superiorities of the GASPT scheme, MOETPT scheme, GAMOPT scheme, COMBPT scheme, MOET scheme, GAMO scheme and COMB scheme over the STANPT scheme were 8.42%, 3.59%, 14.58%, 18.54%, 4.12%, 14.12%, 16.50% in active sires and 2.70%, 5.00%, 11.05%, 12.78%, 7.51%, 17.12%, 25.38% in lactating cows. Supported by Key Project for Introducing Advanced International Agriculture Science & Technologies (Grant No. 2006-G48), the National Key Basic Research and Development Program of China (Grant No. 2006CB102107) and National Key Technology Research and Development Program of China (Grant No. 2006BAD04A01).     

Precision animal breeding

We accept that we are responsible for the quality of life of animals in our care. We accept that the activities of man affect all the living things with which we share this planet. But we are slow to realize that as a result we have a duty of care for all living things. That duty extends to the breeding of animals for which we are responsible. When animals are bred by man for a purpose, the aim should be to meet certain goals: to improve the precision with which breeding outcomes can be predicted; to avoid the introduction and advance of characteristics deleterious to well-being; and to manage genetic resources and diversity between and within populations as set out in the Convention on Biological Diversity. These goals are summed up in the phrase precision animal breeding. They should apply whether animals are bred as sources of usable products or services for medical or scientific research, for aesthetic or cultural considerations, or as pets. Modern molecular and quantitative genetics and advances in reproductive physiology provide the tools with which these goals can be met.     

Mating strategies with genomic information reduce rates of inbreeding in animal breeding schemes without compromising genetic gain

We tested the hypothesis that mating strategies with genomic information realise lower rates of inbreeding (∆F) than with pedigree information without compromising rates of genetic gain (∆G). We used stochastic simulation to compare ∆F and ∆G realised by two mating strategies with pedigree and genomic information in five breeding schemes. The two mating strategies were minimum-coancestry mating (MC) and minimising the covariance between ancestral genetic contributions (MCAC). We also simulated random mating (RAND) as a reference point. Generations were discrete. Animals were truncation-selected for a single trait that was controlled by 2000 quantitative trait loci, and the trait was observed for all selection candidates before selection. The criterion for selection was genomic-breeding values predicted by a ridge-regression model. Our results showed that MC and MCAC with genomic information realised 6% to 22% less ∆F than MC and MCAC with pedigree information without compromising ∆G across breeding schemes. MC and MCAC realised similar ∆F and ∆G. In turn, MC and MCAC with genomic information realised 28% to 44% less ∆F and up to 14% higher ∆G than RAND. These results indicated that MC and MCAC with genomic information are more effective than with pedigree information in controlling rates of inbreeding. This implies that genomic information should be applied to more than just prediction of breeding values in breeding schemes with truncation selection.     

Optimising multi-tier open nucleus breeding schemes

Summary The constant migration (CM) method and the ebv migration (EBVM) method of optimising the design of multi-tier open nucleus breeding schemes are presented and compared. The equation for the equilibrium rate of genetic gain of a three-tier open nucleus scheme is determined using the CM method. The major advantage of the EBVM method is the reduction in the number of parameters which have to be varied in order to locate the maximum equilibrium rate of genetic gain. For the CM method for the number of variable parameters is 5, 14, 27 and (2n + 1) (n - 1) for unrestricted male and female migration in schemes with 2, 3, 4 and n tiers respectively. The corresponding number of variable parameters for the EBVM method is 1, 2, 3 and n-1 respectively. A procedure is given for the EBVM method so as to accomodate variance loss due to selection and variance gain due to the mixing of groups with a different mean breeding value.     

5. The use of genetic resources in breeding and breeding research

The dramatic increase in yields of agricultural crops over the last 40 years in developed countries has been attributed equally to improved genetic components and improved agronomic practices. The success of plant breeding is based partly on an increased understanding of the parameters involved, to a great extent on improved and more efficient methods of selection, to greater use of available genetic diversity and also to advances in a number of related disciplines including plant pathology, biochemistry, agronomy and genetics. Successes and problems associated with using various genetic resources in plant breeding are illustrated with examples from some of the world's major crops, including potatoes, barley and cotton.     

Theory of nucleus breeding schemes with overlapping generations

Summary Explicit methods are derived for estimating steady-state genetic responses and genetic differences between nucleus and base progeny crops in open nucleus breeding schemes which utilize genetic differences between progeny groups with parents of different ages or between age groups. Explicit methods are also given for estimating proportions which should be selected from the different nucleus and base selection groups so as to maximise genetic responses under each of a range of selection methods. Some basic differences between selection programmes utilizing genetic differences between progeny groups with parents of different ages and those utilizing genetic differences between age groups in nucleus breeding schemes are summarized.     

PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees

In the study of large outbred pedigrees with many founders, individual bi-allelic markers, such as SNP markers, carry little information. After phasing the marker genotypes, multi-allelic loci consisting of groups of closely linked markers can be identified, which are called “haploblocks”. Here, we describe PediHaplotyper, an R package capable of assigning consistent alleles to such haploblocks, allowing for missing and incorrect SNP data. These haploblock genotypes are much easier to interpret by the human investigator than the original SNP data and also allow more efficient QTL analyses that require less memory and computation time.     

The use of hybridization in breeding of eukaryotic microorganisms

The article deals with the genetic bases of breeding of eukaryotic microorganisms. Using the data on the Saccharomyces yeasts, application of different genetic approaches and methods to breeding is discussed, including interstrain, interlinear, and distant interspecific hybridization, as well as heterosis, polyploidy, cytoduction, and meiotic recombination.     

The use of hybridization in breeding of eukaryotic microorganisms

The article deals with the genetic bases of breeding of eukaryotic microorganisms. Using the data on the Saccharomyces yeasts, application of different genetic approaches and methods to breeding is discussed, including interstrain, interlinear, and distant interspecific hybridization, as well as heterosis, polyploidy, cytoduction, and meiotic recombination.     

Potential uses of cloning in breeding schemes: dairy cattle

Cloning by nuclear transfer has many potential applications in a dairy cattle breeding program. It can be used to increase the accuracy of selection and therefore the rate of genetic progress, to speed up the dissemination of the genes from animals of exceptionally high genetic merit to the commercial population, and to reproduce transgenic animals. Today, however, the main limitation of the use of cloning besides governmental regulations is its low success rate and consequently the high cost to produce an animal ready for reproduction. As a result cloning is mostly limited to the reproduction of animals of very high genetic merit or that carry genes of specific interest. Examples of this are top-ranked bulls which do not produce enough semen for the demand due to various reasons. A strategy that could be used by artificial insemination (AI) centers would be to create a bank of somatic cells for every bull entering AI facilities long before they are placed on the young sire proving program. The other use of cloning is to assist in the selection and reproduction of bull dams. Marker assisted selection (MAS) can substantially enhance the accuracy of selection for embryos or young animals without comprehensive performance records, and therefore can greatly increase the value of cloning such embryos or young animals.     

The proposed use of melatonin in controlled sheep breeding

The regulation by melatonin of hypothalamic-pituitary events in the ewe to advance seasonal oestrous activity, with no undesirable effects upon fertility, and its induction of those seasonal responses associated with short days indicates an essential role for melatonin in controlled-breeding programs in major sheep-producing countries. The development of suitable controlled-release systems to provide a choice of practical methods of melatonin delivery under field conditions is discussed as also are geographical and breed factors in controlled breeding with melatonin.     

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.     

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。