A combination of walk-back and optimum contribution selection in fish: a simulation study

The aim of this paper was to study the performance of a novel fish breeding scheme, which is a combination of walk-back and optimum contribution selection using stochastic simulation. In this walk-back selection scheme, batches of different sizes (50, 100, 1000, 5000 and 10 000) with the phenotypically superior fish from one tank with mixed families were genotyped to set up the pedigree. BLUP estimated breeding values were calculated. The optimum contribution selection method was used with the rate of inbreeding (ΔF) constrained to 0.005 or 0.01 per generation. If the constraint on ΔF could not be held, a second batch of fish was genotyped etc. Compared with the genotyping of all selection candidates (1000, 5000 or 10 000), the use of batches saves genotyping costs. The results show that two batches of 50 fish were often necessary. With a batch size of 100, genetic level was 76–92% of the genetic level achieved for schemes with all fish being genotyped and thus candidates for the optimum contribution selection step. More parents were selected for schemes with larger batches, resulting in a higher genetic gain, especially when all selection candidates were genotyped. There was little extra genetic gain in genotyping of 1000 fish instead of 100 for the larger schemes of 5000 and 10 000 candidates. The accuracy of breeding values was similar for all batch sizes (~0.30), but higher (~0.5) when all candidates were included. Since only the phenotypically most superior fish were genotyped, BLUP-EBV were biased. Compared with genotyping of all selection candidates, the use of batches saves genotyping costs, while simultaneously maintaining high genetic gains

Within-family marker-assisted selection for aquaculture species

A within-family marker-assisted selection scheme was designed for typical aquaculture breeding schemes, where most traits are recorded on sibs of the candidates. Here, sibs of candidates were tested for the trait and genotyped to establish genetic marker effects on the trait. BLUP breeding values were calculated, including information of the markers (MAS) or not (NONMAS). These breeding values were identical for all family members in the NONMAS schemes, but differed between family members in the MAS schemes, making within-family selection possible. MAS had up to twice the total genetic gain of the corresponding NONMAS scheme. MAS was somewhat less effective when heritability increased from 0.06 to 0.12 or when the frequency of the positive allele was < 0.5. The relative efficiency of MAS was higher for schemes with more candidates, because of larger fullsib family sizes. MAS was also more efficient when male:female mating ratio changed from 1:1 to 1:5 or when the QTL explained more of the total genetic variation. Four instead of two markers linked to the QTL increased genetic gain somewhat. There was no significant difference in polygenic genetic gain between MAS and NONMAS for most schemes. The rates of inbreeding were lower for MAS than NON-MAS schemes, because fewer full-sibs were selected by MAS

Non-random mating for selection with restricted rates of inbreeding and overlapping generations

Minimum coancestry mating with a maximum of one offspring per mating pair (MC1) is compared with random mating schemes for populations with overlapping generations. Optimum contribution selection is used, whereby ΔF is restricted. For schemes with ΔF restricted to 0.25% per year, 256 animals born per year and heritability of 0.25, genetic gain increased with 18% compared with random mating. The effect of MC1 on genetic gain decreased for larger schemes and schemes with a less stringent restriction on inbreeding. Breeding schemes hardly changed when omitting the iteration on the generation interval to find an optimum distribution of parents over age-classes, which saves computer time, but inbreeding and genetic merit fluctuated more before the schemes had reached a steady-state. When bulls were progeny tested, these progeny tested bulls were selected instead of the young bulls, which led to increased generation intervals, increased selection intensity of bulls and increased genetic gain (35% compared to a scheme without progeny testing for random mating). The effect of MC1 decreased for schemes with progeny testing. MC1 mating increased genetic gain from 11–18% for overlapping and 1–4% for discrete generations, when comparing schemes with similar genetic gain and size

Selection against genetic defects in conservation schemes while controlling inbreeding

We studied different genetic models and evaluation systems to select against a genetic disease with additive, recessive or polygenic inheritance in genetic conservation schemes. When using optimum contribution selection with a restriction on the rate of inbreeding (ΔF) to select against a disease allele, selection directly on DNA-genotypes is, as expected, the most efficient strategy. Selection for BLUP or segregation analysis breeding value estimates both need 1–2 generations more to halve the frequency of the disease allele, while these methods do not require knowledge of the disease mutation at the DNA level. BLUP and segregation analysis methods were equally efficient when selecting against a disease with single gene or complex polygene inheritance, i.e. knowledge about the mode of inheritance of the disease was not needed for efficient selection against the disease. Smaller schemes or schemes with a more stringent restriction on ΔF needed more generations to halve the frequency of the disease alleles or the fraction of diseased animals. Optimum contribution selection maintained ΔF at its predefined level, even when selection of females was at random. It is argued that in the investigated small conservation schemes with selection against a genetic defect, control of ΔF is very important

Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress

The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in the initial founders. Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and, therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during 10 generations of phenotypic selection applied in the subsequent breeding program

Combined detection and introgression of QTL in outbred populations

<p>Abstract</p> <p>Background</p> <p>Detecting a QTL is only the first step in genetic improvement programs. When a QTL with desirable characteristics is found, e.g. in a wild or unimproved population, it may be interesting to introgress the detected QTL into the commercial population. One approach to shorten the time needed for introgression is to combine both QTL identification and introgression, into a single step. This combines the strengths of fine mapping and backcrossing and paves the way for introgression of desirable but unknown QTL into recipient animal and plant lines.</p> <p>Methods</p> <p>The method consisting in combining QTL mapping and gene introgression has been extended from inbred to outbred populations in which QTL allele frequencies vary both in recipient and donor lines in different scenarios and for which polygenic effects are included in order to model background genes. The effectiveness of the combined QTL detection and introgression procedure was evaluated by simulation through four backcross generations.</p> <p>Results</p> <p>The allele substitution effect is underestimated when the favourable QTL allele is not fixed in the donor line. This underestimation is proportional to the frequency differences of the favourable QTL allele between the lines. In most scenarios, the estimates of the QTL location are unbiased and accurate. The retained donor chromosome segment and linkage drag are similar to expected values from other published studies.</p> <p>Conclusions</p> <p>In general, our results show that it is possible to combine QTL detection and introgression even in outbred species. Separating QTL mapping and introgression processes is often thought to be longer and more costly. However, using a combined process saves at least one generation. With respect to the linkage drag and obligatory drag, the results of the combined detection and introgression scheme are very similar to those of traditional introgression schemes.</p

2-этилтиобензимидазола гидробромид предупреждает развитие оксидативного стресса и воспалительной реакции при стрессе

ОКСИДАТИВНЫЙ СТРЕСССТРЕСС2-ЭТИЛТИОБЕНЗИМИДАЗОЛА ГИДРОБРОМИДСЕРДЕЧНО-СОСУДИСТАЯ СИСТЕМА /ДЕЙСТВ ПРЕППЕРЕКИСНОЕ ОКИСЛЕНИЕ ЛИПИДОВОКИСЛИТЕЛЬНО-ВОССТАНОВИТЕЛЬНЫЕ РЕАКЦИИБИОМЕДИЦИНСКИЕ ИССЛЕДОВАНИЯЭКСПЕРИМЕНТЫ НА ЖИВОТНЫХКРЫС

Evaluation of strategies to optimize training populations for genomic prediction in oat (Avena sativa)

publishedVersio

Evaluation of strategies to optimize training populations for genomic prediction in oat (Avena sativa)

publishedVersio