Colonial breeding in Mute swans (Cygnus olor) associated with an allozyme of lactate dehydrogenase

The Mute swan ( Cygnus olor Gmelin (Anatidae)) is a common water bird of lowland freshwaters and coastal shallows. Its typical breeding system involves lifelong monogamous pairs which vigorously defend large breeding territories, sometimes killing intruding swans that are unable to escape. However, in some unusual circumstances (superabundant food coupled with limited nesting sites) Mute swans may nest colonially. At the only two colonies in southern England a rare allele for lactate dehydrogenase (LDH) was found to be unusually common and colony swans carrying this allele were shown to breed more successfully. This isolated finding could, however, have originated either from a chance 'founder' effect or from human management of the main colony. We now show that this allele is also significantly commoner at two recently formed colonies in Denmark, implying that the association between the allele and colonial breeding may be widespread and longstanding.     

An invertebrate histocompatibility complex

We have developed defined genetic lines of the hydroid Hydractinia symbiolongicarpus and confirmed earlier results showing that allorecognition is controlled by a single chromosomal region within these lines. In a large backcross population, we detected recombinants that display a fusibility phenotype distinct from typical fusion and rejection. We show that this transitory fusion phenotype segregates in a fashion expected of a single Mendelian trait, establishing that the chromosomal interval contains at least two genes that interact to determine fusibility. Using bulked segregant analysis, we have identified amplified fragment length polymorphisms (AFLP) cosegregating with fusibility, used these markers to independently confirm linkage of the two loci, and constructed a 3.4-cM map of an invertebrate histocompatibility complex.     

Relationship between yield components and partial resistance to Lecanicillium fungicola in the button mushroom, Agaricus bisporus, assessed by quantitative trait locus mapping

Dry bubble, caused by Lecanicillium fungicola, is one of the most detrimental diseases affecting button mushroom cultivation. In a previous study, we demonstrated that breeding for resistance to this pathogen is quite challenging due to its quantitative inheritance. A second-generation hybrid progeny derived from an intervarietal cross between a wild strain and a commercial cultivar was characterized for L. fungicola resistance under artificial inoculation in three independent experiments. Analysis of quantitative trait loci (QTL) was used to determine the locations, numbers, and effects of genomic regions associated with dry-bubble resistance. Four traits related to resistance were analyzed. Two to four QTL were detected per trait, depending on the experiment. Two genomic regions, on linkage group X (LGX) and LGVIII, were consistently detected in the three experiments. The genomic region on LGX was detected for three of the four variables studied. The total phenotypic variance accounted for by all QTL ranged from 19.3% to 42.1% over all traits in all experiments. For most of the QTL, the favorable allele for resistance came from the wild parent, but for some QTL, the allele that contributed to a higher level of resistance was carried by the cultivar. Comparative mapping with QTL for yield-related traits revealed five colocations between resistance and yield component loci, suggesting that the resistance results from both genetic factors and fitness expression. The consequences for mushroom breeding programs are discussed.     

Allele coding in genomic evaluation

Background

Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference.

Results

Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding, provided that the model has a fixed general mean. For the equivalent models, the same results hold, even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient matrix depend on the allele coding because different allele coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being the best.

Conclusions

Different allele coding methods lead to the same inference in the marker-based and equivalent models when a fixed general mean is included in the model. However, reliabilities of genomic breeding values are affected by the allele coding method used. The centered coding has some numerical advantages when Markov chain Monte Carlo methods are used.     

Is drift ‘directional’? Unequal breeding sex ratio revisited

Unequal breeding sex ratio can significantly reduce effective population size, allowing a rare neutral allele to jump to a high frequency through genetic drift. However, this one-way alteration to allele frequency appears inconsistent with the concept that drift is non-directional. Based on binomial sampling distribution, this study developed a method to directly and exhaustively measure drift by calculating the mean deviation of change in allele frequency, then applied it to cases of unequal breeding sex ratio. The result shows that, under those cases, (1) the mean deviation can always be divided into two halves that are equal in size but opposite in direction; (2) each half consists of one or several categories represented by various allele proportions in the rare sex; (3) this proportion is another factor that determines the outcome of drift, in addition to effective population size and allele frequency; (4) drift is non-directional on a global scale, but whether an allele will drift up or down can be predicted based on the above factors. This method enables us to dissect every component of the expected change in allele frequency caused by drift and to find out the combined effect of population size, allele frequency and allele proportion in the rarer sex under neutrality but unequal breeding sex ratio.     

Intronic variation at the CHD1‐Z gene in Black‐tailed Godwits Limosa limosa limosa: correlations with fitness components revisited

Recently, Schroeder et al. (2010, Ibis 152: 368–377) suggested that intronic variation in the CHD1‐Z gene of Black‐tailed Godwits breeding in southwest Friesland, The Netherlands, correlated with fitness components. Here we re‐examine this surprising result using an expanded dataset (2088 birds sampled from 2004 to 2010 vs. 284 birds from 2004 to 2007). We find that the presence of the Z* allele (9% of the birds) is not associated with breeding habitat type, egg size, adult survival, adult body mass or adult body condition. The results presented here, when used in synergy with the previously reported results by Schroeder et al., suggest that there might be a tendency towards female adults with the Z* allele laying earlier clutches than adult females without the Z* allele. The occurrence of the Z* allele was also associated with a higher chick body mass and return rate. Chicks with the Z* allele that had hatched early in the breeding season were heavier at birth than chicks without the Z* allele and chicks with the Z* allele that had hatched late. Collectively, the results suggest that variation in the CHD1‐Z gene may indeed have arisen as a byproduct of selection acting on females during the egg fase and on chicks during the rearing stages of the reproductive cycle.     

不同QTL增效基因初始频率下标记辅助选择的效果

采用随机模拟方法模拟了在一个闭锁群体内连续对单个性状选择10个世代的情形。在假定选择性状受一个位于常染色体上的QTL和多基因共同控制的情况下,采用动物模型标记辅助最佳线性无偏预测方法估计个体育种值并据此进行种畜的选留,并在此基础上系统地比较了QTL增效基因初始频率对标记辅助选择效果的影响。结果表明：当群体中QTL增效基因的初始频率较低时,选择所获得的QTL基因型值的进展会更大,标记辅助选择在单位时间内可获得较大的遗传进展;此时,尽管QTL增效基因在群体中固定所需的世代数会更长一些,但其频率上升的速度却更快。而QTL增效基因初始频率的高低对群体近交增量的影响不是很大。     

Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms

Characterization of genetic diversity is of great value to assist breeders in parental line selection and breeding system design. We screened 770 maize inbred lines with 1,034 single nucleotide polymorphism (SNP) markers and identified 449 high-quality markers with no germplasm-specific biasing effects. Pairwise comparisons across three distinct sets of germplasm, CIMMYT (394), China (282), and Brazil (94), showed that the elite lines from these diverse breeding pools have been developed with only limited utilization of genetic diversity existing in the center of origin. Temperate and tropical/subtropical germplasm clearly clustered into two separate groups. The temperate germplasm could be further divided into six groups consistent with known heterotic patterns. The greatest genetic divergence was observed between temperate and tropical/subtropical lines, followed by the divergence between yellow and white kernel lines, whereas the least divergence was observed between dent and flint lines. Long-term selection for hybrid performance has contributed to significant allele differentiation between heterotic groups at 20% of the SNP loci. There appeared to be substantial levels of genetic variation between different breeding pools as revealed by missing and unique alleles. Two SNPs developed from the same candidate gene were associated with the divergence between two opposite Chinese heterotic groups. Associated allele frequency change at two SNPs and their allele missing in Brazilian germplasm indicated a linkage disequilibrium block of 142 kb. These results confirm the power of SNP markers for diversity analysis and provide a feasible approach to unique allele discovery and use in maize breeding programs.     

Germ cell parasitism as an ecological and evolutionary puzzle: hitchhiking with positively selected genotypes

The phenomenon of intraspecific germ cell parasitism may reveal a theoretical puzzle to the concept of Darwinian selection. In natural chimeras of the colonial protochordate Botryllus schlosseri , parasitic germ lines hitchhike with positively selected allogeneic soma, passing throughout successive generations without being visible to natural selection forces. This may cause the possible development of super-parasitic entities, specialized in allogeneic invasion and germ cell parasitism. Three evolutionary selected mechanisms (diversification of fusibility allele repertoire, the establishment of multichimeric entities, induction of programmed life spans) reduce opportunities for parasitic forms to hitchhike to a high frequency with selected genotypes, and may shape, on the other hand, more benign germ cell parasitic forms that share overlapping future expectations with their hosts. These benign forms are expected to contribute cells for somatic functions, forming entities with fitness that depends on joint genomic fitness of the partners. Population-level feedback thus may stabilize chimeric entities, shaping the evolution of chimerism.     

Linking intronic polymorphism on the CHD1‐Z gene with fitness correlates in Black‐tailed Godwits Limosa l. limosa

We show that variation in an intronic length polymorphism in the CHD1‐Z gene in Black‐tailed Godwits Limosa l. limosa is associated with fitness correlates. This is the second example of the CHDZ‐1 gene being correlated with fitness, a previous study having established that Moorhens Gallinula chloropus carrying the rare Z* allele have reduced survival. In Godwits, however, carriers of the Z* allele (374 bp) fared better than those with the more frequent Z allele (378 bp) with respect to body mass, plumage ornamentation, reproductive parameters and habitat quality. The Z* allele was found in 14% of 251 adult birds from nature reserves, but was absent from 33 birds breeding in intensively managed agricultural lands. Males and females with the Z* allele had less extensive breeding plumage, and females had a higher body mass, bred earlier and had larger eggs. There were no significant differences in annual survival between birds with and without the Z* allele. DNA isolated from museum skins demonstrated that this polymorphism was present at low frequency in 1929. We speculate that strong asymmetrical overdominance may explain the low frequency of the Z* allele and that genetic linkage to causal genes might be an explanation for the phenotypic correlations. Our findings suggest a degree of cryptic genetic population structuring in the Dutch Godwit population.     

Mining data from potato pedigrees: tracking the origin of susceptibility and resistance to<Emphasis Type="Italic"> Verticillium dahliae</Emphasis> in North American cultivars through molecular marker analysis

Potato (Solanum tuberosum L.) cultivated in North America is an autotetraploid species with a narrow genetic base. Most of the popular commercial cultivars are susceptible to Verticillium dahliae, a fungal pathogen causing Verticillium wilt disease, though some cultivars with relatively high resistance also exist. We have used the available pedigree information to track the origin of susceptibility and resistance to Verticillium wilt present in cultivated potatoes. One hundred thirty-nine potato cultivars and breeding selections were analyzed for resistance to the pathogen and for the presence of the microsatellite marker allele STM1051–193 that is closely linked to the resistance quantitative trait locus located on the short arm of chromosome 9. We detected an unusually high frequency of susceptible genotypes in the progeny descending from the breeding selection USDA X96–56. Molecular analysis revealed that USDA X96–56 does not have the STM1051–193 allele. Most of the first-generation progeny of this breeding selection also lack the allele. On the other hand, pedigree analysis indicated that breeding selection USDA 41956 often transfers V. dahliae resistance to its progeny. Molecular analysis detected presence of (at least) three STM1051–193 alleles in this breeding selection. These two genotypes (USDA X96–56 and USDA 41956) appear to have contributed greatly to the susceptibility or resistance, respectively, found in present commercial cultivars. Our results also indicate that the maturity class substantially affects the plant resistance response. In the intermediate to very late maturing class, the presence of the STM1051–193 allele significantly increases the resistance. Early to very early potatoes are usually more susceptible to the disease regardless of the allelic status, though the pattern of the allele effect is always the same. The results indicate that the STM1051–193 allele can be used for marker-assisted selection, but the potato maturity class also needs to be considered when making the final decision about the plant resistance level.Communicated by G. Wenzel     

The evolution of gynodioecy on a lattice

Gynodioecy is a breeding system in plants where populations consist of hermaphrodites and females. The females result from a genetic mutation which impairs pollen production in hermaphrodite plants. Most previous models for the evolution of gynodioecy do not take into account any spatial detail, which might be expected to play an important role in populations with short range interactions caused by poor or no locomotion.In this article we present a generalised mean-field analysis (which ignores any spatial detail), together with stochastic spatial simulations, to investigate the spatial effect on the evolution of gynodioecy. We show that, in a population of hermaphrodites where male sterility is caused by a dominant allele in a nuclear gene, mean-field calculations greatly underestimate the reproductive advantage females require to become viable under spatial constraints. This suggests that gynodioecy is less likely to evolve in plants with more localised pollination and seed setting. This may have implications for the evolution of dioecy, a breeding system in plants where the population consists of males and females, as gynodioecy is thought to be a route to dioecy. Our results also demonstrate that a lower frequency of females should be expected for gynodioecious populations when interactions are local. This is relevant when comparing the results of breeding experiments with observations of female frequency in the wild.     

Breeding colony refinement through phenotypic and genotypic characterization of the SPRD-Pkdr1/Rrrc rat model of polycystic kidney disease

The SPRD-Pkdr1 rat model is widely used for the study of human autosomal dominant polycystic kidney disease. This rat model carries the Cy allele of the Pkdr1 gene, which results in polycystic kidney disease. Because the Cy allele is lethal in the homozygous state at weanling age, the breeding colony must be maintained in the heterozygous state. A random breeding scheme in which production of homozygous pups with enlarged kidneys indicates heterozygous breeders is commonly used. This study was performed to determine whether biochemical markers (blood urea nitrogen [BUN] or creatinine), ultrasonography, or genetic analysis could be used to select breeding animals in the SPRD-Pkdr1/Rrrc colony and thus replace the random breeding scheme with a more efficient selective breeding scheme. BUN was predictive of the Cy allele in 8- to 9-wk-old male but not female rats. Ultrasonography identified animals with polycystic kidney disease in both sexes by 9 wk of age. Microsatellite marker polymorphism analysis could not be used to determine carrier status for the Cy allele, but restriction fragment length polymorphism analysis appropriately detected the Cy allele in 100% of the animals examined. In conclusion, multiple methods can be used for detecting the Cy allele, making possible a selective breeding scheme that markedly reduces the necessary number of breeder animals and eliminates the euthanasia of offspring needed with a random test-mating scheme.     

Whole-body enantiomorphy and maternal inheritance of chiral reversal in the pond snail Lymnaea stagnalis

Sinistral and dextral snails have repeatedly evolved by left-right reversal of bilateral asymmetry as well as coiling direction. However, in most snail species, populations are fixed for either enantiomorph and laboratory breeding is difficult even if chiral variants are found. Thus, only few experimental models of chiral variation within species have been available to study the evolution of the primary asymmetry. We have established laboratory lines of enantiomorphs of the pond snail Lymnaea stagnalis starting from a wild population. Crossing experiments demonstrated that the primary asymmetry of L. stagnalis is determined by the maternal genotype at a single nuclear locus where the dextral allele is dominant to the sinistral allele. Field surveys revealed that the sinistral allele has persisted for at least 10 years, that is, about 10 generations. The frequency of the sinistral allele showed large fluctuations, reaching as frequent as 0.156 in estimate under the assumption of Hardy-Weinberg equilibrium. The frequency shifts suggest that selection against chiral reversal was not strong enough to counterbalance genetic drift in an ephemeral small pond. Because of the advantages as a model animal, enantiomorphs of L. stagnalis can be a unique system to study aspects of chirality in diverse biological disciplines.     

Individual MHC class I and MHC class IIB diversities are associated with male and female reproductive traits in the three-spined stickleback

Genes of the major histocompatibility complex (MHC) are indispensable for pathogen defence in vertebrates. With wild-caught three-spined sticklebacks (Gasterosteus aculeatus) we conducted the first study to relate individual reproductive parameters to both MHC class I and II diversities. An optimal MHC class IIB diversity was found for male nest quality. However, male breeding colouration was most intense at a maximal MHC class I diversity. One MHC class I allele was associated with male redness. Similarly, one MHC class IIB allele was associated with continuous rather than early female reproduction, possibly extending the reproductive period. Both alleles occurred more frequently with increasing individual allele diversity. We suggest that if an allele is currently not part of the optimum, it had not been propagated by choosy females. The parasite against which this allele provides resistance is therefore unlikely to have been predominant the previous year - a step to negative frequency-dependent selection.     

Genome Wide Allele Frequency Fingerprints (GWAFFs) of Populations via Genotyping by Sequencing

Genotyping-by-Sequencing (GBS) is an excellent tool for characterising genetic variation between plant genomes. To date, its use has been reported only for genotyping of single individuals. However, there are many applications where resolving allele frequencies within populations on a genome-wide scale would be very powerful, examples include the breeding of outbreeding species, varietal protection in outbreeding species, monitoring changes in population allele frequencies. This motivated us to test the potential to use GBS to evaluate allele frequencies within populations. Perennial ryegrass is an outbreeding species, and breeding programs are based upon selection on populations. We tested two restriction enzymes for their efficiency in complexity reduction of the perennial ryegrass genome. The resulting profiles have been termed Genome Wide Allele Frequency Fingerprints (GWAFFs), and we have shown how these fingerprints can be used to distinguish between plant populations. Even at current costs and throughput, using sequencing to directly evaluate populations on a genome-wide scale is viable. GWAFFs should find many applications, from varietal development in outbreeding species right through to playing a role in protecting plant breeders’ rights.     

A worldwide polymorphism in aldehyde dehydrogenase in Drosophila melanogaster: evidence for selection mediated by dietary ethanol

Clinally varying traits in Drosophila melanogaster provide good opportunities for elucidating the genetic basis of adaptation. Resistance to ethanol, a natural component of D. melanogaster's breeding sites, increases with latitude on multiple continents, indicating that the trait is under selection. Although the well-studied Alcohol dehydrogenase (Adh) polymorphism makes a contribution to the clines, it accounts for only a small proportion of the phenotypic variation. We describe an amino acid replacement polymorphism in Aldehyde dehydrogenase (Aldh), the gene encoding the second enzyme in the ethanol degradation pathway, that shows hallmarks of also contributing to the clines. The derived Aldh allele, like the Adh-Fast allele, increases in frequency in laboratory populations selected for ethanol resistance, and increases in frequency with latitude in wild populations. Moreover, strains with the derived allele have significantly higher ALDH enzyme activity with acetaldehyde (the breakdown product of ethanol) as a substrate than strains with the ancestral allele. As is the case with the Adh-Fast allele, chromosomes with the derived Aldh allele show markedly reduced molecular variation in the vicinity of the replacement polymorphism compared to those with the ancestral allele, suggesting a single, relatively recent origin. Nonetheless, the Aldh polymorphism differs from the Adh polymorphism in that the ethanol-associated allele remains in relatively low frequency in most populations. We present evidence that this is likely to be the result of a trade-off in catalytic activity, with the advantage of the derived allele in acetaldehyde detoxification being offset by a disadvantage in detoxification of other aldehydes.     

Dot-blot-SNP analysis for practical plant breeding and cultivar identification in rice

We report dot-blot hybridization with allele-specific oligonucleotides for single nucleotide polymorphisms (SNPs) analysis to be applicable for practical plant breeding and cultivar identification. Competitive hybridization of a digoxigenin-labeled oligonucleotide having the sequence of a mutant allele (or a wild-type allele) together with an unlabeled oligonucleotide having the sequence of a wild-type allele (or a mutant allele) was highly effective to reduce background signals in dot-blot hybridization. All 100 tested genes (200 alleles) in rice having SNPs or insertions/deletions were detected in an allele-specific manner. Genotypes of 43 rice cultivars were identified by this technique, and eight SNP markers were found to be sufficient for distinguishing all the cultivars from each other. Dot-blot analysis was also applied to genotyping of Wx and Sd1 of F₄ plants in a conventional breeding program. Since dot-blot analysis with competitive hybridization provides a highly reliable, simple, and cost-effective technique for SNP analysis of a large number of samples, this technique is expected to realize the practical use of a novel breeding method, in which plants or breeding lines are selected by SNP analyses of many genes in a laboratory.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding

Genomic selection (GS) is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV) in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S_2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD) and minor allele frequency (MAF) thresholds for selecting markers, the relative size of the training population (TP) and of the validation population (VP), the selected trait and the genomic prediction models (frequentist and Bayesian) on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r² = 0.59 at 25 kb) and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%), and differentiation between the four synthetic populations was low (F_ST ≤0.06). The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed.     

Systematic differences in the response of genetic variation to pedigree and genome-based selection methods

Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and plant breeding, and offers a potentially superior alternative to traditional breeding methods that rely on pedigree and phenotype information. Using a 60 K SNP chip with markers spaced throughout the entire chicken genome, we compared the impact of GS and traditional BLUP (best linear unbiased prediction) selection methods applied side-by-side in three different lines of egg-laying chickens. Differences were demonstrated between methods, both at the level and genomic distribution of allele frequency changes. In all three lines, the average allele frequency changes were larger with GS, 0.056 0.064 and 0.066, compared with BLUP, 0.044, 0.045 and 0.036 for lines B1, B2 and W1, respectively. With BLUP, 35 selected regions (empirical P<0.05) were identified across the three lines. With GS, 70 selected regions were identified. Empirical thresholds for local allele frequency changes were determined from gene dropping, and differed considerably between GS (0.167–0.198) and BLUP (0.105–0.126). Between lines, the genomic regions with large changes in allele frequencies showed limited overlap. Our results show that GS applies selection pressure much more locally than BLUP, resulting in larger allele frequency changes. With these results, novel insights into the nature of selection on quantitative traits have been gained and important questions regarding the long-term impact of GS are raised. The rapid changes to a part of the genetic architecture, while another part may not be selected, at least in the short term, require careful consideration, especially when selection occurs before phenotypes are observed.