Genomic prediction of starch content and chipping quality in tetraploid potato using genotyping-by-sequencing

peer-reviewedGenomic prediction models for starch content and chipping quality show promising results, suggesting that genomic selection is a feasible breeding strategy in tetraploid potato. Genomic selection uses genome-wide molecular markers to predict performance of individuals and allows selections in the absence of direct phenotyping. It is regarded as a useful tool to accelerate genetic gain in breeding programs, and is becoming increasingly viable for crops as genotyping costs continue to fall. In this study, we have generated genomic prediction models for starch content and chipping quality in tetraploid potato to facilitate varietal development. Chipping quality was evaluated as the colour of a potato chip after frying following cold induced sweetening. We used genotyping-by-sequencing to genotype 762 offspring, derived from a population generated from biparental crosses of 18 tetraploid parents. Additionally, 74 breeding clones were genotyped, representing a test panel for model validation. We generated genomic prediction models from 171,859 single-nucleotide polymorphisms to calculate genomic estimated breeding values. Cross-validated prediction correlations of 0.56 and 0.73 were obtained within the training population for starch content and chipping quality, respectively, while correlations were lower when predicting performance in the test panel, at 0.30-0.31 and 0.42-0.43, respectively. Predictions in the test panel were slightly improved when including representatives from the test panel in the training population but worsened when preceded by marker selection. Our results suggest that genomic prediction is feasible, however, the extremely high allelic diversity of tetraploid potato necessitates large training populations to efficiently capture the genetic diversity of elite potato germplasm and enable accurate prediction across the entire spectrum of elite potatoes. Nonetheless, our results demonstrate that GS is a promising breeding strategy for tetraploid potato.The Danish Council of Strategic Researc

Applying the GBS technique for the genomic characterization of a Danish population of European hedgehogs (Erinaceus europaeus)

The objective of the study was to establish and refine a method for the genomic characterization of European hedgehogs in Denmark using the second-generation genotyping technique, genotyping by sequencing (GBS). Single nucleotide polymorphisms (SNPs) were filtered with a read coverage between 20 - 100 and a maximum number of missing data of 25 %. Individuals with > 25 % missing data were removed yielding a total of 2.4 million SNPs, and after filtering for Minor allele frequency (MAF) >1 %, 2902 SNPs remained. Approximately half of the individuals analysed contained less than 75% of the selected SNPs, and were removed, resulting in a sample size of 30. We estimated inbreeding coefficients (F), observed (HO), expected (HE) and unbiased expected (uHE) heterozygosity and the percent of polymorphic loci (P%). We tested for deviations from Hardy-Weinberg equilibrium (HWE) and patterns of isolation by distance (IBD). We assessed the genetic structure of the sampled individuals based on a Bayesian clustering method, and tested for recent population expansion or decline. We found a P% = 94.5%, a uHE and HE of mean ± SE; 0.31 ± 0.04 and 0.30 ± 0.02, respectively and an HO of 0.290 ± 0.03. The heterozygosity deficiency was reflected in a positive F-value; 0.1 ± 0.01 and a significant deviation for HWE (p < 0.05). The Mantel test for association between the genetical and geographical distances of populations was not significant (b = 0.007, R = 0.145, p > 0.05). The significant and positive F-value found, was explained by inbreeding, genetic substructure and low effective population size (Ne) which are all consequences of habitat fragmentation. We failed to detect recent signs of a population bottleneck or expansion. Further studies on a larger scale are needed to obtain a general view of the conservation status of the Danish hedgehog populatio

Áhrif stýrðrar kennslu Engelmanns og fimiþjálfunar á lestrarfærni 7 ára drengs með athyglisbrest með ofvirkni

Lestur er gríðarlega mikilvægur og er grundvöllur allrar menntunar. Því er mikilvægt að ýta undir lestrarfærni barna snemma á ævinni með árangursríkri lestrarkennslu. Stýrð kennsla (e. Direct Instruction) er raunprófuð kennsluaðferð sem byggir á störfum Siegfried Engelmann og hefur reynst árangursrík við að kenna lestur. Aðferðin byggir á notkun nákvæms handrits sem er byggt upp svo einstaklingur nái tökum á grunnfærni áður en flóknara efni er kennt. Áhersla er lögð á að hrósa fyrir rétt svör og leiðrétta röng, tafarlaust og á skýran hátt. Fimiþjálfun (e. precicion teaching) er önnur raunprófuð kennsluaðferð sem hefur það markmið að auka fimi (e. fluency), sem vísar í hraða, örugga og villulausa svörun. Fylgst er með árangri að settu markmiði, með daglegri skráningu frammistöðu á hröðunarkort, svo hægt sé að breyta kennsluháttum strax ef þörf er á. Aðferðirnar eru oft notaðar saman og hafa reynst árangursríkar við að bæta lestrarfærni barna. Þessar aðferðir mynda saman ágæta heild, þar sem stýrð kennsla er notuð til að kenna færni en fimiþjálfun til að auka fimi og mæla framfarir. Markmið rannsóknarinnar var að nota stýrða kennslu og fimiþjálfun til að auka lestrarfærni barns sem hefur verið greint með athyglisbrest með ofvirkni (AMO), þar sem kenndir eru grunnþættir lestrar, líkt og hljóðun einstakra stafa og einfaldra orða. Niðurstöður sýndu fram á árangur þessara kennsluaðferða í að auka lestrarfærni og fimi þátttakanda í öllum þáttum sem metnir voru, og styðja því notkun stýrðrar kennslu og fimiþjálfunar í íslensku skólakerfi og með börnum sem greind eru með AMO

Genomic variation predicts adaptive evolutionary responses better than population bottleneck history.

The relationship between population size, inbreeding, loss of genetic variation and evolutionary potential of fitness traits is still unresolved, and large-scale empirical studies testing theoretical expectations are surprisingly scarce. Here we present a highly replicated experimental evolution setup with 120 lines of Drosophila melanogaster having experienced inbreeding caused by low population size for a variable number of generations. Genetic variation in inbred lines and in outbred control lines was assessed by genotyping-by-sequencing (GBS) of pooled samples consisting of 15 males per line. All lines were reared on a novel stressful medium for 10 generations during which body mass, productivity, and extinctions were scored in each generation. In addition, we investigated egg-to-adult viability in the benign and the stressful environments before and after rearing at the stressful conditions for 10 generations. We found strong positive correlations between levels of genetic variation and evolutionary response in all investigated traits, and showed that genomic variation was more informative in predicting evolutionary responses than population history reflected by expected inbreeding levels. We also found that lines with lower genetic diversity were at greater risk of extinction. For viability, the results suggested a trade-off in the costs of adapting to the stressful environments when tested in a benign environment. This work presents convincing support for long-standing evolutionary theory, and it provides novel insights into the association between genetic variation and evolutionary capacity in a gradient of diversity rather than dichotomous inbred/outbred groups