30,662 research outputs found

    Linkage analysis between dominant and co-dominant makers in full-sib families of out-breeding species

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    As high-throughput genomic tools, such as the DNA microarray platform, have lead to the development of novel genotyping procedures, such as Diversity Arrays Technology (DArT) and Single Nucleotide Polymorphisms (SNPs), it is likely that, in the future, high density linkage maps will be constructed from both dominant and co-dominant markers. Recently, a strictly genetic approach was described for estimating recombination frequency (r) between co-dominant markers in full-sib families. The complete set of maximum likelihood estimators for r in full-sib families was almost obtained, but unfortunately, one particular configuration involving dominant markers, segregating in a 3:1 ratio and co-dominant markers, was not considered. Here we add nine further estimators to the previously published set, thereby making it possible to cover all combinations of molecular markers with two to four alleles (without epistasis) in a full-sib family. This includes segregation in one or both parents, dominance and all linkage phase configurations

    Effects of reciprocal full-sib selection in maize

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    Fifty full-sib families and 100 S(,1) lines were developed from randomly chosen parents in each of the maize (Zea mays L.) populations BS10C0, BS10(FR)C6, BS11C0, and BS11(FR)C6 to investigate the effects of six cycles of reciprocal full-sib selection on population means and variances. Progenies were evaluated in experiments at two Iowa locations in 1983 and 1984. Data were collected for grain yield, ears per plant, percentage of root and stalk lodged plants, date of 50% silk emergence, ear and plant height, and number of tassel branches;Significant increases in yield and ears per plant among full-sib families and S(,1) lines were detected from the C0 to C6 cycles of BS10 and BS11. At both inbreeding levels, population means were significantly reduced from the C0 to C6 cycles for percentage of stalk lodging in both populations, and for percentage of root lodging and silking date in BS11. Among full-sib families in BS10 and BS11 mean ear and plant height decreased from the C0 to C6 cycles. Increases in mean ear and plant height were observed among S(,1) lines from BS10C0 to BS10(FR)C6, while population means of these traits decreased significantly from BS11C0 to BS11(FR)C6. At both inbreeding levels, population means for number of tassel branches increased from BS10C0 to BS10(FR)C6 and decreased from BS11C0 to BS11(FR)C6;Inbreeding depression for most traits decreased in response to selection. Reductions were significant for ear and plant height in BS10, and for yield, silking date, plant height, and number of tassel branches in BS11;For most traits, magnitudes of variances among full-sib families and S(,1) lines responded similarly to reciprocal full-sib selection. Magnitudes of additive genetic variance tended to decrease from the C0 to C6 cycles of BS10 and BS11 for yield, percentage of stalk lodging, ear and plant height, and number of tassel branches and seemed to increase for ears per plant and percentage of root lodging from BS10C0 to BS10(FR)C6 and for plant height from BS11C0 to BS11(FR)C6. Estimates of dominance variance generally increased, but decreases were observed for percentage of root lodging in BS10 and for yield, percentage of stalk lodging, and plant height in BS11. If actual changes in genetic variances have occurred, they have been small. Several negative estimates of dominance, environments x additive, and environments x dominance variances were obtained

    Preliminary data on the sex ratio in full-sib families of tambaqui Colossoma macropomum.

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    This preliminary study aimed to investigate the sex ratio in full sib families of C. macropomum to gain insight into the sex determination system and differential growth related to sex

    Accuracy and responses of genomic selection on key traits in apple breeding

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    open13siThe application of genomic selection in fruit tree crops is expected to enhance breeding efficiency by increasing prediction accuracy, increasing selection intensity and decreasing generation interval. The objectives of this study were to assess the accuracy of prediction and selection response in commercial apple breeding programmes for key traits. The training population comprised 977 individuals derived from 20 pedigreed full-sib families. Historic phenotypic data were available on 10 traits related to productivity and fruit external appearance and genotypic data for 7829 SNPs obtained with an Illumina 20K SNP array. From these data, a genome-wide prediction model was built and subsequently used to calculate genomic breeding values of five application full-sib families. The application families had genotypes at 364 SNPs from a dedicated 512 SNP array, and these genotypic data were extended to the high-density level by imputation. These five families were phenotyped for 1 year and their phenotypes were compared to the predicted breeding values. Accuracy of genomic prediction across the 10 traits reached a maximum value of 0.5 and had a median value of 0.19. The accuracies were strongly affected by the phenotypic distribution and heritability of traits. In the largest family, significant selection response was observed for traits with high heritability and symmetric phenotypic distribution. Traits that showed non-significant response often had reduced and skewed phenotypic variation or low heritability. Among the five application families the accuracies were uncorrelated to the degree of relatedness to the training population. The results underline the potential of genomic prediction to accelerate breeding progress in outbred fruit tree crops that still need to overcome long generation intervals and extensive phenotyping costs.openMuranty, H.; Troggio, M.; Sadok, I.B.; Mehdi A.R.; Auwerkerken, A.; Banchi, E.; Velasco, R.; Stevanato, P.; Eric van de Weg, W.; Di Guardo, M.; Kumar, S.; Laurens, F.; Bink, M.C.A.M.Muranty, H.; Troggio, M.; Sadok, I. B.; Mehdi, A. R.; Auwerkerken, A.; Banchi, E.; Velasco, R.; Stevanato, Piergiorgio; Eric van de Weg, W.; Di Guardo, M.; Kumar, S.; Laurens, F.; Bink, M. C. A. M

    Breeding strategies for recurrent selection of maize

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    Os objetivos deste trabalho foram analisar ganhos gen√©ticos te√≥ricos de milho como resultado da sele√ß√£o entre fam√≠lias de irm√£os completos e de meios-irm√£os, obtidas pelos Delineamentos I, de Irm√£os Completos e de Meios-Irm√£os, e a variabilidade genot√≠pica e perda de genes com sele√ß√£o a longo prazo. Os delineamentos foram avaliados por simula√ß√£o, com base nos ganhos m√©dios estimados ap√≥s dez ciclos de sele√ß√£o. O processo de simula√ß√£o considerou sete sistemas g√™nicos com dez genes (com distintos graus de domin√Ęncia), tr√™s classes de popula√ß√Ķes (com diferentes freq√ľ√™ncias g√™nicas), sob tr√™s condi√ß√Ķes de ambiente (valores de herdabilidade), e quatro estrat√©gias de sele√ß√£o. Cada combina√ß√£o foi repetida dez vezes, totalizando 25.200 simula√ß√Ķes. Sele√ß√£o entre fam√≠lias de irm√£os completos √© geralmente mais eficiente do que sele√ß√£o com base em prog√™nies de meios-irm√£os. Empregar fam√≠lias de irm√£os completos obtidas pelo Delineamento I √© geralmente mais eficiente que usar prog√™nies derivadas do Delineamento de Irm√£os Completos. O Delineamento I, com 50 machos e 200 f√™meas (tamanho efetivo de 160), n√£o determinou popula√ß√£o melhorada com variabilidade genot√≠pica m√≠nima. Nas popula√ß√Ķes melhoradas com menor tamanho efetivo (160 e 400), a perda de genes favor√°veis √© restrita √†queles recessivos em baixa freq√ľ√™ncia.The objectives of this work were to analyze theoretical genetic gains of maize due to recurrent selection among full-sib and half-sib families, obtained by Design I, Full-Sib Design and Half-Sib Design, and genotypic variability and gene loss with long term selection. The designs were evaluated by simulation, based on average estimated gains after ten selection cycles. The simulation process was based on seven gene systems with ten genes (with distinct degrees of dominance), three population classes (with different gene frequencies), under three environmental conditions (heritability values), and four selection strategies. Each combination was repeated ten times, amounting to 25, 200 simulations. Full-sib selection is generally more efficient than half-sib selection, mainly with favorable dominant genes. The use of full-sib families derived by Design I is generally more efficient than using progenies obtained by Full-Sib Design. Using Design I with 50 males and 200 females (effective size of 160) did not result in improved populations with minimum genotypic variability. In the populations with lower effective size (160 and 400) the loss of favorable genes was restricted to recessive genes with reduced frequencies

    Den förlängda fenotypen i granens krontak

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    The extended phenotype may help us understand how genetically determined trait variation in foundation species can influence associated organisms. Today, there is no existing demonstration of how genetically determined trait variation in Norway spruce (Picea abies) may affect associated organisms in tree canopies. As a majority of all planted Norway spruce seedlings used, in Swedish forestry today, originates from breeding programs it is interesting to know how the genetic material used in these programs may affect associated organisms. For example, according to the growth rate hypothesis the nutritional status of a plant should correspond negatively with tree growth, and the nutritional status of the plant should affect associated organisms. In this study, I aim to evaluate if the genetic origin of Norway spruce affect plant growth and nutritional status of needles (in this case the C:N ratio) and in extension associated communities (abundance of aphids) in the tree canopies. More specifically I will test the following six hypotheses; (1) there is a genetic influence on growth so that breast height diameter (DBH) differ among full-sib families, (2) the growth rate of the trees expressed as their DBH have a significant negative effect on needle C and positive effect on N and consequently negative effect on the C:N ratio, (3) there is a genetic component influencing C:N ratio of the needles so that the ratio differs between full-sib families, (4) growth rate of different full-sib families effect the C:N ratio of needles, (5) the abundance of aphids is influenced by full-sib family and the C:N ratio of needles and (6) growth rate of different full-sib families effect the abundance of aphids. To address these hypotheses twig and insect samples was sampled from Norway spruce trees in 90 two-by-two tree plots from 9 full-sib families. Aphids were determined to species level and needles was analyzed for C and N content with an elemental analyzer. The data on tree growth, needle chemistry, and aphid abundance were used in statistical tests using the statistical software JMP PRO 12.1.0. I found a clear genetic influence on growth in Norway spruce; fast growing full-sib families reached a DBH almost three times larger than that of slow growing full-sib families after 37 years (3.8 cm vs. 9.8 cm). In line with the growth rate hypothesis differences in growth rate also corresponded negatively with the C:N ratio of needles suggesting that needles of fast growing trees are more nutritious than slow growing trees. Despite this relation fast growing full-sib families did not necessarily have the highest nutritional status suggesting that the growth rate ‚Äď nutrition relationship follow different developmental trajectories in different families. Further, aphid abundance in the canopy of Norway spruce was significantly influenced by full-sib family, but this effect could not be related to tree growth nor C:N ratio of the needles of the different full-sub families. Given these results, it seems possible that selection of plant material of certain genetic origin (e.g. fast growing plants) such as currently conducted in Sweden can influence how other plant traits are expressed in populations. If these other traits are of ecological significance we would also expect them to influence ecological processes

    Selection on structural allelic variation biases plasticity estimates

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    Wang and Althoff (2019) explored the capacity of Drosophila melanogaster to exhibit adaptive plasticity in a novel environment. In a full-sib, half-sib design, they scored the activity of the enzyme alcohol dehydrogenase (ADH) and plastic responses, measured as changes in ADH activity across ethanol concentrations in the range of 0-10% (natural variation) and 16% (the novel environment). ADH activity increased with alcohol concentration, and there was a positive association between larval viability and ADH activity in the novel environment. They also reported that families exhibiting greater plasticity had higher larval survival in the novel environment, concluding that ADH plasticity is adaptive. However, the four authors now concur that, since the study estimated plasticity from phenotypic differences across environments using full-sib families, it is not possible to disentangle the contributions of allele frequency changes at the Adh locus from regulatory control at loci known to influence ADH activity. Selective changes in allele frequencies may thus conflate estimates of plasticity; any type of "plasticity" (adaptive, neutral, or maladaptive) could be inferred depending on allele frequencies. The problem of scoring sib-groups after selection should be considered in any plasticity study that cannot use replicated genotypes. Researchers should monitor changes in allele frequencies as one mechanism to deal with this issue.info:eu-repo/semantics/publishedVersio

    Prediction of genetic gains by selection indices using mixed models in elephant grass for energy purposes.

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    Genetically improved cultivars of elephant grass need to be adapted to different ecosystems with a faster growth speed and lower seasonality of biomass production over the year. This study aimed to use selection indices using mixed models (REML/BLUP) for selecting families and progenies within full-sib families of elephant grass (Pennisetum purpureum) for biomass production. One hundred and twenty full-sib progenies were assessed from 2014 to 2015 in a randomized block design with three replications. During this period, the traits dry matter production, the number of tillers, plant height, stem diameter, and neutral detergent fiber were assessed. Families 3 and 1were the best classified, being the most indicated for selection effect. Progenies 40, 45, 46, and 49 got the first positions in the three indices assessed in the first cut. The gain for individual 40 was 161.76% using Mulamba and Mock index. The use of selection indices using mixed models is advantageous in elephant grass since they provide high gains with the selection, which are distributed among all the assessed traits in the most appropriate situation to breeding programs

    The power of genomic estimated breeding values for selection when using a finite population size in genetic improvement of tetraploid potato

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    Potato breeding relies heavily on visual phenotypic scoring for clonal selection. Obtaining robust phenotypic data can be labor intensive and expensive, especially in the early cycles of a potato breeding program where the number of genotypes is very large. We have investigated the power of genomic estimated breeding values (GEBVs) for selection from a limited population size in potato breeding. We collected genotypic data from 669 tetraploid potato clones from all cycles of a potato breeding program, as well as phenotypic data for eight important breeding traits. The genotypes were partitioned into a training and a test population distinguished by cycle of selection in the breeding program. GEBVs for seven traits were predicted for individuals from the first stage of the breeding program (T1) which had not undergone any selection, or individuals selected at least once in the field (T2). An additional approach in which GEBVs were predicted within and across full-sib families from unselected material (T1) was tested for four breeding traits. GEBVs were obtained by using a Bayesian Ridge Regression model estimating single marker effects and phenotypic data from individuals at later stages of selection of the breeding program. Our results suggest that, for most traits included in this study, information from individuals from later stages of selection cannot be utilized to make selections based on GEBVs in earlier clonal generations. Predictions of GEBVs across full-sib families yielded similarly low prediction accuracies as across generations. The most promising approach for selection using GEBVs was found to be making predictions within full-sib families
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