Indirect response in genome wide selection using selected markers

The goal of this work was to compare the effect of the accuracy and residual variance in genome wide selection using marker selection as well as using the effect of the indirect selection, using simulated and real data. In simulated data was used one sample with 200 individuals with 1,000 molecular markers in F2 population. The real data was obtained in maize with F2 population with 441 individuals and genotyping with 261 SSR markers. There was 11 traits evaluated (ear length, ear width, row number, kernels per row, 100-kernel weight, ear weight, grain yield, length of branch, number of branch, plant height and ear height). All data was analyzed using rrBLUP method and 10-fold cross-validation. In simulated and maize data the results were similar: the residual variance with few markers is lower than with the 1000 markers and the accuracy with few markers is bigger than with 1000 markers. For maize data multi trait selection, the accuracy increased when the correlation between traits is greater than 0.50 and residual variance decreased when the correlation is greater than 0.70. In this sense, these results showed that marker selection could be used as a first step in genome wide selection, improving the prediction and compute demand

Optimum population size for genetic mapping in full sibling families

O objetivo deste trabalho foi avaliar o tamanho ótimo de populações de irmãos completos, para estudos de mapas de marcadores moleculares, por meio de simulações de genomas e tamanhos de populações.Foram simulados genomas parentais e amostras de populações de família de irmãos completos do tipo completamente informativas, e também não completamente informativas. As amostras geradas foram de 100, 200,400 e 600 indivíduos, com três grupos de ligação cada, e 11 marcas moleculares codominantes e multialélicas, espaçadas a dez centimorgans por grupo de ligação. Foram realizadas 100 repetições por amostra. Para populações completamente informativas, o tamanho populacional de 200 indivíduos é suficiente para recuperar as informações originais, contudo, para a população não completamente informativa, é necessária a utilização de uma população maior, de 600 indivíduos.The objective of this work was to evaluate the optimum size of populations for the study of genetic mapping of full sibling families, through data simulation of genome and populations. Parental genomes and population samples of full sibling families of both completely and non-completely informative types, were simulated. The generated samples had 100, 200, 400 and 600 individuals, with three linkage groups each, and 11 codominant multi-allelic molecular marks, spaced by ten centimorgans in each linkage group. One-hundred repetitions were accomplished by sample. In completely informative populations, the optimum size of 200 individuals is enough to rescue the original information, however, for the non-completely informative population, it is necessary a larger population, with 600 individuals

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

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

Breeding Jatropha curcas by genomic selection: A pilot assessment of the accuracy of predictive models

Genomic wide selection is a promising approach for improving the selection accuracy in plant breeding, particularly in species with long life cycles, such as Jatropha. Therefore, the objectives of this study were to estimate the genetic parameters for grain yield (GY) and the weight of 100 seeds (W100S) using restricted maximum likelihood (REML); to compare the performance of GWS methods to predict GY and W100S; and to estimate how many markers are needed to train the GWS model to obtain the maximum accuracy. Eight GWS models were compared in terms of predictive ability. The impact that the marker density had on the predictive ability was investigated using a varying number of markers, from 2 to 1,248. Because the genetic variance between evaluated genotypes was significant, it was possible to obtain selection gain. All of the GWS methods tested in this study can be used to predict GY and W100S in Jatropha. A training model fitted using 1,000 and 800 markers is sufficient to capture the maximum genetic variance and, consequently, maximum prediction ability of GY and W100S, respectively. This study demonstrated the applicability of genome-wide prediction to identify useful genetic sources of GY and W100S for Jatropha breeding. Further research is needed to confirm the applicability of the proposed approach to other complex traits

Potential of maize (Zea mays L.) populations derived from commercial single-cross hybrids for extraction of partially inbred lines under different nitrogen availability

Extraction of inbred lines is a very important step in maize breeding since these lines will be used to obtain hybrids intended for the market. However, this expensive process, hinders genotype evaluation in contrasting environments, especially regarding nitrogen (N) content. This study aimed to evaluate the potential of maize populations for line extraction and select partially inbred lines under different soil nitrogen (N) availability. Five populations were evaluated regarding their potential for line extraction. Fifty-five S1 partially inbred lines were extracted from these populations. The top-cross method was used to evaluate lines by crossing them with two testers. Hybrids evaluation used 110 top-cross hybrids, five base populations, and six checks. Two trials were carried out in Dourados and Caarapó. One trial had adequate fertilization (high N) while the other was under stress condition (low N). Hybrid DKB 789 showed potential for extraction of partially inbred lines, aiming at selecting N use efficiency. Base population BP (07) was the most suitable for the extraction of partially inbred lines aiming at N use efficiency. Partially inbred lines BP (07) 13, BP (07) 14, and BP (07) 17 are the most suitable for the extraction of top-cross hybrids with high grain yield, efficiency, and responsiveness to N. Highlights Extraction of inbred lines is a very important step in maize breeding. Hybrid DKB 789 showed potential for extraction of partially inbred lines. BP (07) 13, BP (07) 14, and BP (07) 17 are the most suitable for the extraction of top-cross hybrids.Extraction of inbred lines is a very important step in maize breeding since these lines will be used to obtain hybrids intended for the market. However, this expensive process, hinders genotype evaluation in contrasting environments, especially regarding nitrogen (N) content. This study aimed to evaluate the potential of maize populations for line extraction and select partially inbred lines under different soil nitrogen (N) availability. Five populations were evaluated regarding their potential for line extraction. Fifty-five S1 partially inbred lines were extracted from these populations. The top-cross method was used to evaluate lines by crossing them with two testers. Hybrids evaluation used 110 top-cross hybrids, five base populations, and six checks. Two trials were carried out in Dourados and Caarapó. One trial had adequate fertilization (high N) while the other was under stress condition (low N). Hybrid DKB 789 showed potential for extraction of partially inbred lines, aiming at selecting N use efficiency. Base population BP (07) was the most suitable for the extraction of partially inbred lines aiming at N use efficiency. Partially inbred lines BP (07) 13, BP (07) 14, and BP (07) 17 are the most suitable for the extraction of top-cross hybrids with high grain yield, efficiency, and responsiveness to N. Highlights Extraction of inbred lines is a very important step in maize breeding. Hybrid DKB 789 showed potential for extraction of partially inbred lines. BP (07) 13, BP (07) 14, and BP (07) 17 are the most suitable for the extraction of top-cross hybrids

Strategies for sampling and establishment of core collections

O objetivo deste trabalho foi avaliar a influência da intensidade de amostragem, do tamanho da coleção de germoplasma inicial e da variância da amostragem sobre a qualidade das respectivas coleções nucleares, quanto à representatividade das coleções iniciais. Foram simulados sete tamanhos de coleções iniciais e utilizadas seis intensidades de amostragem para estabelecimento de coleções nucleares, utilizando caracteres morfoagronômicos. Determinaram-se o número de grupos formados, o coeficiente de coincidência entre a coleção nuclear e a coleção inicial e o coeficiente de determinação dos acessos amostrados para comporem a coleção nuclear. Também foi proposto o uso de uma estratégia alternativa para estabelecer coleções nucleares, de forma a maximizar a diversidade entre os acessos. O tamanho da coleção inicial influencia a intensidade de amostragem empregada na obtenção da coleção nuclear. A amostragem de acessos pelo método de Tocher, com critério de aglomeração inverso, mostrou-se eficiente na obtenção de coleções nucleares. As diferentes magnitudes de variância das coleções iniciais não influenciaram os coeficientes de determinação (R2) nem os coeficientes de coincidência entre a coleção inicial e as respectivas coleções nucleares.The objective of this work was to evaluate the effect of sampling intensity, initial collection's size and its variance over the quality of the respective core collections, in terms of representation of the initial collections. Therefore, simulations were performed for seven sizes of the initial collections and six sampling intensities for the establishment of core collections were used, comprising morpho-agronomic traits. Groups formed were determined, as well as the coincidence coefficient between the core and the initial collection, and the determination coefficient of the accessions sampling to compose the core collection. The use of an alternative strategy was proposed to establish core collections, this strategy maximizes the diversity among the accessions. The size of initial collections affects the sampling intensity to be used to obtain a core collection. The selection of accessions with the method of Tocher, comprising criteria of inverse grouping, was efficient for the formation of the core collections. The different magnitudes of variance of the initial collections did not affect either the coefficient of determination (R2) or the coincidence rate between initial collections and respective core collection

Alternative methodology for Scott-Knott test

The test proposed by Scott Knott (1974), a procedure of means grouping, is an effective alternative to performprocedures of multiple comparisons without ambiguity. This study aimed to propose a modification related to the partitioningand means grouping in the said procedure, to obtain results without ambiguity among treatments, organized in morehomogeneous groups. In the proposed methodology, treatments that did not participate in the initial group are joined for a newanalysis, which allows for a better group distribution. In a comparative study, four experiments were simulated in a randomizedcomplete block design. The first consisted of 10 and the other 3 of 100 treatments. All experiments were performed in threereplications at a significance level of 0.05 for the means grouping test. Only in the third experiment of those of 100 treatmentsthe groups formed by Scott-Knott did not differ from the methodology proposed here. The proposed methodology is consideredeffective, aiming at the identification of elite cultivar groups for recommendation

Genotypic diversity and genetic parameters of 'Tahiti' acid lime using different rootstocks

O objetivo deste trabalho foi estimar os parâmetros genéticos e avaliar a diversidade genética de 12 genótipos de lima ácida 'Tahiti' (Citrus latifolia) enxertados em dois porta-enxertos. O experimento foi conduzido de julho de 2017 a janeiro de 2019, no município de São Mateus, no estado de Espírito Santo, Brasil. Foram mensuradas características vegetativas (diâmetro de caule, diâmetro de projeção de copa e altura de planta), produtivas (rendimento e número de frutos) e de qualidade de frutos (diâmetros de fruto, teor de sólidos solúveis e rendimento de suco). Utilizou-se modelo misto para estimar os coeficientes de herdabilidade e repetibilidade, bem como predizer os valores genéticos. A diversidade entre os enxertos foi obtida por meio da diferença da distância euclidiana média padronizada, e os genótipos foram agrupados pelo método de Tocher modificado. A qualidade do agrupamento e a importância dos caracteres foi avaliada pela análise de componentes principais (ACP). Observou-se variabilidade genética, o que indica a possibilidade de seleção de genótipos superiores. O método de Tocher mostrou a presença de três grupos de genótipos, o que foi congruente com os resultados da ACP. O uso de técnicas multivariadas permite a seleção e a recomendação de genótipos superiores de lima ácida 'Tahiti'.The objective of this work was to estimate the genetic parameters and to evaluate the genotypic diversity of 12 'Tahiti' acid lime (Citrus latifolia) genotypes grafted onto two rootstocks. The experiment was carried out from July 2017 to January 2019, in the municipality of São Mateus, in the state of Espírito Santo, Brazil. Vegetative (stem diameter, canopy projection diameter, and plant height), productive (yield and fruit number), and fruit quality (fruit diameter, soluble solids content, and juice yield) traits were determined. A mixed model was used to estimate heritability and repeatability coefficients, as well as to predict clonal values. Scion diversity was determined through the standardized mean difference of Euclidean distances, and genotypes were clustered by modified Tocher. Clustering quality and trait importance were evaluated using the principal component analysis (PCA). Genotypic variance was observed, which is indicative of the possibility of selection of superior genotypes. The Tocher method showed the presence of three clusters, which is in alignment with the PCA results. The multivariate analyses allows of the selection and the recommendation of superior 'Tahiti' acid lime genotypes

Selection of okra parents based on performance and genetic divergence

A total of 200 okra accessions with wide variability and a potential for genetic improvement were stored in the Vegetables Germplasm Bank of the Federal University of Viçosa (UFV-BGH) in Viçosa, Minas Gerais State, Brazil. The objective of this work was to select parents by genetic divergence and behavior per se in 70 okra accessions from the BGH-UFV by quantitative and qualitative descriptors of economic interest. Analysis of individual and combined variance, by clustering of means by Scott-Knott test, of the accessions by Tocher’s method and selection based on qualitative descriptors and behavior per se using the methodology of sum of inverted positions was made. The variability of the characteristics of the accessions as verified by the Scott-Knott test formed different groups and subgroups by Tocher’s method. Fifteen accessions were selected with the qualitative descriptors, and based on the sum of inverted positions for quantitative descriptors the BGH-132, BGH-547, BGH-693, BGH-740, BGH-961, BGH-7863, BGH- 7865, BGH-3196 and BGH-4890 okra accessions were selected as potential parents.Key words: Abelmoschus esculentus (L.) Moench, germplasm bank, genetic resource, genetic improvement

Efficiency of the multilocus analysis for the construction of genetic maps

The use of genetic maps is a useful tool in genetic research. The association between map distance andrecombination frequency is expressed by a genetic mapping function. However, several of these functions do not presupposethe joint recombination percentage. In other words, they are not multilocus probabilities. This work aimed to compare,through simulations, the efficiency in the use of different mapping functions with and without multilocus analysis as a tool inthe construction of genetic maps. A genome constituted of three linkage groups (50, 100 and 200 cM) was simulated for acomparative study. Four mapping populations were simulated, F2, with 50, 100, 200 and 400 individuals, with 10 replicaseach. It was verified, after the analyses, that the multilocus analysis was not efficient to rescue the size of the connectiongroups, concluding that the non use of the multilocus analysis would be viable