Gabriel Borges Mundim

Efficacy of population structure analysis with breeding populations and inbred lines.

AbstractThe objective was to assess by simulation the efficacy of population structure analysis in plant breeding. Twelve populations and 300 inbred lines were simulated and genotyped using 100 microsatellite loci. The experimental material included populations with and without admixture, ancestry relationship and linkage disequilibrium, and with distinct levels of genetic differentiation and effective sizes. The analyses were performed using Structure software and employed all available models. For all the group number (K) tested, for both populations and inbred lines, the admixture model with correlated allelic frequencies provided the highest value for the logarithm of the marginal likelihood. Fitting appropriate model and using adequate sample size for individuals and markers, Structure was effective in identifying the correct population structure, migrants and individuals with genome from distinct populations. The linkage model did not result in an improvement in clustering relative to the admixture model with correlated allelic frequencies. The inclusion of prior information did not change the results; for some K values the analyses showed slight higher values of the marginal likelihood. The reduction in the number of individuals and markers negatively affected the results. There was a high variation in the most probable K value between the evaluated methods.

Genetic diversity and path analysis for nitrogen use efficiency in popcorn inbred lines

Popcorn inbred lines with more efficient nitrogen use are better able to uptake nitrogen from the soil and convert it into higher grain yield, resulting in lower environmental and economic impacts caused by nitrogen fertilization. The objectives of this study were to (i) identify inbred lines superior in nitrogen use (ii) assess the genetic diversity between popcorn inbred lines under high and low N conditions and (iii) investigate the causal effects of several traits in nitrogen use efficiency (NUE). We evaluated 25 popcorn inbred lines under high and low N, and several traits related to NUE and its components were measured. Efficient and inefficient inbred lines under both N levels were identified and can be useful for generating a segregating population for quantitative trait loci mapping. The genetic diversity assessment based on phenotypic traits grouped the inbred lines into four clusters under both N levels, and the efficient inbred lines were grouped together, as were the inefficient lines. The most divergent inbred lines under high N were classified as efficient and intermediate and can be useful to generate a divergent breeding population with a high frequency of favorable genes for NUE. Nitrogen uptake efficiency (NUpE) was considered the most important trait for NUE. To improve the accuracy of selection for NUE, a selection index involving the total root length (TRL), daily growth and NUpE traits under both N levels is recommended, as these traits had high correlations with and direct effects on NUE.

Inferring tropical popcorn gene pools based on molecular and phenotypic data

Studies on tropical popcorn (Zea mays L. ssp. mays) gene pools are still scarce. The objective of this study was to infer tropical popcorn gene pools by employing molecular and phenotypic information. Forty-eight inbred lines and 140 individuals belonging to the Viçosa and Beija-Flor popcorn populations were genotyped using 90 simple sequence repeat (SSR) and 93 single nucleotide polymorphism (SNP) markers, respectively. Grain yield and expansion volume were analyzed for the inbred lines and the hybrids obtained from intra- and interpopulation diallels. The cluster analysis based on SSR markers grouped 46 inbred lines into two groups according to their origin population. Principal coordinate and population structure analyses based on SSR and SNP markers confirmed the results from the clustering. For grain yield, midparent heterosis was greater in the interpopulation hybrids than in the intrapopulation hybrids. The genetic distance did not correlate with the specific combining ability effects and showed a week to intermediate correlation with hybrid performance and midparent heterosis. Based on the results from clustering, population structure, genetic diversity, heterosis and diallel analyses, Viçosa and Beija-Flor populations belong to distinct gene pools. Furthermore, inferring tropical popcorn gene pools might be more efficient if molecular marker and phenotypic data are combined.

Linkage disequilibrium, SNP frequency change due to selection, and association mapping in popcorn chromosome regions containing QTLs for quality traits

Abstract The objectives of this study were to assess linkage disequilibrium (LD) and selection-induced changes in single nucleotide polymorphism (SNP) frequency, and to perform association mapping in popcorn chromosome regions containing quantitative trait loci (QTLs) for quality traits. Seven tropical and two temperate popcorn populations were genotyped for 96 SNPs chosen in chromosome regions containing QTLs for quality traits. The populations were phenotyped for expansion volume, 100-kernel weight, kernel sphericity, and kernel density. The LD statistics were the difference between the observed and expected haplotype frequencies (D), the proportion of D relative to the expected maximum value in the population, and the square of the correlation between the values of alleles at two loci. Association mapping was based on least squares and Bayesian approaches. In the tropical populations, D-values greater than 0.10 were observed for SNPs separated by 100-150 Mb, while most of the D-values in the temperate populations were less than 0.05. Selection for expansion volume indirectly led to increase in LD values, population differentiation, and significant changes in SNP frequency. Some associations were observed for expansion volume and the other quality traits. The candidate genes are involved with starch, storage protein, lipid, and cell wall polysaccharides synthesis.

Best linear unbiased prediction for genetic evaluation in reciprocal recurrent selection with popcorn populations

SUMMARY The objective of the present study was to present the theory and application of best linear unbiased prediction (BLUP) in reciprocal recurrent selection (RRS). Seven progeny tests from two RRS programmes with popcorn (Zea mays L. ssp. mays [syn. Zea mays L. ssp. everta (Sturtev.) Zhuk.]) populations were conducted and analysed for expansion volume and grain yield. The interpopulation half- and full-sib family models were fitted using ASReml software. Half-sib selection is equivalent to selection for the general combining ability (GCA) of the common parents. With inbred full-sib progeny and BLUP analysis, it is possible to predict the general and specific combining ability effects. The standard error of prediction of the progeny effect was lower than the standard deviation of the best linear unbiased estimation (BLUE) estimate. For half- and full-sib RRS, the BLUE and BLUP provided highly correlated estimates of progeny genotypic values. The coincidence between selected parents ranged from 64 to 95%. With inbred full-sib progeny, the correlations between the BLUE of progeny genotypic values and the BLUP of GCA effects were lower. Consequently, the coincidence between selected parents was lower, ranging from 0 to 57%. The percentage of common selected inbred progeny based on the BLUE and BLUP of the progeny genotypic value ranged from 57 to 100%.

Adaptabilidade e estabilidade de populações de milho-pipoca relacionadas por ciclos de seleção

The objectives of this work were to estimate the adaptability and stability parameters of popcorn populations related through cycles of selection, to infer about the efficiency of the selection methods by which the populations were obtained and to assess the effects of selection on the parameters of adaptability and stability. Twenty-five populations and three commercial controls were evaluated in 14 trials carried out in the 2003/2004, 2004/2005, 2006/2007, 2008/2009 and 2009/2010 growing seasons, in seven locations. The experimental design used was randomized complete blocks with four replicates. The expansion volume, evaluated in a microwave oven and in the Metric Weight Volume Tester (MWVT), as well as grain yield were analyzed. The Eberhart & Russell adaptability and stability method was used. In general the initial and improved populations showed predictable performance in response to changes in the environment. Selection can cause changes in the adaptability and stability patterns, and the different selection strategies performed in order to obtain the populations showed similar efficiencies

Erratum to: Efficiency of genome-wide association studies in random cross populations

This article was originally published with two typos and errors in Table 1. The authors regret the errors and apologize for any inconvenience this causes to the readers. In the Abstract, the correct sample sizes are: Fifty samples of 400 individuals... The power of detection was maximized by increasing the sample size to 800... The correct order of lines in Table 1 is shown below: Mol Breeding (2017) 37: 114 DOI 10.1007/s11032-017-0713-x