Freddy Mora

Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR)

Several studies have confirmed that popcorn ( Zea mays L. var. everta) has a narrow genetic basis, which affects the quality of breeding programs. In this study, we present a genetic characterization of 420 individuals representing 28 popcorn populations from Brazilian germplasm banks. All individuals were genotyped using 11 microsatellite markers from the Maize Genetics and Genomics Database. A Bayesian clustering approach via Monte Carlo Markov chains was performed to examine the genetic differentiation (FST values) among different clusters. The results indicate the existence of three distinct and strongly differentiated genetic groups (K = 3). Moreover, the FST values (calculated among clusters) were significantly different according to Bayesian credible intervals of the posterior FST values. The estimates of posterior mean (and 95% credible interval) of the FST values were 0.086 (0.04-0.14), 0.49 (0.376-0.624) and 0.243 (0.173-0.324) for clusters 1, 2, and 3, respectively. Clusters 1 and 3 showed a high level of genetic diversity in terms of expected heterozygosity and number of alleles, indicating their potential for broadening the genetic basis of popcorn in future breeding programs. Additionally, the 11 microsatellites were informative and presented a suitable number of alleles for determining parameters related to genetic diversity and genetic structure. This information is important for increasing our knowledge regarding genetic relationships, for the identification of heterotic groups, and for developing strategies of gene introgression in popcorn.

SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach

This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5–22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5–35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint.

Heritability of stem straightness and genetic correlations in Eucalyptus cladocalyx in the semi-arid region of Chile

The aim of this study was to determine genetic parameters for straightness of the trunk of Eucalyptus cladocalyx, with a view to the selection of straight trees, while keeping the impact on growth minimal. The tests were conducted at two locations in the semi-arid region of Chile, using a randomized block design, with 30 replications and 49 half-sib families. The parameters were estimated by a bi-character model of individual trees, using Bayesian inference by Gibbs algorithm. The heritability for stem straightness was shown to be moderate, with h2=0.40 [0.29-0.57]. Heritabilities for diameter and height were moderate: 0.30 [0.24-0.38] and 0.30 [0.22-0.44]. Genetic correlations between straightness and growth were statistically not different from zero. The genotype-environment interaction was not significant (p>0.05) for the traits. The moderate degree of genetic control allows significant genetic gains in environments under water stress.

Genetic diversity assessed by microsatellite markers in sweet corn cultivars

Information on genetic diversity is essential to the characterization and utilization of germplasm. The genetic diversity of twenty-two sweet corn cultivars (seventeen open-pollinated varieties, OPV, and five hybrids, H) was investigated by applying simple sequence repeat markers. A total of 257 primers were tested, of which 160 were found to be usable in terms of high reproducibility for all the samples tested; 45 were polymorphic loci, of which 30 were used to assess the genetic diversity of sweet corn cultivars. We detected a total of 86 alleles using 30 microsatellite primers. The mean polymorphism was 82 %. The highest heterozygosity values (Ho = 0.20) were found in the PR030-Doce Flor da Serra and BR427 III OPVs, whereas the lowest values (0.14) were recorded in the MG161-Branco Doce and Doce Cubano OPVs. The polymorphism information content ranged from 0.19 (Umc2319) to 0.71 (Umc2205). The analysis of molecular variance revealed that most of the genetic variability was concentrated within the cultivars of sweet corn (75 %), with less variability between them (25 %). The consensus tree derived from the neighbor-joining (NJ) algorithm using 1,000 bootstrapping replicates revealed seven genetically different groups. Nei’s diversity values varied between 0.103 (Doce do Hawai × CNPH-1 cultivars) and 0.645 (Amarelo Doce × Lili cultivars), indicating a narrow genetic basis. The Lili hybrid was the most distant cultivar, as revealed by Principal Coordinates Analysis and the NJ tree. This study on genetic diversity will be useful for planning future studies on sweet corn genetic resources and can complement the breeding programs for this crop.

Marker-trait associations for survival, growth, and flowering components in Eucalyptus cladocalyx under arid conditions

Understanding the basis of the genetic variations responsible for the complex traits found in Eucalyptus cladocalyx under arid environmental conditions is crucial for designing genetic architecture studies. Forty-five half-sib families from Australia were used to identify inter-simple sequence repeat (ISSR) markers that are associated with growth (height, diameter at breast height, and stem straightness), flowering traits (flowering intensity, flowering precocity, reproductive capacity, and late flowering) and tree survival under arid conditions in southern Atacama Desert, Chile. Each DNA pellet consisted of a pool of five trees from each family. ISSR markers were associated with all the traits studied and accounted for 9.8 to 23.4 % of the phenotypic variation. Several loci were associated with more than one trait. For example, UBC810(450–500 bp), ISO1(600–610 bp), and TGT9(780–800 bp) were associated with three of the traits studied. These identified genomic regions may contribute to the increase of the efficiency of the conventional tree breeding program for E. cladocalyx.

Genome-wide association mapping for flowering and maturity in tropical soybean: implications for breeding strategies

Knowledge of the genetic architecture of flowering and maturity is needed to develop effective breeding strategies in tropical soybean. The aim of this study was to identify haplotypes across multiple environments that contribute to flowering time and maturity, with the purpose of selecting desired alleles, but maintaining a minimal impact on yield-related traits. For this purpose, a genome-wide association study (GWAS) was undertaken to identify genomic regions that control days to flowering (DTF) and maturity (DTM) using a soybean association mapping panel genotyped for single nucleotide polymorphism (SNP) markers. Complementarily, yield-related traits were also assessed to discuss the implications for breeding strategies. To detect either stable or specific associations, the soybean cultivars (N = 141) were field-evaluated across eight tropical environments of Brazil. Seventy-two and forty associations were significant at the genome-wide level relating respectively to DTM and DTF, in two or more environments. Haplotype-based GWAS identified three haplotypes (Gm12_Hap12; Gm19_Hap42 and Gm20_Hap32) significantly co-associated with DTF, DTM and yield-related traits in single and multiple environments. These results indicate that these genomic regions may contain genes that have pleiotropic effects on time to flowering, maturity and yield-related traits, which are tightly linked with multiple other genes with high rates of linkage disequilibrium.

Bayesian analysis of quantitative traits in popcorn (Zea mays L.) through four cycles of recurrent selection

Abstract A Bayesian analysis of genetic parameters for quantitative traits was carried out in full-sib families of popcorn through four cycles (C5, C6, C7, and C8) of recurrent selection. The parameters of Bayesian model were estimated using the independence chain algorithm. Grain yield and plant height were found to be moderately heritable ranging from 0.25 to 0.48 and 0.45 to 0.58, respectively. The highest heritability estimates were found for popping expansion volume at C5 ( = 0.71), and C7 ( = 0.63). The response of recurrent selection was 30.5 and 32.3% for grain yield and popping expansion volume, respectively. In C8, predicted genetic advances (from the Bayesian prediction of genotypic values) were 4.8, 4.3, and 2.9% for plant height, grain yield, and popping expansion volume, respectively. The significant genetic variability among popcorn families in successive cycles of recurrent selection has sustained continued genetic progress in breeding for the traits of interest.

Popcorn germplasm resistance to fungal diseases caused by Exserohilum turcicum and Bipolaris maydis

Compared with the common corn, popcorn shows greater susceptibility to pests and diseases occurrence, being the use of resistant cultivars the most efficient strategy. In this regard, Germplasm Banks deserve special attention because they contain accessions that can be used as sources of resistance in breeding programs. The State University of Northern Rio de Janeiro (UENF) maintains a popcorn Germplasm Bank with accessions from tropical and temperate countries, including Diversity Centers for the species. In this study, we investigated the performance of 37 popcorn accessions landraces, hybrids, and inbreed lines ― from the Germplasm Collection of UENF’s Popcorn Breeding Program with respect to the fungal leaf diseases northern leaf blight (NLB) and southern leaf blight (SLB), PLANT BREEDING Article Popcorn germplasm resistance to fungal diseases caused by Exserohilum turcicum and Bipolaris maydis Railan do Nascimento Ferreira Kurosawa1, Marcelo Vivas1, Antonio Teixeira do Amaral Junior1, Rodrigo Moreira Ribeiro1*, Samila Barbosa Miranda1, Guilherme Ferreira Pena1, Jhean Torres Leite1, Freddy Mora2 1.Universidade Estadual do Norte Fluminense Darcy Ribeiro Centro de Ciências e Tecnologias Agropecuárias Laboratório de Melhoramento Genético Vegetal Campos dos Goytacazes (RJ), Brazil. 2.Universidade de Talca Instituto de Ciências Biológicas Talca Chile. *Corresponding author: rodrigo.moreira85@yahoo.com.br Received: Feb. 1, 2017 – Accepted: Apr. 10, 2017 caused by Exserohilum turcicum and Bipolaris maydis, aiming to select promising accessions for genetic resistance to be used in future crosses to generate new resistant cultivars for farmers. The dendrogram scattering by the UPGMA multivariate technique was efficient in discriminating resistant accessions. Satisfactory results were obtained for resistance to NLB in accessions L71, L75, L76, P7, and PARA-172, which can thus be considered remarkable sources of resistance. For resistance to SLB, the superior accessions that can be indicated as sources of resistance are ARZM-05083, ARZM-07049, and PARA-172.

A classification proposal for coefficients of variation in Eucalyptus experiments involving survival, growth and wood quality variables

The objective of this study was to present a classification proposal for coefficients of variation (CV) in Eucalyptus experiments, aiming at providing a useful tool for experiments involving growth, survival and wood quality traits. Ninety-four studies were selected from a search for peer-reviewed journals yielding a total of 508 data. The CVs were classified as low, moderate, high and very high. The mean, standard deviation, maximum and minimum values, skewness and kurtosis were estimated to describe the distribution shape. The Shapiro-Wilk test confirmed that all variables satisfied the assumption of normality (p < 0.05). The results indicated that the growth traits had the highest variability, being variables strongly affected by the environment. In contrast, all variables related to wood quality (except extractives) had the lowest range of CVs. In summary, the classification proposed in this report provides a useful tool for researchers interested in estimating the accuracy of their experiments.

Thirteen years under arid conditions: exploring marker-trait associations in Eucalyptus cladocalyx for complex traits related to flowering, stem form and growth

We present an association analysis for seven key traits related to flowering, stem form and growth in Eucalyptus cladocalyx, a tree species suitable for low rainfall sites, using a long-term progeny trial with 49 open-pollinated maternal families in the southern Atacama Desert, Chile. The progeny trial was carried out in an arid environment with a mean annual rainfall of 152 mm. Simple sequence repeats (SSR) from a full consensus map of Eucalyptus were used for genotyping 245 individual trees. Twenty-three significant marker-trait associations were identified, explaining between 5.9 and 23.7% of the phenotypic variance. The marker EMBRA101 located on LG10 at 56.5 cM was concomitantly associated with diameter at breast height and tree height. Nine SSR were significantly associated with stem forking and stem straightness, explaining between 5.9 and 14.8% of the phenotypic variation. To our knowledge, this is the first study reporting a SSR-based association mapping analysis for stem form traits in Eucalyptus. These results provide novel and valuable information for understanding the genetic base of key traits in E. cladocalyx for breeding purposes under arid conditions.