Current issues

Table of contents: 2019

Research Article

Soybean rust is considered a highly aggressive disease in soybean crops. Most research has focused on obtaining resistant genotypes based on dominant or recessive alleles, which provide vertical resistance. The identification of promising crosses that may be used to develop genotypes with horizontal resistance from IAC 100 may help to increase the longevity of the recommended cultivars. However, this type of resistance is limited by environmental variables that may hinder selection. We ranked crosses based on their response to soybean rust using genetic estimates and predicted gains. It was also an objective to identify quantitative trait loci (QTLs) associated with resistance to soybean rust in two generations derived from the same cross. Eighty-seven F4 progenies from IAC 100 (partial resistance) x BRS Caiapônia (susceptible) cross were field phenotyped. The data divided the DNA samples into two groups for bulked segregant analysis, which was carried out using simple sequence repeat (SSR) primers. A linkage map for the F4 generation was obtained based on 29 SSR markers, which were distributed into nine linkage groups, covering 285.9 cM of the genome. Six QTLs were mapped in four of these groups and two of them were responsible for 39% of the phenotypic variance in resistance to soybean rust. The linkage map generated for the F7 generation was similar to that of the F4 generation, covering 266 cM. Four of the six QTLs mapped in the F4 generation were also identified in the F7 generation, showing that the genomic regions contributing to horizontal resistance to soybean rust are stable.

 

Genet. Mol. Res. 18(3): GMR18249
DOI: 10.4238/gmr18249
Research Article

Dual purpose wheat could be a good alternative for helping overcome the need to import this cereal in Brazil. To achieve this, development of cultivars with high yield is necessary. The contribution of genetics in defining traits is very important for directing breeding programs for the development of cultivars that provide the desired agronomic ideotype. We estimated heritability for 36 characters of agronomic importance in dual-purpose wheat. The inheritable genetic patterns were examined using linear trends, a Euclidean algorithm, factor analysis and artificial neural networks. The study was carried out during the crop seasons of 2011, 2012 and 2013. The experimental design was randomized block, arranged in a factorial scheme with three growing seasons (2011, 2012 and 2013) and five dual-purpose wheat genotypes (BRS Tarumã, BRS Umbu, BRS Figueira, BRS Guatambu and BRS 277) x three cuttings (first cutting, second cutting and third cutting), with three replicates. Deviance analysis or maximum likelihood was significant for the 36 characters. The length of the head of the main plant, plant height before the first second cutting and dry mass of the seedlings showed high variability. The 36 characters expressed linear genetic dependence based on the Euclidean Algorithm; similar to what was found with the Tocher Optimized Clustering and Artificial Neural Networks K-means methods. Similar genetic trends for heritability profiles were obtained with factor analysis and Artificial Neural Networks by the Kohonem method. The use of Artificial Neural Networks through the Kohonem method gave the greatest efficacy in the definition of the genetic profiles needed to develop the recommended agronomic ideotype for the improvement of dual-purpose wheat.

 

Genet. Mol. Res. 18(3): GMR18266
DOI: 10.4238/gmr18266
Research Article

Highly heterotic onion hybrids exhibit high yield and superior post-harvest quality. In general, to develop heterotic hybrids, it is first necessary to develop inbred lines with high genetic divergence and good specific combining ability (SCA). We investigated the correlation between SCA, heterosis, and genetic divergence of inbred onion lines. Two groups of inbred onion lines were used as parentals in a partial (6x5) diallel cross. Group I included six S3 male-sterile lines of the “Super Precoce” pedigree (L4827, L4830, L4833, L4835, L4837, and L4839), and group II included five S2 fertile lines of the “Hiper Precoce” pedigree, Granex type with some inter-crosses (L4741, L4742, L4743, L4744, and L4746). Genetic divergence among the parental lines was estimated on the basis of seven morpho-agronomic characters and 10 inter-simple sequence repeat (ISSR) markers. Pearson and Spearmann correlations between morphology-based genetic dissimilarity, ISSR-based genetic dissimilarity, heterosis, and SCA were evaluated. Five characters (number of leaves, bulb yield, bulb diameter, soluble solids content, and dry mass) accounted for 82.8% of the genetic variation present in the genotypes. The greatest genetic dissimilarity, as indicated by both ISSR data (80.4%) and morpho-agronomic data (92.5%), was calculated for L4742 and L4744, which demonstrated that these onion inbred lines were genetically divergent. Based on estimates of SCA and heterosis, L4742 was identified as the most promising lineage for developing superior onion hybrids. None of the correlations between SCA, heterosis, and genetic dissimilarity (morpho-agronomic or ISSR) were significant, thereby indicating that genetic dissimilarity cannot be used directly to select parental lines or to predict the best crosses for all characters. However, the genetic dissimilarities estimated using morpho-agronomic characters and ISSR profiles were useful for identifying the best crosses for bulb yield and bulb diameter.

Genet. Mol. Res. 18(3): GMR18316
DOI: 10.4238/gmr18316
Research Article

Sweet corn (Zea mays subsp. saccharata) is considered a special vegetable of high nutritional value. One of the barriers encountered by breeders has been a lack of adequate genetic variability of sweet corn, coupled with a need for appropriate methodologies to evaluate the existing genetic diversity. Our objective was to determine the best method to identify promising genotypes to improve sweet corn production. We used data from 181 open-pollinated sweet corn genotypes, cultivated during 2016 and 2017. Multivariate analyses were carried out to determine the genetic dissimilarity between the genotypes, obtaining the matrix of dissimilarity by Euclidean distance. Prior to calculating the distance between matrices, two data standardizations (Z1 and Z2) were performed for comparison. Genetic divergence was analyzed by four distinct hierarchical methods: Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA), Ward, Weighted Pair-Group Method Using Arithmetic Averages (WPGMA) and Single Linkage. Tocher’s optimization method was also used. The Simple Linkage and UPGMA methods presented similar groupings, consistent with breeding program aims and with the highest values of co-phenetic correlation coefficient (CCC). The Ward’s method was not efficient, because it produced several clusters without isolating different genotypes. Furthermore, it was the method with the lowest CCC for both matrices. The standardized Z2 matrix should be avoided, especially when a large number of genetic traits are measured, in order to prevent possible overlapping between traits, a variables with higher standard variations could contribute more to the clustering.

 

Genet. Mol. Res. 18(3): GMR18384
DOI: 10.4238/gmr18384
Brief Note

Type 1 diabetes mellitus (T1D) is considered a polygenic disease that is influenced by environmental factors and autoimmune responses to autoantibodies, resulting in metabolic abnormalities. Tyrosine kinase 2 (TYK2) is involved in type I interferon signaling in beta cells, and TYK2 polymorphism rs2304256 has been associated with T1D. We investigated polymorphism rs2304256 (TYK2) in a case-control study of Euro-Brazilians with T1D manifested during childhood and adulthood. We studied 307 individuals manifesting clinical signs of type 1 diabetes (151 children below 14 years of age and 156 adults with diagnosis after 18 years of age). The control samples consisted of 169 healthy children and 150 healthy adult subjects. T1D groups had inadequate glycemic control because fasting glucose and mean HbA1C concentrations were significantly higher than in the control groups. Real-time PCR with TaqMan® fluorescent probes was applied for genotyping. The studied polymorphisms were in Hardy–Weinberg equilibrium. The minor allele frequency (A-allele) for children in the T1D and control groups was 24.2% (95% CI, 18 - 32) and 23.4% (95% CI, 17 - 30), respectively (P = 0.812), while for adults in the T1D and control groups values were 19.6% (95% CI, 14 - 27) and 24.7% (95% CI, 20 - 35), respectively (P = 0.127). There was no significant difference in genotypes or allelic frequencies of the polymorphism in the groups. The frequency of the minor allele of the polymorphism was similar to that found in other Caucasian populations, and different than that found in Eastern populations. In conclusion, the polymorphism rs2304256 was not associated with T1D in either group.

Genet. Mol. Res. 18(3): GMR18356
DOI: 10.4238/gmr18356
Research Article

The selection of southern rust-resistant genotypes caused by Puccinia polysora (Pucciniaceae) is considered an efficient way to control this disease, which causes high crop losses in popcorn. To help choose adequate cultivars, we examined the combining ability of lines and the agronomic performance of popcorn hybrids for rust resistance. Eight S7 popcorn lines were used, which were crossed in a complete diallel mating scheme, resulting in 56 hybrids. The disease incidence on the whole plant (INC), severity on a leaf of the main ear (SEV), grain yield (GY), popping expansion (PE) and volume of expanded popcorn per hectare (PV) were evaluated. Analysis of variance was performed and the means were grouped by the Scott-Knott algorithm. The analysis diallel was performed by the method of Griffing, using the Diallel I method. The hybrids L76xP8, P8xL70, L77xP8, P8xP1 and L55xL76 stood out with a GY of >3000 kg.ha-1 and PE of >30 mL.g-1. For the traits GY and VP, the non-additive effects were predominant, and the heterosis effects high. For the trait expression of INC, SEV and PE, the additive effects were more relevant. The estimates of general combining ability of lines L70, L61, P1 and L76 were negative for INC and SEV. For commercial cultivation, L77xL76, L76xP1, L77xL70, L76xL70, L70xL76 and L77xP1 are recommended, in view of their excellent agronomic performance and superior resistance to rust.

Genet. Mol. Res. 18(3): GMR18330
DOI: 10.4238/gmr18330
Research Article

The commerce of potted ornamental plants has grown in Brazil, and ornamental pepper stands out due to a profusion of colors and forms, as well as due to its easy cultivation. However, few studies have been carried out with ornamental pepper for genetic improvement of fruit production, plant size and precocity. Thus, in order to conduct a genetic improvement program, we evaluated the general and specific combining abilities, as well as reciprocal effects in a complete diallel with eight progenitors and 56 ornamental pepper hybrids. Thirteen features related to plant and fruits were evaluated. Significant variation was observed among parents and ornamental pepper hybrids by Scott-Knott criterion at 1% probability. There was predominance of additive effects in control of all characteristics except for fruit mass, since the ratio between quadratic components of the general combining ability and the specific combining ability was close to or greater than one. Reciprocal effects were highly significant for all traits, except for days to flowering and fruiting. The predominance of overall combining ability for most features suggests that simple genetic improvement methods, such as the pedigree method, can be successfully used. Based on good classification of UFSJ 1 and UFSJ 6 progenitors in relation to specific combining abilities, favorable reciprocal effects for at least three characteristics simultaneously and at least one of the parents with good general combining ability, UFSJ 4 X UFSJ 1 and UFSJ 6 X UFSJ 1 hybrids were recommended for ornamental cultivation purposes.

Genet. Mol. Res. 18(3): GMR18415
DOI: 10.4238/gmr18415
Research Article

Mate (Ilex paraguariensis) leaves are popular for consumption as an infusion, which provides various health benefits due to its nutraceutical properties. Leaf samples oxidize after harvesting, requiring special handling to avoid DNA damage or degradation by enzymatic or oxidative activities. The objectives of this work were to evaluate several methods for sample storage and DNA extraction to identify practical and efficient protocols to guarantee the DNA quantity and integrity for molecular studies of mate. Total DNA was extracted from fresh leaves and compared with DNA extracted from leaves stored in silica gel at room temperature for 14 days or in CTAB (cetyltrimethylammonium bromide) buffer. The leaves were cleaned with absorbent paper and stored in 50 mL Falcon tubes containing approximately 25 g of silica gel or in 2 mL Eppendorf tubes containing approximately 1 mL of CTAB buffer. Samples treated with silica gel were stored at room temperature for 14 days, and the ones with CTAB buffer were stored either at 4°C for 14 and 90 days or at room temperature for 90 days. The DNA was quantified using a Nanodrop spectrophotometer and agarose gel electrophoresis. DNA purity (with regard to the presence of enzyme inhibitors) was tested by PCR amplification of fragments of the plastid gene, trnL-trnF. Samples of mate leaves can be stored on silica gel or in CTAB buffer for up to 90 days at room temperature without reduction in DNA quality. Samples stored in CTAB buffer can be refrigerated at 4ºC to minimize oxidation of phenolic compounds. The improved methods for sample storage and DNA extraction with CTAB maintain quantity and integrity for conducting molecular studies of mate.

Genet. Mol. Res. 18(3): GMR18390
DOI: 10.4238/gmr18390
Brief Note

Plant DNA and RNA extraction methods are well established, with a wide range of protocols, depending on the purposes of each laboratory/research. Nowadays, quick, inexpensive and easy plant DNA and RNA extraction methods are highly sought after. We developed an optimized protocol for plant DNA and RNA extraction that uses an inexpensive bench drill and plastic bags and does not require liquid nitrogen. DNA from leaves and RNA from leaves and roots of banana, pineapple, citrus, papaya, passion fruit and cassava, were extracted using a basic cetyltrimethylammonium bromide method. Both nucleic acids were quantified and evaluated for quality based on agarose gel electrophoresis. The DNA and RNA extractions were successful for all species, and RNA quality in pellets was maintained after storage at room temperature for three weeks. This protocol can reduce costs considerably in laboratories with ongoing routine activities of DNA and RNA extraction for genetic diversity and gene expression analyses, where other conventional methods have not been successful due to explant, condition of samples and quantity and quality of nucleic acids. This is especially relevant for many laboratories in developing countries where the cost and availability of liquid nitrogen may be a constraint.

Genet. Mol. Res. 18(3): GMR18394
DOI: 10.4238/gmr18394
Research Article
Authors:

Through use of interspecific hybridization, and in some cases followed by polyploidization, cassava cultivars combining various desirable characteristics have been developed in Brazil. These range from high protein content and increased essential amino acids to tolerance to drought. Some cultivars have highly apomictic behavior. Others show tolerance to bacterial diseases and insect pests. Selection from crosses with indigenous cultivars has led to obtaining varieties with high beta carotene content and excellent palatability. Periclinal chimeras were successfully synthesized and gave very high productivity. Ten outstanding genotypes resulting from this ongoing selection and breeding program are part of the University of Brasilia living Manihot collection and are reviewed here.

 

Genet. Mol. Res. 18(3): GMR18385
DOI: 10.4238/gmr18385
Research Article

Prostate cancer (PCa) is the second most common type of tumor among men over 50 years old and its etiology includes environmental, demographic, and genetic risk factors. We investigated a possible association between GSTM1 and GSTT1 polymorphisms, sociodemographic, and clinical factors with PCa in a population of southwestern Bahia, Brazil. The research used a case-control design and was carried out with 268 men aged 50 years or older (134 cases and 134 controls). The mean age was 74 years old (± 7.9) in the case group and 55 years old (± 4.3) in the control group. Polymorphisms were determined by multiplex PCR, followed by electrophoresis. The genotypic frequencies found were 0.45 for GSTM1 -/- (null), 0.55 for GSTM1 +/- or +/+ (non-null), 0.37 for GSTT1 -/- (null) and 0.62 for GSTT1 +/- or +/+ (non-null). The estimated allele frequencies were: GSTM1 - (null allele) 0.60 for the case group and 0.67 for the control group, and GSTT1 - (null allele) 0.49 for the case group and 0.65 for the control group. These polymorphisms were not significantly associated (P-values 0.68 and 0.21, respectively) with PCa. However, non-white ethnicity (self-reported), sexually transmitted infections, and cigarette consumption were significantly associated with PCa (P-value: 0.03, 0.05 and < 0.01 respectively). Vasectomy exhibited an inverse association (P-value < 0.01), thus behaving as a protective factor for PCa.

Genet. Mol. Res. 18(3): GMR18296
DOI: 10.4238/gmr18296
Research Article

Brucella spp. are the pathogens responsible for brucellosis, which is a cosmopolitan and serious disease for animals and humans. Recent studies have revealed the presence of Brucella DNA in the reproductive tract tissues of buffaloes based on microbiological cultures collected from vaginal swabs. We tested for Brucella abortus DNA in the uterus, perivaginal lymph nodes, and uterine mucus of buffalo cows naturally infected with Brucella spp., as defined by a positive complement fixation test. Uterine tissue, uterine mucus, and perivaginal lymph node samples from 16 Brucella seropositive female buffaloes were analyzed. Brucella DNA was found in five of the uterine tissue samples, eight of the perivaginal lymph node samples, and 14 of the uterine mucus samples. Furthermore, Bayesian inference analysis indicated that the DNA sequences obtained from these tissues and mucus grouped with corresponding sequences of the B. abortus species.

Genet. Mol. Res. 18(3): GMR18376
DOI: 10.4238/gmr18376
Research Article

The Guzerat cattle breed, in past centuries, was utilized in Brazil mainly for work and transport in the coffee industry because of its rusticity; however, in recent decades it has become important for milk and meat production. Cattle traits such as rib-eye area, backfat thickness, and intramuscular fat percentage have been continuously evaluated in breeding programs because they are related to meat quality, carcass yield and organoleptic properties; however, the Guzerat breed has not been included in this type of study. In order to overcome these limitations, we estimated variance components, genetic correlations and heritability for ribeye area (REA), backfat thickness (BFT), rump fat thickness (RFT), intramuscular fat percentage (IMF), dry matter intake (DMI), average daily gain (ADG), scrotal circumference (SC), metabolic weight (MW), visual score for finishing (VSF), residual feed intake (RFI) and margin (MAR) from 1499 animals of the Guzerat breed. Genetic parameters and trait heritabilities were estimated using data collected from various breeders for each trait. The dataset was analyzed by the AIREMLF90 program. REA and MAR were the carcass and production traits with the greatest additive genetic variance; they also had the highest heritability values. The average inbreeding of animals in pedigree was 0.81%; more than 71% of animals had 0% inbreeding and only 0.04% of the animals had a coefficient over 25%. Carcass and production traits of Guzerat cattle analyzed in this study showed sufficient genetic variability to respond to a selection program, especially for the traits REA, RFT, IMF and ADG. Thus, selecting animals based on data obtained from this study will help improve Guzerat carcass quality, production efficiency and profit margins.

Genet. Mol. Res. 18(3): GMR18413
DOI: 10.4238/gmr18413
Research Article

Genotoxicity caused by heavy metals can negatively affect vital processes of crop plants, though remedial measures can be used to reduce such damage. We examined the possible stimulatory and phytotoxicity impacts of three nanosized titanium dioxide (nTiO2) doses on soybean (Glycine max) and how adsorption of lead (Pb) onto the surface of nTiO2 may attenuate the toxic action of Pb on soybean by comparing the toxicity of three Pb doses before and after the adsorption process. The exposure time was 48 h. Phenotypic parameters (seedling growth, phytotoxicity, tolerance and vigor indices), cytogenetic tests of pollen grain performance, and DNA status (using flow cytometry, comet assays and analysis of RAPDs) were used as bioassays to assess the effect of the treatments. The optimal nTiO2 dose was 10 mg.L-1 because it i) stimulated and accelerated seedling development parameters, fertility and germination of pollen grains, ii) increased nuclear DNA content and decreased the extent of DNA damage, and iii) generated the maximum number of amplified DNA bands as an indicator for appearances of new DNA bands (genes) more than the control. Doses of nTiO2 higher and lower than the optimal dose resulted in a gradual decline in these parameters, especially the higher dose. The three doses of Pb induced notable inhibitory and genotoxic impacts on all biomarkers used, in a dose-dependent manner. We conclude that the powdered state of optimal dose (10 mg) had a good ability to adsorb Pb onto its surface and consequently mitigated its toxicity. This was evident through the significant amelioration of parameters of each biomarker after application of the three Pb adsorbate solutions on soybean seeds. Therefore, we suggest that stimulatory and adsorbent nTiO2 dose may be used in the future to protect against heavy metal toxicity in economically important plants.

Genet. Mol. Res. 18(3): GMR18350
DOI: 10.4238/gmr18350
Research Article

Local cassava varieties play an important role in food security and the autonomy of subsistence farmers. They can be important resources for breeding and conservation programs. We examined the genetic diversity of cassava through ethnobotanical knowledge and microsatellite markers to understand the dynamics of conservation and management of the varieties used local small-scale farmers of a rural quilombo (a slave-descendant community) in Mato Grosso, Brazil. To obtain ethnobotanical information, semi-structured interviews were applied to 10 family units who cultivated cassava. Each family cultivated from one to five varieties, with 2.3 ± 1.16 varieties/farmer, on average. Genetic analysis was was made of the 11 local varieties with microsatellite markers (12 loci). Despite low ethnobotanical diversity (H' = 2.05), high genetic diversity was found (Na = 6.75, HO = 0.92, H­E = 0.75, on average) in these local varieties. These farmers, who derive their income mainly from cassava cultivation and flour production for the market, direct their variety choices to those that are most productive. Brava variety was the most frequent (found in eight family units) and was considered the most profitable for the production of flour Network analysis showed that propagule circulation and information occurs between the residents and also with other communities of the region, which are important sources of new varieties. Two farmers were identified as the most active in this network, showing potential as key elements for the circulation of propagating material. According to the cluster analysis using the genetic data, the most recently introduced varieties (Baixinha, Liberatona, Broto roxo, Mansa, Ramo branco, Carneiro and Cuiabana) are separated from those introduced a long time ago. The varieties pointed out as bitter by the farmers were also grouped together. The results showed the importance of traditional farmers in maintaining a high genetic diversity of manioc varieties, despite the directing of the choice of varieties to meet market needs.

 

Genet. Mol. Res. 18(3): GMR18326
DOI: 10.4238/gmr18326

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