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Table of contents: 2019

Research Article

The cowpea, Vigna unguiculata (Fabeaceae) is widely cultivated in semi-arid regions, such as northeast Brazil. Due to the low crop yields in this region, it would be useful to develop cultivars adapted to these climate conditions. Landraces are seen as an important source of germplasm to be used in breeding programs of this species due to their good adaptation to the environment, but for this strategy to be viable, their genetic variability must be studied. To this end, we evaluated the genetic diversity, using ISSR molecular markers, of 52 samples of cowpea landraces collected mostly from small producers from all over the state of Ceará, Brazil. The DNA of the genotypes was extracted and analyzed using 25 primers. Based on the electrophoresis profiles of the bands, a genetic dissimilarity matrix was prepared, and a cluster analysis made using the UPGMA and modified Tocher methods. Fourteen primers amplified 80 bands, of which 61 were polymorphic, generating a polymorphism rate of 76%. The selected markers were efficient in identifying genetic variability among the varieties under evaluation, providing a large amount of information. The polymorphic information content varied from 0.13 to 0.66 and the band frequency ranged from 0.01 to 1.00. The two clustering methods agreed in the number of groups formed (n = 6), with the genetic distances ranging from 0.05 to 0.31, values considered low, suggesting a narrow genetic base for the landraces of this species in Ceará state.

 

Genet. Mol. Res. 18(1): GMR18082
DOI: 10.4238/gmr18082
Research Article

The objectives of this study were to select promising common bean populations for high iron and zinc contents (FeC and ZnC), seed yield and 100-seed weight, to study the genetic control of these traits and to select parents for high FeC and ZnC based on a diallele analysis. Fifteen populations were obtained from crosses among six parents selected for high FeC and ZnC using a complete diallel scheme. The 15 populations were evaluated together with two control cultivars/lines (Pérola and Piratã 1). The following traits were evaluated: FeC and ZnC in four environments/generations and seed yield and 100-seed weight, in three environments/generations. Individual and joint analyzes of variance were performed for the four traits and individual and joint diallel analyzes for FeC and ZnC. Significant differences were found among populations for all traits, which demonstrates genetic variability that can be exploited. For FeC, the additive effects were more important and the white seeded line G 2358 stood out for high general combining ability (5.63), being for this reason indicated as a parent. For ZnC, both additive and non-additive effects were important. The populations selected as simultaneously superior for the four traits were Porto Real x G 2358 and BRSMG Majestoso x G 2358, with at least one parent with carioca seeds; and BRS Requinte x BRSMG Majestoso, Porto Real x BRS Requinte and Porto Real x BRSMG Majestoso, with carioca seeds. The BRS Requinte x G 2358 population is recommended to obtain lines with high FeC and ZnC.

Genet. Mol. Res. 18(1): GMR18146
DOI: 10.4238/gmr18146
Research Article
Authors:

Many of the plants that grow in arid and semi-arid regions under harsh conditions (drought, salinity and misuse) are of medical importance. Desert plants also provide other benefits; so conservation efforts should be strengthened in these areas. In this study, three DNA barcodes – chloroplast maturase-K (matK), ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and secondary internal transcribed spacer (ITS2) – were tested in order to determine the ability of these markers to distinguish between various species. A total of 93 fresh and dry samples belonging to 30 plant families were examined. These are native to the arid lands around Makkah in the Kingdom of Saudi Arabia. Various tools and tests were used to evaluate the efficiency of the barcode markers; these included the basic local alignment search tool (BLAST), as well as the use of inter- and intraspecific distances, barcode gap, prediction of the secondary structure of the ITS2 and phylogenetic methods. The results confirmed the efficiency and superiority of the ITS2 loci over two chloroplast genes: matK and rbcL. ITS2 had a 97% success rate with amplification and a 95% success rate with sequencing, showing 100% identification at the family level, 77% identification at the genus level and 70% species resolution. A clear barcode gap was observed between inter- and intraspecific distances. Identification was achieved even in cases of degraded samples or old herbarium specimens. This study contributes to DNA barcode data by adding 224 DNA sequences of desert plants to the National Center for Biotechnology Information NCBI database. The results of this study are important and useful for application in each of the following fields: validation of medicinal plant identity, conservation, and taxonomic and evolutionary studies.

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Genet. Mol. Res. 18(1): GMR18133
DOI: 10.4238/gmr18133
Research Article

This is the first scientific record of Melanagromyza sojae in Bolivia, confirmed through molecular characterization of the mtDNA COI gene. Commonly known as the soybean stem fly, M. sojae belongs to the family Agromyzidae and is a highly polyphagous pest, attacking several plant species of the Fabaceae family, such as soybeans and other beans. Previously reported in Brazil and Paraguay, the soybean stem fly presence was confirmed in soybean fields of the municipalities of Fernández Alonso, Cuatro Cañadas, Santa Cruz de la Sierra, Yapacani and Santa Rosa del Sara, which are located in Santa Cruz Department, Bolivia. This soybean stem fly detection in Bolivia will affect soybean crop practices in South America.

 

Genet. Mol. Res. 18(1): GMR18222
DOI: 10.4238/gmr18222
Research Article

Passiflora cristalina, Passiflora miniata and Passiflora coccinea are wild species with similar floral characteristics, especially color and floral structure, as well as the color of their fruits. Due to their similarities, mainly the floral characteristics, these species are often confused in the field. Given that hybridization is commonplace between Passiflora species in the same region, hybrids could result from crosses involving mainly P. coccinea. We examined genetic distance and possible hybrid nature across P. cristalina, P. miniata, and P. coccinea, via ISSR and SSR markers. Genomic DNA was extracted from leaf samples of five Passiflora species (P. cristalina, P. coccinea, P. miniata, P. setacea, and P. edulis), the latter two being used as witness species. Following quantification, the amplification conditions were tested and optimized. Eighteen ISSR primers presented satisfactory amplification products, with 81 bands being amplified and 99% polymorphism. Through genetic distance and cluster analysis, P. cristalina and P. coccinea were found to be genetically close, while P. miniata remained in an isolated cluster, nevertheless with low dissimilarity with P. cristalina. Twenty-three SSR primers were tested, of which 18 were polymorphic. There was a high transferability rate, 95.65%, demonstrating that genetic proximity between tax is directly related to successful transferability. The main coordinates, genetic distance and cluster analyses showed a clear separation of species presenting similar floral characteristics (P. cristalina, P. coccinea, and P. miniata) from the remaining ones used as controls (P. edulis and P. setacea). SSR markers identified P. cristalina as a possible natural hybrid between P. miniata and P. coccinea.

Genet. Mol. Res. 18(1): GMR18040
DOI: 10.4238/gmr18040
Research Article

Worldwide, several women become victims of rape every day. Many of those women are also murdered, with their bodies sometimes being found in an advanced state of decomposition, resulting in loss of evidence important to criminal investigations. Diptera is one of the main orders associated with human body decomposition. Fly species that belong to the family Calliphoridae are usually scavengers and are frequently found on decomposing bodies, thereby playing an important role in forensic entomology. The recovery and genotyping of human Y-STR DNA from the gastrointestinal contents of the calliphorid Chrysomya albiceps larvae has promising applications in the investigation of sexual crimes, such as rape, and in cases of murder and abandonment of the victim’s body, which may be found in a state of decomposition. We studied this species of fly with the aim of supporting such investigations. After establishment of a colony, larvae were fed with decomposing human semen mixed in ground bovine meat (1 mL per 200 g beef). Larvae (10–15) were collected every 24 h and kept in 70% ethanol, to give a total of 96 larvae obtained after eight days of decomposition. The digestive system of each larva was resected. Molecular typing was conducted, which comprised sample extraction, quantification, amplification, and capillary electrophoresis with 16 STR loci from the Y chromosome. We succeeded in establishing a Y-STR DNA profile, with amplification of up to 11 loci, from individual samples, or up to 15 loci, when a combination of samples corresponding to the time-points 48, 72, 120, 144, and 192 h was used.

 

Genet. Mol. Res. 18(1): GMR18189
DOI: 10.4238/gmr18189
Research Article

The mangaba, Hancornia speciosa, (Apocynaceae) is a fruit tree native to Brazil with predominantly extractivist production. The fruit can be consumed in natura; however, it is widely consumed as frozen pulp and ice cream produced by agro-industry companies. We evaluated the genetic diversity of 213 individuals that make up the mangaba GeneBank of Embrapa Tabuleiros Costeiros, using nine microsatellite markers (SSR). A total of 147 alleles were identified, with a mean of 16 alleles per locus; 100% polymorphism was observed among accessions. Reliability of the result was verified based on stress (0.042) and correlation (0.988) values. The alleles presented a high frequency of heterozygosity (He > Ho). The Fst (0.22) and f (0.07) values indicated moderate population structure, with great diversity within accessions. Bayesian analysis indicated the most adequate grouping with k = 2. The Unweighted Pair Group Method analysis showed three distinct groups according to similarity. The BI accession had the best genetic structure. The PM5/GX2, CN1/CN9, G18/PA1, JA14/JA15, and OI8/OI9 pairs of individuals are the closest genetically. We conclude that the Mangaba GeneBank has high diversity; this knowledge is relevant to develop strategies for the management of these genetic resources.

 

Genet. Mol. Res. 18(1): GMR18108
DOI: 10.4238/gmr18108
Research Article

Pepper has considerable genetic diversity and versatility. Knowledge of the genetic control of traits in peppers is of great importance for breeding programs given the large variety of types, sizes, colors and flavors. To this end, we examined the inheritance of seedling and plant traits in ornamental pepper (Capsicum annuum). The experiment was conducted in a greenhouse in Areia, Paraíba, Brazil. Seven ornamental pepper accessions (C. annuum) belonging to the Federal University of Paraiba’s Germplasm Bank were investigated: UFPB001, UFPB004, UFPB77.3, UFPB099, UFPB134, UFPB137 and UFPB390. Morphoagronomic characterization was performed based on Capsicum descriptors, and 12 quantitative traits were evaluated in seedlings and plants. The data were subjected to variance analysis and subsequent diallel analysis performed according to Hayman's method. The t statistic was used to test the adequacy of the additive-dominance model. The traits seedling height, hypocotyl diameter, cotyledon leaf length, plant height, bifurcation height, leaf length and width and chlorophyll a and b are in agreement with the additive-dominant model. Correlations were positive and significant for seedling height (0.470) and hypocotyl diameter (0.885). Cotyledonary leaf length and width showed negative and significant values of -0.088 and -0.669, respectively. The correlations were positive for the following traits: plant height, stem diameter, first bifurcation height, canopy diameter, leaf length and chlorophyll b, with values ranging from 0.094 to 0.965. Leaf width and chlorophyll a exhibited negative r correlation values. In the genetic parameters estimate, the positive r correlation for most of the traits indicates that the recessive alleles were generally responsible for the increase in these traits. Genetic gains for plant traits in ornamental peppers are possible using breeding programs. The parents UFPB001 and UFPB134 exhibited the highest concentration of favorable alleles for size traits and are indicated for selection for continued improvement programs.

Genet. Mol. Res. 18(1):
DOI: 10.4238/gmr18120
Research Article

Many studies have explored variability to select cattle with high genetic potential for economic interest traits. Genetic variability is a powerful tool to improve production indexes in cattle, as it also is associated with variations in meat and carcass quality traits. We made a Genome-Wide Association Study of beef cattle of Bos indicus origin, in particular Nelore animals, to identify regions and genes associated with carcass quality, by examining phenotypic and genotypic data from 909 animals. Several genes in associated regions were observed to have above 1% of the portion of explained genetic variance explained: for hot carcass weight, genes LRGUK, TRIM24, SVOPL, TEX37, CA10, OXSR1; for ribeye area, genes TWIST2, SFXN1, CMYA5, CPQ and MRS2; for backfat thickness, genes OR2S2, 5S_rRNA, LOC100299372, LOC523083, LOC532403, LOC613441, SNORA69 and ITGA9; and for marbling, genes EMCN, LNX1, EIF5, SNORA28 and DSC3. The various genomic regions associated with small effects show the complexity of these phenotypes and that they do not depend only on the effects of a few genes to determine their variations.

 

 

Genet. Mol. Res. 18(1): GMR18226
DOI: 10.4238/gmr18226
Research Article

The objective of this study was to investigate, using path analysis, the genotypic correlations of primary and secondary production components as well as their decomposition into direct and indirect effects on the yield of coffee crops subjected to programed cycle pruning (PCP). Twenty-two Conilon coffe genotypes belonging to the breeding program developed by Incaper were subjected to PCP and 17 morpho-agronomic traits were measured in new branches. The traits plagiotropic branch length and number of plagiotropic leaves were discarded to eliminate collinearity problems. Path analysis was efficient in identifying the traits with greatest influence on yield. The most important traits linked to yield were number of orthotropic branches and orthotropic branch dry matter, while the secondary traits were orthotropic branch diameter, orthotropic internode length, and length of the plagiotropic branch internode. To increase coffee crop yield, producers should select genotypes that produce an intermediate number of orthotropic branches, which have a higher dry matter yield. Subsequently, they should select genotypes with larger orthotropic branch diameters, and among these, those which have shorter orthotropic and plagiotropic internode lengths.

 

Genet. Mol. Res. 18(1): GMR18114
DOI: 10.4238/gmr18114
Research Article

The parasitic protozoan Perkinsus marinus (Perkinsidae) is known to infect marine bivalves; unfortunately, treatment options are quite limited. The parasite is associated with mass mortalities worldwide and it requires notification to the World Organization for Animal Health (OIE). In Brazil, since the first report of P. marinus infecting Crassosstrea rhizophorae in the state of Paraíba in 2013, populations of oysters have been subject to continuous surveillance programs by the Ministry of Agriculture, Livestock and Food Supply for OIE-listed pathogens. Here, we report the first official case of P. marinus detection in native Crassosstrea sp. and in Crassostrea gigas from southern Brazil by PCR followed by sequencing of amplified fragments of the rDNA ITS region. For a better understanding of the epidemiology of P. marinus, we studied the parasite’s phylogenetic intraspecific variability based on its rDNA NTS region by comparisons of our isolates with other isolates from two Mexican regions on the Pacific coast. All Brazilian isolates clustered together with the Mexican isolates. As expected, high similarities were seen between all Brazilian isolates. Additional studies on P. marinus genotyping using new genomic target tools should be conducted for a better understanding of this parasite’s epidemiology.

Genet. Mol. Res. 18(1):
DOI: 10.4238/gmr18015
Research Article

Genipap (Genipa americana - Rubiaceae) is native to tropical America, occurring in Brazil in practically all biomes, except in the Pampas. It has socioeconomic importance, mainly due to the use of fruits in the manufacture of sweets and juices besides the medicinal properties of its leaves. We evaluated the genetic diversity of 73 individuals from 15 natural populations in the state of Sergipe using ISSR markers. The choice of areas was made randomly and genetic material was extracted from young leaves. PCR analysis using nine markers generated 113 fragments, which were used to estimate genetic diversity. The Shannon index was 0.36 and the similarity of individuals varied between 0.11 and 0.81. The individuals Salgado 3 (SAL3) and Salgado 4 (SAL4) were the most similar (0.81) and seven pairs had low similarity (0.11). The genetic distance the UPGMA analysis, which divided individuals into two distinct groups. The level of genetic variability found allows differentiation between genotypes that can be used to enrich the Genipap Active GermPlasm Bank in Sergipe, and the information generated will be useful for the conservation of these genetic resources and in future breeding programs for this species.

 

Genet. Mol. Res. 18(1): GMR18119
DOI: 10.4238/gmr18119
Research Article

The soybean crop is undoubtedly important to not only Brazil but also for most parts of the globe, as economic and social dependency upon this crop becomes evident. However, the scenario of the soybean crop production has faced challenges with environmental changes, which have escalated the incidence of pests. Due to the abundance of stink bugs, especially Euschistus heros in tropical regions, they can considerably impact the productivity of the crop compromising total grain yield and seed quality. Therefore, this research was aimed to evaluate soybean lines with desirable agronomic traits under high natural infestation of Euschistus heros and to access the genotypic and phenotypic correlations between important agronomic traits for soybean breeding. Twenty-three soybean F8 lines developed by the Soybean Breeding Program of Federal University of Uberlândia and four cultivars (Msoy 8527, UFUS Xavante, Msoy 8787, and UFUS Milionária) were evaluated under randomized complete block design with three repetitions during the growing season of 2015/2016 and 16 agronomic traits were accessed. There was genetic variability for all traits but Asian soybean rust severity at 1% probability level through F test. For all traits in the study but the total number of pods and Asian soybean rust severity, the coefficient of genotypic determination was superior to 70%, indicating that the most part of phenotypic variability was due to genetic differences among the genotypes in study. Grain yield was demonstrated to be a useful trait for indirect selection of soybean genotypes with resistance to brown stink bugs. Also, early cycle genotypes, heavy seeds and a higher number of pods revealed a positive correlation with grain yield over the same conditions. The lines G1, G2, and G24 are very promising genotypes as they have shown valuable agronomic traits for stink bug resistance.

Genet. Mol. Res. 18(1): GMR18182
DOI: 10.4238/gmr18182
Research Article

The DMRT3 gene has been described as the main gene influencing gait in horses; however, most studies have examined its effects by comparing information from trotted and gaited individuals. Within the Brazilian Mangalarga Marchador breed, animals can present two types of gaits (marcha batida and marcha picada), which differ in the movement form – diagonal (marcha batida) or lateral (marcha picada). We examined a possible association of the g.22999655C>A DMRT3 SNP with the type of gait, in this two-gaits breed. The relationship between individuals was calculated for the two phenotypic groups, as well as the inbreeding coefficient and its trend over generations. The allelic and genotypic frequencies were estimated based on genotype data from 310 horses (205 marcha batida; 105 marcha picada).Two threshold models were used to determine the proportion of phenotypic variance explained by DMRT3 genotypes. The average coancestry for animals with marcha batida was 0.04 ± 0.00, whereas in marcha picada it was 0.05 ± 0.01 (higher than the population mean of 0.04 ± 0.00). The inbreeding coefficient was 1.71% and 3.48% for marcha batida and marcha picada animals, respectively. Effects of the DMRT3 gene ranged from 9.94 to 10.77% (as a proportion of phenotypic variance) when included as an uncorrelated random effect and as a covariable, respectively. The genotypic frequencies of the DMRT3 and the patterns of kinship and inbreeding could be a result of selection in this breed, resulting in statistical confusion between the DMRT3 effects and population structure.

 

Genet. Mol. Res. 18(1): GMR18217
DOI: 10.4238/gmr18217
Research Article

Atherosclerosis is a multifactorial chronic inflammatory disease that occurs in response to endothelial aggression. Systemic arterial hypertension is the main risk factor for the formation of atheromas, increasing the risk of cardiovascular diseases. Several genes are involved in atherogenesis and hypertension. We analyzed polymorphisms of candidate genes that potentially participate in processes related to this pathology, including G894T and T786C of eNOS, as well as GSTT1 and GSTM1 in 167 hypertensive patients and 100 controls. Blood samples were from patients attended at the Angiogenesis/Vascular Surgery and Cardiology Department of the Angiogyn clinic in Goiania. There was significant prevalence of the genotype GT (76%) and the mutant allele T (56%) of the T786C (eNOS) polymorphism in the patients. For the polymorphism T786C (eNOS), the heterozygote genotype (TC) was found in 58% of the samples; allele C was found in 61%, but there was no significant difference compared to controls. The GSTT1 genotype was found in 84% and GSTM1 was found in 73%; for both their predominance was significant. There are many possible explanations for how these polymorphisms affect the development of atherosclerosis and hypertension, but more studies are necessary for their elucidation.

 

Genet. Mol. Res. 18(1): GMR18089
DOI: 10.4238/gmr18089

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