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Table of contents: 2021

Research Article

The aim of this study was to select Coffea arabica lines with improved adaptability to tropical edaphic conditions. Competitive trials were set up at three locations of the states of Rondônia and Acre. Each trial was composed of 21 lines in the F5 generation and four reference cultivars evaluated as controls. To analyze beverage quality, six liters of coffee fruit at the M3 maturity stage was collected for each line in the environments of Alta Floresta do Oeste, RO (E1), Porto Velho, RO (E2), and Rio Branco, AC (E3). On the same day, after collection, the fruit was washed and placed to dry (natural processing) in full sun over canvas, until the samples reached 11-12% moisture. Sensory analysis of the samples was carried out by three judges/cuppers (Q Grader), according to the sensory analysis method of the Specialty Coffee Association of America. Analysis of variance showed that the effect of the genotype x environment interaction was significant, indicating differentiated performance of the lines grown in the different locations. Environments E2 and E3 were not favorable for beverage quality, whereas environment E1 showed better conditions for production of specialty coffees. In sensory analysis, six lines had higher final beverage quality scores than the controls. Line 2 had a final score of 80, line 11 had a final score of 79, and line 12 had a final score of 77. In addition to good beverage quality, lines 2, 11 and 12 also had yields higher than 30 bags ha-1 in the average of three harvest periods, indicating the possibility of selecting lines with improved adaptation to tropical regions.

Genet. Mol. Res. 20(2): GMR18809
DOI: 10.4238/gmr18809
Research Article

Autism spectrum disorder (ASD)in children is on the rise and is a concern for parents and the community. There has been no research on the epidemiology of autism in children in general and children under six years old in particular in Nghe An, Vietnam. We examined the prevalence of ASD among children under 6 years of age in this region. We retrospectively studied the medical records of perinatal centers and children's outpatient clinics and hospitals. A relationship was found between cases of autism and risk factors, including congenital asphyxia, sepsis during pregnancy, multiple pregnancies, late reproductive age of the mother, children’s watching television time, and parents’ spending less time with children.

Genet. Mol. Res. 20(2): GMR18738
DOI: 10.4238/gmr18738
Short Communication

Genetic polymorphisms involved in carcinogen metabolism contribute to leukemogenesis risk. Epidemiological studies have revealed genetic alterations in chronic lymphocytic leukemia (CLL), including chromosome alterations, noncoding RNA alterations, and genetic polymorphisms. The bioactivation and detoxification of chemical agents is mediated by xenobiotic metabolism enzymes, and genetic polymorphisms may explain interindividual differences in hematological cancer susceptibility. Glutathione S-transferase (GST) enzymes are capable of metabolizing xenobiotics into less toxic and more easily eliminated substances. Some studies have suggested involvement of GSTs polymorphisms in leukemogenesis susceptibility. We investigated possible genetic associations between GSTM1/GSTT1 deletion and GSTP1 rs1695 polymorphisms with CLL risk in a central Brazilian population. For GSTM1/GSTT1 deletion polymorphism, genotyping was performed with multiplex real-time PCR (qPCR), and for GSTP1 rs1695 polymorphism, PCR-RFLP was used. The GSTM1 null genotype presented a trend towards CLL risk. However, GSTT1 deletion polymorphism presented a protective effect for CLL (OR=0.26, p<0.005).The GSTP1 rs1695 was not associated with disease susceptibility. Among confounding factors, male gender and age was associated with a 2.42-fold and 1.06-fold increased risk of CLL, respectively. In conclusion, among the polymorphisms that were evaluated, the GSTM1 deletion polymorphism apparently helpsin the detoxification process and has a protective effect against CLL.

Genet. Mol. Res. 20(2): GMR18754
DOI: 10.4238/gmr18754
Research Article

An inadequate supply of phosphorus (P) is one of the most limiting factors for plant nutrition, resulting in morphophysiological adjustments and reduced production. We evaluated 42 common bean germplasm bank accesses of the Instituto Agronômico Brazil that are divergent in root traits, using a hydroponic system to determine their performance under P deficiency. The plants were grown with a low P concentration (4.00 mg L-1) in a completely randomized experimental design, with three replications. Evaluations for shoot, root system and grain production traits were carried out, followed by individual analyses of variance, Scott-Knott mean test, Pearson correlation, and GGE-biplot analysis. Leaf chemical analysis showed a mean content of 2.20 g kg-1 of P, a value below the recommended range, as expected.  Analyses of variance showed a significant effect on most of the traits evaluated; the coefficients ranged from 7.1 to 19.8%. The genotypes were clustered for most of the variables based on the Scott-Knott mean test. Two genotypes (G 2333 and Rubi) stood out as the highest yielding, with a greater relative chlorophyll index and better development of the root system. A significant correlation was found between the the root traits length, surface area, and volume with production components. Based on GGE-biplot analysis, 12 genotypes were selected that simultaneously performed better for grain yield and root system.

Genet. Mol. Res. 20(2): GMR18753
DOI: 10.4238/gmr18753
Research Article

The boll weevil, Anthonomus grandis (Curculionidae) is the main pest of cotton culture. To establish more efficient forms of control, it is important to understand its genetic structure and the diversity of its populations. We examined the genetic diversity of various populations of boll weevils, collected from several Brazilian locations, through morphometric and molecular analyses. Flower buds were collected from cotton plantations in three municipalities in the Caatinga region and seven municipalities in the Brazilian Cerrado region. Fifty specimens from each population (municipality) were randomly selected for morphometric characterization and 15 specimens, among the 50 insects characterized morphometrically, were randomly selected for molecular characterization. In the analysis of the principal components, based on 13 morphometric characteristics, the variables that had the most impact on the first two eigenvectors of males and females were total body length and maximum prothorax width. Based on the band count obtained from the ISSR markers, and subsequent construction of the binary matrix, the averages of the number of loci, percentage of polymorphic bands and expected heterozygosity were 71, 53%, and 0.126, respectively. The genetic variation within and between populations was 42.69 and 57.30%, respectively. Using the unweighted pair group method, formation of two population groups was observed after adopting the 95% cut-off point; the clusters formed using molecular data were different from the clusters of males and females formed using morphometric data. The low genetic diversity and the weak geographical structure of the boll weevil in Brazil is apparently due to its being an exotic pest that has been recently introduced, composed of a small portion of the population of origin. The low diversity also indicates that geographically closer populations are not necessarily genetically similar.

Genet. Mol. Res. 20(2): GMR18771
DOI: 10.4238/gmr18771
Research Article

Several studies have described an association between cytotoxic T-lymphocyte antigen-4 (CTLA-4) gene polymorphism and type 1 diabetes mellitus (T1D) in some ethnic populations, and a lack of association in other populations. Differences in the contribution of the genetic background of T1D onset are age dependent. We conducted a case-control study of a T1D Brazilian population, in which a possible association of rs231775 (+49A/G) and rs5792909 (-318C/T) polymorphisms in CTLA-4 with T1D was evaluated. These polymorphisms were genotyped in 150 childhood-onset (age £ 14 years old) and 150 adult-onset (age >18 years) patients with diabetes and non-diabetic healthy individuals (150 children and 150 adults). PCR-restriction fragment length polymorphism (rs5792909) and TaqMan® fluorescent probe (rs231775) methodologies were used for genotyping. The polymorphisms were in Hardy-Weinberg equilibrium. There was no difference in genotype and allele frequency between the patients with T1D and non-diabetic controls. The frequencies for childhood-T1D and adulthood-T1D, for the rs231775 G-allele (95% CI) were 39.0% (31–47) and 37.3% (30–46), and for the T-allele of the rs5792909 polymorphism they were 5.0% (3–7%) and 2.7% (1–4%), respectively. We did not identify an association of CTLA-4 rs231775 and rs5742909 polymorphisms with adult- or childhood-onset T1D in a Euro-Brazilian population in Southern Brazil.

Genet. Mol. Res. 20(2): GMR18817
DOI: 10.4238/gmr18817
Research Article

The umbu tree (Spondias tuberosa) is endemic to the Brazilian semiarid region. This species is not cultivated and commercialized fruits are a result of extrativism; consequently little has been done to develop new and more productive cultivars. Hybrids of different accessions are a result of natural open pollination, so identifying putative male parents among progenies of umbu tree accessions is difficult. Eight accessions were pre-selected for larger fruit size and clones were established at Petrolina, PE. Female plants were randomly chosen among accessions of an established umbu tree experimental plot. Alleles of putative male parents were evaluated based on simple sequence repeat (SSR) loci. Of the 32 SSR loci evaluated, 10 showed polymorphism. Thirty-four alleles were identified, with an average of 3.4/locus. Polymorphism information content ranged from 0.195 to 0.744; the expected ranged from 0.233 to 0.825 and the observed heterozygosity ranged from 0.250 to 0.825. Accessions similarity ranged from 0.44 to 0.68, distributed into two groups: (I) common umbu, BGU30, BGU37, BGU44, BGU55 and BGU68, and (II) BGU 48 and BGU52. Hybrids and self-fertilized plants were identified among BGU30 and BGU37 progenies;   17 out of 20 and 14 out of 44 hybrids were identified by SSR loci in the BGU30 and BGU37 progenies, respectively. The putative hybrids BGU30 × BGU48, BGU30 × BGU55, BGU30 × BGU44, BGU30 × BGU68, BGU37 × BGU44, BGU37 × BGU55 and BGU37 × BGU52 have potential for future evaluations, as they were more divergent in the dendrogram or had male parents with higher weight fruits. The 10 SSR loci were sufficient to identify a single parent in 12 of 20 BGU30 hybrids and all 14 BGU37 hybrids, demonstrating the potential of this procedure.

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Genet. Mol. Res. 20(2): GMR18816
DOI: 10.4238/gmr18816
Research Article

High temperature is one of the main environmental factors that limit crop performance. It may also influence seed formation and quality. We compared the effect of high temperatures on seed darkening and cooking time of 12 genotypes of common beans. The experiments were sown in summer and in fall/winter growing seasons in three municipalities of São Paulo state (Campinas, Votuporanga, and Ribeirão Preto). A randomized block experimental design was adopted with four replications, analyzed in a 2 x 3 x 12 factorial arrangement; the factors were two crop seasons, three locations and 12 genotypes. After harvest, the following seed traits were evaluated: cooking time soon after harvest (CTH), after 30 days of storage (CT30), and after 60 days of storage (CT60); seed color soon after harvest (COLH), after 30 days of storage (COL30), and after 60 days of storage (COL60). Individual variance analyses were performed followed by average test and GGE-biplot interaction of factors analysis. Seed darkening was significantly affected by the crop season factor at all evaluation times, though there was no significant effect on cooking time. Significant effects on all variables were also found for location and genotypes. In the summer growing season, darker seeds were obtained, and among the locations, the seeds produced in Campinas were lighter in color. Increases in cooking time and in seed darkening were found with increases in storage time. The genotypes BRS Estilo, IAC Diplomata, Pérola, BRS Agreste, and IAC Imperador exhibited better seed quality (shorter cooking times and colors in the desired range ) at all locations in the summer season.

Genet. Mol. Res. 20(2): GMR18779
DOI: 10.4238/gmr18779
Research Article

Bombyx mori nucleopolyhedrovirus (BmNPV) is an entomopathogenic virus of the family Baculoviridae that causes disease in the silkworm, Bombyx mori, leading to a series of metabolic disorders that severely affect silk production. The main external sign of BmNPV infection can be observed in the integument of infected caterpillars, which is an important diagnostic indicator that can help direct control measures to prevent viral dispersion in rearing facilities. We analyzed the integument of B. mori caterpillars infected with BmNPV in a cytopathological study of epidermal cells and cuticle, to help identify signs of infection. Fifth instar larvae were inoculated with viral suspension and integument segments were processed for light microscopy and transmission electron microscopy. Signs of infection were monitored daily until cocooning. Cytopathology of epidermal cells showed signs of baculovirus infection, leading to cytolysis and release of viral polyhedra into the hemocoel, similar to what occurs in other BmNPV target cells. Considerable modifications were observed in the apical region of the epidermal cells, with disarrangement and involution of the microvilli, and loss of contact of the plasma membrane plaques with the endocuticle. Plasma membrane plaques are involved in the transport of precursors for chitin synthesis and assembly of chitin myofibrils. The disorganization of the integument of silkworms infected with BmNPV shows the fragility of this organ, which easily ruptures due to infection, leading to the release of BmNPV polyhedra to the external environment, perpetuating the infection.

Genet. Mol. Res. 20(2): GMR18758
DOI: 10.4238/gmr18758
Research Article

Conservation of seeds ex situ is an important strategy for maintaining genetic resources. Mulatinho type common beans are widely cultivated and consumed in regions with extreme climatic conditions with semi-arid characteristics, including low fertility soils, and a dry and hot climate, such as in northern Minas Gerais state and the northeast region of Brazil. This bean type also has socio-economic importance, as a protein source for the food security of families. Part of the harvest is consumed and another part is selected as seed and stored for the next crop. Our objective was to create a reduced collection ensuring the conservation of distinct alleles , based on information on morphologic, agronomic, and ecogeographic characteristics to help support ex situ and on farm seed conservation programs. Two greenhouse studies were conducted at the Embrapa facility, located in Santo Antônio de Goiás, Brazil. Morphologic and agronomic descriptors, both qualitative and quantitative, were transformed into binary variables through the creation of fictitious variables. Descriptors were used to estimate the coefficient of similarity between two accessions and obtain the dissimilarity distance between the semi-partial correlation squared values. Experiment I was comprised of genetic material from 745 accessions of common beans and was planted in pots with three plants for each accession. In Experiment II, 240 accessions were selected from Experiment I, using four pots with three plants for each accession. The phenotypic data in this reduced group showed increased phenotypic dissimilarity, contributing information for research in plant breeding and for farmers who may need seeds. The  mulatinho type common beans types can be reduced to 96 accessions, maintaining the conservation of distinct alleles, with a significantly higher mean number of pods and seeds, and of plant mass, compared to the initial collection of 745 accessions.

Genet. Mol. Res. 20(2): GMR18770
DOI: 10.4238/gmr18770
Research Article

Safflower, Carthamus tinctorius (Asteraceae), is an oilseed plant with good adaptability to warm and dry climatic conditions. It is used for biodiesel production, human food, animal feed, and in the pharmaceutical industry. Recently, the crop has been highlighted, mainly for its oil quality and for biofuel production. We compared 124 safflower genotypes, which are a part of the State University of Mato Grosso germplasm collection, based on their agronomic characteristics, to provide the initial guidelines for a breeding program. Evaluations were carried out during the crop cycle and parameters were defined according to the descriptions recommended by International Board for Plant Genetic Resources and by the Ministry of Agriculture, Livestock and Supply. Multivariate analysis was used to assess the divergence among genotypes, by using Average Euclidean Distance, which ranged from 0.07 to 0.57, showing considerable genetic diversity among safflower genotypes for the agronomic characteristics that were evaluated (flowering, plant cycle, number of branches per plant, plant height, number of chapters per plant, number of seeds per chapter, chapter diameter, stem diameter, weight of 100 seeds, seed size and plant yield. Tocher and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) clustering methods were partially consistent in ordering similar genotypes. The agronomic characteristics: plant yield, number of chapters per plant and plant height provided the greatest contribution to genetic divergence among the genotypes. According to the groupings established with each methodology and depending on the variation structures within each group, several genotypes stood out in terms of agronomic performance and may be indicated for future crosses aiming to obtain improved safflower cultivars for Brazil.

Genet. Mol. Res. 20(1): GMR18698
DOI: 10.4238/gmr18698
Research Article

Various theories have been developed regarding the pathology and etiology of hypertensive disorders of pregnancy (HDP). The impaired placenta secretes antiangiogenic factors into maternal blood, resulting in the development of pregnancy-induced hypertension (PIH). Both µ-calpain and m-calpain are proteins known to be involved in placentation, with the catalytic subunits encoded by the CAPN1 and CAPN2 genes, respectively. The purpose of this study was to find disease susceptibility genes for PIH by conducting an association analysis for HDP using specific gene markers comprising individual single nucleotide variants (SNVs) and haplotypes within the CAPN2 gene. We selected five SNVs in the human CAPN2 gene and performed an association study with 95 HDP patients and 177 age-matched non-HDP subjects. In the analyses conducted for the CAPN2 SNVs, the recessive model of rs1153968 differed significantly between the gestational hypertension (GH, a category of HDP) and control groups. However, rs1153968 deviated from Hardy-Weinberg equilibrium and was deemed unlikely to be a significant factor. No significant differences were seen in any of the other SNVs analyzed. However, association analyses involving the rs1892077-rs98041140-rs17599-rs1153954 haplotype in the CAPN2 gene haplotypes revealed that G-A-A-T was found at a significantly lower frequency, and G-A-C-T and G-G-A-A at significantly greater frequencies, in patients with PIH. These findings may be useful in preventing PIH onset, as well as for the early discovery and treatment of patients who are carriers of the haplotype likely to be associated with this condition.

Genet. Mol. Res. 20(1): GMR18639
DOI: 10.4238/gmr18639
Research Article

The forensic community is concerned about the quality control of mitotypes reported, as probability estimates may be biased to the disadvantage of a suspect when there is incomplete data. This is particularly important when using new technology such as Massively Parallel Sequencing (MPS), which performs simultaneous analysis of millions of DNA fragments, generating vast amounts of data from small amounts of sample, providing more extensive genetic information. The use of MPS for complex forensic evidence analysis could save time and resources, and provide reliable data for extremely degraded DNA samples. However, data analysis methods can be challenging to implement in a forensic labs routine. Here, we propose a reliable and straightforward pipeline for mtDNA data analysis in forensic samples using MPS, and we used this pipeline to solve a human identification case by Rio de Janeiro Police who had recovered a severely putrefied body that could not be identified by conventional autosomal STR analysis. Mitochondrial DNA (mtDNA) from samples were sequenced on Ion Torrent PGM. Raw data from the sequencing was analyzed in two main pipeline protocols: quality control and forensic analysis. The first includes the analyses of raw data and contamination control. The second generates haplotypes, allowing haplogroup classification, and biogeographic inference, as well as verification of a matrilineal relationship. This straightforward freeware pipeline for mtDNA data analysis should facilitate the implementation of this type of system in forensic lab routine. Using our pipeline, the definition of the samples being of African origin was more precise when considering the whole mtGenome and not only the control region, which is usually used for routine forensic analysis. The final analysis was consistent with the existence of a matrilineal relationship between the alleged son (bone sample recovered from the sea) and the mother.

Genet. Mol. Res. 20(1): GMR18757
DOI: 10.4238/gmr18757
Research Article

The cultivation of passion fruit occupies an important place in Brazilian fruit culture; however, there have been successive declines in production. The main cause of this retraction in production is an increase in the incidence of Cowpea aphid-borne mosaic virus. This virus can cause severe deformation of the fruit and make passion fruit production inviable. Due to a lack of cultivars resistant to this virus, the Universidade Estadual do Norte Fluminense Darcy Ribeiro passion fruit breeding program has sought to develop resistant cultivars. The objective of this work was to evaluate the resistance to CABMV of a passion fruit second generation backcross (BC2) segregating population via the REML/BLUP procedure aiming at selecting resistant genotypes with agronomic characteristics to start a recurrent selection program and possibly produce a new passion fruit cultivar. Virus resistance was measured by the average area under the disease progress curve using a score scale, evaluating the percentage of symptoms in the plant and young leaves. The total fruit mass produced per plant was used to assess fruit production. Based on this information, the components of variance and genetic value were estimated via REML/BLUP. The highest values estimated for genetic parameters, for the two characteristics evaluated, were based on the average of each family. The BC2 - 17 family showed the best additive genetic gain concerning resistance to CABMV and the worst for fruit production. The BC2 - 293 family, had the highest estimated value of genetic gain for fruit production. The genetic variability found in the BC2 segregating population allows us to select superior genotypes. Twenty-nine genotypes were selected to start the recurrent selection program aimed at resistance to CABMV. The - Two genotypes (BC2 - 89 and BC2 - 323) showed potential to be launched as CABMV resistant passion fruit cultivars.

Genet. Mol. Res. 20(1): GMR18687
DOI: 10.4238/gmr18687
Research Article

The pigeonpea is an important grain legume in various regions of the world. It is a pulse that is cultivated mainly by small farmers in semi-arid tropical regions for various purposes, including food security, livestock feed, and agroforestry systems. We examined the genetic diversity and structure of 73 pigeonpea accessions from 10 origins, including regions of Brazil, Central America, and India. Allelic diversity and polymorphism, molecular analysis of variance (AMOVA), Bayesian analysis (Structure) and a dendrogram were estimated based on data concerning 11 microsatellite loci. AMOVA revealed wide genetic differentiation among the pigeonpea populations, with FST ranging from 0.22 to 0.25. Expected heterozygosity in the accessions was greater than the observed heterozygosity in eight of the 11 loci, with the observed heterozygosity ranging from 0.06 to 0.55. Polymorphic information content ranged from 0.13 to 0.67 among the 11 loci. Genetic similarity among pigeonpea accessions ranged from 0.26 to 0.93, indicating considerable variability among them, with the formation of three groups, one of which included all Brazilian accessions. Two groups were formed in the Structure analysis, indicating reduced allele sharing between the populations of Northeast Brazil and other populations. This information highlights the importance of incorporating germplasm from the Brazilian Northeast into pigeonpea breeding programs in Brazil, to increase the variability in germplasm collections.

Genet. Mol. Res. 20(1): GMR18807
DOI: 10.4238/gmr18807