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Table of contents: 2018

Research Article

The ability to avoid self-pollination is a trait that evolved as a manner of reducing the deleterious effects of inbreeding in various allogamous plant species, including Coffea canephora. The aim of this study was to perform directed hybridizations to characterize the compatibility groups of superior C. canephora clones, since plant selection can reduce variability for this trait. For that purpose, directed hybridizations were carried out in cross arrangements using a balanced diallel without self-fertilization and without reciprocals. The genotypes evaluated were derived from open pollination and from directed hybridizations using Encapa03 as a male parent donor of pollen grains and Robusta640, Robusta 2258, and Robusta1675 as female parent receptors of pollen grains. To control the occurrence of type I and type II errors, the likelihood ratio test was used. Compatible crosses were predominant (73.7%). Compatible crosses exhibited a mean rate of fruit set of 44%, with amplitude from 26% to 77%. Of the total of 80 crosses performed, three crosses exhibited unexpected results according to the grouping proposed (P08 x P16, P09 x P15, P09 x P16). From the degree of kinship, the genealogy of the S gene and the segregation of the alleles from one generation to another was estimated. The genotypes P12, P14, and P10 exhibited the highest estimates of LOD score associated with their clustering in groups I, II, and III. These genotypes may be used as tester plants of their compatibility groups

Genet. Mol. Res. 17(1): gmr16039876
DOI: 10.4238/gmr16039876
Research Article

Knowing the mating patterns is important to determine the number of trees necessary for seed collection for conservation ex situ, tree breeding and environmental reforestation purposes. We investigated B. excelsa individuals and fruits, to check mating system index variations in a population by using open-pollinated seeds which were hierarchically sampled within and among fruits from nine trees genotyped for ten microsatellite loci. Outcrossing rate ( )changed between trees (0.49–1.0) and fruits (0.53–1.0), but seeds were predominantly produced by outcrossing (0.92) at mean population level. Mating between related trees ( ) was detected in six trees (0.04–0.08) and in 32 fruits in trees (0.03–0.22), thus it suggests that the population presented some related trees in our intra-population spatial genetic structure. Individual fixation index values of seed trees ( ) were lower than the seedling fixation index values ( ), fact that suggests the selection against inbred individuals between the seed and adult stages. The correlated mating showed that seeds sampled at population level were predominantly composed of half-sibs (66%) and full-sibs (20%). Paternity correlation was significantly higher within ( ) than among ( ) fruits at population level, mostly in individual trees. Results evidenced that mating was not random due to self-fertilization, to mating between related trees and correlated mating, and families comprised different relatedness levels such as half-sibs, full-sibs, self-sibs and self-half-sibs; some cases, mating presented inbreeding. These results were addressed to discuss strategies for seed collection applied to conservation ex situ, tree breeding and environmental reforestation.

Genet. Mol. Res. 17(1): gmr16039872
DOI: 10.4238/gmr16039872
Research Article

Milk protein genetic polymorphisms of the genus Bos provoke a significant scientific interest, mainly associated with their evolution, population structure, breeding and hybridization. The aim of present study is to investigate the influence of the genetic variants of αS1- casein gene with respect to milk production and quality of native for Bulgaria cattle breed - Bulgarian Rhodopean cattle. A total of 87 unrelated animals of that breed were examined for genetic variants of the αS1- casein gene through PCR-RFLP analysis. The results showed that three genotypes BB, CC and BC were presented with 26.4 %, 2.3 % and 71.3 %, respectively. The frequency of B allele (62.1 %) was almost twice higher as compare with C allele of the gene (37.9 %). The effect of estimated genotypes on qualitative and quantitative milk traits could be summarized as follow: milk production and milk butter, BC>BB>CC; fat and protein contents, CC>BB>BC. The presence of correlation between genetic variants of αS1- casein gene and qualitative and quantitative bovine milk traits gives a reliable approach for selection of animals with desirable milk traits and genetic elaboration of that native breed as a part of national genetic fund.

Genet. Mol. Res. 17(1): gmr16039868
DOI: 10.4238/gmr16039868
Research Article

The common bacterial blight, caused by Xanthomonas axonopodis pv. phaseoli (Xap) and X. fuscans subsp. fuscans (Xff), is one of the most important dry bean diseases of bacterial etiology. The present work aimed to study the genetic structure among and within populations, and also identify the pathogenic variability of Xap and Xff isolates evaluating the horizontal and vertical resistance of the host. A total of 42 Xap and Xff isolates were obtained were submitted to molecular characterization by rep-PCR markers, and inoculated in the genotypes CNFP 10120, BRS Notável, and Rosinha G-2, for differential interaction studies. In the analysis of genetic structure, the coefficient of genetic differentiation (GST=0.5154) revealed diversity both within and among the pathogenic populations, confirming the result obtained by AMOVA (FST=0.5198). Of a total of 51 loci, 98% were polymorphic, among Xap 59% and within Xff only 21% were polymorphic. In studies of pathogenic variability, diallelic analyses showed significant effects of the general combination ability (GCA), of the general aggression ability (GAA), and of the specific interaction ability (SIA). Therefore, seven races were classified through the differential behavior of all isolates in the three genotypes of bean.

Genet. Mol. Res. 17(1): gmr16039871
DOI: 10.4238/gmr16039871
Research Article

The five most common cultivars from the genus Allium cepa L. in Bosnia and Herzegovina (BiH) were analysed, focusing on Konjic onion. Seven SSR markers for genetic similarity analysis were used to address the genetic backgrounds. The polymorphic relationship between the SSR markers was analyzed by using Polymorphic Information Content (PIC) and Heterozygosity (H) by using the online available PICcalc program. For the complete data analysis and phylogenetic tree construction, the DARwin 6.0.13 software was used. The total number of obtained SSR alleles was 30 bands, where 56.7% were polymorphic with the range of allele size of 130 to 650 base pairs (bp). The mean polymorphic information content (PIC) was 0.435 and the expected heterozygosity (H) values ranged from 0 to 0.785. Jaccard's coefficient of similarity values ranged from 0.14 to 0.55. The results in this study represent the first genetic diversity data on the onion cultivars in BiH and show significant dissimilarity among the onion cultivars. This study confirmed that the molecular SSR analysis represents an efficient tool for Allium cepa L. landrace genetic similarity analysis.

Genet. Mol. Res. 17(1): gmr16039870
DOI: 10.4238/gmr16039870
Research Article

Sixty-eight sugarcane genotypes were evaluated to determine the number of harvests required to select new genotypes in the sugarcane belt in the state of Pernambuco, northeast Brazil. Using a random block design, the following parameters were evaluated: (i) polarizable sugars (POL) per hectare, in metric tons (TPH); (ii) culm productivity per hectare (TCH); (iii) fiber content (FIB); (iv) adjusted percent POL (PCC); (v) soluble solids (BRIX); (vi) total recoverable sugars (ATR); and (viii) metric tons of ATR per hectare (ATR t.ha-1). A variance analysis and genetic parameter estimation were carried out. Means were analyzed using the Scott and Knott test. The repeatability coefficient and the number of harvests were determined using analysis of variance, principal component analysis, and structured data analyses. The best cultivars were SP79-1011, RB952692, RB952675, RB813804, SP78-4764, RB952522, RB952511, RB953265, RB952754, RB952875, SP80-1816, RB763710, and RB892575. Two evaluations are enough to select elite genotypes in the early experimental stages, reducing the time-to-market of these cultivars by three years under the edaphic and climatic conditions in the sugarcane belt evaluated

Genet. Mol. Res. 17(1): gmr16039869
DOI: 10.4238/gmr16039869
Research Article

Soybean (Glycine max) is considered one of the most economically important agricultural crops in Brazil. Due to the high protein content of its grains, this crop demands a greater amount of nitrogen (N) for production. In general, for soybean, nitrogen fertilization costs through chemical fertilizers are considered high. However, the biological nitrogen fixation (BNF) through the use of biological inoculants, such as the strains of Bradyrhizobium genus, a rhyzobacterium, represents a viable alternative for soybean crops in Brazil and dismisses nitrogen fertilization. Because of the need to constantly increase soybean crop productivity, it is necessary to find more efficient Bradyrhizobium genus strains for BNF. Genes related to soybean BNF have been utilized as molecular markers in selection programs that aim to obtain more efficient bacterial strains in this process. Therefore, this study aimed to characterize the gens related to BNF efficiency (nopP, aapP, ilvD and bll3106) by PCR-RFLP in Bradyrhizobium japonicum strains. The nopP and aapP genes were sequenced and submitted to similarity analysis with genes deposited on the Genbank (NCBI). The results showed the presence of highly conservative sequences in nopP and aapP genes between the analyzed B. japonicum strains. The occurrence of these preserved nucleotide sequences can be related to the adaptive function that they can have during the evolutionary process of plant growth promoting rhizobacteria.

Genet. Mol. Res. 17(1): gmr16039867
DOI: 10.4238/gmr16039867
Research Article

Gitelman syndrome (GS) is a genetic disorder that affects kidney and causes an imbalance of charged atoms (ions) in the body, including ions of potassium, magnesium, and calcium. GS is characterized by hypokalemia and metabolic alkalosis. GS is a rare autosomal recessive renal tubulopathy disease caused by loss-of-function mutations in the SLC12A3 gene. Objective of the present study is to find the genetic causes involved in a consanguineous Saudi family. Whole exome sequencing was done to find out the genetic mutation in the affected members of the family and the putative mutation was further validated by subsequent Sanger sequencing in other member of the family. We identified a novel homozygous mutation c.2686C>T as a result in p.Arg896* stop gained in exon 23 of SLC12A3 gene. The mutation was ruled out in 100 unrelated healthy controls. A novel homozygous stop gain mutation detected in this study has not yet been reported as pathogenic in literature or variant databases. Functional prediction of this mutation was performed using various online in silico prediction tools and all predicted it be disease causing. In conclusion, the here detected homozygous SLC12A3 mutation in the SLC12A3 gene as a result a truncated protein produced with a premature stop gain would expected to lead to functional loss to cause GS in Saudi family. This study will add more knowledge about GS in Arab populations’ database of genetic disorders and will help in the genetic counselling of the families in Saudi Arabia.

Genet. Mol. Res. 17(1): gmr16039858
DOI: 10.4238/gmr16039858
Research Article

Drought is a major threat to agricultural crop growth and productivity. However, the molecular mechanism behind such effects remains largely unknown. Plant CBL (Calcineurin B-Like)-interacting protein kinases (CIPKs) are believed to play an important role in plant drought tolerance and signalling transduction. Here, we report the influence of a member of the CIPK family, AtCIPK23, in drought stress responses in tobacco. Transgenic tobacco plants over-expressing AtCIPK23 showed enhanced tolerance to drought stress compared with wild-type plants. After drought stress treatment, the survival rates and levels of chlorophyll, proline, and soluble sugar in three transgenic lines were significantly higher than those in WT plants. Additionally, in the transgenic plant lines the accumulation of H2O2 was lower, and the expression levels of NtSOD, NtCAT and NtAPX were higher compared with wild-type plants under drought stress. A quantitative RT-PCR analysis revealed that over-expression of AtCIPK23 in tobacco induced the expression of the NtDREB, NtLEA5 and NtCDPK2 genes. Therefore, AtCIPK23 perhaps is involved in the plant response to drought stress via regulating the expression of stress-related genes.

Genet. Mol. Res. 17(1): gmr16039864
DOI: 10.4238/gmr16039864
Research Article

Calceolaria is a diversified American genus whose species are mainly visited by oil-collecting bees, representing a highly specialized plant-pollinator system. However, although this is a unique plant system, different aspects of its ecology and evolution remain unexplored. In this study we characterized fifteen polymorphic microsatellites for four Andean Calceolaria species using next-generation sequencing. The number of alleles per locus (Na) for the study species ranged from 2 to 11, and the observed (Ho) and expected (He) heterozygosity ranged from 0 to 0.85 and 0.3 to 0.87, respectively, while FIS ranged from 0.03 to 1.0. Among the four species, C. cana showed the greatest genetic diversity, followed by C. filicaulis. C. arachnoidea and C. lanigera showed similar, lower genetic diversity. These makers are a useful tool to conduct futures studies on population structure and gene flow. Specifically, this set of markers will be helpful to estimate selfing rates as a first approximation to the understanding of the role of specialization in plant mating system evolution

Genet. Mol. Res. 17(1): gmr16039863
DOI: 10.4238/gmr16039863
Research Article

Among the factors affecting cassava yield, the leaf nutrients content has received little attention since cassava genotypes may grow well under inappropriate nutrient supply, however showing inadequate nutritional quality of tuberous roots. Considering this aspect, the genetic diversity should be explored in order to determine standard leaf nutrients in cassava genotypes. Thus, this study aimed at verifying leaf nutrient content (NC) as well as relationships among leaf nutrients (NR) in order to establish standard leaf nutrient level in twelve cassava genotypes. The experiment was performed during 2014/2015 crop seasons in northern region of Espírito Santo State, Brazil. A total of 24 samples were collected from each cassava genotype for quantification of leaf nutrient contents (N, P, K, Ca, Mg, S, Fe, Zn, Cu, Mn and B). UPGMA method for quantifying genetic diversity as well as Scott-Knott for grouping averages were used. Our results reported low genetic diversity for both NC and NR, corroborating with grouping Scott-Knott test. Therefore, our leaf nutrients content values can represent an adequate nutritional status of cassava genotypes, which can be used as reference values for such specie

Genet. Mol. Res. 17(1): gmr16039862
DOI: 10.4238/gmr16039862
Research Article

Halophytes occupy coastal and sub-coastal area of marine environment. They potential candidates for search of novel and new bacterial flora that have immense potential to yield novel therapeutic agents. Six different endophytic bacteria have been isolated from pneumatophores and roots of three halophytes (Salsola imbricata, Avicennia marina and Haplopeplis perfoliata) collected from western coastal area of Jeddah, Saudi Arabia. After testing against five fungal pathogens all were active against oomycetes fungal pathogens, Phytophthora capsici and Pythium ultimum. Molecular identification of the bacteria was done on the basis of 16S rRNA gene sequences which revealed 95.9–99.4% sequence identity to related type strains and were placed in four major genera and two major classes: Actinobacteria (Streptomyces and Nocardioides) and α-Proteobacteria (Inquilinus and Labrezia). Active metabolites of these six bacterial endophytes including EA61, EA83, EA85, EA87, EA97 and EA220 were identified by subjecting to chemical analyses using liquid chromatography-mass spectrometry (LC-MS). LC-MS analyses showed presence of different active compounds in the culture extracts of these isolates. Some of these metabolites are already reported as synthetic molecules and has diverse biological functions as antimicrobial, anti-inflammatory and anthelmintic compounds such as such as Sulfamethoxypyridazine, Sulfamonomethoxine, Sulfamerazine and Dimetridazole, Sulfadiazin

Genet. Mol. Res. 17(1): gmr16039857
DOI: 10.4238/gmr16039857
Research Article

Members of the pistillata-like (PI-like) subfamily of plant MADS-box genes play multiple roles in regulation of reproductive meristems and the specification of sepal and petal identities. However, the function of PI-like genes in the Sedirea japonica is largely unknown. In this study, a full-length of PI-like gene in Sedirea japonica (designated PI-like, GenBank No. KM975642) was cloned using 5’/3’-RACE. The PI-like gene were 921 bp length with an open reading frame (ORF) of 633 bp, which encodes a protein of 210 amino acids, with a putative molecular weight of 24.5 kDa and a theoretical isoelectric point (pI) of 9.3. It also contains a 96-bp 5′ untranslated region (UTR), and a 192-bp 3′ UTR. The result of multiple sequence alignment indicated that PI-like belongs to a Class-B MADS-box gene. In addition, the phylogenetic tree analysis revealed that PI-like gene was highly like PI-like in Phalaenopsis. The qRT-PCR results revealed that the expression of PI-like gene was higher in the tissues on florescence compared to vegetative phase, suggesting that the PI-like gene of S. japonica performed important physiological functions on florescence

Genet. Mol. Res. 17(1): gmr16039855
DOI: 10.4238/gmr16039855
Research Article

Biodiversity stems from speciation, and species identification allows scientists to measure species biodiversity. However, some closely related species, particularly amphibians that choose to inhabit the same environment, are difficult to identify. Juvenile specimens of Limnonectes gyldenstolpei (Lg) and L. taylori (Lt) were used as models to study the speciation process in populations with a parapatric distribution. Samples of the two species were collected from six provinces in the north and northeast of Thailand. Inter-simple sequence repeat (ISSR) data of five loci showed 96 polymorphic bands and species-specific bands of the primers UBC811 (Lg) and UBC824 (Lt). There was limited genetic variation within the same population, 8% in Lg and 2% in Lt, whereas a high genetic variation was observed between populations from different provinces 90% and 97% in Lg and Lt, respectively. An unweighted pair-group method using arithmetic averages (UPGMA) tree was constructed for each population using Jaccard’s similarity efficient. The tree demonstrated genetic differentiation between the two species. Principal coordinates analysis also supported the UPGMA diagram by showing no clear clusters with close genetic distances. The results of the molecular variance analysis within the population were high, indicating that they were genetically similar, and that microhabitat is an important factor influencing genetic distribution. Overall, the present study proves the hypothesis that the distribution of the two species is in a Parapatric form and that the ISSR technique is inappropriate tool to study the differentiation of a species complex.

Genet. Mol. Res. 17(1): gmr16039856
DOI: 10.4238/gmr16039856

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