GENETIC VARIABILITY IN Sechium spp. (Cucurbitaceae) EVALUATED WITH AFLP MARKERS

There are few studies in Mexico aimed at evaluating the genetic variability of Sechium spp. Despite certain biological variants are reported with very high potential to develop antineoplastic supplements to treat public health conditions. Using the Amplified Fragment Length Polymorphism (AFLP) technique, the genetic variability of a sample of 95 accessions of three species of Sechium (S. edule, S. chinantlense, S. compositum) was evaluated, with leaf DNA from the Banco Nacional de Germoplasma de Sechium edule en Mexico. Four combinations of AFPL were applied (EcoRI + ACC/MseI + CAC, EcoRI + ACC/MseI + CAT, EcoRI + ACC/MseI + CGC, and EcoRI + ACC/MseI + CGG). DNA samples were classified into three groups based on the flavour of the fruit (sweet, neutral, bitter). An average of 47.91% polymorphism, 0.16 heterozygosity, 32.83 number of polymorphic bands, and a zero Wright fixation index (Fst) was obtained. The evidence showed that the domesticated accessions (sweet, neutral) were separated from the bitter-taste genotypes. A monophyletic tree was generated with the genetic distance matrix and the neighbour-joining methodology. Analyses showed S. edule as the root taxon, deriving S. compositum and S. chinantlense as subgroups, and suggesting that there is not enough differentiation to treat them as separate species. The evaluated sample showed that there is no apparent reproductive barrier for genetic cross breeding. Genotypes behaved as a complex with evolutive dynamism; that genetic complexity would allow the design of new variants.

Genetic polymorphism of myostatin (MSTN) in Nigerian sheep breeds

Myostatin (MSTN) also known as growth differentiation factor 8 (GDF-8) has been implicated to play an important role in growth regulation, and it is a candidate gene in marker assisted selection (MAS). This study was carried out to identify the polymorphism of MSTN gene as a genetic marker for growth traits in Nigerian indigenous sheep. Genomic DNA (gDNA) was extracted from blood samples of Balami, Yankasa, Uda and West African Dwarf (WAD) breeds of sheep. Parts of 5’UTR, intron and exon1 (614bp) was amplified using a primer sequence designed by FastPCR-primer software. The amplicons were digested with restriction enzyme HaeIII and the fragments produced were stained with luminescent dye and run on gel electrophoresis. The genetic structure of the sampled population was investigated after analysis with POPGENE32 software. The HaeIII digested results showed that Myostatin has three polymorphs (AA, AB and BB), controlled by two alleles (A and B), with B having a higher allelic frequency (82.84%) and BB genotype has the highest frequency of 73%. The sampled population showed a deviation from Hardy-Weinberg equilibrium (p<0.05) while the F-statistics results of the Nigerian breeds of sheep showed the breeds are genetically identical (33.40%) within them. The genetic distance matrix established that Uda and Yankasa show the greatest distant (3.00%) while Uda and WAD are almost identical (99.85%). The four breeds of sheep studied showed polymorphism for Myostatin gene in the intron 1 and exon 1. Myostatin, therefore, could be considered a candidate gene for MAS

Population Structure of 93 Varieties of Rice ( Oryza Sativa L. subsp. Hsien Ting) in Qinba, China

BackgroundThe Qinba region is the transition region between indica and japonica varieties with a long history of indica varieties planting. 72,824 SNPs data based on GBS method, 48 pairs core primers of SSRs, and 15 agronomic traits were employed to explore the population structure of 93 rice varieties. The Mantel test was used to analyze the distance matrix generated using NlaIII-GBS only, MseI-GBS only, by combining NlaIII-GBS and MseI-GBS data and SSR.ResultIn this study, a total of 379 alleles were obtained using 48 pairs core primer of SSR, encompassing an average of 8.0 alleles per primer. The PPB and PIC was 88.65% and 0.77, respectively. Among these, RM278 possess the highest TNB and NPB, and the PPB in 29 pairs of SSR markers was 100%. RM176 showed the highest PIC. MAF was set to 0.05, and 39,872, 35,547 and 67,621 SNPs were obtained via NlaIII-GBS only, MseI-GBS only, and merged NlaIII-GBS and MseI-GBS data, respectively. The IBS genetic similarity coefficient average was 0.74. The results showed that the correlation between the genetic distance matrix based on NlaIII-GBS and MseI-GBS was the largest (R2=0.88), followed by NlaIII-GBS and SSR (R2=0.35), then by merged NlaIII-GBS and MseI-GBS data and SSR (R2=0.33), and the smallest by MseI-GBS and SSR (R2=0.27). The results showed that the 93 rice varieties could be clustered into two subgroups. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations. Tajima’s D value was 1.66, and the FST between the two populations was 0.61, and the Nm was 0.16.ConclusionThe population genetic variation explained by SNP was larger than that explained by SSR. Through cluster analysis, the 93 samples were divided into 2 subgroups, with more than 97% of the samples clustered into one subgroup. The gene flow of 93 samples used in this study is larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of indica varieties in the Qinba region. However, the genetic structure of the rice population is simple and lacked rare alleles.

Genetic diversity among 435 barley accessions based in morpho-agronomical characteristics under irrigation in the Brazilian savannah

The success of barley (Hordeum vulgare L.) cultivation and its adaptation to cropping systems relies on the knowledge and utilization of existing variability in germplasm banks. The objective of this work was to analyse diversity among pre-selected barley accessions to organize a working collection and to identify genotypes for a breeding program for irrigated barley in the Brazilian Savannah. The field experiment was conducted under irrigation in Planaltina, DF, Brazil. The plant population consisted of 433 accessions plus BRS 180 and BRS 195 as checks. The accessions were evaluated using fifteen morpho agronomic descriptors, in which 11 quantitative and four discrete. The interpolated control design was used for the statistical analysis. A genetic distance matrix was calculated using Gower’s coefficient. From the matrix, a grouping analysis was conducted, using the optimizing Tocher method and the graphic dispersion distance. The genetic distances varied between 0.025 and 0.572, with a mean of 0.256. The accessions were distributed in 18 groups by the Tocher method, which was directly related to the graphic dispersion. The existing genetic divergence in the collection under study helped the definition of accessions in crossing blocks from breeding programs directed to the savannah environment.

A geometrical framework for f –statistics

A detailed derivation of the f–statistics formalism is made from a geometrical framework. It is shown that the f–statistics appear when a genetic distance matrix is constrained to describe a four population phylogenetic tree. The choice of genetic metric is crucial and plays an outstanding role as regards the tree–like–ness criterion. The case of lack of treeness is interpreted in the formalism as presence of population admixture. In this respect, four formulas are given to estimate the admixture proportions. One of them is the so–called f4–ratio estimate and we show that a second one is related to a known result developed in terms of the fixation index FST. An illustrative numerical simulation of admixture proportion estimates is included. Relationships of the formalism with coalescence times and pairwise sequence differences are also provided.

Genetic divergence in Tunisian castor bean genotypes based on trap markers

In the present study, the representatives of the genus Ricinus communis collected from 12 different parts of Tunisia were differentiated by the DNA fingerprinting patterns using 30 TRAP primers. The efficacy of the TRAP technique in this study is further supported by the obtained PIC values of the primers used in the analysis. PCR amplification of DNA using 30 primers for TRAP analysis produced 490 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 3 (TRAP 04 x arb 1, TRAP 22 x arb 3 and TRAP 23 x arb 3) to 13 (TRAP 56 x arb 2), and the amplicon size ranged from 100 to 1600 bp. Of the 490 amplified bands, 377 were polymorphic, with an average of 5.71 polymorphic bands per primer. To determine the level of polymorphism in the analysed group of Tunisian castor genotypes polymorphic information content (PIC) was calculated. The lowest values of polymorphic information content were recorded for TRAP 10 x arb 1 (0.555) and the highest PIC values were detected for TRAP 44 x arb 2 (0.961) with an average of 0.770. A dendrogram was constructed from a genetic distance matrix based on profiles of the 30 TRAP primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 56 Tunisian castor genotypes were clustered into five main clusters. Moreover, functional TRAP markers would be efficiently useful in genetic studies for castor genetic improvement.

Agromorphological and molecular analysis discloses wide genetic variability in sunflower breeding lines from USDA, USA

The present study investigates genetic divergence among 84 fertility restorers and 32 cytoplasmic male sterile (CMS) lines of sunflower augmented from USDA, USA along with the popular Indian parental lines using simple sequence repeats (SSR). Thirty-nine polymorphic SSR primers produced 139 alleles with an average of 3.56 alleles per locus. The polymorphic information content ranged from 0.23 to 0.69 with an average of 0.45. The average genetic distance was 0.45 and 0.42 for the R and CMS lines, respectively. Dendrogram based on the dissimilarity coefficient matrix grouped the CMS and R lines into separate clusters except for Cluster A which consisted of all CMS lines along with five R lines. Genetic distance matrix estimated from three sets of mitochondrial primers (BOX, ERIC and REP) grouped the 32 CMS lines into eight clusters. The results suggest the existence of considerable genetic diversity among the restorer and CMS lines of sunflower obtained from USDA, USA.

Elit Domuz Ayrığı (Dactylis glomerata L.) Genotiplerinde Genetik Çeşitliliğin SSR Markörleri ile Belirlenmesi

Orchardgrass (Dactylis glomerata L.) is an economically important, and widely cultivated perennial forage grass. The aim of this study was to determine the genetic diversity and genetic relationship among the orchardgrass breeding lines developed in Aegean Agricultural Research Institute, using simple sequence repeat (SSR, microsatellite) molecular markers. The genetic diversity of 32 orchardgrass was assessed using a set of 24 SSR markers. SSR primer pair combinations yielded 126 alleles for all genotypes. The number of alleles per locus ranged from three to seven with an average of 5.25 alleles across 24 loci. The alleles size ranged from 101 to 354 and the polymorphism rate was 100%. Jaccard genetic distance coefficient varied from 0.21 to 0.84 among genotypes. The degree of genetic diversity among the genotypes was high. Total number of rare alleles was 28 alleles across 126 loci. Dendrogram constructed using neighbor-joining analysis based on Jaccard genetic distance matrix were clustered into three main groups A, B and C. Group A was the largest group contained 15 genotypes, while B had 13 genotypes originated mainly from same region. The group C was the smallest group contained genotypes originated from northern part of Turkey. The molecular analysis revealed that a significant genetic variation existed in this orhardgrass collection, and the genotypes studied have potential for ensure rich genetic resources in orchardgrass breeding program. In addition to this, it was concluded that SSR markers are suitable markers for the molecular identification of different orchardgrass genotypes.

Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes

In the present study, 111 castor genotypes were differentiated by the DNA fingerprinting patterns using 37 SCoT primers. The selected primers amplified DNA fragments across the 111 genotypes studied with the number of amplified fragments varying from 3 (SCoT 14) to 10 (SCoT 30 and SCoT 44) and the amplicon size varied from 100 to 3000 bp. Of the 246 amplified bands, 186 were polymorphic with an average of 5.03 fragments per primer. The percentage of polymorphic bands ranged from 57.14 % (SCoT 34) to 100.00 % (SCoT 28 and SCoT 33) with an average of 77.50%. The polymorphic information content (PIC) values varied from 0.372 (SCoT 14) to 0.818 (SCoT 30) with an average of 0.677. A dendrogram was constructed from a genetic distance matrix based on profiles of the 37 SCoT primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 111 diverse accessions of castor was clustered into two main clusters (1 and 2). The first cluster were subdivided into two subclusters (1a and 1b). Subclaster 1a contained 11 genotypes of castor and subclaster 1b contained 6 genotypes of castor. Subclaster 2 were subdivided into two subclusters (2a and 2b). Subclaster 2a contained 44 castor genotypes and subclaster 2b contained 50 castor genotypes. Results showed the utility of SCoT markers for estimation of genetic diversity of castor genotypes leading to genotype identification.

BARKODING DNA BURUNG ELANG (FAMILI ACCIPITRIDAE) DI INDONESIA

The cytochrome c oxidase subunit I (COI) gene is a reprensentative of all the protein-coding genes of the mitochondrial DNA genome that has been widely used as an animal species identification tool. In this study, 86 sequences of DNA barcodes of members of the family Accipitridae in Indonesia including Nisaetus bartelsi, Nisaetus cirrhatus, Haliaeetus leucogaster, Spilornis cheela, Haliastur indus, and 11 sequences from Genbank were examined. Each species was confirmed through the Basic Local Alignment Search Tool (BLAST). The construction of phylogeny trees based on COI gene sequences was performed by the Neighbors-joining method where the calculation of the genetic distance matrix with the Kimura 2-parameter model was implemented in pairwise distance calculation in the Mega version 6.05 programe. The results of the analysis showed that the divergence within species ranged from 0 to 0.3% (0.13 ± 0.12%), between species ranged from 1.6 to 18.5% (12.8 ± 3.73%), between genera ranged from 13 to 18.6%, and the average in the Accipitridae Family was 11.8%. Therefore, it could form clusters in each species cohesively and clearly separated between the taxa analyzed.