Population structure,genetic diversity,and sexual state of the rice brown spot pathogen Bipolaris oryzae from three Asian countries

Bipolaris oryzae causes brown spot in rice (Oryza sativa) inflicting substantial grain yield losses worldwide. Knowledge of the population structure, genetic diversity and sexual recombination of the fungal pathogen can help to implement effective disease management strategies. In this study, B. oryzae isolates sampled from Iran, the Philippines and Japan were analysed with 12 simple‐sequence repeat (SSR) markers, newly developed from the genome sequence of the fungus. Among the 288 B. oryzae isolates genotyped, 278 unique haplotypes were identified. High genotype numbers (richness) with even distribution (evenness) were found within the collection sites. Both mating types, MAT1‐1 and MAT1‐2, were present in each collection area, and the sexual state was induced under controlled conditions with production of viable ascospores. However, the tests of linkage disequilibrium rejected of the hypothesis of random mating. Discriminant analysis of principal components (DAPC) revealed that the B. oryzae collection formed three clusters, each consisting of isolates from different collection sites. Analysis of molecular variance (amova ) showed that genetic variation among clusters was 18.7%, with the rest of the variation distributed within clusters (R_ST = 0.187, P < 0.001). Statistically significant pairwise genetic differentiation was found between the clusters. These results show that Asian B. oryzae isolates are genetically diverse, and, overall, distributed in three groups. These findings will be helpful in managing the disease and guide the use of representative isolates needed for selection of resistant rice varieties.     

Use of PCR-based methodologies for the determination of DNA diversity between Saccharum varieties

Summary In this study, two PCR-based methodologies were evaluated for potential use in the determination of DNA diversity between 20 commercial sugarcane hybrids and 6 outgroup varieties of S. spontaneum, S. officinarum and hybrids from early in the genealogy. The first method involved PCR amplification of sugarcane DNA in the presence of random, decamer primers (RAPDs), while the second protocol utilized specific microsatellite and telomere sequences as primers. A total of 41 RAPD primers (356 loci) were screened across the varieties of which 15 (160 loci) were used in the calculation of DNA diversity (expressed% similarity). This varied from 61 to 95%, with most of the commercial varieties showing more than 80% similarity in their DNA. The RAPD data indicated that there had been a gradual decline in DNA diversity (84% reduction) from the early inter-specific crosses to the commercial hybrids, probably as a result of backcrossing and in-breeding strategies used in the previous 5 to 6 generations of sugarcane breeding. The microsatellite and telomere data produced a much greater range in DNA similarity values (25–91%), probably due to the fact that these primers detect highly variable regions of the genome. It is suggested that these specific primers would not be suitable for determination of DNA diversity, but could be used more effectively in the development of a methodology for routine, rapid identification of sugarcane varieties.     

Can genetic diversity be maintained during mass selection of the Chinese mitten crab,Eriocheir sinensis?

The Chinese mitten crab (Eriocheir sinensis) is an important aquaculture species and food source in Eastern Asia. This study assesses the changes in genetic diversity in successive generations of early‐ and late‐maturing strains of E. sinensis using 30 microsatellite markers with high polymorphism. The mean average number of alleles (N) in the founder population (G0), first generation (G1), second generation (G2) and third generation (G3) of the early‐maturing strain were 18.367, 14.800, 16.400 and 16.533, respectively; while in late‐maturing strain the values were 18.500, 16.267, 14.367 and 16.533 respectively. Likewise, there was a slight decline in average allelic richness (R_s) in the three successive generations. In both strains, the mean observed heterozygosity (H_o) remained relatively constant for the early‐maturing strain and the values were 0.655, 0.667, 0.685 and 0.705, respectively; and for the late‐maturing strain these were 0.665, 0.672, 0.688 and 0.702 respectively. Similarly, the expected heterozygosity (H_e) remained constant, ranging from 0.823 to 0.854. There was a decrease in effective population sizes (N_e) of the early‐maturing strain with successive generations: values were 492.2, 35.0, 134.7 and 193.2, respectively; while the values in the late‐maturing strain were 1268.5, 75.6, 111.5 and 97.2 respectively. All pairwise population distances were very close in both strains. In conclusion, these results suggest that mass selection of E. sinensis did not significantly diminish genetic diversity although there was a decline for the N_e. Therefore, it is important to maintain sufficient broodstock numbers and a large effective population when following a selective breeding programme.     

Genetic diversity of Puccinia striiformis from cereals in Alberta,Canada

Stripe rust of wheat caused by Puccinia striiformis f. sp. tritici has recently become a production problem on wheat in Alberta, Canada, and stripe rust of barley caused by P. striiformis f. sp. hordei occurs regularly. A total of 261 isolates of P. striiformis were collected from wheat, barley, Hordeum jubatum and triticale plants in Alberta, Canada from 2007 to 2012, and compared to isolates from other provinces and the USA. The genetic diversity of the pathogen was assessed using 11 simple sequence repeat (SSR) markers and by examining a length polymorphism in the ribosomal DNA (rDNA) intergenic spacer 1 (IGS1) region. A total of 28 SSR genotypes were detected within Alberta. The 13 genotypes common on wheat (P. striiformis f. sp. tritici) were distinct from the 15 genotypes common on barley (P. striiformis f. sp. hordei). Four SSR genotypes, two within each forma specialis, represented 85% of the isolates recovered. Genotypic diversity was low, population genetic analysis indicated a clonal structure, and the genotypes were widely dispersed. In both formae speciales, the dominant genotype varied between years. The second most common P. striiformis f. sp. hordei genotype was found to be more closely related to older P. striiformis f. sp. tritici genotypes from the USA than to other P. striiformis f. sp. hordei genotypes.     

Estimates of Heritability of Larval and Early Juvenile Growth Traits in Red Drum (Sciaenops ocellatus)

ABSTRACT

Eighteen to 29 families of red drum were generated via spontaneous spawning of multiple sets of three dams?×?two sires. In 2002, offspring from spawning events were grown in separate larval ponds to a mean TL of 30.4 mm. In 2003, offspring from spawning events were individually passive integrated transponder (PIT)-tagged and grown in “common-garden” tanks from 121.9 to 166.6 mm. Offspring in both experiments were assigned to parents based on genotypes at four microsatellite loci. Heritability estimates were 0.24?±?0.06 (larval TL) and 0.48?±?0.16 (juvenile-specific growth rate in length) and indicate a significant genetic component for both traits.     

Triploid Induction in Atlantic Cod (Gadus morhua L.) by the Use of Different Pressure Levels

Different levels of pressure were investigated to see if it was possible to induce triploidy at a lower pressure than previously used (600 bar) for Atlantic cod (Gadus morhua). Newly fertilized eggs were exposed to different levels of pressure: 400, 500, and 600 bar, and one control group (no pressure). Induction of triploidy occurred at each pressure level used in this experiment. Mean weight and length at the termination of the trial period was significantly lower, in the 400 bar group, compared to the other treatment groups. Microsatellite loci analysis revealed over 90% triploid outcome in each experimental group. Lower incidence of deformities was seen in the 400 bar group compared to the 500 and 600 bar groups. Overall this study demonstrated successful triploid induction at both low (400 bar) and medium (500 bar) pressures.     

Characterization and genomic annotation of polymorphic EST‐SSR loci in Litopenaeus vannamei shrimp

In the present work, EST‐SSR (expressed sequence tag‐simple sequence repeat) loci were obtained by screening 45 000 ESTs from the Pacific white shrimp Litopenaeus vannamei, which was available in a database of the ShEST (Shrimp EST Genome Project) consortium. Fifty‐two of 600 EST‐SSR loci were selected. From this total, 21 EST‐SSRs were polymorphic among 40 individuals and had their gene products ascribed. Two to 20 alleles per locus were detected and the observed heterozygosity ranged from 0.15 to 0.86. Eight loci presented a significant heterozygote deficit after the Bonferroni correction, which was attributed to null alleles. Seven loci were able to have their protein products, molecular functions and biological processes determined. Our results are promising for future studies that relate the levels of these gene polymorphisms with different biological responses to stress in aquaculture.     

Controlling yellow jackets with fipronil-based protein baits in urban recreational areas

ABSTRACT

The western yellow jacket, Vespula penyslvanica (Saussare), is a serious seasonal pest of outdoor venues in the western United States. In the spring, queens and low numbers of workers were captured in heptyl-butyrate-baited traps until early July, when the number of foragers dramatically increased. Microsatellite data suggest that 18 colonies were actively foraging within the park in 2012. Foragers from 11 different colonies were collected at one trap site. In 2012 and 2013, sufficient numbers of foragers were not captured until early August when baiting trials were initiated. Baits were prepared with canned chicken mixed with fipronil for a final concentration of 0.025%. In 2012, a single baiting provided >96% reduction of foragers for at least two months. A second baiting late in the season provided >80% reductions. In 2013, one baiting trial resulted in a 74% and a 93% reduction. A bait acceptance study was conducted in 2014 to test a bait consisting of the juices from canned chicken and 0.025% fipronil incorporated into a hydrogel, and provided a much longer lasting bait in the field.     

Genetic diversity within two Tunisian wild jirds: Meriones shawi and Meriones libycus (Rodentia,Gerbillinae)

Three Meriones species inhabit Tunisia, namely M. shawi, M. libycus and M. crassus, but little genetic data exist on these gerbils. We collected Meriones from eight localities in Tunisia, and obtained mitochondrial (cytochrome b) and nuclear (IRBP) gene sequence data for 37 and 13 specimens, respectively, belonging to two species: M. shawi and M. libycus. We also optimised three microsatellite markers previously described in M. unguiculatus to obtain a finer analysis of their genetic diversity and geographic structure, given their wide distribution. Phylogenetic inferences of cyt b and IRBP data for these species, in the context of other gerbillin data, corroborate their taxonomic affinities reported by previous studies. High cyt b haplotype diversity was observed in both species (25 haplotypes in 29 and 27 sequences for M. shawi and M. libycus, respectively) with little geographical structure for M. shawi but three divergent groups in M. libycus. The average microsatellite diversity within each population was high (H_O ≥ 0.6, H_E ≥ 0.8) with M. libycus populations attaining the highest values. Population differentiation was moderate for several population pairs (F_st ≥ 0.1), the highest being between M. shawi populations. However, genetic distance among populations was not significantly correlated with geographic distance in either M. shawi or M. libycus. Our results contribute to a better characterisation of Tunisian Meriones species, suggesting high geographic structure in mtDNA of M. libycus populations within North Africa.