Assessing sequence variation, haplotype analysis and molecular characterisation of aspartate kinase2 (ask2) gene regulating methionine biosynthesis in diverse maize inbreds.

Traditional maize grain is deficient in methionine, an essential amino acid required for proper growth and development in humans and poultry birds. Thus, development of high methionine maize (HMM) assumes great significance in alleviating malnutrition through sustainable and cost-effective approach. Of various genetic loci, aspartate kinase2 (ask2) gene plays a pivotal role in regulating methionine accumulation in maize. Here, we sequenced the entire ask2 gene of 5394 bp with 13 exons in five wild and five mutant maize inbreds to understand variation at nucleotide level. Sequence analysis revealed that an SNP in exon-13 caused thymine to adenine transversion giving rise to a favourable mutant allele associated with leucine to glutamine substitution in mutant ASK2 protein. Gene-based diversity analysis with 11 InDel markers grouped 48 diverse inbreds into three major clusters with an average genetic dissimilarity of 0.570 (range, 0.0-0.9). The average major allele frequency, gene diversity and PIC are 0.693, 0.408 and 0.341, respectively. A total of 45 haplotypes of the ask2 gene were identified among the maize inbreds. Evolutionary relationship analysis performed among 22 orthologues grouped them into five major clusters. The number of exons varied from 7 to 17, with length varying from 12 to 495 bp among orthologues. ASK2 protein with 565 amino acids was predicted to be in homo-dimeric state with lysine and tartaric acid as binding ligands. Amino acid kinase and ACT domains were found to be conserved in maize and orthologues. The study depicted the presence of enough genetic diversity in ask2 gene in maize, and development of HMM can be accelerated through introgression of favourable allele of ask2 into the parental lines of elite hybrids using molecular breeding.

When is the allele-sharing dissimilarity between two populations exceeded by the allele-sharing dissimilarity of a population with itself?

Allele-sharing statistics for a genetic locus measure the dissimilarity between two populations as a mean of the dissimilarity between random pairs of individuals, one from each population. Owing to within-population variation in genotype, allele-sharing dissimilarities can have the property that they have a nonzero value when computed between a population and itself. We consider the mathematical properties of allele-sharing dissimilarities in a pair of populations, treating the allele frequencies in the two populations parametrically. Examining two formulations of allele-sharing dissimilarity, we obtain the distributions of within-population and between-population dissimilarities for pairs of individuals. We then mathematically explore the scenarios in which, for certain allele-frequency distributions, the within-population dissimilarity - the mean dissimilarity between randomly chosen members of a population - can exceed the dissimilarity between two populations. Such scenarios assist in explaining observations in population-genetic data that members of a population can be empirically more genetically dissimilar from each other on average than they are from members of another population. For a population pair, however, the mathematical analysis finds that at least one of the two populations always possesses smaller within-population dissimilarity than the value of the between-population dissimilarity. We illustrate the mathematical results with an application to human population-genetic data.

Genetic diversity among cassava genotypes (Manihot esculenta crantz) collected in the south-central mesoregion of the state of Mato Grosso-Brazil

The aim of this research was to evaluate the genetic divergence between 164 genotypes of Manihot esculenta from the South-Central mesoregion of the State of Mato Grosso. The genotypes are from projects conducted by the Laboratory of Genetic Resources & Biotechnology of the University of the State of Mato Grosso, Cáceres-Mato Grosso (UNEMAT), and the Brazilian Public Agricultural Research Corporation - Agrosilvopastoral (EMBRAPA). The agronomic descriptors evaluated were plant height, height of first branching, branching levels, weight of the aerial part of the plant, total weight of the plant, number of roots per plant, average weight of roots per plant, yield of commercial roots, yield of non-commercial roots, number of rotten roots per plant and harvest index. For the analysis of genetic divergence, multivariate analysis based on the standardized Euclidean mean distance was employed, later performing the Hierarchical UPGMA and Tocher Optimization agglomerative methods. The degree of preservation of the genetic distances in the dendrogram was verified using the Cophenetic Correlation Coefficient. The Singh criterion was used to quantify the relative contribution of characteristics to genetic divergence. The genotypes presented genetic dissimilarity for the evaluated characteristics and based on the results of the dissimilarity matrix and groupings, it is recommended the crossings between the genotypes allocated in group II with the genotype allocated in group V, for the development of segregated populations with high genetic variability.

Artificial neural networks and genetic dissimilarity among saladette type dwarf tomato plant populations.

Studies have shown that dwarf plants have the potential for use in obtaining hybrids. The aim of this study was to evaluate the agronomic potential and genetic dissimilarity of saladette type dwarf tomato plant populations through the use of artificial neural networks (ANNs). The following traits were analyzed: mean fruit weight, transverse and longitudinal fruit diameter, fruit shape, pulp thickness, locule number, internode length, soluble solids content, and ß-carotene, lycopene, and leaf zingiberene contents. A dendrogram obtained by the unweighted pair-group method with arithmetic mean (UPGMA) and Kohonen self-organizing maps (SOM) agreed in the distinction of the BC1F3 populations from the dwarf donor parent. SOM was more consistent in identifying the genetic similarities among the BC1F3 dwarf tomato plant populations and allowed for the determination of weights of each variable in the cluster formation. The UFU SDi 13-1 BC1F3 population was revealed to be a promising option for obtaining saladette type dwarf tomato plant lines.

Dissimilarity of individual microsatellite profiles under different mutation models: Empirical approach.

Microsatellites (simple sequence repeats, SSRs) still remain popular molecular markers for studying neutral genetic variation. Two alternative models outline how new microsatellite alleles evolve. Infinite alleles model (IAM) assumes that all possible alleles are equally likely to result from a mutation, while stepwise mutation model (SMM) describes microsatellite evolution as stepwise adding or subtracting single repeat units. Genetic relationships between individuals can be analyzed in higher precision when assuming the SMM scenario with allele size differences as a proxy of genetic distance. If population structure is not predetermined in advance, an empirical data analysis usually includes (a) estimating proximity between individual SSR profiles with a selected dissimilarity measure and (b) determining putative genetic structure of a given set of individuals using methods of clustering and/or ordination for the obtained dissimilarity matrix. We developed new dissimilarity indices between SSR profiles of haploid, diploid, or polyploid organisms assuming different mutation models and compared the performance of these indices for determining genetic structure with population data and with simulations. More specifically, we compared SMM with a constant or variable mutation rate at different SSR loci to IAM using data from natural populations of a freshwater bryozoan Cristatella mucedo (diploid), wheat leaf rust Puccinia triticina (dikaryon), and wheat powdery mildew Blumeria graminis (monokaryon). We show that inferences about population genetic structure are sensitive to the assumed mutation model. With simulations, we found that Bruvo's distance performs generally poorly, while the new metrics are capturing the differences in the genetic structure of the populations.

Genetic differentiation between bitter and sweet asafetida plants using ISSR markers.

Bitter (Ferula pseudalliacea) and sweet (Ferula assa-foetida) asafetida (Apiaceae family) are well-known economic and medicinal herbs owing to their gum. This study investigates genetic differentiation of F. pseudalliacea and F. assa-foetida using ISSR markers, to determine the effective primer and to assess the possibility of separating sweet and bitter plant populations from each other. Results showed that among 22 primers, eight markers reproduced obvious DNA patterns and revealed 234 scorable DNA bands. ISSR-16 and ISSR-55 primers had better performance than other primers according to the number of bands, PIC and Marker Index. Bitter population showed polymorphic loci (224), percentage of polymorphic loci (95.73%) and observed number of alleles (1.96 ± 0.2), while sweet populations showed the amount of these parameters as 218, 93.16% and 1.93 ± 0.25, respectively. Estimated Gst of sweet population was 0.09 and Gst of bitter population was 0.06. Comparing gene flow in bitter and sweet populations showed a lower level of gene flow between sweet populations (Nm = 4.93) compared to bitter ones (Nm = 7.89). Within group genetic similarity of sweet asafetida population was higher than between group variation of bitter and sweet populations. The highest similarity was observed between bitter populations (0.95). The highest genetic dissimilarity was also estimated between bitter and sweet populations (0.08). Cluster analysis grouped four studied populations into 13 clusters using Jaccard's similarity coefficient and UPGMA method. Principal coordinate analysis showed that 61.02% of total variance was explained using three components and it could completely separate populations as well as cluster analysis. These grouping correspond nearly with geographical distribution. Analysis of molecular variance showed that genetic variation within populations (87%) was more than among populations (13%). The results indicated that ISSR marker is suitable to investigate genetic diversity of asafetida populations and could separate populations of the same genera with similar germplasm.

[Correlation between genetic differences of mates and pathogenicity of Schistosoma japonicum in definitive host].

OBJECTIVE: To explore the correlation between the genetic dissimilarity and heterozygosity of mates and the pathogenicity of Schistosoma japonicum in the definitive host. METHODS: By using seven microsatellite loci markers, S. japonicum genotyping of sixteen pairs randomly mated was performed, the genetic dissimilarity and heterozygosity were calculated between the mates, and the correlation between the genetic dissimilarity and heterozygosity of the mates and the pathogenicity of S. japonicum in the definitive host was evaluated. RESULTS: There was a significant correlation between the genetic similarity of S. japonicum mates and the mean number of eggs per worm pair in the liver and intestinal tissue (r = 0.501 6, P < 0.05; r = 0.796 5, P < 0.01, respectively) and the hatching rate of deposited eggs in the liver (r = 0.508 3, P < 0.05), respectively. There was no correlation between the genetic similarity of the mates and hepatosplenomegaly per worm pair (r = 0.109 5, P > 0.05; r = 0.265 3, P > 0.05, respectively) and the average diameter of granuloma in the liver (r = -0.272 7, P > 0.05), respectively. There was no correlation between the heterozygosity of the mates and all the pathological parameters of S. japonicum in the definitive host (P > 0.05). CONCLUSIONS: There is the correlation between the genetic dissimilarity of the mates and the pathogenicity of S. japonicum in the definitive host, and the genetic dissimilarity is greater, pathogenicity is weaker. There is no correlation between heterozygosity of the mates and the pathogenicity of S. japonicum in the definitive host.

Correlation between genetic differences of mates and pathogenicity of Schis-tosoma japonicum in definitive host / 中国血吸虫病防治杂志

Objective To explore the correlation between the genetic dissimilarity and heterozygosity of mates and the patho?genicity of Schistosoma japonicum in the definitive host. Methods By using seven microsatellite loci markers,S. japonicum genotyping of sixteen pairs randomly mated was performed,the genetic dissimilarity and heterozygosity were calculated between the mates,and the correlation between the genetic dissimilarity and heterozygosity of the mates and the pathogenicity of S. japon?icum in the definitive host was evaluated. Results There was a significant correlation between the genetic similarity of S. ja?ponicum mates and the mean number of eggs per worm pair in the liver and intestinal tissue (r = 0.501 6 ,P 0.05;r=0.265 3,P>0.05,respectively)and the average diameter of granuloma in the liver(r=-0.272 7,P>0.05),respec?tively. There was no correlation between the heterozygosity of the mates and all the pathological parameters of S. japonicum in the definitive host(P > 0.05). Conclusions There is the correlation between the genetic dissimilarity of the mates and the pathogenicity of S. japonicum in the definitive host,and the genetic dissimilarity is greater,pathogenicity is weaker. There is no correlation between heterozygosity of the mates and the pathogenicity of S. japonicum in the definitive host.

Effects of genetic similarity on the life-history strategy of co-infecting trematodes: are parasites capable of intrahost kin recognition?

For conspecific parasites sharing the same host, kin recognition can be advantageous when the fitness of one individual depends on what another does; yet, evidence of kin recognition among parasites remains limited. Some trematodes, like Coitocaecum parvum, have plastic life cycles including two alternative life-history strategies. The parasite can wait for its intermediate host to be eaten by a fish definitive host, thus completing the classical three-host life cycle, or mature precociously and produce eggs while still inside its intermediate host as a facultative shortcut. Two different amphipod species are used as intermediate hosts by C. parvum, one small and highly mobile and the other larger, sedentary, and burrow dwelling. Amphipods often harbour two or more C. parvum individuals, all capable of using one or the other developmental strategy, thus creating potential conflicts or cooperation opportunities over transmission routes. This model was used to test the kin recognition hypothesis according to which cooperation between two conspecific individuals relies on the individuals' ability to evaluate their degree of genetic similarity. First, data showed that levels of intrahost genetic similarity between co-infecting C. parvum individuals differed between host species. Second, genetic similarity between parasites sharing the same host was strongly linked to their likelihood of adopting identical developmental strategies. Two nonexclusive hypotheses that could explain this pattern are discussed: kin recognition and cooperation between genetically similar parasites and/or matching genotypes involving parasite genotype-host compatibility filters.

Extra-group mating increases inbreeding risk in a cooperatively breeding bird.

In many cooperatively breeding species, females mate extra-group, the adaptive value of which remains poorly understood. One hypothesis posits that females employ extra-group mating to access mates whose genotypes are more dissimilar to their own than their social mates, so as to increase offspring heterozygosity. We test this hypothesis using life history and genetic data from 36 cooperatively breeding white-browed sparrow weaver (Plocepasser mahali) groups. Contrary to prediction, a dominant female's relatedness to her social mate did not drive extra-group mating decisions and, moreover, extra-group mating females were significantly more related to their extra-group sires than their social mates. Instead, dominant females were substantially more likely to mate extra-group when paired to a dominant male of low heterozygosity, and their extra-group mates (typically dominants themselves) were significantly more heterozygous than the males they cuckolded. The combined effects of mating with extra-group males of closer relatedness, but higher heterozygosity resulted in extra-group-sired offspring that were no more heterozygous than their within-group-sired half-siblings. Our findings are consistent with a role for male-male competition in driving extra-group mating and suggest that the local kin structure typical of cooperative breeders could counter potential benefits to females of mating extra-group by exposing them to a risk of inbreeding.

Variabilidade em matrizes de acessos de espinheira-santa / Variability in matrices of espinheira-santa accessions

Maytenus ilicifolia e M. aquifolium são espécies nativas do Brasil, popularmente conhecidas como espinheira-santa, sendo indicadas para gastrite e para úlcera estomacal. A Embrapa Clima Temperado e a Universidade Federal de Pelotas (UFPel) mantêm um banco de germoplasma destas espécies. Com o objetivo de identificar a variabilidade fenotípica para alguns caracteres morfológicos em matrizes de espinheira-santa, estimar a dissimilaridade e agrupar os acessos através de análises multivariadas, 105 acessos foram caracterizados morfologicamente. Foram avaliados os caracteres comprimento e largura de fruto, número de sementes por fruto, comprimento e largura de folha, relação comprimento/largura de folha e número de espinhos por folha. Foi estimada a distância euclidiana e os acessos foram agrupados pelo método de otimização de Tocher. Foi observada uma ampla variabilidade para todos os caracteres analisados. O número de espinhos por folha foi o caráter que mais contribuiu para a divergência. Os caracteres morfológicos permitiram separar os acessos em sete grupos. A maior dissimilaridade foi entre os acessos 57 (M. ilicifolia) e 91 (M. aquifolium). Não foi evidenciada uma separação de acordo com a localização geográfica dos acessos. Na análise de agrupamento foram identificados dois grupos que apresentavam tanto acessos de M. ilicifolia quanto de M. aquifolium, o que indica proximidade filogenética entre estas espécies.

Maytenus ilicifolia and M. aquifolium are native Brazilian species popularly known as espinheira-santa, being indicated for gastritis and stomach ulcer. Embrapa Clima Temperado and Universidade Federal de Pelotas (UFPel) keep a gene bank of these species. With the objective of identifing phenotypic variability for some morphological characters in matrices of espinheira-santa, estimating dissimilarity and clustering accessions through multivariate analysis, 105 accessions had been morphologically characterized. The characteristics evaluated were fruit length, fruit width, number of seeds per fruit, leaf length, leaf width, leaf length/leaf width ratio and number of thorns per leaf. The euclidean distance was estimated and accessions were clustered by Tocher optimization method. A wide variability for all the characteristics analyzed was observed. The number of thorns per leaf was the characteristics that more contributed to the divergence. The morphological characteristics enabled to separate the accesses in seven clusters. The higher dissimilarity was between accessions 57 (M. ilicifolia) and 91 (M. aquifolium). There was no evidence of a separation in accordance to the geographic localization of the accessions. In the clustering analysis were identified two clusters that had accessions of both species, M. ilicifolia and M. aquifolium, indicating phylogenetic relatedness between these species.