Phenotypic and Genetic Diversity Evaluation of Sengon (Falcataria moluccana (Miq.) Barneby & JW Grimes) from Solomon Provenance on Progeny Trial in Cirangsad Experimental Forest, West Java

Initial evaluation of phenotypic variability and genetic diversity was conducted on the progeny test of 2 years-old sengon from Solomon provenance, which derived from nine families of mother tree and were then planted in 4 blocks in the Cirangsad Experimental Forest. Phenotypic assessment on eight traits was conducted on 36 trees using a scoring system, while genetic diversity of 15 selected individuals which represented high and low-score phenotypic traits was analyzed using 5 selected RAPD primers. The result on phenotypic assessment showed that family 3 (57.25 points) has the highest average score of phenotypic quality and family 4 has the lowest average score (7.50 points). Furthermore, genetic analysis showed that the low-scoring sengon population had a greater mean genetic diversity (He = 0.2535) than the high-score population (He = 0.2345). The analysis of molecular variance (AMOVA) revealed a significant genetic differences (p-value < 0.001) among high and low-score populations and the dendrogram of genetic distance revealed clustering of individuals having similar superior phenotypic against those having non-superior, indicating the selection based on phenotypes in this study had succeeded in pooling the good quantitative alleles in the selected population. This evaluation results can be used as a reference in determining the best families to produce superior sengon (from Solomon provenance) offspring in the future that have desired adaptability, productivity, and diversity.

Population structure of Moniliophthora perniciosa in the main cacao producing departments of Colombia

The witches’ broom (Moniliophthora perniciosa) is considered as one of the main threats for cacao production and, consequently, for chocolate production worldwide.. In this work, the genetic diversity and population structure of M. perniciosa were analyzed for 59 isolates collected in five departments of Colombia and using 10 microsatellite markers. Analyses revealed 35 multilocus genotypes (MLGs) and clonal populations structure according to linkage disequilibrium analysis. One of the objectives of this study was to determine whether populations were differentiated by geographic origin or T. cacao host genotype. Analysis of molecular variance, Discriminant Analysis of Principal Components (DAPC) and Bruvo genetic distance suggested that the genetic structure was driven by geographic origin and not by T. cacao genotype. The results of this study were consistent with previous findings obtained in other cocoa producing countries. Important insights were discussed regarding the dispersal patterns of the pathogen in Colombia and the genetic change of its populations due to different environmental conditions.

Genetic Profiling of Sida rhombifolia Originated from Several Indonesian Ethnicities Based on Sequence-Related Amplified Polymorphism Markers

Sida rhombifolia is one of wild flowering plants that grows easily in many habitats with moderate humidity, with some usefulness in traditional medicine. Genetic characterization of Sida rhombifolia accessions originated from 12 ethnicities of Indonesia was analyzed based on Sequence-Related Amplified Polymorphism (SRAP) Markers. The genomic DNA were extracted from leaf samples and then were characterized by using the SRAP marker system according to Li and Quiros (2001). Nine pairs of SRAP primer resulted high polymorphic bands and were used in the genetic profiling. The data analysis was performed using GenAlEx to calculate genetic distance, Principal coordinate analysis, and Analysis of Molecular Variance (AMOVA), also using POPGENE to assess genetic diversity (Hs and Ht) and Nm to predict gene flow among populations. The coordinate analysis showed that the accessions originated from ethnicities along Wallacean line tend to differ genetically from most other locations. However, the results of analysis of molecular variance suggested that there were only slight differences (0.1%) found between ethnicities, while most genetic variances (99.9%) were found mostly among accessions within populations. The results suggested that there was an extensive genetic flow and plant spreading among Sida rhombifolia plant populations, resulting more homogenous genetic characters among most populations, while high diversity within population. The calculation of the number of migration (Nm = 1.7341) confirmed that the high rate of gene flow had occurred between populations.

Phylogeography and population differentiation in Hepatozoon canis (Apicomplexa: Hepatozoidae) reveal expansion and gene flow in world populations

Background Hepatozoon canis is a protozoan transmitted to dogs and other wild carnivores by the ingestion of ticks containing mature oocysts and is considered the principal cause of canine hepatozoonosis in the world. Here, we examined ribosomal RNA 18S gene sequence variation to determine the genetic differences and phylogeographic diversity of H. canis from various geographical areas around the world. Methods We used 550 publicly available sequences of H. canis from 46 countries to assess haplotype relationships, geographical structure, genetic diversity indices, and relationships among populations. We performed neutrality tests and pairwise comparisons of fixation index (FST) values between groups and pairwise comparisons of FST values between populations. To determine whether populations are structured, analyses of molecular variance (AMOVAs) and spatial analysis of molecular variance (SAMOVA) were performed. Results The dataset of H. canis yielded 76 haplotypes. Differentiation among populations indicated that there is no phylogeographical structure (GST = 0.302 ± 0.0475). Moreover, when samples were grouped by continents a significant FST was obtained, meaning that populations were genetically differentiated. The AMOVA showed that 57.4% of the genetic variation was explained by differences within populations when all locations were treated as a single group and revealed that there is no population structure when populations are grouped into two, three, and four groups (FCT, p > 0.05), suggesting that dispersal between populations is high. SAMOVA revealed significant FCT values for groups K = 5. The Tajima’s D and Fu’s Fs show that populations have undergone recent expansion, and the mismatch distribution analysis showed population expansion (multimodal distribution). Conclusions The current molecular data confirmed that H. canis does not show phylogeographic or population structure. The haplotypes exhibit low genetic differentiation, suggesting a recent expansion due to gene flow among populations. These results provide pivotal information required for future detailed population genetic analysis or to establish control strategies of this parasite. Graphical abstract

Evaluation of the genetic variability of Ophrys insectifera L. populations growing in Belarus using molecular iPBS markers

An analysis of genetic heterogeneity was performed for two populations of Ophrys insectifera L. located in the Berezinsky Biosphere Reserve and the Verkudy village. The species are critically endangered (CR). The analysis of data obtained using iPBS markers detected the higher risk of extinction of the population in the Berezinsky Biosphere Reserve than the population from the Verkudy village, since the level of population genetic heterogeneity from the Verkudy is higher compared to the Berezinsky Biosphere Reserve. Molecular variance analysis (AMOVA) and other parameters of genetic variation showed the major fraction of intrapopulation variation (64 %, Gst = 0.26). Principal Coordinates Analysis (PCoA) revealed two groups that coincided with natural populations, and confirmed a larger genetic heterogeneity in the population from the Verkudy.

Assessment of genetic differentiation of populations by analysis of molecular variance (analytical review)

Different approaches to using the analysis of molecular variance (AMOVA) to assess the genetic differentiation of populations have been compared in the research. Data on 11 microsatellite loci of 84 bulls of seven breeds were used. The results were compared for three options of the AMOVA module of the GenAlEx 6.502 program: the allele distance matrix (calculated FST(W&C)(=θ) statistics – variant AMOVA1); the genotype distance matrix (ΦPT– AMOVA2); and the allele size difference matrix (RST– AMOVA3). Similar summary estimates of the genetic differentiation of breeds were obtained: FST(W&C)= 0.108, ΦPT= 0.115, RST= 0.110 (all with pperm≤ 0.001). Between the estimates of FST(W&C)and ΦPTfor each locus, the correlation coefficient was 0.99 (pvalue<0.0001); no statistically significant correlations with RSTwere found. A high correlation of FST(W&C)and ΦPTwith the estimates of differentiation according to Nei’s (0.96) was found. Programs other than GenAlEx (Arlequin v.3.5, GenePop v.4.7.3, RST22) gave similar AMOVA estimates. The negative linear dependence of FST(W&C)and ΦPTon the level of the average heterozygosity of the breed samples was established (R2= 0.6, rS= -0.75 for pvalue < 0.02) and the absence of such dependence for RST(R2= 0.04, rS= -0.23 for pvalue= 0.47). The standardization of the FST(W&C)and ΦPTestimates according to Hedrick’s eliminated this dependence and raised the initial estimates to 0.35 and 0.37, respectively. The latter were comparable to the estimates obtained by the Nei-Hedrick’s (0.364-0.375), Jost’s (0.292), and Morisit-Horn’s (0.308) methods. The Mantel correlations between the matrices of paired genetic distances (GD) calculated by different measures were >0.9 in most cases. The projections of the GD matrices in the principal coordinate analysis (PCoA) on the 2D plane were generally similar. The PCoA identified a cluster of Holstein «ecotypes», a cluster of «Red» breeds, and a branch of the Jersey breed. In the two-factor AMOVA of data on clusters (as two «regions»), the interregional GD was 0.357; the differentiation of breeds within the «regions» did not exceed 0.027. Modeling the association of breeds with close to zero GD resulted in an increase in the number of alleles per locus in the «new» breeds by 29 %, and an increase in the combined estimate of genetic differentiation by 29-46 %. The results obtained can be used in the development of measures for the conservation of endangered breeds.

Identification of Main Oyster Species and Comparison of Their Genetic Diversity in Zhejiang Coast, South of Yangtze River Estuary

Oysters are an important aquaculture species distributed worldwide, including in Zhejiang Province, located on the east coast of China. Because of the high diversity and complicated introduction history of oysters and their seedlings, there has been much disagreement regarding the origin of each species, and the dominant and indigenous species remain unclear. We sampled 16 batches of oysters from seven sites in three aquaculture bays and found two main oyster species, Crassostrea sikamea and Crassostrea angulata. The former occupied the higher intertidal zone and comprised more than 70% of the cultured oysters. Based on the cytochrome oxidase C subunit I (COI) and mitochondrial noncoding region (MNR), C. sikamea showed higher genetic diversity than C. angulata. The analysis of molecular variance among COI sequences of these species from the Xiangshan Bay populations were comparable to those of other populations and showed that most of the molecular variance was within groups, which was consistent with the low pairwise fixation index FST values. The neutrality test revealed that C. sikamea experienced population expansion events, whereas for C. angulata, the significant Fu’s Fs and non-significant Tajima’s D test results may indicate a possible population expansion event, implying that C. sikamea is likely an indigenous species. The method established based on internal transcribed spacer 1 digestion by the HindIII restriction enzyme is useful for identifying C. sikamea and C. angulata in the local region. The specific primers on the MNR sequence show potential for distinguishing C. sikamea from four other important Crassostrea oysters. These results highlight the abundance of C. sikamea on the Zhejiang coast and lay the foundation for protecting and utilizing the local oyster germplasm resources and for the sustainable development of the oyster industry.

Genetic Diversity, Identification and Utilization of Novel Genetic Resources for Resistance to Meloidogyne incognita in Mulberry (Morus spp.)

Mulberry (Morus spp.) is an important crop in the sericulture industry as the leaves constitute the primary feed for the silkworm. The availability of diverse genetic sources of resistance to root- knot nematode (RKN; Meloidogyne spp.) are very scanty and therefore, a set of 415 varied exotic and indigenous germplasm accessions were screened under glasshouse conditions. Twenty one accessions were identified as highly resistant and 48 were resistant, the highest numbers of highly resistant/resistant accessions were found in Morus alba. Further, thirty accessions based on rooting ability were evaluated for field resistance at four different locations with infested soil. Finally, eight germplasm accessions; BR-8, Karanjtoli-1, Hosur-C8, Nagalur Estate, Tippu, Calabresa, Thai Pecah and SRDC-3 were identified as potential genetic sources in RKN resistance breeding programs or as resistant rootstock for the establishment of mulberry gardens. Sixteen SSR markers analyzed among the 77 resistant and susceptible accessions, generated 55 alleles, ranging from 2 to 5 with an average of 3.43 alleles per locus. Principle coordinate analysis grouped the accessions on the basis of RKN susceptible and resistant to a greater extent. The RKN susceptible accessions exhibited higher variability as compared to resistant accessions and they were more dispersed. Analysis of molecular variance showed that maximum molecular variance (78%) within the population and 22% between populations. Results of this study indicate that SSR markers are reliable for assessing genetic variability among the RKN resistant and susceptible mulberry accessions.

Breeding Strategy for Resistance to Striga Asiatica Based on Genetic Diversity and Population Structure of Tropical Maize Lines

Maize (Zea mays L.) is a major staple crop in southern Africa and is produced on millions of hectares. However, its yield is greatly reduced by Striga spp, a parasitic weed which is causing US$ 7 billion losses annually. Use of host resistance could be an effective way of controlling Striga and resistance to Striga is quantitative, mainly controlled by additive gene action. Understanding the population structure and genetic diversity is therefore key in designing an effective breeding program targeting grain yield heterosis and resistance to Striga. The aim of this study was to determine the genetic diversity and population structure of the key germplasm from tropical Africa. This information could guide in the identification of heterotic groups and potential testers required to kick start a maize breeding program for Striga asiatica in southern Africa. A total of 222 maize inbred lines from IITA and CIMMYT were used in this study. The materials were genotyped using the genotyping-by-sequencing method. A total of 45 000 SNP markers were revealed, and these were subjected to analysis of molecular variance, structure analysis and clustering using the Gower’s distance and neighbor joining algorithm. Molecular variance was lager within individuals (91%) than among populations (9%). The inbred lines clustered into three major groups, with the IITA germplasm clustering separately from CIMMYT germplasm. A breeding strategy for Striga asiatica resistance was proposed with the aim of increasing genetic gains in both the resistance and grain yield.

The most important fishery resource in the Amazon, the migratory catfish Brachyplatystoma vaillantii (Siluriformes: Pimelodidae), is composed by an unique and genetically diverse population in the Solimões-Amazonas River System

ABSTRACT The migratory catfish Brachyplatystoma vaillantii is one of the most important fishery resources in the Amazon. Intense capture occurs associated to its life cycle. In order to know the genetic status, we sequenced the mitochondrial DNA control region from 150 individuals of B. vaillantii, collected in five fishing landing locations, covering the length of the Solimões-Amazonas River in Brazil. Genetic diversity parameters suggest there is no genetic differentiation between the five localities. Population’s expansion indicated by R 2 and Fu’s Fs tests was also confirmed by the high number of unique haplotypes found. The Analyses of molecular variance indicated that nearly all variability was contained within locations (99.86%), and estimates of gene flow among B. vaillantii were high (F ST = 0.0014). These results suggest that Brachyplatystoma vaillantii forms a panmitic population along the Solimões-Amazonas River and, has greater genetic variability than other species of the Brachyplatystoma genus available so far. Although the influence of different tributaries on B. vaillantii migration patterns remains uncertain, a single population in the main channel should be consider in future policies for management of this resource. However, since the species’ life cycle uses habitats in several countries, its management and conservation depend greatly of internationally joined efforts.