Population Genetics of Polyploid Complex Psidium cattleyanum Sabine (Myrtaceae): Preliminary Analyses Based on New Species-Specific Microsatellite Loci and Extension to Other Species of the Genus.

Polyploidy is a phenomenon that alters the genetic diversity of populations and has been reported as one of the most important evolutionary forces for plant diversification. The Psidium cattleyanum complex comprises a group of wild populations with several ploidy levels reported in the literature. The multiple cytotypes, associated with its wide distribution area, make this species a potential key model for understanding evolutionary processes related to polyploidization. In this study, we isolated and characterized nuclear microsatellite markers of P. cattleyanum and tested their transferability to other nine species of the genus. We performed a preliminary analysis of genetic diversity and population structure in three populations of P. cattleyanum. The three populations analyzed had different chromosome numbers, being polyploid cytotypes (2n = 6x = 66, 2n = 7x = 77 and 2n = 8x = 88). We designed 46 primer pairs and successfully amplified 37 markers, from which the 10 best were selected for analysis. Considering both the PIC and DP values, most of markers were highly informative. The new SSR markers were used to assess the levels of genetic diversity of the populations and detected one population with predominance of sexual reproduction. DAPC analysis pointed the formation of three groups, which corresponded to the populations analyzed. The markers were successfully amplified in related species, with some species presenting 80% transferability. By producing this panel of polymorphic microsatellites, we contribute to the understanding evolution in groups of natural polyploids for future studies.

Development of microsatellite markers for the predatory mite Phytoseiulus macropilis and cross-amplification in three other species of phytoseiid mites.

Phytoseiid mites are efficient predators of mites and small pest insects. Understanding the dispersion and distribution pattern of phytoseiid mites is essential to promote the conservation of these natural enemies and support their use in biological control. Population genetic studies using molecular markers such as microsatellites have proved to be extremely informative to address questions about population structure and dispersion patterns of predatory mites. The objective of this work was to develop specific microsatellite markers for the predatory mite Phytoseiulus macropilis, aiming at improving field dispersion studies. For this purpose, the genomic DNA was extracted from the whole body of a pool of 260 adult females and used to build the genomic microsatellites-enriched library, using biotinylated probes (CT)8 and (GT)8. In total 26 pairs of primers were synthesized and screened across 30 adult females of P. macropilis for characterization. Seven loci were polymorphic, revealing from two to six alleles per locus. Cross amplifications were successfully obtained in the species Phytoseiulus persimilis, Amblyseius swirskii and Proprioseiopsis sp. The molecular markers obtained are the first developed for P. macropilis-they are effective for the detection and quantification of genetic variation, and show high transferability, thus can be used in genetic and molecular studies of this and other species of the same genus and also of close genera.

Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas.

BACKGROUND: Urochloa humidicola (Koronivia grass) is a polyploid (6x to 9x) species that is used as forage in the tropics. Facultative apospory apomixis is present in most of the genotypes of this species, although one individual has been described as sexual. Molecular studies have been restricted to molecular marker approaches for genetic diversity estimations and linkage map construction. The objectives of the present study were to describe and compare the leaf transcriptome of two important genotypes that are highly divergent in terms of their phenotypes and reproduction modes: the sexual BH031 and the aposporous apomictic cultivar BRS Tupi. RESULTS: We sequenced the leaf transcriptome of Koronivia grass using an Illumina GAIIx system, which produced 13.09 Gb of data that consisted of 163,575,526 paired-end reads between the two libraries. We de novo-assembled 76,196 transcripts with an average length of 1,152 bp and filtered 35,093 non-redundant unigenes. A similarity search against the non-redundant National Center of Biotechnology Information (NCBI) protein database returned 65 % hits. We annotated 24,133 unigenes in the Phytozome database and 14,082 unigenes in the UniProtKB/Swiss-Prot database, assigned 108,334 gene ontology terms to 17,255 unigenes and identified 5,324 unigenes in 327 known metabolic pathways. Comparisons with other grasses via a reciprocal BLAST search revealed a larger number of orthologous genes for the Panicum species. The unigenes were involved in C4 photosynthesis, lignocellulose biosynthesis and flooding stress responses. A search for functional molecular markers revealed 4,489 microsatellites and 560,298 single nucleotide polymorphisms (SNPs). A quantitative real-time PCR analysis validated the RNA-seq expression analysis and allowed for the identification of transcriptomic differences between the two evaluated genotypes. Moreover, 192 unannotated sequences were classified as containing complete open reading frames, suggesting that the new, potentially exclusive genes should be further investigated. CONCLUSION: The present study represents the first whole-transcriptome sequencing of U. humidicola leaves, providing an important public information source of transcripts and functional molecular markers. The qPCR analysis indicated that the expression of certain transcripts confirmed the differential expression observed in silico, which demonstrated that RNA-seq is useful for identifying differentially expressed and unique genes. These results corroborate the findings from previous studies and suggest a hybrid origin for BH031.

Guiding seed movement: environmental heterogeneity drives genetic differentiation in Plathymenia reticulata, providing insights for restoration.

Forest and landscape restoration is one of the main strategies for overcoming the environmental crisis. This activity is particularly relevant for biodiversity-rich areas threatened by deforestation, such as tropical forests. Efficient long-term restoration requires understanding the composition and genetic structure of native populations, as well as the factors that influence these genetic components. This is because these populations serve as the seed sources and, therefore, the gene reservoirs for areas under restoration. In the present study, we investigated the influence of environmental, climatic and spatial distance factors on the genetic patterns of Plathymenia reticulata, aiming to support seed translocation strategies for restoration areas. We collected plant samples from nine populations of P. reticulata in the state of Bahia, Brazil, located in areas of Atlantic Forest and Savanna, across four climatic types, and genotyped them using nine nuclear and three chloroplast microsatellite markers. The populations of P. reticulata evaluated generally showed low to moderate genotypic variability and low haplotypic diversity. The populations within the Savanna phytophysiognomy showed values above average for six of the eight evaluated genetic diversity parameters. Using this classification based on phytophysiognomy demonstrated a high predictive power for genetic differentiation in P. reticulata. Furthermore, the interplay of climate, soil and geographic distance influenced the spread of alleles across the landscape. Based on our findings, we propose seed translocation, taking into account the biome, with restricted use of seed sources acquired or collected from the same environment as the areas to be restored (Savanna or Atlantic Forest).

Genetic structure and molecular diversity of Brazilian grapevine germplasm: Management and use in breeding programs.

The management of germplasm banks is complex, especially when many accessions are involved. Microsatellite markers are an efficient tool for assessing the genetic diversity of germplasm collections, optimizing their use in breeding programs. This study genetically characterizes a large collection of 410 grapevine accessions maintained at the Agronomic Institute of Campinas (IAC) (Brazil). The accessions were genotyped with 17 highly polymorphic microsatellite markers. Genetic data were analyzed to determine the genetic structure of the germplasm, quantify its allelic diversity, suggest the composition of a core collection, and discover cases of synonymy, duplication, and misnaming. A total of 304 alleles were obtained, and 334 unique genotypes were identified. The molecular profiles of 145 accessions were confirmed according to the literature and databases, and the molecular profiles of more than 100 genotypes were reported for the first time. The analysis of the genetic structure revealed different levels of stratification. The primary division was between accessions related to Vitis vinifera and V. labrusca, followed by their separation from wild grapevine. A core collection of 120 genotypes captured 100% of all detected alleles. The accessions selected for the core collection may be used in future phenotyping efforts, in genome association studies, and for conservation purposes. Genetic divergence among accessions has practical applications in grape breeding programs, as the choice of relatively divergent parents will maximize the frequency of progeny with superior characteristics. Together, our results can enhance the management of grapevine germplasm and guide the efficient exploitation of genetic diversity to facilitate the development of new grape cultivars for fresh fruits, wine, and rootstock.