B. B. Z. Vigna

Genetic Diversity and Population Structure of the Brachiaria brizantha Germplasm

Brachiaria brizantha (Hochst. ex A. Rich.) Stapf. (syn. Urochloa brizantha (Hochst. ex A. Rich.) R.D. Webster) is a species used primarily as forage in tropical America and Southeast Asia. B. brizantha has been extensively researched since the 1980s with the initiation of the Tropical Forages Breeding Program conducted by the Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária; EMBRAPA), holding one of the largest germplasm collections in the world. This work has identified 15 new microsatellite markers for this species, which have been used in addition to five previously reported markers, to estimate the genetic similarities among 172 accessions and six cultivars of this species. Similarity index values ranged from 0.40 to 1.00. Two duplications were found in the germplasm. A Bayesian analysis performed using the STRUCTURE 2.3.3 program revealed the presence of three clusters with different allelic pools. This analysis is valuable for the performance of crosses to explore heterosis; however, the mode of reproduction of the accessions and ploidy barriers must be observed for effective exploration. A grouping analysis using the neighbor-joining method was consistent with the STRUCTURE analysis, and a combination approach suggested that this germplasm collection does not exhibit considerable genetic variability despite the presence of three distinct allelic pools. The lack of correlation between the genetic and geographic distances is also discussed.

Microsatellite markers for Urochloa humidicola (Poaceae) and their transferability to other Urochloa species

BackgroundUrochloa humidicola is a warm-season grass commonly used as forage in the tropics and is recognized for its tolerance to seasonal flooding. This grass is an important forage species for the Cerrado and Amazon regions of Brazil. U. humidicola is a polyploid species with variable ploidy (6X–9X) and facultative apomixis with high phenotypic plasticity. However, this apomixis and ploidy, as well as the limited knowledge of the genetic basis of the germplasm collection, have constrained genetic breeding activities, yet microsatellite markers may enable a better understanding of the species’ genetic composition. This study aimed to develop and characterize new polymorphic microsatellite molecular markers in U. humidicola and to evaluate their transferability to other Urochloa species.FindingsA set of microsatellite markers for U. humidicola was identified from two new enriched genomic DNA libraries: the first library was constructed from a single sexual genotype and the second from a pool of eight apomictic genotypes selected on the basis of previous results. Of the 114 loci developed, 72 primer pairs presented a good amplification product, and 64 were polymorphic among the 34 genotypes tested. The number of bands per simple sequence repeat (SSR) locus ranged from 1 to 29, with a mean of 9.6 bands per locus. The mean polymorphism information content (PIC) of all loci was 0.77, and the mean discrimination power (DP) was 0.87. STRUCTURE analysis revealed differences among U. humidicola accessions, hybrids, and other Urochloa accessions. The transferability of these microsatellites was evaluated in four species of the genus, U. brizantha, U. decumbens, U. ruziziensis, and U. dictyoneura, and the percentage of transferability ranged from 58.33% to 69.44% depending on the species.ConclusionsThis work reports new polymorphic microsatellite markers for U. humidicola that can be used for breeding programs of this and other Urochloa species, including genetic linkage mapping, quantitative trait loci identification, and marker-assisted selection.

Genetic structure and diversity of populations of polyploid Tibouchina pulchra Cogn. (Melastomataceae) under different environmental conditions in extremes of an elevational gradient

The genetic structure and diversity of plants may change significantly in an elevational gradient because different elevations regulate different ecological conditions. Several factors may influence genetic variation, such as mutations, selection, genetic drift, and gene flow. The aim of the present study was to evaluate the genetic structure and diversity of populations of Tibouchina pulchra Cogn. (Melastomataceae) trees in two extremes of an elevational gradient experiencing different environmental conditions. Nine polymorphic microsatellite loci were used to measure the genetic diversity of 14 adult populations, whose structure was evaluated using frequentist and Bayesian analyses. We also carried out progeny structure and paternity analyses comparing the number of fathers of each progeny and the probability of the progeny genotypes to be the result of selfing in order to evaluate the possible current processes leading to such genetic structure. Genetic structure analyses indicated the existence of genetic differentiation between populations in adults and progenies, but with a contact interface between them. The population from the higher region showed smaller genetic diversity when compared to the population at the lower region. However, the pollen variability delivered to the stigmas at the higher region was not different from that of the lower region. These results may be explained by the dynamics of gene flow mediated by pollen, especially by the different amounts of pollination events in each region, as well as local adaptation, distribution, and reproduction characteristics of T. pulchra.

Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping

The African species Urochloa humidicola (Rendle) Morrone & Zuloaga (syn. Brachiaria humidicola (Rendle) Schweick.) is an important perennial forage grass found throughout the tropics. This species is polyploid, ranging from tetra to nonaploid, and apomictic, which makes genetic studies challenging; therefore, the number of currently available genetic resources is limited. The genomic architecture and evolution of U. humidicola and the molecular markers linked to apomixis were investigated in a full-sib F1 population obtained by crossing the sexual accession H031 and the apomictic cultivar U. humidicola cv. BRS Tupi, both of which are hexaploid. A simple sequence repeat (SSR)-based linkage map was constructed for the species from 102 polymorphic and specific SSR markers based on simplex and double-simplex markers. The map consisted of 49 linkage groups (LGs) and had a total length of 1702.82 cM, with 89 microsatellite loci and an average map density of 10.6 cM. Eight homology groups (HGs) were formed, comprising 22 LGs, and the other LGs remained ungrouped. The locus that controls apospory (apo-locus) was mapped in LG02 and was located 19.4 cM from the locus Bh027.c.D2. In the cytological analyses of some hybrids, bi- to hexavalents at diakinesis were observed, as well as two nucleoli in some meiocytes, smaller chromosomes with preferential allocation within the first metaphase plate and asynchronous chromosome migration to the poles during anaphase. The linkage map and the meiocyte analyses confirm previous reports of hybridization and suggest an allopolyploid origin of the hexaploid U. humidicola. This is the first linkage map of an Urochloa species, and it will be useful for future quantitative trait locus (QTL) analysis after saturation of the map and for genome assembly and evolutionary studies in Urochloa spp. Moreover, the results of the apomixis mapping are consistent with previous reports and confirm the need for additional studies to search for a co-segregating marker.

Microsatellite markers for the endangered orchids Cattleya labiata Lindl. and C. warneri T. Moore (Orchidaceae)

In this study, we developed a new set of microsatellite markers for endangered Cattleya labiata and Cattleya warneri. Also the first microsatellite loci for Cattleya, these markers can be useful for studies in the conservation genetics of these species. Twenty-one new microsatellite primers pairs were characterized by cloning an enriched library, and two libraries were obtained by cloning inter-simple sequence repeats. Thirteen polymorphic primers were found, and the remaining eight were monomorphic for both species. Our results indicate that these new microsatellite markers have the potential to be used as a tool for studying the genetic diversity of C. labiata and C. warneri and for future studies focusing mating systems and the detection of hybrids.

Apomixis-related genes identified from a coexpression network in Paspalum notatum, a Neotropical grass

Apomixis is a highly desirable trait in modern agriculture; however, incorporating it into breeding programs requires a deeper comprehension of apomictic regulatory mechanisms. Paspalum notatum is considered a good model for such studies because it exhibits both sexual and apomictic cytotypes. A transcriptomic approach to identifying differentially expressed genes between these cytotypes would constitute an important tool for the identification of genes in the apomictic pathway. We generated leaf and inflorescence transcriptomes of apomictic tetraploids and sexual diploids/tetraploids of P. notatum accessions. We de novo assembled and annotated 114,306 unigenes. Coexpression network and ontological annotation were applied to recover the interactions and biological processes of exclusive and differentially expressed genes from the apomictic libraries. Additionally, genes potentially linked to the apomixis-controlling region and several genes reported in the literature were identified. The reference transcriptome obtained in this study represents a robust set of expression data for P. notatum. Our approach to sequencing florets and leaves from different cytotypes enabled us to isolate a set of candidate genes. Using a gene expression network, we recovered transcriptionally coordinated genes related to mechanisms regulating apomixis. These findings provide an important contribution to our knowledge of apomixis and are valuable for Paspalum breeding programs.

First microsatellite markers for Paspalum plicatulum (Poaceae) characterization and cross-amplification in different Paspalum species of the Plicatula group

BackgroundPaspalum plicatulum is a perennial rhizomatous grass with natural diploid and polyploid cytotypes. It is a member of Plicatula, which has historically been recognized as a highly complex group containing species of ecological, ornamental and forage importance. The complex nature of the P. plicatulum genome makes it a challenging species for genetic research. This study aimed to develop and characterize microsatellite molecular markers in P. plicatulum and to evaluate their transferability to other Plicatula group species.FindingsMicrosatellite sequences were identified from three enriched libraries from P. plicatulum. Specific primers were designed, and 25 displayed polymorphism when screened across 48 polyploid Paspalum spp. genotypes. The number of bands per locus ranged from 2 to 17, with a mean of 8.65. Private bands for each species were identified; the highest number of private bands was observed for P. plicatulum in 52% of the loci analyzed. The mean polymorphism information content of all loci was 0.69, and the mean discriminatory power was 0.82. Microsatellite markers were satisfactorily cross-amplified for the eight tested Plicatula-group Paspalum species, with P. atratum exhibiting the highest transferability rate (89.86%). STRUCTURE and Discriminant Analysis of Principal Components separated accessions into three groups but did not reveal separation of the accessions according to species.ConclusionsThis study describes the first microsatellite markers in P. plicatulum, which are polymorphic, efficient for the detection and quantification of genetic variation, and show high transferability into other species of the Plicatula group. This set of markers can be used in future genetic and molecular studies necessary for the proper development of conservation and breeding programs. Private bands within the markers can be used to assist in species identification.