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Like other eukaryotes, the nuclear genome of plants consists of DNA with a small proportion of low-copy DNA (genes and regulatory sequences) and very abundant DNA sequence motifs that are repeated thousands up to millions of times in the genomes including transposable elements (TEs) and satellite DNA. Retrotransposons, one class of TEs, are sequences that amplify via an RNA intermediate and reinsert into the genome, are often the major fraction of a genome. Here, we put research on retrotransposons into the larger context of plant repetitive DNA and genome behaviour, showing features of genome evolution in a grass genus, Brachiaria, in relation to other plant species. We show the contrasting amplification of different retroelement fractions across the genome with characteristics for various families and domains. The genus Brachiaria includes both diploid and polyploid species, with similar chromosome types and chromosome basic numbers x = 6, 7, 8 and 9. The polyploids reproduce asexually and are apomictic, but there are also sexual species. Cytogenetic studies and flow cytometry indicate a large variation in DNA content (C-value), chromosome sizes and genome organization. In order to evaluate the role of transposable elements in the genome and karyotype organization of species of Brachiaria, we searched for sequences similar to conserved regions of TEs in RNAseq reads library produced in Brachiaria decumbens. Of the 9649 TE-like contigs, 4454 corresponded to LTR-retrotransposons, and of these, 79.5 % were similar to members of the gypsy superfamily. Sequences of conserved protein domains of gypsy were used to design primers for producing the probes. The probes were used in FISH against chromosomes of accesses of B. decumbens, Brachiaria brizantha, Brachiaria ruziziensis and Brachiaria humidicola. Probes showed hybridization signals predominantly in proximal regions, especially those for retrotransposons of the clades CRM and Athila, while elements of Del and Tat exhibited dispersed signals, in addition to those proximal signals. These results show that the proximal region of Brachiaria chromosomes is a hotspot for retrotransposon insertion, particularly for the gypsy family. The combination of high-throughput sequencing and a chromosome-centric cytogenetic approach allows the abundance, organization and nature of transposable elements to be characterized in unprecedented detail. By their amplification and dispersal, retrotransposons can affect gene expression; they can lead to rapid diversification of chromosomes between species and, hence, are useful for studies of genome evolution and speciation in the Brachiaria genus. Centromeric regions can be identified and mapped, and retrotransposon markers can also assisting breeders in the developing and exploiting interspecific hybrids.

Genomic selection is an efficient approach to get shorter breeding cycles in recurrent selection programs and greater genetic gains with selection of superior individuals. Despite advances in genotyping techniques, genetic studies for polyploid species have been limited to a rough approximation of studies in diploid species. The major challenge is to distinguish the different types of heterozygotes present in polyploid populations. In this work, we evaluated different genomic prediction models applied to a recurrent selection population of 530 genotypes of Panicum maximum , an autotetraploid forage grass. We also investigated the effect of the allele dosage in the prediction, i.e. , considering tetraploid (GS-TD) or diploid (GS-DD) allele dosage. A longitudinal linear mixed model was fitted for each one of the six phenotypic traits, considering different covariance matrices for genetic and residual effects. A total of 41,424 genotyping-by-sequencing markers were obtained using 96-plex and Pst 1 restriction enzyme, and quantitative genotype calling was performed. Six predictive models were generalized to tetraploid species and predictive ability was estimated by a replicated fivefold cross-validation process. GS-TD and GS-DD models were performed considering 1,223 informative markers. Overall, GS-TD data yielded higher predictive abilities than with GS-DD data. However, different predictive models had similar predictive ability performance. In this work, we provide bioinformatic and modeling guidelines to consider tetraploid dosage and observed that genomic selection may lead to additional gains in recurrent selection program of P. maximum .

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Urochloa decumbens (Stapf) R. D. Webster is one of the most important African forage grasses in Brazilian beef production. Currently available genetic-genomic resources for this species are restricted mainly due to polyploidy and apomixis. Therefore, crucial genomic-molecular studies such as the construction of genetic maps and the mapping of quantitative trait loci (QTLs) are very challenging and consequently affect the advancement of molecular breeding. The objectives of this work were to (i) construct an integrated U. decumbens genetic map for a full-sibling progeny using GBS-based markers with allele dosage information, (ii) detect QTLs for spittlebug ( Notozulia entreriana ) resistance, and (iii) seek putative candidate genes involved in defense against biotic stresses. We used the Setaria viridis genome a reference to align GBS reads and selected 4,240 high-quality SNP markers with allele dosage information. Of these markers, 1,000 were distributed throughout nine homologous groups with a cumulative map length of 1,335.09 cM and an average marker density of 1.33 cM. We detected QTLs for resistance to spittlebug, an important pasture insect pest, that explained between 4.66 and 6.24% of the phenotypic variation. These QTLs are in regions containing putative candidate genes related to defense against biotic stresses. Because this is the first genetic map with SNP autotetraploid dosage data and QTL detection in U. decumbens , it will be useful for future evolutionary studies, genome assembly, and other QTL analyses in Urochloa spp. Moreover, the results might facilitate the isolation of spittlebug-related candidate genes and help clarify the mechanism of spittlebug resistance. These approaches will improve selection efficiency and accuracy in U. decumbens molecular breeding and shorten the breeding cycle.

A bulked segregant analysis using RAPD technique was carried out to identify molecular markers linked to apomixis in a Brachiaria humidicola F 1 population that segregated 1 : 1 for the mode of reproduction (apomixis and sexual). A marker related to the apo-locus was found. Segregation data, together with this marker were used to generate a map of the region. This marker was located at 4.61 cM of the target locus, and it can be used in deploying marker-assisted selection for mode of reproduction in the hybrid progenies of this species.Brazil is the worldÕs largest beef exporter and also has the biggest cattle herd, numbering about 200 million heads. This large herd feeds almost exclusively on pastures. Cultivated pastures in Brazil cover an estimated 120 million ha, and about 85% of this area is planted to Brachiaria species (Macedo 2006). This paper describes the work carried out with a hybrid population of B. humidicola (Rendle) Schweickert, also known as koronivia grass, a perennial savanna grass native to Africa. This species is well adapted to poorly drained and infertile acid soils (Keller-Grein et al. 1996). Most B. humidicola ecotypes are polyploid and reproduce by apomixis, an asexual mode of reproduction through seeds (do Valle and Savidan 1996).Apomixis in B. humidicola is facultative, pseudogamous and embryo sacs show apospory of the Panicum type, where the apospore develops into a diploid, monopolar four-nucleate embryo sac with a three-celled egg apparatus and a central cell with one nucleus (Savidan 1982). Pseudogamy means that for endosperm development the secondary nucleus of the embryo sac needs to be fertilized by a male gamete (Alves et al. 2001). Facultative apomictic plants develop both aposporous and meiotic sacs within the same inflorescence and even within the same pistil (Nogler 1984). The two reproductive modes are not mutually exclusive, therefore, some segregation may be observed in the progeny of an apomictic Brachiaria genitor.In the main Brachiaria species apomixis is simply inherited (do Valle and Savidan 1996), thus apomictic and sexual hybrids are generated at each sexual · apomictic cross in the proportion of 1 : 1.The objective of this work was to identify RAPD markers tightly linked to apomixis in B. humidicola hybrids to improve efficiency and accuracy in the determination of the reproduction mode on the breeding programme of this species. Materials and MethodsPlant material: One hundred and seven plants belonging to an F 1 population obtained by crossing a polyploid apomictic cultivar (B. humidicola cv. BRS Tupi) with a polyploid sexual parent (BRA005811-H31) were analysed. The hybrid nature of the F 1 plants was confirmed using RAPD markers.Analysis of mode of reproduction: Flowers of these hybrids were collected at anthesis. Sixty ovules were dissected from each hybrid and then clarified using methyl salicylate according to the Young et al. (1979) procedure. At least 50 cleared ovules were analysed per plant using an interference contrast microscope. A chi-squared test w...

Stylosanthes guianensis is an important tropical pasture legume. Knowledge of genetic diversity and structure of S. guianensis populations is of great importance for the conservation and germplasm management of this species. Thus, 20 microsatellite markers were developed from a S. guianensis enriched library. The microsatellites were characterized in 20 accessions from the germplasm collection of the Empresa Brasileira de Pesquisa Agropecuária (Embrapa). The average number of alleles per locus varied from 2 to 7, with an average of 4 alleles per locus. The observed and expected heterozygosities ranged from 0 to 0.60 and 0.10 to 0.85, respectively. This new set of microsatellites will contribute towards studies of genetic diversity and conservation of S. guianensis.

BackgroundForage grasses of the African genus Urochloa (syn. Brachiaria) are the basis of Brazilian beef production, and there is a strong demand for high quality, productive and adapted forage plants. Among the approximately 100 species of the genus Urochloa, Urochloa decumbens is one of the most important tropical forage grasses used for pastures due to several of its agronomic attributes. However, the level of understanding of these attributes and the tools with which to control them at the genetic level are limited, mainly due to the apomixis and ploidy level of this species. In this context, the present study aimed to identify and characterize molecular microsatellite markers of U. decumbens and to evaluate their cross-amplification in other Urochloa species.FindingsMicrosatellite loci were isolated from a previously constructed enriched library from one U. decumbens genotype. Specific primers were designed for one hundred thirteen loci, and ninety-three primer pairs successfully amplified microsatellite regions, yielding an average of 4.93 alleles per locus. The polymorphism information content (PIC) values of these loci ranged from 0.26 to 0.85 (average 0.68), and the associated discriminating power (DP) values ranged from 0.22 to 0.97 (average 0.77). Cross-amplification studies demonstrated the potential transferability of these microsatellites to four other Urochloa species. Structure analysis revealed the existence of three distinct groups, providing evidence in the allelic pool that U. decumbens is closely related to Urochloa ruziziensis and Urochloa brizantha. The genetic distance values determined using Jaccard’s coefficient ranged from 0.06 to 0.76.ConclusionsThe microsatellite markers identified in this study are the first set of molecular markers for U. decumbens species. Their availability will facilitate understanding the genetics of this and other Urochloa species and breeding them, and will be useful for germplasm characterization, linkage mapping and marker-assisted selection.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-1967-9) contains supplementary material, which is available to authorized users.