Dataset Information

Genetic variation in polyploid forage grass: assessing the molecular genetic variability in the Paspalum genus.

ABSTRACT: BACKGROUND: Paspalum (Poaceae) is an important genus of the tribe Paniceae, which includes several species of economic importance for foraging, turf and ornamental purposes, and has a complex taxonomical classification. Because of the widespread interest in several species of this genus, many accessions have been conserved in germplasm banks and distributed throughout various countries around the world, mainly for the purposes of cultivar development and cytogenetic studies. Correct identification of germplasms and quantification of their variability are necessary for the proper development of conservation and breeding programs. Evaluation of microsatellite markers in different species of Paspalum conserved in a germplasm bank allowed assessment of the genetic differences among them and assisted in their proper botanical classification. RESULTS: Seventeen new polymorphic microsatellites were developed for Paspalum atratum Swallen and Paspalum notatum Flüggé, twelve of which were transferred to 35 Paspalum species and used to evaluate their variability. Variable degrees of polymorphism were observed within the species. Based on distance-based methods and a Bayesian clustering approach, the accessions were divided into three main species groups, two of which corresponded to the previously described Plicatula and Notata Paspalum groups. In more accurate analyses of P. notatum accessions, the genetic variation that was evaluated used thirty simple sequence repeat (SSR) loci and revealed seven distinct genetic groups and a correspondence of these groups to the three botanical varieties of the species (P. notatum var. notatum, P. notatum var. saurae and P. notatum var. latiflorum). CONCLUSIONS: The molecular genetic approach employed in this study was able to distinguish many of the different taxa examined, except for species that belong to the Plicatula group, which has historically been recognized as a highly complex group. Our molecular genetic approach represents a valuable tool for species identification in the initial assessment of germplasm as well as for characterization, conservation and successful species hybridization.

SUBMITTER: Cidade FW

PROVIDER: S-EPMC3682885 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Genetic variation in polyploid forage grass: assessing the molecular genetic variability in the Paspalum genus.

Cidade Fernanda W FW Vigna Bianca Bz BB de Souza Francisco Hd FH Valls José Francisco M JF Dall'Agnol Miguel M Zucchi Maria I MI de Souza-Chies Tatiana T TT Souza Anete P AP

BMC genetics 20130608

<h4>Background</h4>Paspalum (Poaceae) is an important genus of the tribe Paniceae, which includes several species of economic importance for foraging, turf and ornamental purposes, and has a complex taxonomical classification. Because of the widespread interest in several species of this genus, many accessions have been conserved in germplasm banks and distributed throughout various countries around the world, mainly for the purposes of cultivar development and cytogenetic studies. Correct ident ...[more]

PMID: 23759066

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Project description: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.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.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.

Project description:BACKGROUND AND AIMS: The diploid cytotype of Paspalum rufum (Poaceae) reproduces sexually and is self-sterile; however, recurrent autopolyploidization through 2n + n fertilization and the ability for reproduction via apomixis have been documented in one genotype of the species. The objectives of this work were to analyse the variation in the functionality of apomixis components in diploid genotypes of P. rufum and to identify individuals with contrasting reproductive behaviours. METHODS: Samples of five individuals from each of three natural populations of P. rufum (designated R2, R5 and R6) were used. Seeds were obtained after open pollination, selfing, conspecific interploidy crosses and interspecific interploidy self-pollination induction. The reproductive behaviour of each plant was determined by using the flow cytometric seed screen (FCSS) method. Embryo sacs were cleared using a series of ethanol and methyl salicylate solutions and observed microscopically. KEY RESULTS: In open pollination, all genotypes formed seeds by sexual means and no evidence of apomeiotic reproduction was detected. However, in conspecific interploidy crosses and interspecific interploidy self-pollination induction, variations in the reproductive pathways were observed. While all plants from populations R2 and R6 formed seeds exclusively by sexual means, three genotypes from the R5 population developed seeds from both meiotic and aposporous embryo sacs, and one of them (R5#49) through the complete apomictic pathway (apospory + parthenogenesis + pseudogamy). Cytoembryological observations revealed the presence of both meiotic and aposporous embryo sacs in all the genotypes analysed, suggesting that parthenogenesis could be uncoupled from apospory in some genotypes. CONCLUSIONS: The results presented demonstrate the existence of variation in the functionality of apomixis components in natural diploid genotypes of P. rufum and have identified individuals with contrasting reproductive behaviours. Genotypes identified here can be crossed to generate segregating populations in order to study apomixis determinants at the diploid level. Moreover, analysis of their expression patterns, quantification of their transcript levels and an understanding of their regulation mechanisms could help to design new strategies for recreating apomixis in a diploid genome environment.

Dataset Information

Genetic variation in polyploid forage grass: assessing the molecular genetic variability in the Paspalum genus.

Publications

Genetic variation in polyploid forage grass: assessing the molecular genetic variability in the Paspalum genus.

Similar Datasets

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