Chloroplast DNA variation in the grass tribe Festuceae

Isolation of Intact Chloroplast for Sequencing Plastid Genomes of Five Festuca Species

Isolation of good quality chloroplast DNA (cpDNA) is a challenge in different plant species, although several methods for isolation are known. Attempts were undertaken to isolate cpDNA from Festuca grass species by using available standard protocols; however, they failed due to difficulties separating intact chloroplasts from the polysaccharides, oleoresin, and contaminated nuclear DNA that are present in the crude homogenate. In this study, we present a quick and inexpensive protocol for isolating intact chloroplasts from seven grass varieties/accessions of five Festuca species using a single layer of 30% Percoll solution. This protocol was successful in isolating high quality cpDNA with the least amount of contamination of other DNA. We performed Illumina MiSeq paired-end sequencing (2 × 300 bp) using 200 ng of cpDNA of each variety/accession. Chloroplast genome mapping showed that 0.28%–11.37% were chloroplast reads, which covered 94%–96% of the reference plastid genomes of the closely related grass species. This improved method delivered high quality cpDNA from seven grass varieties/accessions of five Festuca species and could be useful for other grass species with similar genome complexity.

Genetic relationships within and among Iberian fescues (Festuca L.) based on PCR-amplified markers

The genus Festuca comprises approximately 450 species and is widely distributed around the world. The Iberian Penninsula, with more than 100 taxa colonizing very diverse habitats, is one of its main centers of diversification. This study was conducted to assess molecular genetic variation and genetic relatedness among 91 populations of 31 taxa of Iberian fescues, based on several molecular markers (random amplified polymorphic DNA, amplified fragment length polymorphisms, and trnL sequences). The analyses showed the paraphyletic origin of the broad-leaved (subgenus Festuca , sections Scariosae and Subbulbosae, and subgenus Schedonorus ) and the fine-leaved fescues (subgenus Festuca, sections Aulaxyper, Eskia, and Festuca). Schedonorus showed a weak relationship with Lolium rigidum and appeared to be the most recent of the broad-leaved clade. Section Eskia was the most ancient and Festuca the most recent of the fine-leaved clade. Festuca and Aulaxyper were the most related sections, in concordance with their taxonomic affinities. All taxa grouped into their sections, except F. ampla and F. capillifolia (section Festuca), which appeared to be more closely related to Aulaxyper and to a new independent section, respectively. Most populations clustered at the species level, but some subspecies and varieties mixed their populations. This study demonstrated the value in combining different molecular markers to uncover hidden genetic relationships between populations of Festuca.

Low variability of internal transcribed spacer rDNA and trnL (UAA) intron sequences of several taxa in the Festuca ovina aggregate (POACEAE)

Identification and classification of numerous Festuca species is still a difficult problem due to the close morphological resemblance. The most difficult fine fescues to identify belong to the Festuca ovina aggregate, which is the largest group in the genus Festuca. Many taxons are considered to be separate species based on quantitative taxonomic characters, differences in ploidy level or the structure of sclerenchyma cells. In order to evaluate the taxonomic value of DNA-based markers, sequence analysis of the internal transcribed spacer (ITS1-5.8S-ITS2) region and the chloroplast trnL (UAA) intron was performed in the ten most problematic fine fescues belonging to the Festuca ovina aggregate. Intraspecific ITS variants were found in a single case while in other cases only intragenomic ITS polymorphisms were detected with 1-2 ambiguous positions. Among the sequences of the trnL (UAA) intron even intragenomic polymorphisms were not detected in any of the Festuca species studied. Thus, the results do not support the species status of these ten taxa.

Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses

Microsatellites or simple sequence repeats (SSRs) are highly useful molecular markers for plant improvement. Expressed sequence tag (EST)-SSR markers have a higher rate of transferability across species than genomic SSR markers and are thus well suited for application in cross-species phylogenetic studies. Our objectives were to examine the amplification of tall fescue EST-SSR markers in 12 grass species representing 8 genera of 4 tribes from 2 subfamilies of Poaceae and the applicability of these markers for phylogenetic analysis of grass species. About 43% of the 145 EST-SSR primer pairs produced PCR bands in all 12 grass species and had high levels of polymorphism in all forage grasses studied. Thus, these markers will be useful in a variety of forage grass species, including the ones tested in this study. SSR marker data were useful in grouping genotypes within each species. Lolium temulentum, a potential model species for cool-season forage grasses, showed a close relation with the major Festuca-Lolium species in the study. Tall wheat grass was found to be closely related to hexaploid wheat, thereby confirming the known taxonomic relations between these species. While clustering of closely related species was found, the effectiveness of such data in evaluating distantly related species needs further investigations. The phylogenetic trees based on DNA sequences of selected SSR bands were in agreement with the phylogenetic relations based on length polymorphism of SSRs markers. Tall fescue EST-SSR markers depicted phylogenetic relations among a wide range of cool-season forage grass species and thus are an important resource for researchers working with such grass species.

A decade of “chromosome painting” in Lolium and Festuca

GISH has been a particularly useful technique for studying the Lolium-Festuca species complex of forage grasses. The reason for this utility is two-fold: (i) the complex is unique amongst crop plants in which fertile hybrids, and backcross progenies, can be produced which recombine genomes and promiscuously exchange their genes through homoeologous recombination; (ii) dispersed repetitive DNAs differ between species, and this allows tracking of the identity of chromosomes and chromosome segments. This tracking property has enabled several fruitful lines of research to produce a harvest of new information for both fundamental and practical purposes. We review this first decade of GISH (genomic in situ hybridization) in Lolium-Festuca, and discuss and summarize the achievements which have accrued.

Chloroplast DNA variation in dactylis glomerata L. taxa endemic to the macaronesian islands

In the Dactylis glomerata infraspecific polyploid grass complex, restriction fragment length polymorphisms (RFLPs) of chloroplast DNA (cpDNA) were studied in diploid and tetraploid populations of several taxa endemic to Macaronesia (Madeira and the Canary islands) and in populations from the African and European continental areas closest to Macaronesia. Two chlorotypes, which differed by a single 290-bp length mutation, were observed in the Macaronesian and the continental populations. Chlorotype I, which is predominant in the whole D. glomerata complex, was found in the majority of continental populations. It was also observed in the most western Macaronesian islands, in the two diploid taxa endemic to the lowland scrub and the high elevation heath of Tenerife, respectively, and in tetraploids endemic to Madeira and La Palma. These island populations were growing under the influence of humid trade winds. Chlorotype II was found in the eastern part of the Archipelago (closer to Africa), which experienced subarid Mediterranean climate conditions, and in very few diploid and tetraploid Mediterranean populations growing at high elevation on the continent. This geographical and climatic distribution of chlorotype variation in Macaronesia is consistent with that reported previously for morphological, allozyme and phenolic variation in the same plant material. Chlorotype II was, however, also observed in tetraploid populations from La Gomera island and in one of the seven tetraploid populations analysed from Madeira, which all showed clearly subtropical characters for morphology, allozymes and phenolic compounds. This result suggests that cpDNA introgression has occurred more than once from the Mediterranean material into the subtropical one and may indicate that colonization between the mainland and islands, or among the islands, probably played a major role in the geographical pattern observed for that marker.

Use of random PCR (RAPD) technology to analyse phylogenetic relationships in the Lolium/Festuca complex

The RAPD PCR technique has been employed to investigate phylogenetic relationships between species of the genera Lolium and Festuca. Several decamer primers were used to generate patterns from groups of genotypes of several different species. The degree of band sharing was used to evaluate genetic distances between species and to construct a phylogenetic tree which is in good overall agreement with classical taxonomy, but contains a number of novel insights. The degree of homoplasy inherent in this approach has been investigated using Southern hybridization. These results are discussed in the context of current work in molecular biosystematics.

Isozyme variation and species relationships in the genus Lolium L. (ryegrasses, Graminaceae)

Thirty-two natural populations belonging to the eight species of the genus Lolium (ryegrass) or to Festuca pratensis (meadow fescue) were recorded for allelic frequencies at 13 isozyme loci. Cultivated ryegrass (L. perenne and L. multiflorum), meadow fescue, and the annual L. rigidum, are true outbreeders. The other species are true inbreeders, except for L. canariense, which shows a moderate level of cross fertilisation (20%). Hierarchical clustering from Nei's unbiased distance leads to four groups. The three self-pollinating, weed species, L. temulentum, L. remotum and L. persicum, belong to the first cluster, which is the most differentiated one. The second cluster comprises L. multiflorum, L. subulatum and most populations of L. rigidum. All L. perenne populations belong to the third cluster, as do two of L. rigidum. The average genetic distance within the L. perenne group is very low. Surprisingly, the fourth cluster groups together L. canariense and Festuca pratensis. The data suggest that L. rigidum is the species with the greatest diversity, and could be a common ancestor of the genus. Knowledge of historical processes of domestication could help to calibrate the molecular clock.

Phylogenetic relationships of turfgrasses as revealed by restriction fragment analysis of chloroplast DNA

Chloroplast DNAs (cpDNAs) were analyzed in order to clarify the phylogenetic relationships among turfgrasses. Physical maps of cpDNAs from Agrostis stolonifera and Zoysia japonica, which are representative species of cool (C3 type) and warm (C4 type) season turfgrasses, respectively, were constructed with four restriction enzymes, i.e., PstI, SalI, SacI, and XhoI. The genome structures of these cpDNAs were found to be similar to each other in terms of genome size and gene orders, showing thereby a similarity to other grass cpDNAs. CpDNAs of 5 species of cool season turfgrasses and 6 species of warm season turfgrasses as well as four species of cereals, distributed among 14 genera of Gramineae, were digested with PstI, XhoI, and BamHI, and their restriction fragment patterns were compared. Their genome sizes were estimated to be 135-140 kbp. Each species showed characteristic RFLP patterns. On the basis of the frequency of commonly shared fragments, a dendrogram showing the phylogenetic relationships among their cpDNAs was constructed. This dendrogram shows that turfgrasses can be divided into three major groups; these correspond to the subfamilies. Cool and warm season turfgrasses are clearly distinguishable from each other, and the latter can be further classified into two subgroups that correspond to Eragrostoideae and Panicoideae. Our classification of turfgrasses and cereals by RFLP analysis of cpDNA agreed in principal with their conventional taxonomy, except for the location of Festuca and Lolium.

Chloroplast DNA diversity in wild and cultivated species of rice (Genus Oryza, section Oryza). Cladistic-mutation and genetic-distance analysis

Using a novel nonaqueous procedure, chloroplast DNA was isolated from 318 individual adult rice plants, representing 247 accessions and the breadth of the diversity in section Oryza of genus Oryza. Among them, 32 different cpDNA restriction patterns were distinguished using the restriction endonucleases EcoRI and AvaI, and they were further characterized by restriction with BamHI, HindIII, SmaI, PstI, and BstEII enzymes. The differences in the electrophoretic band patterns were parsimoniously interpreted as being the result of 110 mutations, including 47 restriction site mutations. The relationships between band patterns were studied by a cladistic analysis based on shared mutations and by the computation of genetic distances based on shared bands. The deduced relationships were compared with earlier taxonomical studies. The maternal parents for BC genome allotetraploids were deduced. Within species, cpDNA diversity was found larger in those species with an evolutionary history of recent introgression and/or allotetraploidization. Occasional paternal inheritance and recombination of cpDNA in rice was suggested.

Species relationships in the Hordeum murinum aggregate viewed from chloroplast DNA restriction fragment patterns

Three annual widespread species of Hordeum were investigated by the fragment pattern method on their chloroplast (cp) DNA. The species were H. glaucum, H. leporinum and H. murinum; H. vulgare was surveyed for comparison. Twelve restriction enzymes were used, nine recognizing 6 bp, one 5 bp and two 4 bp, thus, randomly surveyed, a total of 2,113 bp or 1.6% of the cp genome. Differences in patterns were found in three enzymes, HindIII, CfoI and MspI. CfoI characterizes H. glaucum from the other two species. HindIII and MspI revealed polymorphisms within species. These results confirm previous numerical taxonomic relationships among these three closely related species. Furthermore, cpDNA polymorphism in Hordeum is discussed in view of earlier reports on cpDNA polymorphism in H. vulgare. The taxonomic implications of cpDNA polymorphism are discussed after reviewing several articles using the fragment pattern method on cpDNA. The importance of using material from several populations representative of a species is stressed.

Autopolyploidy in Dactylis glomerata L.: further evidence from studies of chloroplast DNA variation

Chloroplast DNA variation has been used to examine some of the maternal lineages involved in the evolution of the intraspecific polyploid complex, Dactylis glomerata L. Diploid (2x) and tetraploid (4x) individuals were collected from natural populations of the subspecies glomerata (4x), marina (4x) and lusitanica (2x), as well as from sympatric 2x/4x populations of the Galician type. Digestion of their ctDNA with 11 restriction endonucleases revealed enough variation to characterise three ctDNA variants, designated MBMK, MBmK and mBMK. The distribution of these ctDNA variants reflects different stages in their spread among the populations. The MBMK ctDNA variant predominated at both ploidy levels in subspecies glomerata, lusitanica and marina, and in recent tetraploid Galician/glomerata hybrids. The MBmK variant was detected in a single tetraploid individual and probably results from a relatively recent mutation. Fixation of the mBMK minority variant in the diploid and tetraploid Galician populations adds to the evidence concerning the possible origin of the Galician tetraploids. It means that the Galician diploids were maternal ancestors of the tetraploids. This result complements evidence from earlier studies based on morphology or biochemical markers, and reduces the likelihood that the tetraploids arose by hybridisation between an ancient Galician diploid and an alien tetraploid. It is, however, consistent with a true autopolyploid origin of the tetraploids.