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Digitaria isanensis is described as a new species apparently endemic to sandy soils in open areas of northeastern Thailand. In addition, D. thwaitesii var. tonkinensis is reinstated and presented as a new record for Thailand. Descriptions and illustrations of both taxa are provided. [ABSTRACT FROM AUTHOR]

Phenotyping of genetic resources remains the bottleneck in the characterization of genetic resources, since the advent of modern next-generation sequencing technologies has made genotyping much more cost- and time-effective. This article reports on the phenotyping of agriculturally important traits in perennial ryegrass (Lolium perenne). In the present study, water-soluble carbohydrate (WSC), crude protein and dry matter contents were recorded for 1320 individuals, pooled into 132 samples from 33 perennial ryegrass ecotypes and cultivars at five different harvest time points across the 2004 growing season. While, in general, the cultivars had higher WSC contents than the ecotypes, individual ecotypes did show potential to be used in breeding programmes, as they had higher values than all other accessions at particular cutting time points. In correlation analyses, positive relationships were observed between dry matter and glucose contents both early and late in the growing season. Principal components analysis allowed the split either between cultivars and ecotypes or between tetraploid cultivars and the rest of the accessions at four of the five cutting time points. In the analysis of variance, cutting time was the most significant factor influencing the variation in traits. [ABSTRACT FROM PUBLISHER]

A new bicarpellate Buxus species, Buxus sirindhorniana W. K. Soh, M. von Sternburg, Hodk.. J. Parn., is described from northern Thailand. This is the first reported bicarpellate species of Buxus. The pollen morphology and the degree of pollen viability of the species are reported. DNA was extracted from herbarium samples and the internal transcribed spacer (ITS) region of nuclear ribosomal DNA sequenced. The palynological evidence and the phylogenetic reconstruction support the contention that this new species belongs to the genus Buxus. The morphological diversity of reproductive organs in the Buxaceae, in relation to this new species, is briefly discussed. [ABSTRACT FROM AUTHOR]

Background: Salix caprea is a cold-tolerant pioneer species that is ecologically important in Europe and western and central Asia. However, little data is available on its population genetic structure and molecular ecology. We describe the levels of geographic population genetic structure in natural Irish populations of S. caprea and determine the extent of gene flow and sexual reproduction using both chloroplast and nuclear simple sequence repeats (SSRs). Results: A total of 183 individuals from 21 semi-natural woodlands were collected and genotyped. Gene diversity across populations was high for the chloroplast SSRs (HT = 0.21-0.58) and 79 different haplotypes were discovered, among them 48% were unique to a single individual. Genetic differentiation of populations was found to be between moderate and high (mean GST = 0.38). For the nuclear SSRs, GST was low at 0.07 and observed heterozygosity across populations was high (HO = 0.32-0.51); only 9.8% of the genotypes discovered were present in two or more individuals. For both types of markers, AMOVA showed that most of the variation was within populations. Minor geographic pattern was confirmed by a Bayesian clustering analysis. Gene flow via pollen was found to be approximately 7 times more important than via seeds. Conclusions: The data are consistent with outbreeding and indicate that there are no significant barriers for gene flow within Ireland over large geographic distances. Both pollen-mediated and seed-mediated gene flow were found to be high, with some of the populations being more than 200 km apart from each other. These findings could simply be due to human intervention through seed trade or accidental transportation of both seeds and pollen. These results are of value to breeders wishing to exploit natural genetic variation and foresters having to choose planting material. [ABSTRACT FROM AUTHOR]

A taxonomic review of the genus Pseudostachyum Munro in Thailand is presented including a description of its morphology, geographic distribution and habitat. An illustrated description of the newly recorded species P. polymorphum Munro, discovered in Thailand, is provided and a doubtful species, P. wakha Brandis ex Camus, is reduced to a synonym of P. polymorphum. [ABSTRACT FROM AUTHOR]

Simple Summary: Ash sawfly, Tomostethus nigritus, larvae feed on the leaves of Fraxinus excelsior. In the last 20 years, outbreaks of these insects have become more common, and they cause severe defoliation of the tree crown. This pest is native to Europe, and it was recorded for the first time on the island of Ireland in Belfast, Northern Ireland (UK) in 2016. This article is the first report of T. nigritus in the Republic of Ireland (IE). Damaged leaves and larvae were observed on ash trees in Co. Kildare in summer 2021. The larvae were collected and then identified using molecular analyses. Similar damaged leaves were observed on trees in Co. Dublin, which showed mild defoliation of the crown. However, severe defoliation of ash trees has also been recorded in Co. Meath in 2021. No control treatments are available against the insects, and little is known about the cause of the outbreaks. Severe outbreaks by T. nigritus could further affect the delicate situation that the Irish ash tree population is currently facing caused by another severe antagonist of Fraxinus, the ash dieback pathogen Hymenoscyphus fraxineus. This is the first report of the ash sawfly, Tomostethus nigritus, in the Republic of Ireland. We observed defoliated leaves of Fraxinus excelsior L. and T. nigritus larvae at a forestry plantation in Co. Kildare. Morphological observation of the larvae and DNA analysis using mitochondrial COI barcoding confirmed the identification of this pest of ash. [ABSTRACT FROM AUTHOR]

C4 photosynthesis is a series of anatomical and biochemical modifications to the typical C3 pathway that increases the productivity of plants in warm, sunny, and dry conditions. Despite its complexity, it evolved more than 62 times independently in flowering plants. However, C4 origins are absent from most plant lineages and clustered in others, suggesting that some characteristics increase C4 evolvability in certain phylogenetic groups. The C4 trait has evolved 22-24 times in grasses, and all origins occurred within the PACMAD clade, whereas the similarly sized BEP clade contains only C3 taxa. Here, multiple foliar anatomy traits of 157 species from both BEP and PACMAD clades are quantified and analyzed in a phylogenetic framework. Statistical modeling indicates that C4 evolvability strongly increases when the proportion of vascular bundle sheath (BS) tissue is higher than 15%, which results from a combination of short distance between BS and large BS cells. A reduction in the distance between BS occurred before the split of the BEP and PACMAD clades, but a decrease in BS cell size later occurred in BEP taxa. Therefore, when environmental changes promoted C4 evolution, suitable anatomy was present only in members of the PACMAD clade, explaining the clustering of C4 origins in this lineage. These results show that key alterations of foliar anatomy occurring in a C3 context and preceding the emergence of the C4 syndrome by millions of years facilitated the repeated evolution of one of the most successful physiological innovations in angiosperm history. [ABSTRACT FROM AUTHOR]

C4 grasses constitute the main component of savannas and are pervasive in other dry tropical ecosystems where they serve as the main diet for grazing animals. Among potential factors driving C4 evolution of grasses, the interaction between grasses and grazers has not been investigated. To evaluate if increased grazing pressure may have selected for higher leaf silica production as the grasses diverged, we reconstructed the phylogeny of all 800 genera of the grass family with both molecular (combined multiplastid DNA regions) and morphological characters. Using molecular clocks, we also calculated the age and number of origins of C4 clades and found that shifts from C3 to C4 photosynthesis occurred at least 12 times starting 30.9 million years ago and found evidence that the most severe drop in atmospheric carbon dioxide in the late Oligocene (between 33 and 30 million years ago) matches the first origin of C4 photosynthesis in Chloridoideae. By combining fossil and phylogenetic data for ungulates and implementing a randomization procedure, our results showed that the appearance of C4 grass clades and ungulate adaptations to C4-dominated habitats match significantly in time. An increase of leaf epidermal density of silica bodies was found to correspond to postulated shifts in diversification rates in the late Miocene [24 significant shifts in diversification ( P<0.05) were detected between 23 and 3.7 million years ago]. For aristidoid and chloridoid grasses, increased grazing pressure may have selected for a higher leaf epidermal silica production in the late Miocene. [ABSTRACT FROM AUTHOR]

Lolium perenne L. (perennial ryegrass) is globally one of the most important forage and grassland crops. We sequenced the chloroplast (cp) genome of Lolium perenne cultivar Cashel. The L. perenne cp genome is 135 282 bp with a typical quadripartite structure. It contains genes for 76 unique proteins, 30 tRNAs and four rRNAs. As in other grasses, the genes accD, ycf1 and ycf2 are absent. The genome is of average size within its subfamily Pooideae and of medium size within the Poaceae. Genome size differences are mainly due to length variations in non-coding regions. However, considerable length differences of 1–27 codons in comparison of L. perenne to other Poaceae and 1–68 codons among all Poaceae were also detected. Within the cp genome of this outcrossing cultivar, 10 insertion/deletion polymorphisms and 40 single nucleotide polymorphisms were detected. Two of the polymorphisms involve tiny inversions within hairpin structures. By comparing the genome sequence with RT–PCR products of transcripts for 33 genes, 31 mRNA editing sites were identified, five of them unique to Lolium. The cp genome sequence of L. perenne is available under Accession number AM777385 at the European Molecular Biology Laboratory, National Center for Biotechnology Information and DNA DataBank of Japan. [ABSTRACT FROM PUBLISHER]

Cyperaceae are the third largest monocotyledon family, with considerable economic and conservation importance. In subfamily Mapanioideae there is particular specialization of the inflorescence into units termed spicoids. The structural homology of the spicoid is difficult to interpret, making determination of intrafamilial relationships problematic. To address this, pollen from eight species in Mapanioideae was investigated using light microscopy and scanning and transmission electron microscopy. Pollen development was also examined to identify the type of pollen present in these species. We also analyzed DNA sequence data using the trnL-F and rps16 regions from 25 genera and 35 species of Cyperaceae, Juncaceae, and Thurniaceae. Two types of pollen, Mapania-type and pseudomonad, were identified. Analysis of combined DNA and pollen data resolved a clade sister to the rest of Cyperaceae, corresponding to Mapanioideae. Within this, two further clades were resolved. One comprised taxa assigned to tribe Hypolytreae, which had Mapania-type pollen. The other comprised taxa mainly assigned to tribe Chrysitricheae, but included two taxa from Hypolytreae, Capitularina and Exocarya. All taxa in this clade had pseudomonad pollen. Thus new groupings within the subfamily have been discovered based on the specialization of some taxa in terms of their pollination biology. [ABSTRACT FROM AUTHOR]

Presents information on a study which investigated the origin of two clones of Miscanthus using DNA sequencing and amplified fragment length polymorphism. Information on Miscanthus as a biomass source; Role of fluorescent in situ hybridization and genomic in situ hybridization in investigating genome organization.

Large and comprehensive phylogenetic trees are desirable for studying macroevolutionary processes and for classification purposes. Such trees can be obtained in two different ways. Either the widest possible range of taxa can be sampled and used in a phylogenetic analysis to produce a "big tree," or preexisting topologies can be used to create a supertree. Although large multigene analyses are often favored, combinable data are not always available, and supertrees offer a suitable solution. The most commonly used method of supertree reconstruction, matrix representation with parsimony (MRP), is presented here. We used a combined data set for the Poaceae to (1) assess the differences between an approach that uses combined data and one that uses different MRP modifications based on the character partitions and (2) investigate the advantages and disadvantages of these modifications. Baum and Ragan and Purvis modifications gave similar results. Incorporating bootstrap support associated with pre-existing topologies improved Baum and Ragan modification and its similarity with a combined analysis. Finally, we used the supertree reconstruction approach on 55 published phylogenies to build one of most comprehensive phylogenetic trees published for the grass family including 403 taxa and discuss its strengths and weaknesses in relation to other published hypotheses. [ABSTRACT FROM AUTHOR]

Previously, we found a significant negative correlation between DNA C-value and altitude among eight natural populations of Dactylis glomerata L. (Creber et al., New Phytologist 128: 555–561, 1994). We have examined the extent to which similar negative relationships exist in other altitudinal transects, one in southern France and the other in Italy. Using Feulgen microdensitometry, C-values were negatively correlated with altitude both for the French and Italian populations. A combined plot of DNA C-values against altitude for all of the transects (representing C-values for 17 natural populations), exhibited a highly significant negative relationship; there was a 1·3-fold variation in DNA C-value from the largest genome-lowest altitude to the smallest genome-highest altitude natural population. Such a consistent marked altitudinal cline suggests strong nucleotypic selection acting upon these populations with increasing altitude. Preliminary examination of amplified fragment length polymorphisms between populations selected from the upper and lower limits of the French and Italian transects has shown that these populations are genetically distinct. The extent to which this genetic separation is related to altitude or genome size, or both, is discussed. [ABSTRACT FROM AUTHOR]

Background: Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability. Results: Using these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set. Conclusion: Using a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications. [ABSTRACT FROM AUTHOR]

We revised the genus Piper (Piperaceae) for the forthcoming volume of the Flora of Thailand. Three new species, namely P. kerrii, P. phangngaense and P.rugocarpum are described and illustrated. In addition, two records of species new to Thailand, P. laosanum and P. obtusissimum, are presented. New complete taxonomic descriptions of P. crassipes and P. obtusissimum are provided. We also designate lectotypes and epitypes of P. laosanum and P. obtusissimum, respectively. An emended key to species including the new species, new records for Thai Piper species and additional taxonomic notes are provided. [ABSTRACT FROM AUTHOR]

Digitaria is a large pantropical genus, which includes a number of economically problematic agricultural weeds. Difficulties in species identification and the circumscription of the genus have previously hindered progress in understanding its evolution and developing a stable classification. We investigate the evolutionary history of Digitaria by combining two approaches: (i) phylogenetic analyses of the currently available Sanger sequence data with previously unpublished sequences mainly from South East Asia, and (ii) newly generated genomic data from low-copy nuclear genes obtained using the Angiosperms353 probe kit, with new data mainly from Madagascar. Both methods gave congruent results. The combination of these results allowed us to confirm a new clade structure within Digitaria lineages, in partial agreement with the previous morphology-based classifications. We confirm that Digitaria as traditionally circumscribed is not monophyletic, comprising Anthephora , Baptorhachis , Chaetopoa , and Chlorocalymma. We present an inference of key character evolution with morphological support for clades with spikelets arranged in binate and ternate groups, with variable trichome morphology, spikelet length, and culm length. Geographical clade structure is also observed. No phylogenetic signal of weedy function was observed. [ABSTRACT FROM AUTHOR]

Phyllanthus kaweesakii Pornp., Chantar. & J.Parn. sp. nov. is newly described from the limestone mountain ridges in the northeast of Thailand. Comparison of morphology, anatomy, pollen morphology, and DNA sequences of this species with the most similar existing species P. mirabilis Müll.Arg. was undertaken. The results indicated that the two taxa are different in morphology, especially habit, stem base, and inflorescence, but that their pollen morphology and anatomy are similar. The molecular phylogenetic analysis, based on sequences of the plastid matK and nuclear ribosomal ITS regions, supported separation of the two taxa. This new species is described and illustrated, and its conservation status is discussed. [ABSTRACT FROM AUTHOR]

Molecular data was reviewed for the woody bamboo account in the English language Flora of China. The implications for recognition of suprageneric taxa and genera, for macro-morphological characters used in classification systems, and for the inferred biogeographical history of Asian bamboos are discussed. Support was not found for large supertribes based on inflorescence structure. Instead a restricted number of suprageneric taxa was suggested, with only 3 subtribes for Asian woody bamboos. The presence of both iterauctant and semelauctant inflorescences within subtribes shows that bamboos with these contrasting forms can be closely related, suggesting that simpler evolutionary pathways are required to explain them. Differences in sequence divergence between tropical and temperate subtribes suggests different biogeographical histories. It is hypothesised that temperate bamboos diversified later in Asia, only after the collision of the Indian and African tectonic plates with the Eurasian plate, and that the poor resolution of temperate taxa from sequence data is largely the result of rapid diversification after this biotic interchange. Sequence data provided somewhat equivocal evidence for recognition of genera. It was useful in demonstrating the polyphyly of broad interpretations of genera Sinarundinaria, Thamnocalamus, Schizostachyum, Racemobambos, Drepanostachyum, Arundinaria and Bashania. However, in the temperate Arundinariinae, sequence data was not capable of refining boundaries between closely related genera, for which different molecular markers may prove more useful. [ABSTRACT FROM AUTHOR]

Background and Aims Improved understanding of the secondary gene pools of crops is essential for advancing genetic gain in breeding programmes. Common bean, Phaseolus vulgaris, is a staple crop with several wild relatives in its secondary gene pool. The year-long bean, P. dumosus, an important crop in Guatemala, is considered particularly closely related to P. vulgaris and a potential source of novel variation. However, the genetic diversity and relationship to other Phaseolus species of P. dumosus remain unclear. Methods We conducted the first comprehensive investigation of P. dumosus genetic diversity using both nuclear and chloroplast genome markers. Our nuclear marker set included over 700 markers present within the Phaseolus DArT (Diversity Arrays Technology) array, which we applied to P. dumosus and other relatives of P. vulgaris (including every secondary gene pool species: P. acutifolius, P. albescens, P. coccineus and P. costaricensis). Key Results Phaseolus dumosus arose from hybridization of P. vulgaris and P. coccineus, followed by at least two later hybridizations with sympatric congener populations. Existing P. dumosus collections have low genetic diversity. Conclusions The under-utilized crop P. dumosus has a complex hybrid origin. Further sampling in the region in which it arose may uncover additional germplasm for introgressing favourable traits into crops within the P. vulgaris gene pool. [ABSTRACT FROM AUTHOR]