Differentially methylated genes involved in reproduction and ploidy levels in recent diploidized and tetraploidized Eragrostis curvula genotypes.

Epigenetics studies changes in gene activity without changes in the DNA sequence. Methylation is an epigenetic mechanism important in many pathways, such as biotic and abiotic stresses, cell division, and reproduction. Eragrostis curvula is a grass species reproducing by apomixis, a clonal reproduction by seeds. This work employed the MCSeEd technique to identify deferentially methylated positions, regions, and genes in the CG, CHG, and CHH contexts in E. curvula genotypes with similar genomic backgrounds but with different reproductive modes and ploidy levels. In this way, we focused the analysis on the cvs. Tanganyika INTA (4x, apomictic), Victoria (2x, sexual), and Bahiense (4x, apomictic). Victoria was obtained from the diploidization of Tanganyika INTA, while Bahiense was produced from the tetraploidization of Victoria. This study showed that polyploid/apomictic genotypes had more differentially methylated positions and regions than the diploid sexual ones. Interestingly, it was possible to observe fewer differentially methylated positions and regions in CG than in the other contexts, meaning CG methylation is conserved across the genotypes regardless of the ploidy level and reproductive mode. In the comparisons between sexual and apomictic genotypes, we identified differentially methylated genes involved in the reproductive pathways, specifically in meiosis, cell division, and fertilization. Another interesting observation was that several differentially methylated genes between the diploid and the original tetraploid genotype recovered their methylation status after tetraploidization, suggesting that methylation is an important mechanism involved in reproduction and ploidy changes.

A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality.

The Poaceae constitute a taxon of flowering plants (grasses) that cover almost all Earth's inhabitable range and comprises some of the genera most commonly used for human and animal nutrition. Many of these crops have been sequenced, like rice, Brachypodium, maize and, more recently, wheat. Some important members are still considered orphan crops, lacking a sequenced genome, but having important traits that make them attractive for sequencing. Among these traits is apomixis, clonal reproduction by seeds, present in some members of the Poaceae like Eragrostis curvula. A de novo, high-quality genome assembly and annotation for E. curvula have been obtained by sequencing 602 Mb of a diploid genotype using a strategy that combined long-read length sequencing with chromosome conformation capture. The scaffold N50 for this assembly was 43.41 Mb and the annotation yielded 56,469 genes. The availability of this genome assembly has allowed us to identify regions associated with forage quality and to develop strategies to sequence and assemble the complex tetraploid genotypes which harbor the apomixis control region(s). Understanding and subsequently manipulating the genetic drivers underlying apomixis could revolutionize agriculture.

Temporal and spatial expression of genes involved in DNA methylation during reproductive development of sexual and apomictic Eragrostis curvula.

Recent reports in model plant species have highlighted a role for DNA methylation pathways in the regulation of the somatic-to-reproductive transition in the ovule, suggesting that apomixis (asexual reproduction through seeds) likely relies on RdDM downregulation. Our aim was therefore to explore this hypothesis by characterizing genes involved in DNA methylation in the apomictic grass Eragrostis curvula. We explored floral transcriptomes to identify homologs of three candidate genes, for which mutations in Arabidopsis and maize mimic apomixis (AtAGO9/ZmAGO104, AtCMT3/ZmDMT102/ZmDMT105, and AtDDM1/ZmCHR106), and compared both their spatial and temporal expression patterns during reproduction in sexual and apomictic genotypes. Quantitative expression analyses revealed contrasting expression patterns for the three genes in apomictic vs sexual plants. In situ hybridization corroborated these results for two candidates, EcAGO104 and EcDMT102, and revealed an unexpected ectopic pattern for the AGO gene during germ line differentiation in apomicts. Although our data partially support previous results obtained in sexual plant models, they suggest that rather than an RdDM breakdown in the ovule, altered localization of AtAGO9/ZmAGO104 expression is required for achieving diplospory in E. curvula. The differences in the RdDM machinery acquired during plant evolution might have promoted the emergence of the numerous apomictic paths observed in plants.

QTL analysis of pasta quality using a composite microsatellite and SNP map of durum wheat.

Bright yellow color, firmness and low cooking loss are important factors for the production of good-quality pasta products. However, the genetic factors underlying those traits are still poorly understood. To fill this gap we developed a population of 93 recombinant inbred lines (RIL) from the cross between experimental line UC1113 (intermediate pasta quality) with the cultivar Kofa (excellent pasta quality). A total of 269 markers, including 23 SNP markers, were arranged on 14 linkage groups covering a total length of 2,140 cM. Samples from each RIL from five different environments were used for complete pasta quality testing and the results from each year were used for QTL analyses. The combined effect of different loci, environment and their interactions were analyzed using factorial ANOVAs for each trait. We identified major QTLs for pasta color on chromosomes 1B, 4B, 6A, 7A and 7B. The 4B QTL was linked to a polymorphic deletion in the Lpx-B1.1 lipoxygenase locus, suggesting that it was associated with pigment degradation during pasta processing. The 7B QTL for pasta color was linked to the Phytoene synthase 1 (Psy-B1) locus suggesting difference in pigment biosynthesis. QTLs affecting pasta firmness and cooking loss were detected on chromosomes 5A and 7B, and in both cases they were overlapping with QTL for grain protein content and wet gluten content. These last two parameters were highly correlated with pasta firmness (R > 0.71) and inversely correlated to cooking loss (R < -0.37). The location and effect of other QTLs affecting grain size and weight, gluten strength, mixing properties, and ash content are also discussed.

Construction and evaluation of cDNA libraries for large-scale expressed sequence tag sequencing in wheat (Triticum aestivum L.).

A total of 37 original cDNA libraries and 9 derivative libraries enriched for rare sequences were produced from Chinese Spring wheat (Triticum aestivum L.), five other hexaploid wheat genotypes (Cheyenne, Brevor, TAM W101, BH1146, Butte 86), tetraploid durum wheat (T. turgidum L.), diploid wheat (T. monococcum L.), and two other diploid members of the grass tribe Triticeae (Aegilops speltoides Tausch and Secale cereale L.). The emphasis in the choice of plant materials for library construction was reproductive development subjected to environmental factors that ultimately affect grain quality and yield, but roots and other tissues were also included. Partial cDNA expressed sequence tags (ESTs) were examined by various measures to assess the quality of these libraries. All ESTs were processed to remove cloning system sequences and contaminants and then assembled using CAP3. Following these processing steps, this assembly yielded 101,107 sequences derived from 89,043 clones, which defined 16,740 contigs and 33,213 singletons, a total of 49,953 "unigenes." Analysis of the distribution of these unigenes among the libraries led to the conclusion that the enrichment methods were effective in reducing the most abundant unigenes and to the observation that the most diverse libraries were from tissues exposed to environmental stresses including heat, drought, salinity, or low temperature.

Precise mapping of a locus affecting grain protein content in durum wheat.

Grain protein content (GPC) is an important factor in pasta and breadmaking quality, and in human nutrition. It is also an important trait for wheat growers because premium prices are frequently paid for wheat with high GPC. A promising source for alleles to increase GPC was detected on chromosome 6B of Triticum turgidum var. dicoccoides accession FA-15-3 (DIC). Two previous quantitative trait locus (QTL) studies found that the positive effect of DIC-6B was associated to a single locus located between the centromere and the Nor-B2 locus on the short arm of chromosome 6B. Microsatellite markers Xgwm508 and Xgwm193 flanking the QTL region were used in this study to develop 20 new homozygous recombinant substitution lines (RSLs) with crossovers between these markers. These 20 RSLs, plus nine RSLs developed in previous studies were characterized with four new RFLP markers located within this chromosome segment. Grain protein content was determined in three field experiments organized as randomized complete block designs with ten replications each. The QTL peaks for protein content were located in the central region of a 2.7-cM interval between RFLP markers Xcdo365 and Xucw67 in the three experiments. Statistical analyses showed that almost all lines could be classified unequivocally within low- and high- protein groups, facilitating the mapping of this trait as a single Mendelian locus designated Gpc-6B1. The Gpc-6B1 locus was mapped 1.5-cM proximal to Xcdo365 and 1.2-cM distal to Xucw67. These new markers can be used to reduce the size of the DIC chromosome segment selected in marker-assisted selection programs. Markers Nor-B2 and Xucw66 flanking the previous two markers can be used to select against the DIC segment and reduce the linkage drag during the transfer of Gpc-6B1 into commercial bread and pasta wheat varieties. The precise mapping of the high GPC gene, the high frequency of recombinants recovered in the targeted region, and the recent development of a tetraploid BAC library including the Gpc-6B1 DIC allele are the first steps towards the map-based cloning of this gene.

Cereal genes similar to Snf2 define a new subfamily that includes human and mouse genes.

Genes from the SNF2 family play important roles in transcriptional regulation, maintenance of chromosome integrity and DNA repair. This study describes the molecular cloning and characterization of cereal genes from this family. The predicted proteins exhibit a novel C-terminal domain that defines a new subfamily designated SNF2P that includes human and mouse proteins. Comparison between genomic and cDNA sequences showed that cereal Snf2P genes consisted of 17 exons, including one only 8 bp long. Two barley alleles differed by the presence of a 7.7-kb non-LTR retrotransposon in intron 6. An alternative annotation of the orthologous Arabidopsis gene would improve its similarity with the other members of the subfamily. Intron 2 was not spliced out in approximately half of the rice Snf2P mRNAs present in leaves, resulting in a premature stop codon. Transcripts from the barley and wheat Snf2P genes were found in apexes, leaves, sheaths, roots and spikes. The Snf2P genes exist as single copies on wheat chromosome arm 5A(m)L and in the colinear regions on barley chromosome arm 4HL and rice chromosome 3. High-density genetic mapping and RT-PCR suggest that Snf2P is not a candidate gene for the tightly linked vernalization gene Vrn2.

Water relations and leaf growth rate of three Agropyron genotypes under water stress

The effects of water stress on leaf water relations and growth are reported for three perennial tussock grass genotypes under glasshouse conditions. Studies were performed in genotypes El Palmar INTA and Selección Anguil of Agropyron scabrifolium (Dõell) Parodi, and El Vizcachero of A. elongatum (Host) Beauv. Agropyron scabrifolium El Palmar INTA is native to a region with warm-temperate and humid climate without a dry season, and an average annual precipitation of 900 mm. Agropyron scabrifolium Selección Anguil comes from a region with a sub-humid, dry to semiarid climate and a mean annual precipitation of 600 mm. Agropyron elongatum is a widespread forage in semiarid Argentina with well-known water stress resistance. A mild water stress treatment was imposed slowly; plants reached a minimum pre-dawn leaf water potential of about -1.83 MPa by day 21 after watering was withheld. In all genotypes, water stress led to a reduction of leaf growth. There was a tendency for a greater epicuticular wax accumulation on water-stressed plants of A. scabrifolium Selección Anguil and A. elongatum than on those of A. scabrifolium El Palmar INTA. This may have contributed to obtain greater turgor pressures and relative water contents in the first two than in the later genotype. In turn, this may have contributed to determine smaller leaf growth rate reductions in A. scabrifolium Selección Anguil and A. elongatum than in A. scabrifolium El Palmar INTA under water stress. This study demonstrated variation in water stress resistance between genotypes in A. scabrifolium, and between A. scabrifolium Selección Anguil and A. elongatum versus A. scabrifolium El Palmar INTA, which was related to their differential responses in water relations.

Water relations and leaf growth rate of three Agropyron genotypes under water stress

The effects of water stress on leaf water relations and growth are reported for three perennial tussock grass genotypes under glasshouse conditions. Studies were performed in genotypes El Palmar INTA and Selección Anguil of Agropyron scabrifolium (D÷ell) Parodi, and El Vizcachero of A. elongatum (Host) Beauv. Agropyron scabrifolium El Palmar INTA is native to a region with warm-temperate and humid climate without a dry season, and an average annual precipitation of 900 mm. Agropyron scabrifolium Selección Anguil comes from a region with a sub-humid, dry to semiarid climate and a mean annual precipitation of 600 mm. Agropyron elongatum is a widespread forage in semiarid Argentina with well-known water stress resistance. A mild water stress treatment was imposed slowly; plants reached a minimum pre-dawn leaf water potential of about -1.83 MPa by day 21 after watering was withheld. In all genotypes, water stress led to a reduction of leaf growth. There was a tendency for a greater epicuticular wax accumulation on water-stressed plants of A. scabrifolium Selección Anguil and A. elongatum than on those of A. scabrifolium El Palmar INTA. This may have contributed to obtain greater turgor pressures and relative water contents in the first two than in the later genotype. In turn, this may have contributed to determine smaller leaf growth rate reductions in A. scabrifolium Selección Anguil and A. elongatum than in A. scabrifolium El Palmar INTA under water stress. This study demonstrated variation in water stress resistance between genotypes in A. scabrifolium, and between A. scabrifolium Selección Anguil and A. elongatum versus A. scabrifolium El Palmar INTA, which was related to their differential responses in water relations. (AU)

Frequencies of Ty1- copia and Ty3- gypsy retroelements within the Triticeae EST databases.

The frequency of Ty1- copia-type and Ty3- gypsy-type retrotransposons in the International Triticeae EST Consortium (ITEC) database (61,942 sequences: 82% wheat, 10% barley, 8% rye) and the DuPont EST database (86,628 wheat sequences) was estimated using BLASTN searches. These ESTs were obtained from 94 cDNA libraries from different tissues (leaves, roots, spikes, flowers and seeds) and different growing conditions, excluding subtracted and normalized cDNA libraries. Triticeae EST databases were screened using four different Ty1- -copia-type, 12 reverse transcriptase sequences, and three Ty3- gypsy-type Triticeae retrotransposon sequences. Using a selection threshold of BLASTN scores higher than 100 or E values smaller than e(-20), 0.145% of the ESTs were found to be significantly similar to at least one of the retrotransposons used in the search (0.064% Ty1- copia, 0.081% Ty3- gypsy). This percentage increased to 0.176% when the BLASTN threshold was changed to E

Embryogenic cell suspensions from different explants and cultivars of Eragrostis curvula (Schrad.) Nees.

The aim of this work was the establishment of embryogenic calli and cell suspensions from different explants and cultivars of weeping lovegrass, Eragrostis curvula (Schrad.) Nees, to be used as targets for biolistic transformation. Calli were initiated from immature inflorescences, seeds, embryos, leaf bases and root tips. Modified MS medium (Murashige and Skoog, 1962) was used for calli induction and proliferation. Cell suspensions were established and maintained in AAF medium (Wang et al., 1993). Morphogenic calli, embryogenic cell suspensions of moderate growth rate--consisting mainly of compact proembryogenic cell clusters- and green plants were obtained from all the explants and cultivars assayed, except root tips. Both, explant and genotype were very important factors to be considered in order to obtain a morphogenic response and to establish cell suspensions from this grass. The statistical analysis detected interaction between both factors, explants and genotypes. Immature inflourescences were the best source of explant and Kromdraai was the cultivar that showed the best morphogenic response (expressed as the percentage of calli/explant and the percentage of calli with green spots--every green spot developed into green plants-) with inflourescences, embryos and leaf bases. For Morpa and Don Pablo embryos as explants were less responsive than seeds and leaf bases. There were no differences in leaf bases for all the three cultivars analysed.

Embryogenic cell suspensions from different explants and cultivars of Eragrostis curvula (Schrad.) Nees.

The aim of this work was the establishment of embryogenic calli and cell suspensions from different explants and cultivars of weeping lovegrass, Eragrostis curvula (Schrad.) Nees, to be used as targets for biolistic transformation. Calli were initiated from immature inflorescences, seeds, embryos, leaf bases and root tips. Modified MS medium (Murashige and Skoog, 1962) was used for calli induction and proliferation. Cell suspensions were established and maintained in AAF medium (Wang et al., 1993). Morphogenic calli, embryogenic cell suspensions of moderate growth rate--consisting mainly of compact proembryogenic cell clusters- and green plants were obtained from all the explants and cultivars assayed, except root tips. Both, explant and genotype were very important factors to be considered in order to obtain a morphogenic response and to establish cell suspensions from this grass. The statistical analysis detected interaction between both factors, explants and genotypes. Immature inflourescences were the best source of explant and Kromdraai was the cultivar that showed the best morphogenic response (expressed as the percentage of calli/explant and the percentage of calli with green spots--every green spot developed into green plants-) with inflourescences, embryos and leaf bases. For Morpa and Don Pablo embryos as explants were less responsive than seeds and leaf bases. There were no differences in leaf bases for all the three cultivars analysed.