Oat species and interspecific amphiploids show predominance of diploid nuclei in the syncytial endosperm

Apart from apomictic types, the Polygonum-type eight-nuclear embryo sac is considered to be dominant in grasses. A triploid endosperm is formed as a result of double fertilisation. This study showed, for the first time, the dominance of diploid nuclei in the syncytial stage of the central cell of embryo sac in oat species and amphiploids. The dominance of diploid nuclei, which were the basis for the formation of polyploid nuclei, was weaker in amphiploids due to aneuploid events. The genomic in situ hybridisation method applied in the study did not distinguish the maternal and paternal haploid nuclei of embryo sac. However, this method demonstrated the lack of a set of genomes of one haploid nucleus. Embryological analyses of the initial stages of oat endosperm development revealed a fertilised egg cell, and two polar nuclei differing in size. It can be assumed that the formation of diploid oat endosperm occurred after the fusion of one polar nucleus and the nucleus of a male gamete, while the second polar nucleus gave rise to 1n nuclei. The levels of ploidy of syncytial nuclei were not influenced by both aneuploid events and correlated with pollen developmental anomalies. The differences in the analysed cytogenetic events distinguished amphiploids and their parental species in the ordination space.

Genome-wide expansion and reorganization during grass evolution: from 30 Mb chromosomes in rice and Brachypodium to 550 Mb in Avena

BACKGROUND

The BOP (Bambusoideae, Oryzoideae, and Pooideae) clade of the Poaceae has a common ancestor, with similarities to the genomes of rice, Oryza sativa (2n = 24; genome size 389 Mb) and Brachypodium, Brachypodium distachyon (2n = 10; 271 Mb). We exploit chromosome-scale genome assemblies to show the nature of genomic expansion, structural variation, and chromosomal rearrangements from rice and Brachypodium, to diploids in the tribe Aveneae (e.g., Avena longiglumis, 2n = 2x = 14; 3,961 Mb assembled to 3,850 Mb in chromosomes).

RESULTS

Most of the Avena chromosome arms show relatively uniform expansion over the 10-fold to 15-fold genome-size increase. Apart from non-coding sequence diversification and accumulation around the centromeres, blocks of genes are not interspersed with blocks of repeats, even in subterminal regions. As in the tribe Triticeae, blocks of conserved synteny are seen between the analyzed species with chromosome fusion, fission, and nesting (insertion) events showing deep evolutionary conservation of chromosome structure during genomic expansion. Unexpectedly, the terminal gene-rich chromosomal segments (representing about 50 Mb) show translocations between chromosomes during speciation, with homogenization of genome-specific repetitive elements within the tribe Aveneae. Newly-formed intergenomic translocations of similar extent are found in the hexaploid A. sativa.

CONCLUSIONS

The study provides insight into evolutionary mechanisms and speciation in the BOP clade, which is valuable for measurement of biodiversity, development of a clade-wide pangenome, and exploitation of genomic diversity through breeding programs in Poaceae.

Chromosomal Location of Pm12-A Novel Powdery Mildew Resistance Gene from Avena sterilis

Identification of new, effective disease resistance genes is a very important aspect of plant breeding. Also important is the precise location of individual loci and tagging them with DNA markers for marker assisted selection. The aim of the present study was identification of the molecular markers linked with Pm12, a new effective resistance gene to powdery mildew, and their location in the oat genome. The analysis was performed on 167 F₂ individuals from a hybrid of Fuchs × CN67383, with the status of the locus in each individual verified by progeny test in F₃. Segregation ratios confirmed the monogenic nature of resistance. Making use of the sequence data of DNA markers and the oat OT3098 v2 genome reference assembly, Pm12 is located on chromosome 7C. A comparison was also made with the reference consensus map, to which there are more reports of mapped genes to date. The mapping results suggest that Pm12 is located in the interval 103.8-111.7 cM on this map. No powdery mildew resistance locus has been identified in this region so far, suggesting that Avena sterilis CN67383 carries a novel locus offering effective resistance in oat breeding. The information included in the oat genome annotation allowed for the identification of candidate genes in the close region of the marker cluster for Pm12. This information may provide an interesting source of further analysis of the pathways of various genes in response to the stress of powdery mildew infection.

Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids

Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic translocations, in contrast to wheats where these translocations are relatively rare. We aimed to show genome structural diversity and genome relationships in tetraploid, hexaploid and octoploid Avena species and amphiploids, establishing patterns of intergenomic translocations across different oat taxa using fluorescence in situ hybridization (FISH) with four well-characterized repetitive DNA sequences: pAs120, AF226603, Ast-R171 and Ast-T116. In A. agadiriana (2n=4x=28), the selected probes hybridized to all chromosomes indicating that this species originated from one (autotetraploid) or closely related ancestors with the same genomes. Hexaploid amphiploids were confirmed as having the genomic composition AACCDD, while octoploid amphiploids showed three different genome compositions: AACCCCDD, AAAACCDD or AABBCCDD. The A, B, C, and D genomes of oats differ significantly in their involvement in non-centromeric, intercalary translocations. There was a predominance of distal intergenomic translocations from the C- into the D-genome chromosomes. Translocations from A- to C-, or D- to C-genome chromosomes were less frequent, proving that at least some of the translocations in oat polyploids are non-reciprocal. Rare translocations from A- to D-, D- to A- and C- to B-genome chromosomes were also visualized. The fundamental research has implications for exploiting genomic biodiversity in oat breeding through introgression from wild species potentially with contrasting chromosomal structures and hence deleterious segmental duplications or large deletions in amphiploid parental lines.

Narrative Review on the Effects of Oat and Sprouted Oat Components on Blood Pressure

Hypertension (HTN) is a major risk factor for cardiovascular disease (CVD) and cognitive decline. Elevations in blood pressure (BP) leading to HTN can be found in young adults with increased prevalence as people age. Oats are known to decrease CVD risk via an established effect of β-glucan on the attenuation of blood cholesterol. Many past studies on CVD and oats have also reported a decrease in BP; however, a thorough assessment of oats and BP has not been conducted. Moreover, oats deliver several beneficial dietary components with putative beneficial effects on BP or endothelial function, such as β-glucan, γ-amino butyric acid (GABA), and phytochemicals such as avenanthramides. We conducted a comprehensive search for systematic reviews, meta-analyses, and clinical intervention studies on oats and BP and identified 18 randomized controlled trials (RCTs) and three meta-analyses that supported the role of oats in decreasing BP. Emerging data also suggest oat consumption may reduce the use of anti-hypertensive medications. The majority of these studies utilized whole oats or oat bran, which include a vast array of oat bioactives. Therefore, we also extensively reviewed the literature on these bioactives and their putative effect on BP-relevant mechanisms. The data suggest several oat components, such as GABA, as well as the delivery of high-quality plant protein and fermentable prebiotic fiber, may contribute to the anti-HTN effect of oats. In particular, GABA is enhanced in oat sprouts, which suggests this food may be particularly beneficial for healthy BP management.

Characterization of the complete chloroplast genome of Avena chinensis (Poales: Poaceae)

Avena chinensis is recognized as one of the cereals with high nutritional value in the world. In this study, the complete chloroplast (cp) genome sequence of A. chinensis was reported. The complete cp genome of A. chinensis was 135,899 bp in length with a GC content of 38.51%, including a large single copy (LSC) region of 80,117 bp, a small single copy (SSC) region of 12,576 bp, and a pair of inverted repeated regions of 21,603 bp. The A. chinensis cp genome encoded 128 functional genes, including 82 protein-coding genes, 38 tRNAs, and eight rRNAs. The phylogenetic analysis showed that A. chinensis was closely related to Avena hybrid and Avena occidentalis.

longiglumis

This study analysed cytogenetic events occurring in the syncytial endosperm of the Avena magna H. C. Murphy & Terrell × Avena longiglumis Durieu amphiploid, which is a product of two wild species having different genomes. Selection through the elimination of chromosomes and their fragments, including those translocated, decreased the level of ploidy in the endosperm below the expected 3n, leading to the modal number close to 2n. During intergenomic translocations, fragments of the heterochromatin-rich C-genome were transferred to the D and Al genomes. Terminal and non-reciprocal exchanges dominated, whereas other types of translocations, including microexchanges, were less common. Using two probes and by counterstaining with DAPI, the A. longiglumis and the rare exchanges between the D and Al genomes were detected by GISH. The large discontinuity in the probe labelling in the C chromosomes demonstrated inequality in the distribution of repetitive sequences along the chromosome and probable intragenomic rearrangements. In the nucleus, the spatial arrangement of genomes was non-random and showed a sectorial-concentric pattern, which can vary during the cell cycle, especially in the less stable tissue like the hybrid endosperm.

Growth-promoting effects of Bradyrhizobium soybean symbionts in black oats, white oats, and ryegrass

Although inoculating soybean with rhizobia for biological nitrogen fixation is a common practice in agriculture, rhizobia are also known to associate with grasses. In this study, we evaluate the potential utility of the rhizobial strains SEMIA 587 and 5019 (Bradyrhizobium elkanii), 5079 (Bradyrhizobium japonicum), and 5080 (Bradyrhizobium diazoefficiens), recommended for Brazilian soybean inoculation, in colonizing black oat plants and promoting growth in black and white oats, and ryegrass. Inoculation of white oats with SEMIA 587 increase the seed germination (SG) by 32.09%, whereas the SG of black oats inoculated with SEMIA 587 and 5019 increased by 40.38% and 37.85%, respectively. Similarly, inoculation of ryegrass with all strains increased SG values between 24.63 and 27.59%. In addition, white oats with SEMIA 587 and 5080 had root areas significantly superior to those in other treatments, whereas inoculation with SEMIA 5079 and 5080 resulted in the highest volume of roots. Likewise, SEMIA 5079 and 5080 significantly increased the length, volume, and area of black oats roots, whereas SEMIA 587 increased the volume, area, and dry mass of roots and shoot. Inoculation in ryegrass with SEMIA 587 significantly increased the root volume. Moreover, most strains transformed with gfp and gus were observed to colonize the roots of black oats. Collectively, the findings of this study indicate that rhizobial strains recommended for inoculation of soybean can also be used to promote the growth of the three assessed grass species, and are able to colonize the roots of black oats.

A universal karyotypic system for hexaploid and diploid Avena species brings oat cytogenetics into the genomics era

BACKGROUND

The identification of chromosomes among Avena species have been studied by C-banding and in situ hybridization. However, the complicated results from several cytogenetic nomenclatures for identifying oat chromosomes are often contradictory. A universal karyotyping nomenclature system for precise chromosome identification and comparative evolutionary studies would be essential for genus Avena based on the recently released genome sequences of hexaploid and diploid Avena species.

RESULTS

Tandem repetitive sequences were predicted and physically located on chromosomal regions of the released Avena sativa OT3098 genome assembly v1. Eight new oligonucleotide (oligo) probes for sequential fluorescence in situ hybridization (FISH) were designed and then applied for chromosome karyotyping on mitotic metaphase spreads of A. brevis, A. nuda, A. wiestii, A. ventricosa, A. fatua, and A. sativa species. We established a high-resolution standard karyotype of A. sativa based on the distinct FISH signals of multiple oligo probes. FISH painting with bulked oligos, based on wheat-barley collinear regions, was used to validate the linkage group assignment for individual A. sativa chromosomes. We integrated our new Oligo-FISH based karyotype system with earlier karyotype nomenclatures through sequential C-banding and FISH methods, then subsequently determined the precise breakage points of some chromosome translocations in A. sativa.

CONCLUSIONS

This new universal chromosome identification system will be a powerful tool for describing the genetic diversity, chromosomal rearrangements and evolutionary relationships among Avena species by comparative cytogenetic and genomic approaches.

[Lactic starter cultures to improve the oat bioactive compounds]

The objective of this work was to study lactic fermentation as a biostrategy to enhance the antioxidant activity of oats. The adaptability of 31 strains of lactic bacteria (LB) in an oats/water system (OWS/SAA) was evaluated, measuring growth, acidification and fermentation activity (impedimetric method; detection time [DT], maximum rate of conductance change [MRCC/VMCC] and percentage of conductance change [PCC]). Moreover, the content of phenolic compounds (PC) was determined using the Folin-Ciocalteu method (gallic acid equivalents [GAE]), free peptides and amino acids and free radical scavenging activity (DPPH^• and ABTS^•+ methods) of methanolic and aqueous extracts obtained from fermented OWS/SAAs (fOWS/SAAf) were determined. Six strains have shown the best adaptability to SAA, with high values of VMCC (0.34-0.47 μS/min) and PCC (53.6-66.6%), and low values of DT (≤ 3 h). In these f/OWS/SAAf the chemical composition was also modified (PC concentration, peptides and free amino acids) with strain-dependent behavior. The PC content in f/OWS/SAAf using these six strains (29.1-36.9 μg GAE/ml) was higher than the control content in OWS/SAA control (17.1 ± 1.9 μg GAE/ml). An increase (9-25.5%) in antioxidant activity in f/OWS/SAAf methanolic extracts was detected using both methods. Minor modifications were observed in the peptide and free amino acid content of SAA and their antioxidant activity. Our results show LB ability to adapt to oat as fermentation substrate and increase the content of its antioxidant compounds.

Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

BACKGROUND

Oat (Avena sativa L.) is a recognized health-food, and the contributions of its different candidate A-genome progenitor species remain inconclusive. Here, we report chloroplast genome sequences of eleven Avena species, to examine the plastome evolutionary dynamics and analyze phylogenetic relationships between oat and its congeneric wild related species.

RESULTS

The chloroplast genomes of eleven Avena species (size range of 135,889-135,998 bp) share quadripartite structure, comprising of a large single copy (LSC; 80,014-80,132 bp), a small single copy (SSC; 12,575-12,679 bp) and a pair of inverted repeats (IRs; 21,603-21,614 bp). The plastomes contain 131 genes including 84 protein-coding genes, eight ribosomal RNAs and 39 transfer RNAs. The nucleotide sequence diversities (Pi values) range from 0.0036 (rps19) to 0.0093 (rpl32) for ten most polymorphic genes and from 0.0084 (psbH-petB) to 0.0240 (petG-trnW-CCA) for ten most polymorphic intergenic regions. Gene selective pressure analysis shows that all protein-coding genes have been under purifying selection. The adjacent position relationships between tandem repeats, insertions/deletions and single nucleotide polymorphisms support the evolutionary importance of tandem repeats in causing plastome mutations in Avena. Phylogenomic analyses, based on the complete plastome sequences and the LSC intermolecular recombination sequences, support the monophyly of Avena with two clades in the genus.

CONCLUSIONS

Diversification of Avena plastomes is explained by the presence of highly diverse genes and intergenic regions, LSC intermolecular recombination, and the co-occurrence of tandem repeat and indels or single nucleotide polymorphisms. The study demonstrates that the A-genome diploid-polyploid lineage maintains two subclades derived from different maternal ancestors, with A. longiglumis as the first diverging species in clade I. These genome resources will be helpful in elucidating the chloroplast genome structure, understanding the evolutionary dynamics at genus Avena and family Poaceae levels, and are potentially useful to exploit plastome variation in making hybrids for plant breeding.

Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species

BACKGROUND

Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As- and Cp-subgenomes, Avena atlantica and Avena eriantha respectively. The diploid Avena species serve as important genetic resources for improving common oat's adaptive and food quality characteristics.

RESULTS

The A. atlantica and A. eriantha genome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species-including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance (Pc91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species.

CONCLUSIONS

The genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.

Developing Chloroplast Genomic Resources from 25 Avena Species for the Characterization of Oat Wild Relative Germplasm

Chloroplast (cp) genomics will play an important role in the characterization of crop wild relative germplasm conserved in worldwide gene banks, thanks to the advances in genome sequencing. We applied a multiplexed shotgun sequencing procedure to sequence the cp genomes of 25 Avena species with variable ploidy levels. Bioinformatics analysis of the acquired sequences generated 25 de novo genome assemblies ranging from 135,557 to 136,006 bp. The gene annotations revealed 130 genes and their duplications, along with four to six pseudogenes, for each genome. Little differences in genome structure and gene arrangement were observed across the 25 species. Polymorphism analyses identified 1313 polymorphic sites and revealed an average of 277 microsatellites per genome. Greater nucleotide diversity was observed in the short single-copy region. Genome-wide scanning of selection signals suggested that six cp genes were under positive selection on some amino acids. These research outputs allow for a better understanding of oat cp genomes and evolution, and they form an essential set of cp genomic resources for the studies of oat evolutionary biology and for oat wild relative germplasm characterization.

Rainfall variability maintains grass-forb species coexistence

Environmental variability can structure species coexistence by enhancing niche partitioning. Modern coexistence theory highlights two fluctuation-dependent temporal coexistence mechanisms -the storage effect and relative nonlinearity - but empirical tests are rare. Here, we experimentally test if environmental fluctuations enhance coexistence in a California annual grassland. We manipulate rainfall timing and relative densities of the grass Avena barbata and forb Erodium botrys, parameterise a demographic model, and partition coexistence mechanisms. Rainfall variability was integral to grass-forb coexistence. Variability enhanced growth rates of both species, and early-season drought was essential for Erodium persistence. While theoretical developments have focused on the storage effect, it was not critical for coexistence. In comparison, relative nonlinearity strongly stabilised coexistence, where Erodium experienced disproportionately high growth under early-season drought due to competitive release from Avena. Our results underscore the importance of environmental variability and suggest that relative nonlinearity is a critical if underappreciated coexistence mechanism.

Genetic Transformation of Oat Mediated by Agrobacterium is enhanced with Sonication and Vacuum Infiltration

BACKGROUND

Oat (Avena sativa) with high nutritive value and fiber content is used as the main food grain in many countries for human diet as well as animal feed. Recently, it became difficult to transfer new genes through the conventional breeding due to the lack of desirable traits.

OBJECTIVES

The current study aimed at achieving a standardized protocol for Agrobacterium-mediated transformation in oat.

MATERIALS AND METHODS

For oat transformation, mature seeds were sterilized, germinated, and used for explants generation. Agrobacterium tumefaciens GV3101 with the binary vector pCAMBIA 1305.1, which carries gus as reporter gene, was utilized in the transformation. The co-cultivation treatment assisted with sonication, and vacuum infiltration, and their combination was employed for transformation with different incubation periods of 48, 72, and 96 hours under the dark conditions.

RESULTS

Among the different transformation treatments, the vacuum treatment with 72 hours dark incubation had the best results. Vacuum infiltration of the cultures from leaf base produced a maximum of 25% hygromycin-resistant explants. These explants upon GUS assay and PCR analysis revealed 21.85% and 19.04% transformation efficiency, respectively.

CONCLUSIONS

It could be concluded that vacuum infiltration assisted Agrobacterium-mediated transformation is the most efficient method to conduct the genetic improvement of the oat using transformation protocol.

Instability of endosperm development in amphiploids and their parental species in the genus Avena L

The development of oat endosperm is modified by chromatin and nuclei elimination, intrusive growth of cell walls, and polyploidisation of cell clones. The last event is correlated with somatic crossing-over. Grass endosperm is a variable tissue in terms of its cytogenetics and development. Free-nuclear syncytium and starchy and aleurone endosperm were the main focus of the research. These were studied in oat amphiploids (4x, 6x, and 8x) and parental species (2x, 4x, and 6x). What the levels of cytogenetic disorders and developmental anomalies in species versus hybrids are, and, what the factors are determining phenotypes of both tissue components, are open questions for oats. Chromosome bridges and micronuclei are the main cytogenetic disorders showing the elimination of parts of genomes. Bridges are formed by the AT-heterochromatin-rich and -free ends of chromosomes. In the starchy tissue, various sectors are separated structurally due to the elongation or intrusive growth of aleurone cells. The development of the aleurone layer is highly disturbed locally due to the amplification of aleurone cell divisions. Changes related to their structure and metabolism occur in the aleurone cells, for example, clones of small versus large aleurone cells. Somatic crossing-over (SCO) is expressed in clones of large polyploidised cells (r = 0.80***), giving rise to new aleurone phenotypes. The multivariate description of the endosperm instability showed that endospermal disorders were more frequent in amphiploids than in the oat species. Avena strigosa and the amphiploid A. fatua × A. sterilis appeared to be extreme units in an ordination space. Nuclear DNA elimination, periclinal and multidirectional cytokineses, polyploidisation, intrusive growth, and SCO appeared to be important factors determining oat endospermal variations.

Oats in healthy gluten-free and regular diets: A perspective

During the 20th century, the economic position of oats (Avena sativa L.) decreased strongly in favour of higher yielding crops including winter wheat and maize. Presently, oat represents only ~1.3% of the total world grain production, and its production system is fragmented. Nonetheless, current interest is growing because of recent knowledge on its potential benefits in food, feed and agriculture. This perspective will serve as a further impetus, with special focus on the recently valued advantages of oats in human food and health. Five approved European Food Safety Authority (EFSA) health claims apply to oats. Four relate to the oat-specific soluble fibres, the beta-glucans, and concern the maintenance and reduction of blood cholesterol, better blood glucose balance and increased faecal bulk. The fifth claim concerns the high content of unsaturated fatty acids, especially present in the endosperm, which reduces the risks of heart and vascular diseases. Furthermore, oat starch has a low glycemic index, which is favourable for weight control. Oat-specific polyphenols and avenanthramides have antioxidant and anti-inflammatory properties. Thus, oats can contribute significantly to the presently recommended whole-grain diet. Next to globulins, oats contain a small fraction of prolamin storage proteins, called 'avenins', but at a much lower quantity than gluten proteins in wheat, barley and rye. Oat avenins do not contain any of the known coeliac disease epitopes from gluten of wheat, barley and rye. Long-term food studies confirm the safety of oats for coeliac disease patients and the positive health effects of oat products in a gluten-free diet. These effects are general and independent of oat varieties. In the EU (since 2009), the USA (since 2013) and Canada (since 2015) oat products may be sold as gluten-free provided that any gluten contamination level is below 20ppm. Oats are, however, generally not gluten-free when produced in a conventional production chain, because of regular contamination with wheat, barley or rye. Therefore, establishing a separate gluten-free oat production chain requires controlling all steps in the chain; the strict conditions will be discussed. Genomic tools, including a single nucleotide polymorphism (SNP) marker array and a dense genetic map, have recently been developed and will support marker-assisted breeding. In 2015, the Oat Global initiative emerged enabling a world-wide cooperation starting with a data sharing facility on genotypic, metabolic and phenotypic characteristics. Further, the EU project TRAFOON (Traditional Food Networks) facilitated the transfer of knowledge to small- and medium-sized enterprises (SMEs) to stimulate innovations in oat production, processing, products and marketing, among others with regard to gluten-free. Finally, with focus on counteracting market fragmentation of the global oat market and production chains, interactive innovation strategies between customers (consumers) and companies through co-creation are discussed.

Tyramide Signal Amplification: Fluorescence In Situ Hybridization for Identifying Homoeologous Chromosomes

Tyramide signal amplification (TSA) fluorescence in situ hybridization (FISH) has been shown as a valuable molecular tool for visualizing specific amplified DNA sequences in chromosome preparations. This chapter describes how to perform TSA-FISH, paying special interest to its two critical steps: probe generation and metaphase plate generation. The potential of physically mapping 12S-globulin sequences by TSA-FISH as a means of identifying homeology among chromosome regions of Avena species was tested and is discussed.

Chromosomal distribution patterns of the (AC)10 microsatellite and other repetitive sequences, and their use in chromosome rearrangement analysis of species of the genus Avena

Fluorescence in situ hybridization (FISH) was used to determine the physical location of the (AC)₁₀ microsatellite in metaphase chromosomes of six diploid species (AA or CC genomes), two tetraploid species (AACC genome), and five cultivars of two hexaploid species (AACCDD genome) of the genus Avena, a genus in which genomic relationships remain obscure. A preferential distribution of the (AC)₁₀ microsatellite in the pericentromeric and interstitial regions was seen in both the A- and D-genome chromosomes, while in C-genome chromosomes the majority of signals were located in the pericentromeric heterochromatic regions. New large chromosome rearrangements were detected in two polyploid species: an intergenomic translocation involving chromosomes 17AL and 21DS in Avena sativa 'Araceli' and another involving chromosomes 4CL and 21DS in the analyzed cultivars of Avena byzantina. The latter 4CL-21DS intergenomic translocation differentiates clearly between A. sativa and A. byzantina. Searches for common hybridization patterns on the chromosomes of different species revealed chromosome 10A of Avena magna and 21D of hexaploid oats to be very similar in terms of the distribution of 45S and Am1 sequences. This suggests a common origin for these chromosomes and supports a CCDD rather than an AACC genomic designation for this species.

The starch-bound alpha-amylase/trypsin-inhibitors in Avena

Oat kernels exhibit an extra-soft texture, a trait recently demonstrated to be largely modulated by starch-bound tryptophan-rich 2S proteins, the vromindolines. In this study, fractionation by two-dimensional electrophoresis of starch-bound proteins in 25 oat (Avena sativa) cultivars and 11 diploid or tetraploid Avena species revealed novel 2S proteins called Avena α-amylase/trypsin-inhibitors (AATI) because of their sequence similarity with wheat α-amylase/trypsin inhibitors. Thirty-seven AATI polypeptides, about 14 kDa in size, were split into three families named AATI-1, AATI-2, and AATI-3 with different primary structures and isoelectric points. AATI-1 and AATI-2 proteins showed 55.5-60.0 % sequence similarity with wheat α-amylase inhibitors CM1, CM2, and CM16, which have been found to cause innate immunity responses in celiac disease and non-celiac gluten sensitivity. Diploid A-genome and tetraploid AC-genome oat species possess three and five genes encoding for the AATI proteins, respectively, whereas hexaploid A. sativa exhibits 12 genes dispersed over the A-, C-, and D-genomes. Some AATI proteins expressed in hexaploid oats were assigned to the A-genome based on similarity to their counterparts in diploid species, contributing to further clarify the genetic origin of hexaploid oats. Moreover, AATI may interact with starch-bound vromindolines in determining the extra-soft texture of oat kernels and, due to their balanced amino acid compositions, may contribute to the biological value of oat proteins in a positive manner.

C-Banding of Plant Chromosomes

C-banding is used to differentially stain metaphase chromosomes in organisms having appreciable amounts of constitutive heterochromatin. Its primary benefits are that it is an inexpensive and a relatively fast method of identifying individual chromosomes and morphological or karyotypic variation, including large chromosomal rearrangements and aneuploidies. We currently employ this technique with considerable effect in genome analysis of oat (Avena sativa) and related grass species, though it has been most extensively used for chromosome analysis of wheat (Triticum aestivum) and its relatives of the Triticeae.

Multistep food plant processing at Grotta Paglicci (Southern Italy) around 32,600 cal B.P

Residue analyses on a grinding tool recovered at Grotta Paglicci sublayer 23A [32,614 ± 429 calibrated (cal) B.P.], Southern Italy, have demonstrated that early modern humans collected and processed various plants. The recording of starch grains attributable to Avena (oat) caryopses expands our information about the food plants used for producing flour in Europe during the Paleolithic and about the origins of a food tradition persisting up to the present in the Mediterranean basin. The quantitative distribution of the starch grains on the surface of the grinding stone furnished information about the tool handling, confirming its use as a pestle-grinder, as suggested by the wear-trace analysis. The particular state of preservation of the starch grains suggests the use of a thermal treatment before grinding, possibly to accelerate drying of the plants, making the following process easier and faster. The study clearly indicates that the exploitation of plant resources was very important for hunter-gatherer populations, to the point that the Early Gravettian inhabitants of Paglicci were able to process food plants and already possessed a wealth of knowledge that was to become widespread after the dawn of agriculture.

Phylogenetic analysis of the genus Avena based on chloroplast intergenic spacer psbA-trnH and single-copy nuclear gene Acc1

Two uncorrelated nucleotide sequences, chloroplast intergenic spacer psbA-trnH and acetyl CoA carboxylase gene (Acc1), were used to perform phylogenetic analyses in 75 accessions of the genus Avena, representing 13 diploids, seven tetraploid, and four hexaploids by maximum parsimony and Bayesian inference. Phylogenic analyses based on the chloroplast intergenic spacer psbA-trnH confirmed that the A genome diploid might be the maternal donor of species of the genus Avena. Two haplotypes of the Acc1 gene region were obtained from the AB genome tetraploids, indicating an allopolyploid origin for the tetraploid species. Among the AB genome species, both gene trees revealed differences between Avena agadiriana and the other species, suggesting that an AS genome diploid might be the A genome donor and the other genome diploid donor might be the Ac genome diploid Avena canariensis or the Ad genome diploid Avena damascena. Three haplotypes of the Acc1 gene have been detected among the ACD genome hexaploid species. The haplotype that seems to represent the D genome clustered with the tetraploid species Avena murphyi and Avena maroccana, which supported the CD genomic designation instead of AC for A. murphyi and A. maroccana.

A novel noninvasive procedure for high-throughput screening of major seed traits

The large numbers of samples processed in breeding and biodiversity programmes require the development of efficient methods for the nondestructive evaluation of basic seed properties. Near-infrared spectroscopy is the state-of-the-art solution for this analytical demand, but it also has some limitations. Here, we present a novel, rapid, accurate procedure based on time domain-nuclear magnetic resonance (TD-NMR), designed to simultaneously quantify a number of basic seed traits without any seed destruction. Using a low-field, benchtop (1) H-NMR instrument, the procedure gives a high-accuracy measurement of oil content (R(2) = 0.98), carbohydrate content (R(2) = 0.99), water content (R(2) = 0.98) and both fresh and dry weight of seeds/grains (R(2) = 0.99). The method requires a minimum of ~20 mg biomass per sample and thus enables to screen individual, intact seeds. When combined with an automated sample delivery system, a throughput of ~1400 samples per day is achievable. The procedure has been trialled as a proof of concept on cereal grains (collection of ~3000 accessions of Avena spp. curated at the IPK genebank). A mathematical multitrait selection approach has been designed to simplify the selection of outlying (most contrasting) accessions. To provide deeper insights into storage oil topology, some oat accessions were further analysed by three-dimensional seed modelling and lipid imaging. We conclude that the novel TD-NMR-based screening tool opens perspectives for breeding and plant biology in general.

Expression of the Commelina yellow mottle virus promoter in transgenic oat

The Commelina yellow mottle virus (CoYMV) infects the monocot weed Commelina diffusa. The objective of this study was to investigate the transgene expression conferred by the CoYMV promoter in a monocot species. Friable, embryogenic oat (Avena sativa L.) tissue cultures were stably transformed with the CoYMV promoter fused to the coding region of E. coli β-glucuronidase (uidA, GUS). Developmental and tissue-specific expression of the CoYMV-GUS construct was investigated in regenerated plants and their progeny. Histochemical GUS staining was primarily localized in the vascular tissues of shoots, leaves, floral bracts and in roots. While ovaries stained intensely, no staining was detected in anthers or the endosperm in mature seed. The scutellum of mature and germinating seed exhibited GUS activity.

multiflorum Lam

The pattern of recovery in seedlings of cultivars of Lolium perenne, L. multiflorum and Avena sativa was studied after an artificial freezing test at various stages of hardening. Unhardened plants of the three species were killed at about -6°C. The temperature at which plant mortality of hardened plants occurred was lower and was characteristic of the genotype, the hardening environment and the duration of the hardening treatment. A detailed analysis of the mode of recovery showed that the actively growing apex of the main tiller did not appear to develop increased resistance to freezing since it was killed at about -6°C in all hardening treatments. Improved survival of hardened plants at lower freezing temperatures could not be attributed to improved hardiness of the main apex but depended on the ability to establish viable regrowth from lateral tiller buds during the recovery period. This method of recovery is discussed in relation to possible physiological mechanisms of freezing tolerance including the release of apical dominance after death of the main apex and the sufficiency of post-freezing carbon assimilation.