Avena magna: An Important New Tetraploid Species of Oats

Mapping crown rust resistance in the oat diploid accession PI 258731 (Avena strigosa)

Oat crown rust, caused by Puccinia coronata Corda f. sp. avenae Eriks. (Pca), is a major biotic impediment to global oat production. Crown rust resistance has been described in oat diploid species A. strigosa accession PI 258731 and resistance from this accession has been successfully introgressed into hexaploid A. sativa germplasm. The current study focuses on 1) mapping the location of QTL containing resistance and evaluating the number of quantitative trait loci (QTL) conditioning resistance in PI 258731; 2) understanding the relationship between the original genomic location in A. strigosa and the location of the introgression in the A. sativa genome; 3) identifying molecular markers tightly linked with PI 258731 resistance loci that could be used for marker assisted selection and detection of this resistance in diverse A. strigosa accessions. To achieve this, A. strigosa accessions, PI 258731 and PI 573582 were crossed to produce 168 F5:6 recombinant inbred lines (RILs) through single seed descent. Parents and RILs were genotyped with the 6K Illumina SNP array which generated 168 segregating SNPs. Seedling reactions to two isolates of Pca (races TTTG, QTRG) were conditioned by two genes (0.6 cM apart) in this population. Linkage mapping placed these two resistant loci to 7.7 (QTRG) to 8 (TTTG) cM region on LG7. Field reaction data was used for QTL analysis and the results of interval mapping (MIM) revealed a major QTL (QPc.FD-AS-AA4) for field resistance. SNP marker assays were developed and tested in 125 diverse A. strigosa accessions that were rated for crown rust resistance in Baton Rouge, LA and Gainesville, FL and as seedlings against races TTTG and QTRG. Our data proposed SNP marker GMI_ES17_c6425_188 as a candidate for use in marker-assisted selection, in addition to the marker GMI_ES02_c37788_255 suggested by Rine's group, which provides an additional tool in facilitating the utilization of this gene in oat breeding programs.

Combined transcriptome sequencing reveals the photoperiod insensitivity mechanism of oats

Avena sativa L. is the most important cultivated oat species worldwide. Although photoperiod-insensitive oat varieties exist, the molecular mechanisms underlying their photoperiod sensitivity are poorly understood. This study investigated the effects of day length on the fioral transition of oats and the mechanisms underlying oat photoperiod insensitivity. Photoperiod-sensitive and photoperiod-insensitive varieties, including gp012, were used in shading experiments, and the developing leaves and main shoot apices (MSAs) of the HONGQI2 and gp012 varieties were used for sequencing. Leaves and MSAs were collected in 2016, and their transcriptomes were sequenced. The photoperiod-insensitive varieties headed under both short-day and long-day conditions, while the photoperiod-sensitive varieties headed only under long-day conditions. A total of 60673 transcript sequences were obtained, 7932 of which were differentially expressed; 3194 and 4738 transcripts were differentially expressed in the leaves and MSAs, respectively. A total of 25793 transcripts were classified into 123 pathways based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The carbon metabolism pathways were dominant, followed by ribosome and protein processing in the endoplasmic reticulum. In addition, 203 transcripts were classified into the circadian rhythm pathway. Compared with the expression of pseudo-response regulator protein 37 (PRR37) in photoperiod-sensitive varieties, that in photoperiod-insensitive varieties was upregulated. Among the differentially expressed transcripts (DETs), 8 MADS-box genes were identified. PRR37 is a key regulator of oat photoperiod insensitivity. The obtained transcriptome dataset may provide a reference for analyzing oat transcript expression, and the results should be used as a reference for oat breeding and production.

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat

KEY MESSAGE

Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.

Domestication via hybridization of the wild tetraploid oats Avena magna and A. murphyi

The wild tetraploid (2n=28) oat species Avena magna and A. murphyi have been domesticated by having been transferred from the common oat, A sativa (2n=42), the characteristics of non-shedding spikelets glabrous and yellow lemma, and reduced awn formation. Domestication has been achieved by crossing the common oat with either of the tetraploid species and then backcrossing the pentaploid hybrids with pollen of the tetraploid wild parent. Among the BC plants obtained only a few produced some seeds. Fertile tetraploids exhibiting the domesticated syndrome have been selected for in the F2 generation. Although morphologically they were almost indistinguishable from the common oat, they were tetraploids. Wild x domesticated A. magna hybrids were vigorous and fertile. They retained their spikelets at maturity, lemma color and pubescence were intermediate between the parental lines, and awns were formed only on the lower floret of the spikelet. Each of these characteristics segregated in a 3∶1 fashion, indicating single gene control, as in the common oat. These four characteristics formed a linkage group in one F2 family and two linkage groups in the other two families. The usefulness of the domesticated tetraploids for oat research and production has been discussed. Taxonomically, the domesticated tetraploids were ranked as subspecies: A. magna ssp. domestica, and A. murphyi ssp. rigida.

A case of genome partition in polyploid oats

At the second generation of the interspecific cross between the cultivated hexaploid (2n = 42) oat A. Sativa and the wild tetraploid (2n = 28) A. Murphyi, a plant having hexaploid and diploid (2n = 14) sectors was selected. Meiosis was highly regular in the diploid sector but the tillers failed to proceed beyond the boot stage and no seeds were produced. It is suggested that this diploid sector represents an entire genome of one of the diploid progenitors of the hexaploid oat.

INTROGRESSION BETWEEN THE CULTIVATED HEXAPLOID OAT A. SATIVA AND THE TETRAPLOID WILD A. MAGNA AND A. MURPHYI

Introgression between the hexaploid (2n = 42) oat A. sativa and the newly discovered tetraploid (2n = 28) species A. magna and A. murphyi was studied by the rate of stabilization of chromosome number, restoration of fertility of pentaploid hybrid derivatives and the ultimate gene transfer between the tetraploid and the hexaploid levels. The complete self-sterility of the pentaploid F1 hybrids was overcome by massive back-pollination to the parental species. Great variation in chromosome number (12-48) was found among the viable F1 female gametes. Meiotically stable and reasonably fertile derivatives were selected only at the F2 of the BC and in a relatively small proportion. Gene transfer between the tetraploid and the hexaploid species was demonstrated by introducing the allele for nonshattering seed from the cultivated oat A. sativa to both A. magna and A. murphyi, and lemma hairiness from the tetraploids to the hexaploid level. The possible exploitation of introgression between the polyploid oats for breeding purposes has been pointed out and the potential of A. magna and A. murphyi as cultivated oats has been briefly discussed.

SEED PROTEIN HOMOLOGIES AND THE EVOLUTION OF POLYPLOIDY IN AVENA

Crude seed protein of the nine oat species was fractionated by disc electrophoresis on polyacrylamide gel. Correlation coefficients calculated from optical density curves obtained from the stained gels showed that individual species possessed characteristic, albeit variable, profiles. Pattern variability among and within species was greater in the case of the diploids than in the case of the polyploids. The very few profile types in A. strigosa 4x and in the hexaploid A. sativa suggested that the variation in these polyploids is due more to independent origin of the types than to differentiation following polyploidization. Virtual identity between individual A. strigosa 2x and 4x profiles suggested a strict autopolyploid origin for some 4x types while complementing pairs of A. strigosa 2x profiles indicated an intervarietal origin for other A. strigosa 4x types. A diagnostic band at 11.0 cm in the profiles of A. magna and A. murphyi suggested that these species rather than A. strigosa 4x had functioned as the tetraploid parent of the hexaploid A. sativa. The profile of A. murphyi complemented by a specific A. strigosa 2x profile simulated a specific A. sativa type. The adaptive success of the genus is assessed in the light of variation and homologies in the seed protein patterns of the various species.

LEAF ESTERASE ISOZYMES IN AVENA AND THEIR RELATIONSHIP TO THE GENOMES

Leaf esterase patterns of natural populations of diploid, tetraploid and hexaploid Avena species were separated by disc electrophoresis. The zymotypes of the A genome diploids A. hirtula, A. strigosa and A. longiglumis differed from the C genome diploids A. pilosa and A. ventricosa. The tetraploids A. barbata, A. magna and A. murphyi had distinctive zymotypes. The A. barbata zymotype resembled the A genome diploids which supports the cytological evidence for homoeology between the genomes. Avena magna and A. murphyi were a combination of the A and C diploid patterns with A. murphyi resembling the C more than the A pattern. The zymotypes of the hexaploids A. sterilis and A. sativa revealed the expected A, C and AC genome ancestry. Band affinity ratings within and between genomic groups agreed with the cytological evidence and cross-compatible relationships, the exception being the C — AC species that have high affinity ratings but are apparently cross-incompatible.

ANALYSIS OF SPECIES RELATIONSHIPS IN AVENAE BY THIN-LAYER CHROMATOGRAPHY AND DISC ELECTROPHORESIS

Thin-layer chromatographic studies on flavonoids, and disc electrophoretic studies on proteins and esterase isoenzymes were conducted with Avena to determine species relationships and genome homologies. Distinctness of Avena ventricosa and A. pilosa was observed in comparison to other diploid species. Closeness of the diploid species of the A. strigosa group (including hirtula and wiestii) was evident from the similarity of their protein and esterase spectra. The tetraploid species, A. barbata and A. abyssinica, were found to be very close to A. hirtula and A. strigosa, respectively, by TLC studies. Proteins and esterases also showed that the tetraploid species are very close to the A. strigosa group of diploid species. The contribution of a genome by the A. strigosa group to the tetraploids and hexaploids was confirmed. The hexaploids showed different protein and esterase patterns. The involvement of A. ventricosa as the C genome donor to the hexaploids was shown by the protein and esterase spectra. A few extra protein bands observed may have been from the D genome.

CHROMOSOME RELATIONSHIPS BETWEEN TETRAPLOID (2n=28) AVENA MURPHYI AND SOME DIPLOID, TETRAPLOID AND HEXAPLOID SPECIES OF OATS

On combined evidence of cytology and morphology it is apparent that the newly discovered tetraploid Avena murphyi shares a common genome with the tetraploid A. magna. Lack of crossability and limited pairing in triploid hybrids involving A. murphyi indicate that none of the presently known diploid oats participated in the formation of A. murphyi. Meiotic behavior of A. murphyi × A. sativa pentaploid hybrids shows considerable homology between the chromosomes of the parents. The origin of the hexaploid oats is discussed in the light of the cytogenetic status of A. murphyi.

A PROTEIN ELECTROPHORETIC STUDY OF THREE AMPHIPLOIDS AND EIGHT SPECIES IN AVENA

Seed proteins of three synthetic amphiploids, one autotetraploid and eight species that include representatives of all ploidy levels and karyotypes of Avena were studied by acrylamide gel electrophoresis. Complete or nearly complete additiveness in banding pattern of the parental protein was obtained in the amphiploids and mechanical mixtures. The pattern of autotetraploid A. pilosa was more similar to the amphiploid derived from its diploid and A. sativa than to its diploid form. This was interpreted as a dosage effect indicating the presence of the same genes in both parental species. No distinct zonation of protein bands was apparent in the basic gels, but in the acidic gels a gap separated the fastest moving bands from the slower bands. About 50% of the bands were common to all species studied, indicating extensive residual homology. The A and C genome diploids were readily separated by band differences, the A genome protein patterns were essentially identical and the C genomes differed primarily in band number. The tetraploid protein patterns differed but the hexaploids had high homology and intraspecific polymorphism was detected in the hexaploid cultivars. Almost complete homology occurred between the A genome spectrum and the tetraploid and hexaploid patterns, as well as between the C genome spectrum and the tetraploid A. magna and the hexaploid protein patterns. Protein homology in Avena indicated close genomic relationships.

Complementary ways of meeting the world's protein need

Before considering the various possible protein sources, we must make some sort of estimate of the possible protein need by—say—the end of the century. That estimate controls the amount of effort we should put into work on protein supplies and the degree of novelty that we should envisage. The estimate depends on the number of people to be fed and the amount of protein that each needs. Both quantities are uncertain: the first because it must be guessed, the second because it is hotly disputed.

Complementary ways of meeting the world’s protein need

Before considering the various possible protein sources, we must make some sort of estimate of the possible protein need by—say—the end of the century. That estimate controls the amount of effort we should put into work on protein supplies and the degree of novelty that we should envisage. The estimate depends on the number of people to be fed and the amount of protein that each needs. Both quantities are uncertain: the first because it must be guessed, the second because it is hotly disputed.

THE CYTOGENETIC STATUS OF AVENA MAGNA

The corresponding pairing behaviour of the chromosomes of A. magna and A. abyssinica was determined in triploid and pentaploid hybrids. Much higher overall pairing was found in the A. abyssinica than in the A. magna triploids indicating reduced homology between the A genomes of the diploids and A. magna and the absence of homoeology between the A genome and the second genome of A. magna. In contrast, pairing was much higher in the A. magna pentaploid than that of A. abyssinica. It was concluded that the second genome of A. magna is closely related to one genome other than the A of the hexaploids. On the ground of morphology, cross-compatibility and the pairing behaviour of chromosomes it was proposed that A. magna has the genomes AADD and that it is the putative ancestral tetraploid of the hexaploid species. This hypothesis can be tested by a synthetic allohexaploid derived from A. ventricosa and A. magna.

GENOME RELATIONSHIPS IN TETRAPLOID AVENA

Relationships between the A and B genomes of the tetraploid Avena species (A. magna excluded) and between these and the AS genome of the diploid A. hirtula and strigosa were studied in triploid (ASAB) and tetraploid (ASASAB) hybrids. Chromosome affinities were estimated on the basis of the karyotypes and the pairing behaviour of the chromosomes.The main findings were:1. The AS karyotype of the 2x and the A of the 4x species were identical and the chromosomes of the genomes A and B were similar. No difference was noticeable in the karyotypes of the 4x species studied. A nucleolar chromosome appeared from the B set in the 3x hybrids. It was concluded that the B genome is probably a modified form of A.2. All the chromosomes were capable of pairing in the ASAB and ASASAB hybrids. High degree of homology between the AS and A genomes was indicated by the high frequency of ring bivalents and ring-rod trivalents. The synaptic success of the B genome chromosomes (up to six trivalents) was interpreted as homoeology between the A and B genome chromosomes. The long chains (up to XII) suggested heterozygosity for numerous large segments.3. Attempting to resolve the conflict between homoeology and bivalent pairing in the 4x species, a diploidizing gene system, effective only in the homozygous condition, was assumed.4. The effect of multiple differences for large segments in the evolution of alloploids was briefly discussed.

THE CHROMOSOMES OF AVENA MAGNA

The karyotype of the newly discovered tetraploid species A. magna was described and compared with that of the other tetraploid species. While one set of chromosomes of A. magna is very similar to that of the As genome of some of the diploids and to that of the A genome of the other tetraploids, the second set of A. magna is quite different from the second set (B) of the other tetraploids. Preliminary evidence suggests that A. magna is a truly rare species in the Mediterranean region.