Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated a reference-quality genome assembly of hulless common oat, comprising 21 pseudomolecules with a total length of 10.76 Gb and contig N50 of 75.27 Mb. We also produced genome assemblies for diploid and tetraploid Avena ancestors, which enabled the identification of oat subgenomes and provided insights into oat chromosomal evolution. The origin of hexaploid oat is inferred from whole-genome sequencing, chloroplast genomes and transcriptome assemblies of different Avena species. These findings and the high-quality reference genomes presented here will facilitate the full use of crop genetic resources to accelerate oat improvement.

Saline–alkali stress is one of the major factors limiting oat seed germination. The regulatory role of melatonin (MT) as a naturally occurring active substance is well known, but the mechanism of MT-mediated intrinsic physiological regulation of oat seed germination under saline–alkali stress is unclear. Therefore, this study investigated (1) the variability of different MT seed soaking concentrations and times on the germination of oat seeds under saline–alkali stress, and (2) the possible physiological regulatory mechanisms of MT on the germination of oat seeds under saline–alkali stress. The results showed that seed vigor was significantly reduced under saline–alkali stress, and seed germination of oats was significantly inhibited; different concentrations of MT seed soaking treatments improved the germination rate, germination potential, germination index, vigor index, root length, germ length, fresh weight, and dry weight; and, overall, treatment improved seed germination and exhibited the phenomenon of “low promotion and high inhibition”. The 100 μmol·L⁻¹ MT seed soaking treatment effectively enhanced the activities of seed antioxidant enzymes (SOD, POD, CAT, and APX) and nonenzymatic antioxidants (GSH and AsA), affected the AsA-GSH cycle, and effectively increased the contents of osmoregulatory substances (proline, protein, and soluble sugar) by reducing levels of H₂O₂, OH⁻, and MDA, thus enhancing the tolerance of oats to saline–alkali and promoting seed germination. In conclusion, MT has a positive effect on the saline–alkali tolerance of oat seeds.

In order to solve the difficult problem of the outer shell covering in the processing of Tartary buckwheat, we conducted a genetic analysis in segregating F₂ and F₃ populations derived from a hybrid between ‘Yunqiao No. 1’ and ‘Rice buckwheat’, and the F₃ population was used to analyze the phenotypic and genetic correlation among the traits. The results showed that the variety with a value of trait for seed shell thickness over 0.20 mm is a hard-shelled type (The thick shell type = seed shell rate > 20%), and that with a value of trait for seed shell thickness below 0.15 mm is a easily-shelled type (The thin shell type = seed shell rate < 20%), while that with a value of trait for seed shell thickness ranging from 0.15 mm to 0.20 mm is a hard-shelled type or easily-shelled type. In addition, alleles for traits of number of seed per plant and total seed weight per plant have larger dominance variance relative to their additive variance, indicating that genes controlling these traits have larger dominant effects, it is not suitable for the selection of single plant in offspring plants at the early stage of development, because these traits do not show up then. The alleles for traits of 1000 kernel weight and seed shell thickness have larger additive variance relative to their dominant variance, indicating that genes governing these traits have greater additive effects, with which the single plant can be selected in the progeny at the early stage of development. Although, the value of seed shell thickness has been shown to correlated positively with that of 1000 kernel weight, almost all the seeds of easily-shelled type are those with thin shell. However, ideal single plants with easily-shelled trait are those with intermediate phenotypes of seed shell thickness and 1000 kernel weight, by which the traits of large number of seeds per plant and total seed weight per plant could be selected. In the progeny population of this study, there were excellent single plants with high-yield and easily-shelled traits, of which the value of seed shell thickness was 0.17 mm (0.15 mm to 0.20 mm), the value of 1000 kernel weight was 14 g, the value of number of seeds per plant was 1137 and value of total seed weight per plant was 15.9 g. The results showed that taking the hybrid combinations of easily-shelled trait with the trait of seed shell thickness was the most effective selection indexes to breed the high-yield buckwheat varieties with the trait of easy shelling.

To cope with the yield loss caused by drought stress, new oat varieties with greater drought tolerance need to be selected. In this study, two oat varieties with different drought tolerances were selected for analysis of their phenotypes and physiological indices under moderate and severe soil drought stress. The results revealed significant differences in the degree of wilting, leaf relative water content (RWC), and SOD and CAT activity between the two oat genotypes under severe soil drought stress; moreover, the drought-tolerant variety exhibited a significant increase in the number of stomata and wax crystals on the surface of both the leaf and guard cells; additionally, the morphology of the guard cells was normal, and there was no significant disruption of the grana lamella membrane or the nuclear envelope. Furthermore, transcriptome analysis revealed that the expression of genes related to the biosynthesis of waxes and cell-wall components, as well as those of the WRKY family, significantly increased in the drought-tolerant variety. These findings suggest that several genes involved in the antioxidant pathway could improve drought tolerance in plants by regulating the increase/decrease in wax and cell-wall constituents and maintaining normal cellular water potential, as well as improving the ability of the antioxidant system to scavenge peroxides in oats.

Exogenous melatonin (MT) regulates plant growth and mitigates stress in response to stress. To analyze the machinery of exogenous melatonin, which improves salt and alkaline tolerance in oats, MT’s function was identified in the oat seed germination stage in our previous study. In this study, morphogenesis, photosynthetic physiology, hormone levels, and ion homeostasis were evaluated using the same MT treatment concentration. The results revealed that compared to the S45 treatment, the 100 μmol·L⁻¹ MT treatment efficiently increased the seedling height and main root length of oat seedlings; promoted secondary root development; enhanced the root volume and root surface area; maintained a higher photosynthetic pigment content (carotenoids; chlorophyll a; chlorophyll b); raised the leaf photosynthetic rate (Pn), intercellular CO₂ concentration (Ci), conductance to H₂O (Gs), and transpiration rate (Tr); enhanced the light energy absorption and conversion of leaves; increased the leaf GA3, Tryptamine (TAM), and IAA contents; and decreased ABA levels. Hierarchical cluster analysis revealed that MT treatment also increased the contents of P, K, Ca, Mn, Cu, Mg, Fe, Zn, Mo, Cd, Al, Se, Ni, Co, and Ti; decreased the Na/K ratio; and maintained cellular ionic homeostasis in oat seedlings under saline–alkali stress, as compared with the untreated group. These findings showed that MT treatment enhanced the adaptation of oat to saline–alkali stress through regulating the physiological process of seedling growth. This suggests that MT plays a different role in improving saline–alkali tolerance in the germination and seedling stages of oat.

Groat protein content (GPC) is a key quality trait attribute in oat. Understanding the variation of GPC in oat germplasms and identifying genomic regions associated with GPC are essential for improving this trait. In this study, the GPC of 174 diverse oat accessions was evaluated in three field trials. The results showed a wide variation in GPC, ranging from 6.97% to 22.24% in this panel. Hulless oats displayed a significantly higher GPC compared to hulled oats across all environments. A GWAS analysis was performed based on 38,313 high-quality SNPs, which detected 27 non-redundant QTLs with 41 SNPs significantly associated with GPC. Two QTLs on chromosome 6C (QTL16) and 4D (QTL11) were consistently detected in multiple environments, with QTL16 being the most significant and explaining the highest proportion of the phenotypical variation in all tested environments except in CZ20. Haplotype analysis showed that the favorable haplotypes for GPC are more prevalent in hulless oats. These findings provide a foundation for future efforts to incorporate favorable alleles into new cultivars through introgression, fine mapping, and cloning of promising QTLs.