Genome-Wide Association Mapping of QTL Underlying Groat Protein Content of a Diverse Panel of Oat Accessions.

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.

Genetic diversity and genome-wide association analysis in Chinese hulless oat germplasm.

KEY MESSAGE: Genotyping-by-sequencing (GBS)-derived molecular markers reveal the distinct genetic population structure and relatively narrow genetic diversity of Chinese hulless oat landraces. Four markers linked to the naked grain gene (N1) are identified by genome-wide association study (GWAS). Interest in hulless oat (Avena sativa ssp. nuda), a variant of common oat (A. sativa) domesticated in Western Asia, has increased in recent years due to its free-threshing attribute and its domestication history. However, the genetic diversity and population structure of hulless oat, as well as the genetic mechanism of hullessness, are poorly understood. In this study, the genetic diversity and population structure of a worldwide sample of 805 oat lines including 186 hulless oats were investigated using genotyping-by-sequencing. Population structure analyses showed a strong genetic differentiation between hulless landraces vs other oat lines, including the modern hulless cultivars. The distinct subpopulation stratification of hulless landraces and their low genetic diversity suggests that a domestication bottleneck existed in hulless landraces. Additionally, low genetic diversity within European oats and strong differentiation between the spring oats and southern origin oat lines revealed by previous studies were also observed in this study. Genomic regions contributing to these genetic differentiations suggest that genetic loci related to growth habit and stress resistance may have been under intense selection, rather than the hulless-related genomic regions. Genome-wide association analysis detected four markers that were highly associated with hullessness. Three of these were mapped on linkage group Mrg21 at a genetic position between 195.7 and 212.1 cM, providing robust evidence that the dominant N1 locus located on Mrg21 is the single major factor controlling this trait.

Correlation and genetic analysis of seed shell thickness and yield factors in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.).

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.

Genetic mapping and a new PCR-based marker linked to a dwarfing gene in oat (Avena sativa L.).

Short straw is a desired trait in cultivated hexaploid oat (Avena sativa L.) for some production environments. Marker-assisted selection, a key tool for achieving this objective, is limited by a lack of mapping data and available markers. Here, bulked-segregant analysis was used to identify PCR-based markers associated with a dwarfing gene. Genetic analysis identified a monogenic dominant inheritance of one dwarfing gene from WAOAT2132, temporarily designated DwWA. A simple sequence repeat (SSR) marker (AME117) that was already available and a new codominant PCR-based marker (bi17) developed by homologous cloning in the present study were both associated with the dwarfing gene. The two markers were located 21 and 1.2 cM from DwWA, respectively. The bi17 marker was mapped to neighboring SNP markers on chromosome 18D of the oat consensus map. Since Dw6 was previously mapped on chromosome 18, and since our new marker bi17 is also diagnostic for NILs generated for Dw6, there is strong evidence that the dwarfing gene identified in WAOAT2132 is Dw6. The newly developed markers could find applications in the identification of this gene in oat germplasm and in the fine mapping or positional cloning of the gene.

Effects of different cooking methods of oatmeal on preventing the diet-induced increase of cholesterol level in hypercholesterolemic rats.

BACKGROUND: The aim of present study is to investigate the influences of brewing and boiling on hypocholesterolemic effect of oatmeal in rats fed with a hypercholesterolemic diet. METHODS: Fifty-six male Sprague-Dawley rats were divided into 5 groups of 8 rats each with similar mean body weights and serum cholesterol concentrations. Rats were fed with the experimental diets containing 10% of oatmeal from two Chinese oat varieties which were brewed or boiled for 30 days. The lipids levels in serum, liver, and faeces were determined. RESULTS: The effects of feeding boiled oatmeal on lowering lipid concentrations in plasma and liver were more significant than that of brewed oatmeal (P < 0.05). Feeding boiled oatmeal was also more efficient in increasing fecal total lipids, cholesterol and bile acids as compared to feeding brewed oatmeal (P < 0.05). Boiled oatmeal had higher apparent viscosity and soluble ß-glucan content than the brewed oatmeal did (P < 0.05). CONCLUSION: These results indicated that the capability of boiled oatmeal in improving cholesterol metabolism is better than that of brewed oatmeal, which is mainly attributed to its higher soluble ß-glucan content and apparent viscosity.

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.

Transcriptome Analysis Reveals Drought-Responsive Pathways and Key Genes of Two Oat (Avena sativa) Varieties.

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.

Transcriptomic response for revealing the molecular mechanism of oat flowering under different photoperiods.

Proper flowering is essential for the reproduction of all kinds of plants. Oat is an important cereal and forage crop; however, its cultivation is limited because it is a long-day plant. The molecular mechanism by which oats respond to different photoperiods is still unclear. In this study, oat plants were treated under long-day and short-day photoperiods for 10 days, 15 days, 20 days, 25 days, 30 days, 40 days and 50 days, respectively. Under the long-day treatment, oats entered the reproductive stage, while oats remained vegetative under the short-day treatment. Forty-two samples were subjected to RNA-Seq to compare the gene expression patterns of oat under long- and short-day photoperiods. A total of 634-5,974 differentially expressed genes (DEGs) were identified for each time point, while the floral organ primordium differentiation stage showed the largest number of DEGs, and the spikelet differentiation stage showed the smallest number. Gene Ontology (GO) analysis showed that the plant hormone signaling transduction and hormone metabolism processes significantly changed in the photoperiod regulation of flowering time in oat. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Mapman analysis revealed that the DEGs were mainly concentrated in the circadian rhythm, protein antenna pathways and sucrose metabolism process. Additionally, transcription factors (TFs) involved in various flowering pathways were explored. Combining all this information, we established a molecular model of oat flowering induced by a long-day photoperiod. Taken together, the long-day photoperiod has a large effect at both the morphological and transcriptomic levels, and these responses ultimately promote flowering in oat. Our findings expand the understanding of oat as a long-day plant, and the explored genes could be used in molecular breeding to help break its cultivation limitations in the future.

Design, synthesis and activity against drug-resistant bacteria evaluation of C-20, C-23 modified 5-O-mycaminosyltylonolide derivatives.

With the increasing incidence of antibiotic resistance, there is an urgent need to develop new antibiotics with excellent activity against drug-resistant bacteria. Three novel series of tylosin semisynthetic derivatives were designed, synthesized and evaluated for their antibacterial activities against various Gram-positive and Gram-negative bacteria. Among these derivatives, compound C-2 demonstrated potent antibacterial activity against both gram-positive and gram negative bacteria, and non mutagenic. More importantly, compound C-2 displayed high antimicrobial potency against Gram-positive bacteria in a murine model, and was found to be more efficient than tildipirosin. Thus, compound C-2 had great potential as a promising lead compound for the treatment of bacterial infection.

Reference genome assemblies reveal the origin and evolution of allohexaploid oat.

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.

Effects of water-saving superabsorbent polymer on antioxidant enzyme activities and lipid peroxidation in oat (Avena sativa L.) under drought stress.

BACKGROUND: Drought stress significantly limits oat (Avena sativa L.) growth and productivity. Thus an efficient management of soil moisture and study of metabolic changes in response to drought are important for improved production of oat. The objective was to gain a better understanding of drought tolerance mechanisms and improve soil water management strategies using water-saving superabsorbent polymer (SAP) at 60 kg ha(-1) under three irrigation levels (adequate, moderate and deficit) using a new type of hydraulic pressure-controlled auto irrigator. RESULTS: The results showed that the relative water content and leaf water potential (ψ(1) ) were much higher in oats treated with SAP. Although the SAP had little effect on plant biomass accumulation under adequate and moderate irrigation, it significantly increased the biomass by 52.7% under deficit irrigation. Plants treated with SAP under deficit irrigation showed a significant decrease in superoxide dismutase, catalase, peroxidase, ascorbate peroxidase and glutathione reductase activities in leaves compared with control plants. CONCLUSION: Our results suggested that drought stress leads to production of oxygen radicals, which results in increased lipid peroxidation and oxidative stress in the plant, and the application of SAP could conserve soil water, making same available to plants for increased biomass accumulation and reduced oxidative stress especially under severe water stress.

Oat-Based Foods: Chemical Constituents, Glycemic Index, and the Effect of Processing.

The desire for foods with lower glycemic indices has led to the exploration of functional ingredients and novel food processing techniques. The glycemic index (GI) is a well-recognized tool to assess the capacity of foods to raise blood glucose levels. Among cereal crops, oats have shown the greatest promise for mitigating glycemic response. This review evaluated decades of research on the effects of oat components on the GI level of oat-based foods with specific emphasis on oat starch, ß-glucans, proteins, and phenolics. The effects of commonly used processing techniques in oats on GI level, including heating, cooling, and germination were also discussed. In addition, the GI of oat-based foods in various physical formats such as whole grain, flakes, and flour was systematically summarized. The aim of this review was to synthesize knowledge of the field and to provide a deeper understanding of how the chemical composition and processing of oats affect GI, thereby further benefiting the development of low-GI oat foods.

New evidence confirming the CD genomic constitutions of the tetraploid Avena species in the section Pachycarpa Baum.

The tetraploid Avena species in the section Pachycarpa Baum, including A. insularis, A. maroccana, and A. murphyi, are thought to be involved in the evolution of hexaploid oats; however, their genome designations are still being debated. Repetitive DNA sequences play an important role in genome structuring and evolution, so understanding the chromosomal organization and distribution of these sequences in Avena species could provide valuable information concerning genome evolution in this genus. In this study, the chromosomal organizations and distributions of six repetitive DNA sequences (including three SSR motifs (TTC, AAC, CAG), one 5S rRNA gene fragment, and two oat A and C genome specific repeats) were investigated using non-denaturing fluorescence in situ hybridization (ND-FISH) in the three tetraploid species mentioned above and in two hexaploid oat species. Preferential distribution of the SSRs in centromeric regions was seen in the A and D genomes, whereas few signals were detected in the C genomes. Some intergenomic translocations were observed in the tetraploids; such translocations were also detected between the C and D genomes in the hexaploids. These results provide robust evidence for the presence of the D genome in all three tetraploids, strongly suggesting that the genomic constitution of these species is DC and not AC, as had been thought previously.

Position Validation of the Dwarfing Gene Dw6 in Oat (Avena sativa L.) and Its Correlated Effects on Agronomic Traits.

An F6 : 8 recombinant inbred line (RIL) population derived from the cross between WAOAT2132 (Dw6) and Caracas along with the two parents were used to evaluate the genetic effects of Dw6 dwarfing gene on plant height and other agronomic traits in oat (Avena sativa L.) across three environments, and develop closely linked markers for marker-assisted selection (MAS) for Dw6. The two parents differed in all investigated agronomic traits except for the number of whorls. The RIL lines showed a bimodal distribution for plant height in all three tested environments, supporting the height of this population was controlled by a single gene. Dw6 significantly reduced plant height (37.66∼44.29%) and panicle length (13.99∼22.10%) but without compromising the coleoptile length which was often positively associated with the reduced stature caused by dwarfing genes. Dw6 has also strong negative effects on hundred kernel weight (14.00∼29.55%), and kernel length (4.21∼9.47%), whereas the effects of Dw6 on the kernel width were not uniform across three environments. By contrast, lines with Dw6 produced more productive tillers (10.11∼10.53%) than lines without Dw6. All these together suggested the potential yield penalty associated with Dw6 might be partially due to the decrease of kernel weight which is attributed largely to the reduction of kernel length. Eighty-one simple sequence repeat (SSR) primer pairs from chromosome 6D were tested, five of them were polymorphic in two parents and in two contrasting bulks, confirming the 6D location of Dw6. By using the five polymorphic markers, Dw6 was mapped to an interval of 1.0 cM flanked by markers SSR83 and SSR120. Caution should be applied in using this information since maker order conflicts were observed. The close linkages of these two markers to Dw6 were further validated in a range of oat lines. The newly developed markers will provide a solid basis for future efforts both in the identification of Dw6 in oat germplasm and in the determination of the nature of the gene through positional cloning.

The evolution pattern of rDNA ITS in Avena and phylogenetic relationship of the Avena species (Poaceae: Aveneae).

Ribosomal ITS sequences are commonly used for phylogenetic reconstruction because they are included in rDNA repeats, and these repeats often undergo rapid concerted evolution within and between arrays. Therefore, the rDNA ITS copies appear to be virtually identical and can sometimes be treated as a single gene. In this paper we examined ITS polymorphism within and among 13 diploid (A and C genomes), seven tetraploid (AB, AC and CC genomes) and four hexaploid (ACD genome) to infer the extent and direction of concerted evolution, and to reveal the phylogenetic and genome relationship among species of Avena. A total of 170 clones of the ITS1-5.8S-ITS2 fragment were sequenced to carry out haplotype and phylogenetic analysis. In addition, 111 Avena ITS sequences retrieved from GenBank were combined with 170 clones to construct a phylogeny and a network. We demonstrate the major divergence between the A and C genomes whereas the distinction among the A and B/D genomes was generally not possible. High affinity among the A(d) genome species A. damascena and the ACD genome species A. fatua was found, whereas the rest of the ACD genome hexaploids and the AACC tetraploids were highly affiliated with the A(l) genome diploid A. longiglumis. One of the AACC species A. murphyi showed the closest relationship with most of the hexaploid species. Both C(v) and C(p) genome species have been proposed as paternal donors of the C-genome carrying polyploids. Incomplete concerted evolution is responsible for the observed differences among different clones of a single Avena individual. The elimination of C-genome rRNA sequences and the resulting evolutionary inference of hexaploid species are discussed.

Antioxidant activities of aged oat vinegar in vitro and in mouse serum and liver.

BACKGROUND: The present study focused on the antioxidant activities of aged oat (Avena sativa L.) vinegar. The antioxidant activities of oat and vinegar have been proved by many previous research studies. It should be noted that oat vinegar, as a novel seasoning, has antioxidant activity. RESULTS: Oat vinegar showed stronger radical scavenging activities, reducing power, and inhibition of lipid peroxidation than rice vinegar. The concentrations of polyphenols and flavonoids in oat vinegar were higher than those in rice vinegar. Ethyl acetate extract of oat vinegar possessed the most varieties of phenolic acids and showed the strongest antioxidant activity compared with ethanol and water extracts. At suitable doses of oat vinegar, the malondialdehyde value was decreased, activities of superoxide dismutase and glutathione peroxidase were promoted, and hepatic damage induced by (60)Co gamma-irradiation was ameliorated in aging mice. CONCLUSION: Oat vinegar manifested antioxidant activity which was stronger than that of rice vinegar in vitro and the same as that of vitamin E in vivo.

The effects of steaming and roasting treatments on beta-glucan, lipid and starch in the kernels of naked oat (Avena nuda).

BACKGROUND: Normal pressure steaming (NPS), autoclaved steaming (AS), and hot-air roasting (HAR) are widely used to deactivate oat enzyme in the oat-processing industry. Infrared roasting (IR) is a new oat deactivation method, and is welcomed and employed by increasing numbers of oat-processing plants in China. It is widely known that oat starch plays an important role in the processing function of oat food, and that oat beta-glucan and lipid contribute greatly to the health benefits of oat food. However, the effects of steaming and roasting treatments on the starch, beta-glucan and lipid in oat kernels are poorly known. RESULTS: In this research, the level and distribution of beta-glucan and lipid in oat kernels with and without deactivation treatments were tested. We also measured the viscosity properties of oat flour from kernels after NPS, AS, HAR and IR treatments, and examined the effects of these treatments on oat starch granularity using scanning electron microscopy. The results showed that the deactivation treatments did not have significant effects on oat beta-glucan and lipid levels in oat kernels (P < 0.01). The distribution of beta-glucan and lipid in enzyme-deactivated kernels was very similar to that in normal kernels. NPS, AS, HAR and IR treatments changed the shape of starch granules, crumbled large starch granules, reduced the connection between the protein network and starch granules, and improved starch gelatinization properties. CONCLUSIONS: NPS, AS, HAR and IR treatments can change the structure of oat starch granules and improve the viscosity property of oat starch without causing beta-glucan and lipid loss to oat food.

Rhizodeposition of nitrogen and carbon by mungbean (Vigna radiata L.) and its contribution to intercropped oats (Avena nuda L.).

Compounds released by mungbean roots potentially represent an enormous source of nitrogen (N) and carbon (C) in mungbean-oat intercropping systems. In this study, an in situ experiment was conducted using a 15N - 13C double stem-feeding method to measure N and C derived from the rhizodeposition (NdfR and CdfR) of mungbean and their transfer to oats in an intercropping system. Mungbean plants were sole cropped (S) or intercropped (I) with oat. The plants were labeled 5 weeks after planting and were harvested at the beginning of pod setting (Ip and Sp) and at maturity (Im and Sm). More than 60% and 50% of the applied 15N and 13C, respectively, were recovered in each treatment, with 15N and 13C being quite uniformly distributed in the different plant parts. NdfR represented 9.8% (Sp), 9.2% (Ip), 20.1% (Sm), and 21.2% (Im) of total mungbean plant N, whereas CdfR represented 13.3% (Sp), 42.0% (Ip), 15.4% (Sm), and 22.6% (Im) of total mungbean plant C. When considering the part of rhizodeposition transferred to associated oat, intercropping mungbean released more NdfR and CdfR than mungbean alone. About 53.4-83.2% of below-ground plant N (BGP-N) and 58.4-85.9% of BGP-C originated from NdfR and CdfR, respectively. The N in oats derived from mungbean increased from 7.6% at the pod setting stage to 9.7% at maturity, whereas the C in oats increased from 16.2% to 22.0%, respectively. Only a small percentage of rhizodeposition from mungbean was transferred to oats in the intercropping systems, with a large percentage remaining in the soil. This result indicates that mungbean rhizodeposition might contribute to higher N and C availability in the soil for subsequent crops.

[Oat growth and cation absorption characteristics under salt and alkali stress].

This paper monitored the oat growth and cation absorption characteristics on a saline-alkali soil in the Baicheng region of Jilin Province under low, medium, and high levels of salt stress. No significant differences were observed in the shoot growth and yield components under the three levels of salt stress, but the root biomass and root/shoot ratio decreased significantly with increasing salt stress level. At maturing stage, the root/shoot ratio under medium and high salt stresses was 77.2% and 64.5% of that under low salt stress, respectively. Under the three levels of salt stress, the K+/Na+ and Ca2+/Na+ ratios in oat plant had significant differences at trefoil stage, but no significant differences at heading stage. With the increase of salt stress level, the cation absorption selectivity coefficient of oat at filling stage decreased significantly, but the transportation selectivity coefficient had no significant difference under the three levels of stress. It was concluded that oat could adapt to the salt and alkali stress of soda-alkaline soil to some extent, and the adaptation capability decreased with the increasing level of stress. The decrease of oat root biomass and the stronger ion selective absorption capacity at heading stage under salt and alkali stress could benefit the shoot growth and yield components of oat.