Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat

BACKGROUND

Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated.

RESULTS

Here, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find that Tartary buckwheat originated in the Himalayan region and then spread southwest possibly along with the migration of the Yi people, a minority in Southwestern China that has a long history of planting Tartary buckwheat. Along with the expansion of the Mongol Empire, Tartary buckwheat dispersed to Europe and ultimately to the rest of the world. The different natural growth environments resulted in adaptation, especially significant differences in salt tolerance between northern and southern Chinese Tartary buckwheat populations. By scanning for selective sweeps and using a genome-wide association study, we identify genes responsible for Tartary buckwheat domestication and differentiation, which we then experimentally validate. Comparative genomics and QTL analysis further shed light on the genetic foundation of the easily dehulled trait in a particular variety that was artificially selected by the Wa people, a minority group in Southwestern China known for cultivating Tartary buckwheat specifically for steaming as a staple food to prevent lysine deficiency.

CONCLUSIONS

This study provides both comprehensive insights into the origin and domestication of, and a foundation for molecular breeding for, Tartary buckwheat.

Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility

Common buckwheat (Fagopyrum esculentum) is an ancient crop with a world-wide distribution. Due to its excellent nutritional quality and high economic and ecological value, common buckwheat is becoming increasingly important throughout the world. The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat, but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly. Here we report the assembly of a chromosome-scale high-quality reference genome of F. esculentum var. homotropicum, a homozygous self-pollinating variant of common buckwheat. Comparative genomics revealed that two cultivated buckwheat species, common buckwheat (F. esculentum) and Tartary buckwheat (F. tataricum), underwent metabolomic divergence and ecotype differentiation. The expansion of several gene families in common buckwheat, including FhFAR genes, is associated with its wider distribution than Tartary buckwheat. Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat. Furthermore, we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat. Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups. Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period, a key agronomic trait controlling the yield of outcrossing crops, and that Fh06G015130 is a crucial gene underlying flavor-associated flavonoids. Intriguingly, we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common buckwheat. Collectively, our results elucidate the genetic basis of speciation, ecological adaptation, fertility, and unique flavor of common buckwheat, and provide new resources for future genomics-assisted breeding of this economically important crop.

Characterization of the Slovene Autochthonous Rose Hybrid Rosa pendulina × spinosissima (Rosa reversa Waldst. and Kit) Using Biochemical Patterns of the Plant Blossoms

The Rosa genus is characterized by great variability and, consequently, they easily hybridize. The petals of R. pendulina, R. spinosissima and their hybrid Rosa pendulina × spinosissima, collected in western Slovenia, were included in the research. We performed morphometric analysis using keys to determine roses and genetic analysis to determine the genome size. The phenolic compound content in petals of all rose flowers was measured by liquid chromatography and mass spectrometry (HPLC-MS). Using flow cytometry, we could confirm the native hybridization process due to the amount of 2C DNA. The value of R. pendulina was 1.71 pg, of R. spinosissima 1.60 pg and of the hybrid 1.62 pg. The value for the hybrid was close to values measured for parent plants and, at the same time, those values of parent plants significantly differed from each other. Our results showed that the content of phenolic compounds in petals decreased after crossing. We found that the highest total phenolic content (178.9 g/kg FW) was measured in R. spinossisima, the lowest content was analyzed for the hybrid (84.36 g/kg FW) and the content for R. pendulina was between these two values (110.58 g/kg FW). The content of flavanols and flavonols was lowest in the hybrid petals, whereas the content of anthocyanins was highest in the hybrid petals.

Phytochemistry, Bioactivities of Metabolites, and Traditional Uses of Fagopyrum tataricum

In Tartary buckwheat (Fagopyrum tataricum), the edible parts are mainly grain and sprouts. Tartary buckwheat contains protecting substances, which make it possible for plants to survive on high altitudes and under strong natural ultraviolet radiation. The diversity and high content of phenolic substances are important for Tartary buckwheat to grow and reproduce under unfriendly environmental effects, diseases, and grazing. These substances are mainly flavonoids (rutin, quercetin, quercitrin, vitexin, catechin, epicatechin and epicatechin gallate), phenolic acids, fagopyrins, and emodin. Synthesis of protecting substances depends on genetic layout and on the environmental conditions, mainly UV radiation and temperature. Flavonoids and their glycosides are among Tartary buckwheat plants bioactive metabolites. Flavonoids are compounds of special interest due to their antioxidant properties and potential in preventing tiredness, diabetes mellitus, oxidative stress, and neurodegenerative disorders such as Parkinson's disease. During the processing and production of food items, Tartary buckwheat metabolites are subjected to molecular transformations. The main Tartary buckwheat traditional food products are bread, groats, and sprouts.

Molecular Shield for Protection of Buckwheat Plants from UV-B Radiation

Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) and common buckwheat (Fagopyrum esculentum Moench) are adapted to growing in harsh conditions of high altitudes. Ultraviolet radiation at high altitudes strongly impacts plant growth and development. Under the influence of ultraviolet radiation, protecting substances are synthesized in plants. The synthesis of UV-B defense metabolites is genetically conditioned, and their quantity depends on the intensity of the ultraviolet radiation to which the plants and plant parts are exposed. These substances include flavonoids, and especially rutin. Other substances with aromatic rings of six carbon atoms have a similar function, including fagopyrin, the metabolite specific for buckwheat. Defensive substances are formed in the leaves and flowers of common and Tartary buckwheat, up to about the same concentration in both species. In comparison, the concentration of rutin in the grain of Tartary buckwheat is much higher than in common buckwheat. Flavonoids also have other functions in plants so that they can protect them from pests and diseases. After crushing the grains, rutin is exposed to contact with the molecules of rutin-degrading enzymes. In an environment with the necessary humidity, rutin is turned into bitter quercetin under the action of rutin-degrading enzymes. This bitterness has a deterrent effect against pests. Moreover, flavonoids have important functions in human nutrition to prevent several chronic diseases, including obesity, cardiovascular diseases, gallstone formation, and hypertension.

Tartary Buckwheat in Human Nutrition

Tartary buckwheat (Fagopyrum tataricum Gaertn.) originates in mountain areas of western China, and it is mainly cultivated in China, Bhutan, northern India, Nepal, and central Europe. Tartary buckwheat shows greater cold resistance than common buckwheat, and has traits for drought tolerance. Buckwheat can provide health benefits due to its contents of resistant starch, mineral elements, proteins, and in particular, phenolic substances, which prevent the effects of several chronic human diseases, including hypertension, obesity, cardiovascular diseases, and gallstone formation. The contents of the flavonoids rutin and quercetin are very variable among Tartary buckwheat samples from different origins and parts of the plants. Quercetin is formed after the degradation of rutin by the Tartary buckwheat enzyme rutinosidase, which mainly occurs after grain milling during mixing of the flour with water. High temperature treatments of wet Tartary buckwheat material prevent the conversion of rutin to quercetin.

Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits

BACKGROUND

Tartary buckwheat (Fagopyrum tataricum) is a nutritionally balanced and flavonoid-rich crop plant that has been in cultivation for 4000 years and is now grown globally. Despite its nutraceutical and agricultural value, the characterization of its genetics and its domestication history is limited.

RESULTS

Here, we report a comprehensive database of Tartary buckwheat genomic variation based on whole-genome resequencing of 510 germplasms. Our analysis suggests that two independent domestication events occurred in southwestern and northern China, resulting in diverse characteristics of modern Tartary buckwheat varieties. Genome-wide association studies for important agricultural traits identify several candidate genes, including FtUFGT3 and FtAP2YT1 that significantly correlate with flavonoid accumulation and grain weight, respectively.

CONCLUSIONS

We describe the domestication history of Tartary buckwheat and provide a detailed resource of genomic variation to allow for genomic-assisted breeding in the improvement of elite cultivars.

Breeding Buckwheat for Increased Levels and Improved Quality of Protein

Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) and common buckwheat (Fagopyrum esculentum Moench) are important sources of proteins with balanced amino-acid compositions, and thus of high nutritional value. The polyphenols naturally present in Tartary buckwheat and common buckwheat lower the true digestibility of the proteins. Digestion-resistant peptides are a vehicle for fecal excretion of steroids, and in this way, for bile acid elimination and reduction of cholesterol concentrations in serum. Buckwheat proteins are more effective compared to soy proteins for the prevention of gallstone formation. Tartary and common buckwheat grain that contains appropriate amounts of selenium-containing amino acids can be produced as functional food products. The protein-rich by-products of buckwheat are a good source of bioactive substances that can suppress colon carcinogenesis by reducing cell proliferation. The grain embryo is a rich source of proteins, so breeding buckwheat with larger embryos is a possible strategy to increase protein levels in Tartary and common buckwheat grain. However, chemical analysis of the grain is the most relevant criterion for assessing grain protein levels and quality.

Breeding Buckwheat for Increased Levels of Rutin, Quercetin and Other Bioactive Compounds with Potential Antiviral Effects

Common buckwheat (Fagopyrum esculentum Moench) and Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) are sources of many bioactive compounds, such as rutin, quercetin, emodin, fagopyrin and other (poly)phenolics. In damaged or milled grain under wet conditions, most of the rutin in common and Tartary buckwheat is degraded to quercetin by rutin-degrading enzymes (e.g., rutinosidase). From Tartary buckwheat varieties with low rutinosidase activity it is possible to prepare foods with high levels of rutin, with the preserved initial levels in the grain. The quercetin from rutin degradation in Tartary buckwheat grain is responsible in part for inhibition of α-glucosidase in the intestine, which helps to maintain normal glucose levels in the blood. Rutin and emodin have the potential for antiviral effects. Grain embryos are rich in rutin, so breeding buckwheat with the aim of producing larger embryos may be a promising strategy to increase the levels of rutin in common and Tartary buckwheat grain, and hence to improve its nutritional value.

Breeding buckwheat for nutritional quality

Common buckwheat (Fagopyrum esculentum Moench, CB) and Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn., TB) are used in human nutrition. The idea to screen in the haploid phase for genes affecting low amylose concentration opens the possibility for the effective search of low amylose (waxy) genotypes in CB populations. Self-pollinated homozygous plants of TB might allow us to use a part of endosperm for screening of amylose content. Phenolic substances have a significant inhibitory effect on the digestion of CB and TB proteins, thus metabolites may have impact on protein digestibility. Digestion-resistant peptides are largely responsible for the bile acid elimination. Breeding to diminish polyphenols and anti-nutritional substances might have negative effects on the resistance of plants against pests, diseases and UV-radiation. Bread and pasta are popular CB and TB dishes. During dough making most of CB or TB rutin is degraded to quercetin by rutin-degrading enzymes. The new trace-rutinosidase TB variety makes possible making TB bread with considerable amount of rutin, preserving the initial rutin from flour. Breeding CB and TB for larger embryos would make it possible to increase protein, rutin, and essential minerals concentration in CB and TB grain.

The temperature threshold for the transformation of rutin to quercetin in Tartary buckwheat dough

The aim was to determine conditions under which rutin can be retained during production of Tartary buckwheat (Fagopyrum tataricum) dough. Tartary buckwheat flour was hydrothermally treated by mixing with water at 25, 40, 60, 80 and 95 °C, with unprocessed Tartary buckwheat flour as control. With hydrothermal treatments at 25, 40 and 60 °C, most of the rutin was transformed to quercetin. However, for hydrothermal treatments at 80 and 95 °C, rutin was retained due to denaturation of the rutin-degrading enzymes during hydrothermal treatment. This is the first report to describe a temperature threshold for denaturation of rutin-degrading enzymes in any buckwheat material. Tartary buckwheat dough produced at 95 °C contained 12 mg rutin/g dry matter. Based on these characteristics, dough from hydrothermally treated Tartary buckwheat is a promising, rutin-rich functional food material.

NEW INSIGHTS INTO STRUCTURES AND COMPOSITION OF PLANT FOOD MATERIALS

The aim of this paper is to review principles and potential application of micro-proton induced X-ray emission (micro-PIXE), synchrotron-based micro-X-ray fluorescence (micro-XRF) and inductively coupled plasma-mass spectrometry (ICP-MS) hyphenated with pulsed laser ablation (LA) for analysing plants and plant materials to elucidate feature of constituensts of nutritional value. These are required in order to develop novel high-quality functional and other food products in view of the variability of properties of plant tissues and products.

New polymorphic dinucleotide and trinucleotide microsatellite loci for hop Humulus lupulus L

One hundred and thirty-five microsatellite markers were developed for hop Humulus lupulus L. from di- and trinucleotide-enriched libraries. Seventy-eight primers showed amplification in two tested genotypes. Twenty-four loci were further characterized on a population of 34 hop samples and the number of alleles per locus, observed heterozygosity and expected heterozygosity ranged from two to 20 (9.7 on average), from 0.0294 to 0.9412 (0.6234 on average) and from 0.0294 to 0.9170 (0.6720 on average), respectively. These microsatellite markers will be further used for studying population structures and relationships and for identifying important qualitative and quantitative loci of hop.

Identification of quantitative trait loci for resistance to Verticillium wilt and yield parameters in hop (Humulus lupulus L.)

Verticillium wilt (VW) can cause substantial yield loss in hop particularly with the outbreaks of the lethal strain of Verticillium albo-atrum. To elucidate genetic control of VW resistance in hop, an F1 mapping population derived from a cross of cultivar Wye Target, with the predicted genetic basis of resistance, and susceptible male breeding line BL2/1 was developed to assess wilting symptoms and to perform QTL mapping. The genetic linkage map, constructed with 203 markers of various types using a pseudo-testcross strategy, formed ten major linkage groups (LG) of the maternal and paternal maps, covering 552.98 and 441.1 cM, respectively. A significant QTL for VW resistance was detected at LOD 7 on a single chromosomal region on LG03 of both parental maps, accounting for 24.2-26.0 % of the phenotypic variance. QTL analysis for alpha-acid content and yield parameters was also performed on this map. QTLs for these traits were also detected and confirmed our previously detected QTLs in a different pedigree and environment. The work provides the basis for exploration of QTL flanking markers for possible use in marker-assisted selection.

Quantitative determination of mosaic GFP gene expression in tobacco

A specific form of gene silencing that was observed visually as a mosaic distribution of fluorescent and non-fluorescent cells apparently dispersed at random within tissues was found in a few green fluorescent protein (GFP)-transformed tobacco lines. To characterize this event quantitatively, we studied flow cytometric measurements in GFP-expressing and -silenced cells in T1 and T2 progeny of four selected plants. The proportion of silenced cells varied considerably among the T1 lines but with notable genotype differences. Mosaic expression was inherited into the T2 generation in which the majority of progenies tested exhibited a level of silencing similar to that of their T1 parental plants. However, in some T2 progenies segregation, evident as a decrease or increase in the proportion of fluorescent cells, was observed. We discuss several factors, such as copy number, promoter activity or polyploidy, that may be the possible causes of the gene silencing, but none sufficiently explain the appearance of the mosaic distribution.