Gene flow signature in the S-allele region of cultivated buckwheat

Genetic diversity, population genetic structure and gene flow in the rare and endangered wild plant Cypripedium macranthos revealed by genotyping-by-sequencing

BACKGROUND

Genetic diversity, genetic structure, and gene flow in plant populations and their influencing factors are important in conservation biology. Cypripedium macranthos is one of the few wild orchids with high ornamental value in northern China. However, over the past decade, excessive collection, trading, tourism development, habitat fragmentation, deceptive pollination, and seed germination difficulties have all caused a sharp decline in the number of C. macranthos individuals and its population. In order to propose a scientific and effective conservation strategy, the genetic diversity, genetic structure and gene flow of the current CM population are urgent scientific issues to be clarified.

RESULTS

Here, 99 individuals of C. macranthos from north and northeast China were analyzed to evaluate the genetic diversity, gene flow among populations, and genetic structure by genotyping-by-sequencing. More than 68.44 Gb high-quality clean reads and 41,154 SNPs were obtained. Our data based on bioinformatics methods revealed that C. macranthos has lower genetic diversity, high levels of historical gene flow, and moderate-to-high genetic differentiation between populations. The gene migration model revealed that the direction of gene flow was mainly from northeast populations to north populations in China. The results of genetic structure analysis showed that 11 C. macranthos populations can be considered as two groups, and further divided into four subgroups. Moreover, the Mantel test detected no significant "Isolation by Distance" between populations.

CONCLUSIONS

Our study demonstrates that the present genetic diversity and genetic structure of C. macranthos populations were mainly caused by biological characteristics, human interference, habitat fragmentation, and restricted gene flow. Finally, constructive measures, which can provide a basis for the proposal of conservation strategies, have been suggested.

2S albumin g13 polypeptide, less related to Fag e 2, can be eliminated in common buckwheat (Fagopyrum esculentum Moench) seeds

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2S albumin (g11, g13, g14, and g28) is an important allergen in common buckwheat.

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g13 is hydrophobic, scarce, and less related to g14 than g11/g28 is related to g14.

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g13_null allele homozygote produced no g13 protein in seeds.

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Insert-like sequence of g13_null allele resided frequently in buckwheat genome.

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g13_null homozygote lowered allergenicity in common buckwheat.

2S albumin (g11, g13, g14, and g28) is an important allergen in common buckwheat (Fagopyrum esculentum). g13 is hydrophobic, rare in seeds, and may show distinct allergenicity from the others; therefore, we tried to eliminate this protein. Phylogenetic and property distance analyses indicated g13 is less related to g14 (Fag e 2) than g11/g28 is related to g14, particularly in the second domain containing the II and III α-helices. A null allele with a 531 bp insertion in the coding region was found for g13 at an allele frequency of 2 % in natural populations of common buckwheat. The g13_null allele homozygote accumulated no g13 protein. A BLAST search for the 531 bp insertion suggested the insert-like sequence resided frequently in the buckwheat genome, including the self-incompatibility responsible gene ELF3 in Fagopyrum tataricum. The g13_null insert-like sequence could, therefore, help in producing hypoallergenic cultivars, and expand the genetic diversity of buckwheat.

FaesAP3_1 Regulates the FaesELF3 Gene Involved in Filament-Length Determination of Long-Homostyle Fagopyrum esculentum

The identification downstream genes of floral organ identity regulators are critical to revealing the molecular mechanisms underlying floral morphogenesis. However, a general regulatory pathway between floral organ identity genes and their downstream targets is still unclear because of the lack of studies in nonmodel species. Here, we screened a direct downstream target gene, FaesELF3, of a stamen identity transcription factor, FaesAP3_1, in long-homostyle (LH) Fagopyrum esculentum moench by using yeast one-hybrid (Y1H) and dual-luciferase reporter (DR) assays. Furthermore, FaesAP3_1-silenced LH plants that produced flowers with part stamens or anthers homeotically converted into a tepaloid structure, and FaesELF3-silenced plants that had flowers with part stamens consisting of a short filament and empty anther (male sterile anther). All these suggested that transcription factor (TF) FaesAP3_1 directly activates FaesELF3 in order to regulate filament elongation and pollen grain development in LH buckwheat. Our data also suggested that other stamen development pathways independent of FaesAP3_1 remain in F. esculentum.

Plastome comparison and phylogenomics of Fagopyrum (Polygonaceae): insights into sequence differences between Fagopyrum and its related taxa

BACKGROUND

Fagopyrum (Polygonaceae) is a small plant lineage comprised of more than fifteen economically and medicinally important species. However, the phylogenetic relationships of the genus are not well explored, and the characteristics of Fagopyrum chloroplast genomes (plastomes) remain poorly understood so far. It restricts the comprehension of species diversity in Fagopyrum. Therefore, a comparative plastome analysis and comprehensive phylogenomic analyses are required to reveal the taxonomic relationship among species of Fagopyrum.

RESULTS

In the current study, 12 plastomes were sequenced and assembled from eight species and two varieties of Fagopyrum. In the comparative analysis and phylogenetic analysis, eight previously published plastomes of Fagopyrum were also included. A total of 49 plastomes of other genera in Polygonaceae were retrieved from GenBank and used for comparative analysis with Fagopyrum. The variation of the Fagopyrum plastomes is mainly reflected in the size and boundaries of inverted repeat/single copy (IR/SC) regions. Fagopyrum is a relatively basal taxon in the phylogenomic framework of Polygonaceae comprising a relatively smaller plastome size (158,768-159,985 bp) than another genus of Polygonaceae (158,851-170,232 bp). A few genera of Polygonaceae have nested distribution of the IR/SC boundary variations. Although most species of Fagopyrum show the same IRb/SC boundary with species of Polygonaceae, only a few species show different IRa/SC boundaries. The phylogenomic analyses of Fagopyrum supported the cymosum and urophyllum groups and resolved the systematic position of subclades within the urophyllum group. Moreover, the repeat sequence types and numbers were found different between groups of Fagopyrum. The plastome sequence identity showed significant differences between intra-group and inter-group.

CONCLUSIONS

The deletions of intergenic regions cause a short length of Fagopyrum plastomes, which may be the main reason for plastome size diversity in Polygonaceae species. The phylogenomic reconstruction combined with the characteristics comparison of plastomes supports grouping within Fagopyrum. The outcome of these genome resources may facilitate the taxonomy, germplasm resources identification as well as plant breeding of Fagopyrum.

Milling fractions composition of common (Fagopyrum esculentum Moench) and Tartary (Fagopyrum tataricum (L.) Gaertn.) buckwheat

Buckwheat is a pseudocereal with important nutritional qualities and great potential for broad consumption. The study aimed to determine the biochemical composition, antioxidant properties and multi-mineral composition of the whole grains, hulls, bran, and the light flour of common (Fagopyrum esculentum Moench) and Tartary (Fagopyrum tataricum (L.) Gaertn.) buckwheat harvested in two consecutive years. Significant differences between fractions of both species were observed. On the other hand, the differences between the production years were not so significant. Biochemical and multi-mineral compositions of common and Tartary buckwheat were comparable, while significant differences between species were observed in antioxidant properties. The antioxidant potential (AOP), total phenolic content (TPC), and total flavonoid content (TFC) were higher in all fractions of Tartary buckwheat compared to individual fractions of common buckwheat. Fourteen minerals were quantified in fractions. Contents of all major minerals and most of the trace minerals were the highest in bran fraction.

Comparison of Plant Morphology, Yield and Nutritional Quality of Fagopyrum esculentum and Fagopyrum tataricum Grown under Field Conditions in Belgium

Buckwheat is a pseudocereal with high nutritional and nutraceutical properties. Although common buckwheat (Fagopyrum esculentum) is the main cultivated species, Tartary buckwheat (Fagopyrum tataricum) is gaining interest. In this paper, we compared plant growth, yield-related parameters and seed nutritional qualities of two varieties of F. esculentum and F. tataricum under field conditions in Belgium. Fagopyrum esculentum flowered earlier, produced less nodes, less branches, less inflorescences, but more flowers per inflorescence than F. tataricum. The yield was higher in F. tataricum, while the thousand-grain weight was higher in F. esculentum. Yield ranged between 2037 kg/ha and 3667 kg/ha depending on the species and year. Regarding nutritional qualities, seeds of F. esculentum contained more proteins (15.4% vs. 12.8%) than seeds of F. tataricum although their amino acid profile was similar. Seeds of F. esculentum contained also more Mg (1.36 vs. 1.15 mg/g dry weight (DW)) and less Fe (22.9 vs. 32.6 µg/g DW) and Zn (19.6 vs. 24.5 µg/g DW) than F. tataricum. The main difference between seed nutritional quality was the concentration of flavonoids that was 60 times higher in F. tataricum than in F. esculentum. Both species grow well under Belgian conditions and showed good seed quality.

Targeted amplicon sequencing + next-generation sequencing-based bulked segregant analysis identified genetic loci associated with preharvest sprouting tolerance in common buckwheat (Fagopyrum esculentum)

BACKGROUND

Common buckwheat (2n = 2x = 16) is an outcrossing pseudocereal whose seeds contain abundant nutrients and potential antioxidants. As these beneficial compounds are damaged by preharvest sprouting (PHS) and PHS is likely to increase with global warming, it is important to find efficient ways to develop new PHS-tolerant lines. However, genetic loci and selection markers associated with PHS in buckwheat have not been reported.

RESULTS

By next-generation sequencing (NGS) of whole-genome of parental lines, we developed a genome-wide set of 300 markers. By NGS- based bulked segregant analysis (NGS-BSA), we developed 100 markers linked to PHS tolerance. To confirm the effectiveness of marker development from NGS-BSA data, we developed 100 markers linked to the self-compatibility (SC) trait from previous NGS-BSA data. Using these markers, we developed genetic maps with AmpliSeq technology, which can quickly detect polymorphisms by amplicon-based multiplex targeted NGS, and performed quantitative trait locus (QTL) analysis for PHS tolerance in combination with NGS-BSA. QTL analysis detected two major and two minor QTLs for PHS tolerance in a segregating population developed from a cross between the PHS-tolerant 'Kyukei 29' and the self-compatible susceptible 'Kyukei SC7'. We found different major and minor QTLs in other segregating populations developed from the PHS-tolerant lines 'Kyukei 28' and 'NARO-FE-1'. Candidate markers linked to PHS developed by NGS-BSA were located near these QTL regions. We also investigated the effectiveness of markers linked to these QTLs for selection of PHS-tolerant lines among other segregating populations.

CONCLUSIONS

We efficiently developed genetic maps using a method combined with AmpliSeq technology and NGS-BSA, and detected QTLs associated with preharvest sprouting tolerance in common buckwheat. This is the first report to identify QTLs for PHS tolerance in buckwheat. Our marker development system will accelerate genetic research and breeding in common buckwheat.

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.

Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim. revealed by reduced representation sequencing

BACKGROUND

Studying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such as rare and endangered plants. Tetraena mongolica Maxim. (TM), belongs to Zygophyllaceae family, a rare and endangered plant with narrow distribution. However, for the last decade, due to excessive logging, urban expansion, industrial and tourism development, habitat fragmentation and loss of natural habitats have become major threats to the population of endangered plants.

RESULTS

In this study, genetic diversity, population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, and a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found that the existing TM populations have moderate levels of genetic diversity, and very low genetic differentiation as well as high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups. The Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. Moreover, the migration model indicated that the gene flow is more of a north to south migration pattern in history.

CONCLUSIONS

This study demonstrates that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. Our recommendation with respect to conservation management is that, all 8 populations should be preserved as a whole population, rather than just those in the core area of TM nature reserve. In particular, the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.

Genetic and genomic research for the development of an efficient breeding system in heterostylous self-incompatible common buckwheat (Fagopyrum esculentum)

Common buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is an annual crop that is cultivated widely around the world and contains an abundance of nutrients and bioactive compounds. However, the yield of buckwheat is low compared to that of other major crops, and it contains proteins that cause allergic reactions in some people. Much research has aimed to improve or eliminate these undesirable traits, and some major advances have recently been made. Here, we review recent advances in buckwheat breeding materials, tools, and methods, including the development of self-compatible lines, genetic maps, a buckwheat genome database, and an efficient breeding strategy. We also describe emerging breeding methods for high-value lines.

Nutraceutical crop buckwheat: a concealed wealth in the lap of Himalayas

Buckwheat is a crop that has gained considerable interest worldwide due to its nutritional, economical, and pharmaceutical values. To ensure food and nutritional security in a scenario of global climate change, this pseudocereal is a competent alternative to staple crops. With rising knowledge regarding the nutraceutical potential, the popularity of this species is expected to increase further in coming years. The main bioactive component of this species is rutin that has been proven to have a wide range of health-promoting benefits. Due to breeding constraints, asynchronous maturity, seed shattering, and restricted distribution, this species holds the status of an underutilized or neglected crop in many parts of the world. In the North-western Himalayan zone, it is an integral part of local dietary intake and is grown as a second crop after harvesting barley and peas. Fagopyrum esculentum and F. tataricum are the species of buckwheat cultivated in the North-western Himalayas. However, more studies in the direction of conservation, utilization, and genetic amelioration of plant genetic resources are needed to sustain food security in Southeast Asia. The present review paper accentuates the multicore potential of buckwheat besides highlighting the commercial and pharmaceutical perspective. This article also focuses on the conservation and sustainable utilization of Himalayan gene pools, desirable agronomic traits, and genetic diversity besides focusing on the biochemical and molecular response of Fagopyrum to biotic and abiotic stress including modulation of the rutin content. The role of biotechnological interventions and future prospects are also summarized.

History of the progressive development of genetic marker systems for common buckwheat

Genotyping is an essential procedure for identifying agronomically useful genes and analyzing population structure. Various types of genetic marker systems have been developed in common buckwheat (Fagopyrum esculentum Moench). In the 1980s, morphological and allozyme markers were used to construct linkage maps. Until the early 2000s, allozyme markers were widely used in population genetics studies. Such studies demonstrated that cultivated common buckwheat likely originated in the Sanjiang area of China. In the late 1990s and early 2000s, advances in PCR technology led to the development of various DNA marker systems for use in linkage mapping. However, PCR-based markers did not completely cover the genome, making genetic analysis of buckwheat challenging. The subsequent development of next generation sequencing, a game-changing technology, has allowed genome-wide analysis to be performed for many species. Indeed, 8,884 markers spanning 756 loci were recently mapped onto eight linkage groups of common buckwheat; these markers were successfully used for genomic selection to increase yield. Furthermore, draft genome sequences are now available in the Buckwheat Genome DataBase (BGDB). In this review, I summarize advances in the breeding and genetic analysis of common buckwheat based on contemporary genetic marker systems.

Genomics-assisted breeding in minor and pseudo-cereals

Minor and pseudo-cereals, which can grow with lower input and often produce specific nutrients compared to major cereal crops, are attracting worldwide attention. Since these crops generally have a large genetic diversity in a breeding population, rapid genetic improvement can be possible by the application of genomics-assisted breeding methods. In this review, we discuss studies related to biparental quantitative trait locus (QTL) mapping, genome-wide association study, and genomic selection for minor and pseudo-cereals. Especially, we focus on the current progress in a pseudo-cereal, buckwheat. Prospects for the practical utilization of genomics-assisted breeding in minor and pseudo-cereals are discussed including the issues to overcome especially for these crops.