Construction of a BAC library for buckwheat genome research - an application to positional cloning of agriculturally valuable traits

Buckwheat OMICS: present status and future prospects

Buckwheat (Fagopyrum spp.) is an underutilized resilient crop of North Western Himalayas belonging to the family Polygonaceae and is a source of essential nutrients and therapeutics. Common Buckwheat and Tatary Buckwheat are the two main cultivated species used as food. It is the only grain crop possessing rutin, an important metabolite with high nutraceutical potential. Due to its inherent tolerance to various biotic and abiotic stresses and a short life cycle, Buckwheat has been proposed as a model crop plant. Nutritional security is one of the major concerns, breeding for a nutrient-dense crop such as Buckwheat will provide a sustainable solution. Efforts toward improving Buckwheat for nutrition and yield are limited due to the lack of available: genetic resources, genomics, transcriptomics and metabolomics. In order to harness the agricultural importance of Buckwheat, an integrated breeding and OMICS platforms needs to be established that can pave the way for a better understanding of crop biology and developing commercial varieties. This, coupled with the availability of the genome sequences of both Buckwheat species in the public domain, should facilitate the identification of alleles/QTLs and candidate genes. There is a need to further our understanding of the molecular basis of the genetic regulation that controls various economically important traits. The present review focuses on: the food and nutritional importance of Buckwheat, its various omics resources, utilization of omics approaches in understanding Buckwheat biology and, finally, how an integrated platform of breeding and omics will help in developing commercially high yielding nutrient rich cultivars in Buckwheat.

Elimination of zero-repeat subunit in allergenic seed protein 13S globulin using the novel allele GlbNB2 in common buckwheat (Fagopyrum esculentum Moench)

Common buckwheat (Fagopyrum esculentum Moench) seeds contain 13S globulin, the zero-repeat subunit of which is trypsin-resistant and allergenic. Here, its two novel alleles were analyzed for development of hypoallergenic plants. The GlbNC allele has a Miniature Inverted-repeat Transposable Element (MITE)-like insertion in the 4th exon. However, most of the insertion was spliced-out, resulting in accumulation of zero-repeat subunit in GlbNC homozygotes. Meanwhile, the GlbNB2 has a 164-bp insertion in the 3rd exon, resulting in no accumulation of zero-repeat subunit in GlbNB2 homozygotes (NB2_homo). Both the insertion sequences were predicted to form a hairpin-like structure, and that of GlbNB2 was more rigid than that of GlbNC. Trypsin digestion in NB2_homo showed that the α polypeptide of Met-rich subunit is also hard to digest, that is a next target to eliminate for hypoallergenic buckwheat development.

Two floral forms in the same species-distyly

MAIN CONCLUSION

This paper reviews the progress of research on the morphology, physiology and molecular biology of distyly in plants. It will help to elucidate the mysteries of distyly in plants. Distyly is a unique representative type of heterostyly in plants, primarily characterized by the presence of long style and short style within the flowers of the same species. This interesting trait has always fascinated researchers. With the rapid development of molecular biology, the molecular mechanism for the production of dimorphic styles in plants is also gaining ground. Researchers have been studying plant dimorphic styles from various perspectives. The researchers are gradually unravelling the mechanisms by which plants produce distyly traits. This paper reviews advances in the study of plant dimorphic style characteristics, mainly in terms of the morphology, physiology and molecular biology of plants with dimorphic styles. The aim is to provide a theoretical basis for the study of the mechanism of distyly formation in plants.

Insertion of ten amino acids into 13S globulin zero-repeat subunit improves trypsin digestibility in common buckwheat (Fagopyrum esculentum Moench) seeds

The 13S globulin zero-repeat subunit is resistant to trypsin and may have higher allergenicity than the 1-6 tandem repeat subunits in common buckwheat (Fagopyrum esculentum Moench). To explore alleles useful for lowering allergenicity, amplicon deep sequencing targeting the zero-repeat subunit gene was conducted in bulked genomic DNA from eight cultivars and landraces. The analysis identified a unique allele encoding a zero-repeat subunit with 10 amino acid insertion (10aa) at a position equivalent to the tandem repeat insertion. Prediction of its 3-D structure suggested that 10aa changes the β-hairpin structure in the non-10aa (native) subunit to a random coil, which is also found in 1- and 3- repeat subunits. Homozygotes of the 10aa allele were developed and showed that the 10aa subunit was more digestible than the native subunit. However, the 10aa subunit was still less digestible than the 1-6 repeat subunits, suggesting needs to explore unfunctional alleles.

Biotechnological Methods for Buckwheat Breeding

The Fagopyrum genus includes two cultivated species, namely common buckwheat (F. esculentum Moench) and Tartary buckwheat (F. tataricum Gaertn.), and more than 25 wild buckwheat species. The goal of breeders is to improve the properties of cultivated buckwheat with methods of classical breeding, with the support of biotechnological methods or a combination of both. In this paper, we reviewed the possibility to use transcriptomics, genomics, interspecific hybridization, tissue cultures and plant regeneration, molecular markers, genetic transformation, and genome editing to aid in both the breeding of buckwheat and in the identification and production of metabolites important for preserving human health. The key problems in buckwheat breeding are the unknown mode of inheritance of most traits, associated with crop yield and the synthesis of medicinal compounds, low seed yield, shedding of seeds, differential flowering and seed set on branches, and unknown action of genes responsible for the synthesis of buckwheat metabolites of pharmaceutical and medicinal interest.

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.

Healthy and Resilient Cereals and Pseudo-Cereals for Marginal Agriculture: Molecular Advances for Improving Nutrient Bioavailability

With the ever-increasing world population, an extra 1.5 billion mouths need to be fed by 2050 with continuously dwindling arable land. Hence, it is imperative that extra food come from the marginal lands that are expected to be unsuitable for growing major staple crops under the adverse climate change scenario. Crop diversity provides right alternatives for marginal environments to improve food, feed, and nutritional security. Well-adapted and climate-resilient crops will be the best fit for such a scenario to produce seed and biomass. The minor millets are known for their high nutritional profile and better resilience for several abiotic stresses that make them the suitable crops for arid and salt-affected soils and poor-quality waters. Finger millet (Eleucine coracana) and foxtail millet (Setaria italica), also considered as orphan crops, are highly tolerant grass crop species that grow well in marginal and degraded lands of Africa and Asia with better nutritional profile. Another category of grains, called pseudo-cereals, is considered as rich foods because of their protein quality and content, high mineral content, and healthy and balance food quality. Quinoa (Chenopodium quinoa), amaranth (Amaranthus sp.), and buckwheat (Fagopyrum esculentum) fall under this category. Nevertheless, both minor millets and pseudo-cereals are morphologically different, although similar for micronutrient bioavailability, and their grains are gluten-free. The cultivation of these millets can make dry lands productive and ensure future food as well as nutritional security. Although the natural nutrient profile of these crop plant species is remarkably good, little development has occurred in advances in molecular genetics and breeding efforts to improve the bioavailability of nutrients. Recent advances in NGS have enabled the genome and transcriptome sequencing of these millets and pseudo-cereals for the faster development of molecular markers and application in molecular breeding. Genomic information on finger millet (1,196 Mb with 85,243 genes); S. italica, a model small millet (well-annotated draft genome of 420 Mb with 38,801 protein-coding genes); amaranth (466 Mb genome and 23,059 protein-coding genes); buckwheat (genome size of 1.12 Gb with 35,816 annotated genes); and quinoa (genome size of 1.5 Gb containing 54,438 protein-coding genes) could pave the way for the genetic improvement of these grains. These genomic resources are an important first step toward genetic improvement of these crops. This review highlights the current advances and available resources on genomics to improve nutrient bioavailability in these five suitable crops for the sustained healthy livelihood.

A short story gets longer: recent insights into the molecular basis of heterostyly

Heterostyly is a fascinating adaptation to promote outbreeding and a classical paradigm of botany. In the most common type of heterostyly, plants either form flowers with long styles and short stamens, or short styles and long stamens. This reciprocal organ positioning reduces pollen wastage and promotes cross-pollination, thus increasing male fitness. In addition, in many heterostylous species selfing and the generation of unfit progeny due to inbreeding depression is limited by a self-incompatibility system, thus promoting female fitness. The two floral forms are genetically determined by the S locus as a complex supergene, namely a chromosomal region containing several individual genes that control the different traits, such as style or stamen length, and are held together by very tight linkage due to suppressed recombination. Recent molecular-genetic studies in several systems, including Turnera, Fagopyrum, Linum, and Primula have begun to identify and characterize the causal heterostyly genes residing at the S locus. An emerging theme from several families is that the dominant S haplotype represents a hemizygous region not present on the recessive s haplotype. This provides an explanation for the suppressed recombination and suggests a scenario for the chromosomal evolution of the S locus. In this review, we discuss the results from recent molecular-genetic analyses in light of the classical models on the genetics and evolution of heterostyly.

Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes

Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits.

Oakleaf: an S locus-linked mutation of Primula vulgaris that affects leaf and flower development

In Primula vulgaris outcrossing is promoted through reciprocal herkogamy with insect-mediated cross-pollination between pin and thrum form flowers. Development of heteromorphic flowers is coordinated by genes at the S locus. To underpin construction of a genetic map facilitating isolation of these S locus genes, we have characterised Oakleaf, a novel S locus-linked mutant phenotype. We combine phenotypic observation of flower and leaf development, with classical genetic analysis and next-generation sequencing to address the molecular basis of Oakleaf. Oakleaf is a dominant mutation that affects both leaf and flower development; plants produce distinctive lobed leaves, with occasional ectopic meristems on the veins. This phenotype is reminiscent of overexpression of Class I KNOX-homeodomain transcription factors. We describe the structure and expression of all eight P. vulgaris PvKNOX genes in both wild-type and Oakleaf plants, and present comparative transcriptome analysis of leaves and flowers from Oakleaf and wild-type plants. Oakleaf provides a new phenotypic marker for genetic analysis of the Primula S locus. We show that none of the Class I PvKNOX genes are strongly upregulated in Oakleaf leaves and flowers, and identify cohorts of 507 upregulated and 314 downregulated genes in the Oakleaf mutant.

Integration of genetic and physical maps of the Primula vulgaris S locus and localization by chromosome in situ hybridization

Heteromorphic flower development in Primula is controlled by the S locus. The S locus genes, which control anther position, pistil length and pollen size in pin and thrum flowers, have not yet been characterized. We have integrated S-linked genes, marker sequences and mutant phenotypes to create a map of the P. vulgaris S locus region that will facilitate the identification of key S locus genes. We have generated, sequenced and annotated BAC sequences spanning the S locus, and identified its chromosomal location. We have employed a combination of classical genetics and three-point crosses with molecular genetic analysis of recombinants to generate the map. We have characterized this region by Illumina sequencing and bioinformatic analysis, together with chromosome in situ hybridization. We present an integrated genetic and physical map across the P. vulgaris S locus flanked by phenotypic and DNA sequence markers. BAC contigs encompass a 1.5-Mb genomic region with 1 Mb of sequence containing 82 S-linked genes anchored to overlapping BACs. The S locus is located close to the centromere of the largest metacentric chromosome pair. These data will facilitate the identification of the genes that orchestrate heterostyly in Primula and enable evolutionary analyses of the S locus.

Diversification of 13S globulins, allergenic seed storage proteins, of common buckwheat

The α polypeptide of the 13S globulin subunit of common buckwheat is the counterpart of the major allergenic β polypeptide. Trypsin digestibility varies between variants of the α polypeptide with and without a tandem repeat insert. To evaluate the intra-species diversity of 13S globulin, the comprehensive screening of a genomic DNA library was performed, resulting in the isolation of 14 and 3 genes for Met-poor and Met-rich subunits, respectively. Although most tandem repeat units were 45 bp in length, the two-repeat gene Glb2B and all one-repeat genes contained an additional 3 bp. Secondary structure predictions and polyacrylamide gel electrophoresis demonstrated that the sense strand of Glb2B-CCG, the additional 3 bp-deletion clone of Glb2B, formed a more rigid secondary structure than that of the wild-type. Thus, the large intra-species variation of 13S globulin revealed in this study and its diversification might be attributable to the unique nature of the tandem repeat sequences.

Progress and prospects for interspecific hybridization in buckwheat and the genus Fagopyrum

Cultivated buckwheat, such as common (Fagopyrum esculentum Moench.) and tartary (Fagopyrum tataricum (L.) Gaertn.) buckwheat, is one of the most versatile crops for forage and food and has several benefits for human health. Interspecific hybridization between Fagopyrum species is of great importance to improvement of buckwheat. Hybridization would allow the transfer of agronomical beneficial characteristics from wild Fagopyrum species, including self-pollination and increased fertility, frost tolerance, and higher content of beneficial compounds. However, conventional breeding methods are only partially applicable because of the self-incompatibility and incompatibility barriers between different species. Present review summarizes the morphology of self-incompatibility, the genetic and cellular basis of incompatibility between different Fagopyrum species. In many interspecific crosses hybrid embryos are aborted after successful pollination due to post-zygotic incompatibility. The use of in vitro embryo rescue after interspecific hybridization has been successful in circumventing breeding barriers between Fagopyrum species. Methods applied successfully for the construction of interspecific hybrids are discussed in detail.

S-LOCUS EARLY FLOWERING 3 is exclusively present in the genomes of short-styled buckwheat plants that exhibit heteromorphic self-incompatibility

The different forms of flowers in a species have attracted the attention of many evolutionary biologists, including Charles Darwin. In Fagopyrum esculentum (common buckwheat), the occurrence of dimorphic flowers, namely short-styled and long-styled flowers, is associated with a type of self-incompatibility (SI) called heteromorphic SI. The floral morphology and intra-morph incompatibility are both determined by a single genetic locus named the S-locus. Plants with short-styled flowers are heterozygous (S/s) and plants with long-styled flowers are homozygous recessive (s/s) at the S-locus. Despite recent progress in our understanding of the molecular basis of flower development and plant SI systems, the molecular mechanisms underlying heteromorphic SI remain unresolved. By examining differentially expressed genes from the styles of the two floral morphs, we identified a gene that is expressed only in short-styled plants. The novel gene identified was completely linked to the S-locus in a linkage analysis of 1,373 plants and had homology to EARLY FLOWERING 3. We named this gene S-LOCUS EARLY FLOWERING 3 (S-ELF3). In an ion-beam-induced mutant that harbored a deletion in the genomic region spanning S-ELF3, a phenotype shift from short-styled flowers to long-styled flowers was observed. Furthermore, S-ELF3 was present in the genome of short-styled plants and absent from that of long-styled plants both in world-wide landraces of buckwheat and in two distantly related Fagopyrum species that exhibit heteromorphic SI. Moreover, independent disruptions of S-ELF3 were detected in a recently emerged self-compatible Fagopyrum species and a self-compatible line of buckwheat. The nonessential role of S-ELF3 in the survival of individuals and the prolonged evolutionary presence only in the genomes of short-styled plants exhibiting heteromorphic SI suggests that S-ELF3 is a suitable candidate gene for the control of the short-styled phenotype of buckwheat plants.

Floral heteromorphy in Primula vulgaris: progress towards isolation and characterization of the S locus

BACKGROUND

The common primrose, Primula vulgaris, along with many other species of the Primulaceae, exhibits floral heteromorphy in which different individuals develop one of two possible forms of flower, known as pin and thrum. Both flower types are hermaphrodite and exhibit reciprocal positions of male and female reproductive structures, which together with a sporophytic incompatibility system, prevent self-pollination and promote out-crossing. The development of the two different forms of flower is controlled by a co-adapted linkage group of genes known as the S locus.

SCOPE

Here progress towards identification and characterization of these genes is described to provide a molecular genetic explanation of the different floral characteristics that define heterostyly in Primula as observed and described by Charles Darwin. Previous work to identify and characterize developmental mutations linked to the P. vulgaris S locus, together with the isolation of S locus-linked genes and polymorphic DNA sequences markers, is summarized. The development of tools are described which will facilitate isolation and characterization of the S locus and its environs, including the creation of two expressed sequence tag libraries from pin and thrum flowers, as well as the construction and screening of two bacterial artificial chromosome (BAC) libraries containing thrum genomic DNA. Screening of these libraries with four S locus-linked sequences has enabled us to assemble four BAC contigs representing over 40 individual overlapping BAC clones which represent over 2·2 Mb of S locus-linked genomic sequence. PCR-based approaches for identification of the allelic origin of these BACs are described as well as identification of an additional 14 S locus-linked genes within BAC-end sequences.

CONCLUSIONS

On-going work to assemble the four S locus-linked contigs into one contiguous sequence spanning the S locus is outlined in preparation for sequence analysis and characterization of the genes located within this region.

Positional cloning of the s haplotype determining the floral and incompatibility phenotype of the long-styled morph of distylous Turnera subulata

Heterostyly is a plant breeding system occurring in approximately 28 plant families and it has often been used as a model system in plant genetics and evolution. Although heterostyly has been studied for over a century beginning with Charles Darwin, the genes determining floral architecture and incompatibility are still unknown. To identify the genes residing at the S-locus of distylous Turnera subulata, we used a positional cloning strategy and assembled three BAC contigs across the S-locus region. In total, 31 overlapping BAC clones were assembled into contigs 1, 2 and SL. We developed and mapped numerous co-dominant markers from the ends of BAC clones across the S-locus region and assayed X-ray deletion mutants to delimit the region of the contig containing the S-locus. Deletion mapping revealed that a single BAC clone (L22s) within contig-SL contains the s haplotype, while two additional BAC clones (I1 and K15) may contain parts of the dominant S haplotype. Furthermore, we exploited the contigs assembled and investigated the rates of recombination at the S-locus as well as in two regions on either side of the S-locus. We found that recombination rates (estimated in kb/cM) are 2-5 times lower at the S-locus relative to flanking regions, although they are not statistically significant. The present study represents a landmark in the molecular characterization of the S-locus of a heterostylous species. We are now on the verge of identifying the genes that have remained elusive since Darwin's comprehensive study of heterostylous systems more than 125 years ago.

Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae)

Background

The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae.

Findings

Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S₂S₂ for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S₁S₄. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers.

Conclusions

This indicated that both BAC libraries are valuable tools for molecular studies in chicory, one goal being the positional cloning of the S-locus in this Asteraceae species.

High-resolution mapping of the S-locus in Turnera leads to the discovery of three genes tightly associated with the S-alleles

While the breeding system known as distyly has been used as a model system in genetics, and evolutionary biology for over a century, the genes determining this system remain unknown. To positionally clone genes determining distyly, a high-resolution map of the S-locus region of Turnera has been constructed using segregation data from 2,013 backcross progeny. We discovered three putative genes tightly linked with the S-locus. An N-acetyltransferase (TkNACE) flanks the S-locus at 0.35 cM while a sulfotransferase (TkST1) and a non-LTR retroelement (TsRETRO) show complete linkage to the S-locus. An assay of population samples of six species revealed that TsRETRO, initially discovered in diploid Turnera subulata, is also associated with the S-allele in tetraploid T. subulata and diploid Turnera scabra. The sulfotransferase gene shows some level of differential expression in long versus short styles, indicating it might be involved in some aspect of distyly. The complete linkage of TkST1 and TsRETRO to the S-locus suggests that both genes may reside within, or in the immediate vicinity of the S-locus. Chromosome walking has been initiated using one of the genes discovered in the present study to identify the genes determining distyly.