Genetic linkage facilitates cloning of Ert-m regulating plant architecture in barley and identified a strong candidate of Ant1 involved in anthocyanin biosynthesis

A guide to barley mutants

BACKGROUND

Mutants have had a fundamental impact upon scientific and applied genetics. They have paved the way for the molecular and genomic era, and most of today's crop plants are derived from breeding programs involving mutagenic treatments.

RESULTS

Barley (Hordeum vulgare L.) is one of the most widely grown cereals in the world and has a long history as a crop plant. Barley breeding started more than 100 years ago and large breeding programs have collected and generated a wide range of natural and induced mutants, which often were deposited in genebanks around the world. In recent years, an increased interest in genetic diversity has brought many historic mutants into focus because the collections are regarded as valuable resources for understanding the genetic control of barley biology and barley breeding. The increased interest has been fueled also by recent advances in genomic research, which provided new tools and possibilities to analyze and reveal the genetic diversity of mutant collections.

CONCLUSION

Since detailed knowledge about phenotypic characters of the mutants is the key to success of genetic and genomic studies, we here provide a comprehensive description of mostly morphological barley mutants. The review is closely linked to the International Database for Barley Genes and Barley Genetic Stocks ( bgs.nordgen.org ) where further details and additional images of each mutant described in this review can be found.

Identification of a candidate dwarfing gene in Pallas, the first commercial barley cultivar generated through mutational breeding

Many induced mutants are available in barley (Hordeum vulgare L.). One of the largest groups of induced mutants is the Erectoides (ert) mutants, which is characterized by a compact and upright spike and a shortened culm. One isolated mutant, ert-k.32, generated by X-ray treatment and registered in 1958 under the named "Pallas", was the first ever induced barley mutant to be released on the market. Its value was improved culm strength and enhanced lodging resistance. In this study, we aimed to identify the casual gene of the ert-k.32 mutant by whole genome sequencing of allelic ert-k mutants. The suggested Ert-k candidate gene, HORVU.MOREX.r3.6HG0574880, is located in the centromeric region of chromosome 6H. The gene product is an alpha/beta hydrolase with a catalytic triad in the active site composed of Ser-167, His-261 and Asp-232. In comparison to proteins derived from the Arabidopsis genome, ErtK is most similar to a thioesterase with de-S-acylation activity. This suggests that ErtK catalyzes post-translational modifications by removing fatty acids that are covalently attached to cysteine residues of target proteins involved in regulation of plant architecture and important commercial traits such as culm stability and lodging resistance.

Ant13 Encodes Regulatory Factor WD40 Controlling Anthocyanin and Proanthocyanidin Synthesis in Barley (Hordeum vulgare L.)

Flavonoid compounds like anthocyanins and proanthocyanidins are important plant secondary metabolites having wide biological activities for humans. In this study, the molecular function of the Ant13 locus, which is one of the key loci governing flavonoid synthesis in barley, was determined. It was found that Ant13 encodes a WD40-type regulatory protein, which is required for transcriptional activation of a set of structural genes encoding enzymes of flavonoid biosynthesis at the leaf sheath base (colored by anthocyanins) and in grains (which accumulate proanthocyanidins). Besides its role in flavonoid biosynthesis, pleiotropic effects of this gene in plant growth were revealed. The mutants deficient in the Ant13 locus showed similar germination rates but a decreased rate of root and shoot growth and yield-related parameters in comparison to the parental cultivars. This is the seventh Ant locus (among 30) for which molecular functions in flavonoid biosynthesis regulation have been determined.

Relationship between the anthocyanin content values in the leaf sheath base of barley cultivars and in the grain of the hybrids derived from them

Background. The development of barley cultivars accumulating anthocyanins in grain is an important task for breeding, which is based on the Ant1 and Ant2 genes that control synthesis of these compounds. To optimize the breeding strategy and selection of the initial material, quantitative assay of anthocyanin content in the leaf sheath base of barley cultivars was carried out and the relationship between this parameter for some of the barley cultivars and anthocyanin content in grain of the hybrids derived from them was evaluated.

Materials and methods. The anthocyanin content in the leaf sheath base was studied in 32 barley cultivars in the tillering stage and in mature grains of 11 purple-grain hybrids selected from the hybrid populations using DNA-markers.

Results and discussion. It was shown that there were quantitative differences in the anthocyanin content in the leaf sheath base among barley cultivars, which varied from 1 to 191 mg/kg. A cluster analysis helped to identify three groups of cultivars: with low, medium and high anthocyanin content. The hybrids from crossing cultivars differing in their anthocyanin content in the leaf sheath base with line P18, the donor of the dominant allele of the Ant2 gene, showed variation of the anthocyanin content in grain from 22 to 71 mg/kg. The observed differences among the hybrids were determined by the genotypes of individual plants and the allelic state of Ant2. A weak correlation (rs = 0.37, p = 0.0362) was shown between the anthocyanin contents in the leaf sheath base and in the grain of the obtained hybrids.

Conclusion. The results of the study would help to optimize the breeding strategy for the development of new barley cultivars with high anthocyanin content in the grain and substantiate the need to test the anthocyanin content in the grain of individual lines. 

FIND-IT: Accelerated trait development for a green evolution

Improved agricultural and industrial production organisms are required to meet the future global food demands and minimize the effects of climate change. A new resource for crop and microbe improvement, designated FIND-IT (Fast Identification of Nucleotide variants by droplet DigITal PCR), provides ultrafast identification and isolation of predetermined, targeted genetic variants in a screening cycle of less than 10 days. Using large-scale sample pooling in combination with droplet digital PCR (ddPCR) greatly increases the size of low-mutation density and screenable variant libraries and the probability of identifying the variant of interest. The method is validated by screening variant libraries totaling 500,000 barley (Hordeum vulgare) individuals and isolating more than 125 targeted barley gene knockout lines and miRNA or promoter variants enabling functional gene analysis. FIND-IT variants are directly applicable to elite breeding pipelines and minimize time-consuming technical steps to accelerate the evolution of germplasm.

Analysis of barley mutants ert-c.1 and ert-d.7 reveals two loci with additive effect on plant architecture

Both mutant ert-c.1 and ert-d.7 carry T2-T3 translocations in the Ert-c gene. Principal coordinate analyses revealed the translocation types and translocation breakpoints. Mutant ert-d.7 is an Ert-c Ert-d double mutant. Mutations in the Ert-c and Ert-d loci are among the most common barley mutations affecting plant architecture. The mutants have various degrees of erect and compact spikes, often accompanied with short and stiff culms. In the current study, complementation tests, linkage mapping, principal coordinate analyses and fine mapping were conducted. We conclude that the original ert-d.7 mutant does not only carry an ert-d mutation but also an ert-c mutation. Combined, mutations in Ert-c and Ert-d cause a pyramid-dense spike phenotype, whereas mutations in only Ert-c or Ert-d give a pyramid and dense phenotype, respectively. Associations between the Ert-c gene and T2-T3 translocations were detected in both mutant ert-c.1 and ert-d.7. Different genetic association patterns indicate different translocation breakpoints in these two mutants. Principal coordinate analysis based on genetic distance and screening of recombinants from all four ends of polymorphic regions was an efficient way to narrow down the region of interest in translocation-involved populations. The Ert-c gene was mapped to the marker interval of 2_0801to1_0224 on 3HL near the centromere. The results illuminate a complex connection between two single genes having additive effects on barley spike architecture and will facilitate the identification of the Ert-c and Ert-d genes.

Manipulating a Single Transcription Factor, Ant1, Promotes Anthocyanin Accumulation in Barley Grains

Barley has abundant anthocyanin-rich accessions, which renders it an ideal model to investigate the regulatory mechanism of anthocyanin biosynthesis. This study functionally characterized two transcription factors: Ant1 and Ant2. Sequence alignment showed that the coding sequences of Ant1 and Ant2 are conserved among 11 colored hulless barley and noncolored barley varieties. The expression profiles of Ant1 and Ant2 were divergent between species, and significantly higher expression was found in two colored Qingke accessions. The co-expression of Ant1 and Ant2 resulted in purple pigmentation in transient transformation systems via the promotion of the transcription of four structural genes. Ant1 interacted with Ant2, and overexpression of Ant1 activated the transcription of Ant2. Moreover, overexpression of Ant1 led to anthocyanin accumulation in the pericarp and aleurone layer of transgenic barley grains. Overall, our results suggest that anthocyanin-enriched barley grains can be produced by manipulating Ant1 expression.

Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases

Barley plays an important role in health and civilization of human migration from Africa to Asia, later to Eurasia. We demonstrated the systematic mechanism of functional ingredients in barley to combat chronic diseases, based on PubMed, CNKI, and ISI Web of Science databases from 2004 to 2020. Barley and its extracts are rich in 30 ingredients to combat more than 20 chronic diseases, which include the 14 similar and 9 different chronic diseases between grains and grass, due to the major molecular mechanism of six functional ingredients of barley grass (GABA, flavonoids, SOD, K-Ca, vitamins, and tryptophan) and grains (β-glucans, polyphenols, arabinoxylan, phytosterols, tocols, and resistant starch). The antioxidant activity of barley grass and grain has the same and different functional components. These results support findings that barley grain and its grass are the best functional food, promoting ancient Babylonian and Egyptian civilizations, and further show the depending functional ingredients for diet from Pliocene hominids in Africa and Neanderthals in Europe to modern humans in the world. This review paper not only reveals the formation and action mechanism of barley diet overcoming human chronic diseases, but also provides scientific basis for the development of health products and drugs for the prevention and treatment of human chronic diseases.

Analysis of early-flowering genes at barley chromosome 2H expands the repertoire of mutant alleles at the Mat-c locus

Analyses of barley mat-c loss of function mutants reveal deletions, splice-site mutations and nonsynonymous substitutions in a key gene regulating early flowering. Optimal timing of flowering is critical for reproductive success and crop yield improvement. Several major quantitative trait loci for flowering time variation have been identified in barley. In the present study, we analyzed two near-isogenic lines, BW507 and BW508, which were reported to carry two independent early-flowering mutant loci, mat-b.7 and mat-c.19, respectively. Both introgression segments are co-localized in the pericentromeric region of chromosome 2H. We mapped the mutation in BW507 to a 31 Mbp interval on chromosome 2HL and concluded that BW507 has a deletion of Mat-c, which is an ortholog of Antirrhinum majus CENTRORADIALIS (AmCEN) and Arabidopsis thaliana TERMINAL FLOWER1 (AtTFL1). Contrary to previous reports, our data showed that both BW507 and BW508 are Mat-c deficient and none of them are mat-b.7 derived. This work complements previous studies by identifying the uncharacterized mat-c.19 mutant and seven additional mat-c mutants. Moreover, we explored the X-ray structure of AtTFL1 for prediction of the functional effects of nonsynonymous substitutions caused by mutations in Mat-c.

Purple-grained barley (Hordeum vulgare L.): marker-assisted development of NILs for investigating peculiarities of the anthocyanin biosynthesis regulatory network

BACKGROUND

Anthocyanins are plants secondary metabolites important for plant adaptation to severe environments and potentially beneficial to human health. Purple colour of barley grain is caused by the pigments synthesized in pericarp. One or two genes determine the trait. One of them is Ant2 mapped on chromosome 2HL and is known to encode transcription factor (TF) with a bHLH domain. In plants, bHLH regulates anthocyanin biosynthesis together with TF harboring an R2R3-MYB domain. In wheat, the R2R3-MYBs responsible for purple colour of grain pericarp are encoded by the homoallelic series of the Pp-1 genes that were mapped on the short arms of chromosomes 7. In barley, in orthologous positions to wheat's Pp-1, the Ant1 gene determining red colour of leaf sheath has been mapped. In the current study, we tested whether Ant1 has pleiotropic effect not only on leaf sheath colour but also on pericarp pigmentation.

RESULTS

А set of near isogenic lines (NILs) carrying different combinations of alleles at the Ant1 and Ant2 loci was created using markers-assisted backcrossing approach. The dominant alleles of both the Ant1 and Ant2 genes are required for anthocyanin accumulation in pericarp. A qRT-PCR analysis of the Ant genes in lemma and pericarp of the NILs revealed that some reciprocal interaction occurs between the genes. Expression of each of the two genes was up-regulated in purple-grained line with dominant alleles at the both loci. The lines carrying dominant allele either in the Ant1 or in the Ant2 locus were characterized by the decreased level of expression of the dominant gene and scant activity of the recessive one. The Ant1 and Ant2 expression was barely detected in uncolored line with recessive alleles at both loci. The anthocyanin biosynthesis structural genes were differently regulated: Chs, Chi, F3h, Dfr were transcribed in all lines independently on allelic state of the Ant1 and Ant2 genes, whereas F3'h and Ans were activated in presence on dominant alleles of the both regulatory genes.

CONCLUSIONS

The R2R3-MYB-encoding counterpart (Ant1) of the regulatory Ant2 gene was determined for the first time. The dominant alleles of both of them are required for activation of anthocyanin synthesis in barley lemma and pericarp. The R2R3-MYB + bHLH complex activates the synthesis via affecting expression of the F3'h and Ans structural genes. In addition, positive regulatory loop between Ant1 and Ant2 was detected. Earlier the interaction between the anthocyanin biosynthesis regulatory genes has been revealed in dicot plant species only. Our data demonstrated that the regulatory mechanism is considered to be more common for plant kingdom than it has been reported so far.