RFLP mapping of the dwarfing (Ddw1) and hairy peduncle (Hp) genes on chromosome 5 of rye (Secale cereale L.)

Identification and Fine-Mapping of Quantitative Trait Loci Controlling Plant Height in Central European Winter Triticale (×Triticosecale Wittmack)

The quantitatively inherited trait plant height is routinely evaluated in triticale breeding programs as it substantially influences lodging and disease susceptibility, is a main contributor to biomass yield, and is required to improve hybrid seed production by fine-tuning plant height in the female and male parental pools in hybrid breeding programs. In this study, we evaluated a panel of 846 diverse Central European triticale genotypes to dissect the genetic architecture underlying plant height by genome-wide association mapping. This revealed three medium- to large-effect QTL on chromosomes 5A, 4B, and 5R. Genetic and physical fine-mapping of the putative QTL revealed that the QTL on chromosome 5R most likely corresponds to Ddw1 and that the QTL on chromosome 5A is likely to be Rht12. Furthermore, we observed a temporal trend in registered cultivars with a decreasing plant height during the past decades, accompanied by an increasing use of the height-reducing alleles at the identified QTL. In summary, our results shed new light on the genetic control of plant height in triticale and open new avenues for future improvement by breeding.

How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data

The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F2 population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.0) and three ML algorithms: logistic regression (LR), random forest and extreme gradient boosted trees (XGBoost), were used to select markers closely linked to the gene encoding wax layer. The allele conditioning the nonglaucous appearance of plants, derived from the cultivar Karlikovaja Zelenostebelnaja, was mapped at the chromosome 2R, which is the first report on this localization. The DNA sequence of DArT-Silico 3585843, closely linked to wax segregation detected by using ML methods, was indicated as one of the candidates controlling the studied trait. The putative gene encodes the ABCG11 transporter.

QTL mapping and successful introgression of the spring wheat-derived QTL Fhb1 for Fusarium head blight resistance in three European triticale populations

KEY MESSAGE

The spring wheat-derived QTL Fhb1 was successfully introgressed into triticale and resulted in significantly improved FHB resistance in the three triticale mapping populations. Fusarium head blight (FHB) is a major problem in cereal production particularly because of mycotoxin contaminations. Here we characterized the resistance to FHB in triticale breeding material harboring resistance factors from bread wheat. A highly FHB-resistant experimental line which derives from a triticale × wheat cross was crossed to several modern triticale cultivars. Three populations of recombinant inbred lines were generated and evaluated in field experiments for FHB resistance using spray inoculations during four seasons and were genotyped with genotyping-by-sequencing and SSR markers. FHB severity was assessed in the field by visual scorings and on the harvested grain samples using digital picture analysis for quantifying the whitened kernel surface (WKS). Four QTLs with major effects on FHB resistance were identified, mapping to chromosomes 2B, 3B, 5R, and 7A. Those QTLs were detectable with both Fusarium severity traits. Measuring of WKS allows easy and fast grain symptom quantification and appears as an effective scoring tool for FHB resistance. The QTL on 3B collocated with Fhb1, and the QTL on 5R with the dwarfing gene Ddw1. This is the first report demonstrating the successful introgression of Fhb1 into triticale. It comprises a significant step forward for enhancing FHB resistance in this crop.

Gene Expression Profiling and Fine Mapping Identifies a Gibberellin 2-Oxidase Gene Co-segregating With the Dominant Dwarfing Gene Ddw1 in Rye (Secale cereale L.)

The gibberellin (GA)-sensitive dwarfing gene Ddw1 provides an opportunity to genetically reduce plant height in rye. Genetic analysis in a population of recombinant inbred lines confirmed a monogenetic dominant inheritance of Ddw1. Significant phenotypic differences in PH between homo- and heterozygotic genotypes indicate an incomplete dominance of Ddw1. De novo transcriptome sequencing of Ddw1 mutant as well as tall genotypes resulted in 113,547 contigs with an average length of 318 bp covering 36.18 Mbp rye DNA. A hierarchical cluster analysis based on individual groups of rye homologs of functionally characterized rice genes controlling morphological or physiological traits including plant height, flowering time, and source activity identified the gene expression profile of stems at the begin of heading to most comprehensively mirror effects of Ddw1. Genome-wide expression profiling identified 186 transcripts differentially expressed between semi-dwarf and tall genotypes in stems. In total, 29 novel markers have been established and mapped to a 27.2 cM segment in the distal part of the long arm of chromosome 5R. Ddw1 could be mapped within a 0.4 cM interval co-segregating with a marker representing the C20-GA2-oxidase gene ScGA2ox12, that is up-regulated in stems of Ddw1 genotypes. The increased expression of ScGA2ox12 observed in semi-dwarf rye as well as structural alterations in transcript sequences associated with the ScGA2ox12 gene implicate, that Ddw1 is a dominant gain-of-function mutant. Integration of the target interval in the wheat reference genome sequence indicated perfect micro-colinearity between the Ddw1 locus and a 831 kb segment on chromosome 5A, which resides inside of a 11.21 Mb interval carrying the GA-sensitive dwarfing gene Rht12 in wheat. The potential of Ddw1 as a breeder's option to improve lodging tolerance in rye is discussed.

Effect of Dwarfing Gene Ddw1 on Height and Agronomic Traits in Spring Triticale in Greenhouse and Field Experiments in a Non-Black Earth Region of Russia

Triticale is a relatively new crop which still possesses serious drawbacks that can be significantly improved by breeding. The dwarfing genes proved to be very useful in the development of new lodging resistant and productive cultivars of winter triticale. The aim of our research was to assess the effect of the Ddw1 dwarfing gene from rye on the agronomic valuable traits in spring triticale. The Ddw1 effect was studied in the greenhouse experiment in segregating the F_2:3 population and in the field of F_3:4 and F_4:5 families derived from crossing winter triticale ‘Hongor’ (Ddw1Ddw1) and spring triticale ‘Dublet’ (ddw1ddw1). As a result, in all three generations, a strong decrease in plant height was demonstrated that was accompanied by a decrease in grain weight per spike and 1000-grain weight. In field experiments, a decrease in spike length and increase in spike density and delay in flowering and heading were observed. As a result of decrease in culm vegetative weight due to Ddw1, the harvest index measured in F_4:5 increased. The spike fertility and number of grains were not affected by Ddw1. The comparison of Ddw1 in rye, winter, and spring triticale, and the possible role of Ddw1 in improving spring triticale are discussed.

Identification of a novel, dominant dwarfing gene (Ddw4) and its effect on morphological traits of rye

Shortening rye stems to improve lodging resistance is among the major tasks awaiting breeders of this cereal. The most straightforward way to achieve this goal is the implementation of a dominant dwarfing gene into high yielding cultivars. The choice of dominant dwarfing genes in rye is limited to Ddw1 and Ddw3 loci, which are well characterized with respect to map position and tightly linked molecular markers on the long arms of chromosomes 5RL and 1RL, respectively. This paper reports on the identification and preliminary characterization of a novel dominant dwarfing gene, Ddw4, from line S44. This was mapped within the centromeric region of chromosome 3R. The Ddw4 gene is sensitive to exogenous gibberellin. Its introduction into the rye populational cultivar Dańkowskie Amber decreased plant height by c. 54% without any negative effects on spike length and number of kernels per spike. Further genetic studies are needed to determine the perspectives for application of the newly detected dwarfing gene into breeding programs for short-stem rye.

Hybrid dwarfness in crosses between wheat (Triticum aestivum L.) and rye (Secale cereale L.): a new look at an old phenomenon

The existence of hybrid dwarfs from intraspecific crosses in wheat (Triticum aestivum) was described 100 years ago, and the genetics underlying hybrid dwarfness are well understood. In this study, we report a dwarf phenotype in interspecific hybrids between wheat and rye (Secale cereale). We identified two rye lines that produce hybrid dwarfs with wheat and have none of the hitherto known hybrid dwarfing genes. Genetic analyses revealed that both rye lines carry a single allelic gene responsible for the dwarf phenotype. This gene was designated Hdw-R1 (Hybrid dwarf-R1). Application of gibberellic acid (GA3 ) to both intraspecific (wheat-wheat) and interspecific (wheat-rye) hybrids showed that hybrid dwarfness cannot be overcome by treatment with this phytohormone. Histological analysis of shoot apices showed that wheat-rye hybrids with the dwarf phenotype at 21 and 45 days after germination failed to develop further. Shoot apices of dwarf plants did not elongate, did not form new primordia and had a dome-shaped appearance in the seed. The possible relationship between hybrid dwarfness and the genes responsible for the transition from vegetative to generative growth stage is discussed.

Genetic architecture of fusarium head blight resistance in four winter triticale populations

Fusarium head blight (FHB) is a devastating disease that causes significant reductions in yield and quality in wheat, rye, and triticale. In triticale, knowledge of the genetic architecture of FHB resistance is missing but essential due to modern breeding requirements. In our study, four doubled-haploid triticale populations (N=120 to 200) were evaluated for resistance to FHB caused by artificial inoculation with Fusarium culmorum in four environments. DArT markers were used to genotype triticale populations. Seventeen quantitative trait loci (QTL) for FHB resistance were detected across all populations; six of them were derived from rye genome and located on chromosomes 4R, 5R, and 7R, which are here reported for the first time. The total cross-validated ratio of the explained phenotypic variance for all detected QTL in each population was 41 to 68%. In all, 17 QTL for plant height and 18 QTL for heading stage were also detected across all populations; 3 and 5 of them, respectively, were overlapping with QTL for FHB. In conclusion, FHB resistance in triticale is caused by a multitude of QTL, and pyramiding them contributes to higher resistance.

Adult plant development in triticale (× triticosecale wittmack) is controlled by dynamic genetic patterns of regulation

Many biologically and agronomically important traits are dynamic and show temporal variation. In this study, we used triticale (× Triticosecale Wittmack) as a model crop to assess the genetic dynamics underlying phenotypic plasticity of adult plant development. To this end, a large mapping population with 647 doubled haploid lines derived from four partially connected families from crosses among six parents was scored for developmental stage at three different time points. Using genome-wide association mapping, we identified main effect and epistatic quantitative trait loci (QTL) at all three time points. Interestingly, some of these QTL were identified at all time points, whereas others appear to only contribute to the genetic architecture at certain developmental stages. Our results illustrate the temporal contribution of QTL to the genetic control of adult plant development and more generally, the temporal genetic patterns of regulation that underlie dynamic traits.

Effect of a rye dwarfing gene on plant height, heading stage, and Fusarium head blight in triticale (×Triticosecale Wittmack)

The rye-derived dwarfing gene Ddw1 on chromosome 5R acts in triticale in considerably reducing plant height, increasing FHB severity and delaying heading stage. Triticale, an amphiploid hybrid between durum wheat and rye, is an European cereal mainly grown in Germany, France, Poland, and Belarus for feeding purposes. Dwarfing genes might further improve the genetic potential of triticale concerning lodging resistance and yield. However, they might have pleiotropic effects on other, agronomically important traits including Fusarium head blight. Therefore, we analyzed a population of 199 doubled haploid (DH) lines of the cross HeTi117-06 × Pigmej for plant height, heading stage, and FHB severity across 2 locations and 2 years. The most prominent QTL was detected on chromosome 5R explaining 48, 77, and 71 % of genotypic variation for FHB severity, plant height, and heading stage, respectively. The frequency of recovery in cross validation was ≥90 % for all three traits. Because the markers that detect dwarfing gene Ddw1 in rye are also in our population the most closely linked markers, we assume that this major QTL resembles Ddw1. For FHB severity two, for plant height three, and for heading stage five additional QTL were detected. Caused by the considerable genetic variation for heading stage and FHB severity within the progeny with the dwarfing allele, short-strawed, early heading and FHB-resistant lines can be developed when population size is large enough.

Mapping dynamic QTL for plant height in triticale

BACKGROUND

Plant height is a prime example of a dynamic trait that changes constantly throughout adult development. In this study we utilised a large triticale mapping population, comprising 647 doubled haploid lines derived from 4 families, to phenotype for plant height by a precision phenotyping platform at multiple time points.

RESULTS

Using multiple-line cross QTL mapping we identified main effect and epistatic QTL for plant height for each of the time points. Interestingly, some QTL were detected at all time points whereas others were specific to particular developmental stages. Furthermore, the contribution of the QTL to the genotypic variance of plant height also varied with time as exemplified by a major QTL identified on chromosome 6A.

CONCLUSIONS

Taken together, our results in the small grain cereal triticale reveal the importance of considering temporal genetic patterns in the regulation of complex traits such as plant height.

Multiple-line cross QTL mapping for biomass yield and plant height in triticale (× Triticosecale Wittmack)

QTL mapping in multiple families identifies trait-specific and pleiotropic QTL for biomass yield and plant height in triticale. Triticale shows a broad genetic variation for biomass yield which is of interest for a range of purposes, including bioenergy. Plant height is a major contributor to biomass yield and in this study, we investigated the genetic architecture underlying biomass yield and plant height by multiple-line cross QTL mapping. We employed 647 doubled haploid lines from four mapping populations that have been evaluated in four environments and genotyped with 1710 DArT markers. Twelve QTL were identified for plant height and nine for biomass yield which cross-validated explained 59.6 and 38.2 % of the genotypic variance, respectively. A major QTL for both traits was identified on chromosome 5R which likely corresponds to the dominant dwarfing gene Ddw1. In addition, we detected epistatic QTL for plant height and biomass yield which, however, contributed only little to the genetic architecture of the traits. In conclusion, our results demonstrate the potential of genomic approaches for a knowledge-based improvement of biomass yield in triticale.

Construction of comparative genetic maps of two 4Bs.4Bl-5Rl translocations in bread wheat (Triticum aestivumL.)

The physical length of the rye segment of a 4BS.4BL–5RL translocation derived from the Cornell Wheat Selection 82a1-2-4-7 in a Triticum aestivum 'Chinese Spring' background was measured using genomic in situ hybridization (GISH) and found to be 16% of the long arm. The size of this translocation was similar to previously published GISH measurements of another 4BS.4BL–5RL translocation in a Triticum aestivum 'Viking' wheat background. Molecular maps of both 4BS.4BL–5RL translocations for 2 different wheat backgrounds were developed using RFLP analysis. The locations of the translocation breakpoints of the 2 4BS.4BL–5RL translocations were similar even though they arose in different populations. This suggests a unique property of the region at or near the translocation breakpoint that could be associated with their similarity and spontaneous formation. These segments of rye chromosome 5 also contain a gene for copper efficiency that improves the wheat's ability to cope with low-copper soils. Genetic markers in these maps can also be used to screen for copper efficiency in bread wheat lines derived from the Cornell Wheat Selection 82a1 2-4-7.Key words: Triticum aestivum, wheat–rye translocation, homoeologous group 4, homoeologous group 5, GISH, comparative map, copper efficiency, hairy peduncle.

Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags

The genetic map of rye contains predominantly restriction fragment length polymorphism (RFLP) markers but also a limited number of microsatellite markers, which are known to be more reliable and easier to apply. We report here the saturation of the genomic map of rye with additional microsatellite-derived markers that we obtained from the rye expressed sequence tag (EST) databases and the Gatersleben collection of wheat microsatellite markers (WMS). A total of 99 loci (39 EST and 60 WMS) were mapped into the RFLP frameworks of four rye mapping populations consisting of 139, 64, 58 and 60 RFLPs, respectively. For another ten WMS loci, which amplified PCR products not polymorphic in any of the mapping populations, chromosome and chromosome arm locations were determined using wheat-rye addition lines. Chromosomes 1R, 2R, 3R, 4R, 5R, 6R and 7R were enriched with 9, 19, 9, 13, 27, 16 and 16 microsatellite loci, respectively. The microsatellite loci mapped were evenly distributed along the chromosomes, which is important for the further application of these markers for gene mapping or diversity studies in rye. Forty-four of the WMS loci mapped in rye were found to be homologous to those mapped in bread wheat ( Triticum aestivum L.).

Production of near-isogenic lines and marked monosomic lines in common wheat (Triticum aestivum) cv. Chinese Spring

Sixteen near-isogenic lines (NILs) carrying a marker gene were produced by the recurrent backcrossing method in the genetic background of common wheat (Triticum aestivum) cv. Chinese Spring (CS). Three genes from alien species showed segregation distortion. In NILs carrying a marker gene of rye (Secale cereale) or Aegilops caudata, the alien chromosome segments were detected by fluorescence in situ hybridization (FISH). The NILs were grown with replications and the effect of marker genes on plant morphology in the genetic background of CS was investigated. These NILs were further crossed with the corresponding monosomics of CS and 13 monosomic lines whose monosome carries a respective marker gene were established and named "marked monosomics." Many of the marked monosomics were distinguishable from the disomic NILs because of the different dosage effect of the genes. The NILs are utilized for studies on gene isolation or gene regulation. Marked monosomics are useful not only for monosomic analysis but also for production of homologous chromosome substitution lines because chromosome observation is not required.

Chromosomal location and genetic mapping of the mismatch repair gene homologs MSH2, MSH3, and MSH6 in rye and wheat

The efficiency of homeologous recombination is influenced by mismatch repair genes in bacteria, yeast, and mammals. To elucidate a possible role of these genes in homeologous pairing and cross-compatibility in plants, gene probes of wheat (Triticum aestivum) specific for the mismatch repair gene homologues MSH2, MSH3, and MSH6 were used to map them to their genomic positions in rye (Secale cereale). Whereas MSH2 was mapped to the short arm of chromosome 1R, MSH3 was mapped to the long arm of chromosome 2R and MSH6 to the long arm of chromosome 5R. Southern blots with nullisomic-tetrasomic (NT) lines of wheat indicated the presence of the sequences on the respective homeologous group of wheat chromosomes. Additionally, an MSH6-specific homologue could also be detected on homoeologous group 3 of wheat. However, in the well-known, highly homoeologous pairing wheat mutant ph1b the MSH6-specific sequence is not within the deleted part of chromosome 5BL, indicating that the pairing phenotype is not due to a loss of one of the mismatch repair genes tested.

RFLP mapping of a gene for hairy leaf sheath using a recombinant line from Hordeum vulgare L. ×Hordeum bulbosum L. cross

A gene conditioning hairy leaf sheath character, which was derived from Hordeum bulbosum and designated Hsb, was mapped using a cross between Hordeum vulgare and a H. vulgare/H. bulbosum recombinant line. The Hsb locus was tagged relative to eight RFLP markers detecting three loci on the distal part of chromosome 4HL. The map position suggests that Hsb of H. bulbosum is homoeologous to the gene Hp1 of rye (Secale cereale), which pleiotropically governs the traits hairy leaf sheath and hairy peduncle. It is proposed that the recombination break point between H. vulgare and H. bulbosum chromosomes occured at a position homoeologous compared with the 4L/5L translocation in Triticeae genomes, and may reflect a hot spot for chromosome breakage.Key words: Hordeum vulgare, Hordeum bulbosum, comparative mapping, hairy leaf sheath, RFLP.

Chromosomal location of three wheat sequences with homology to pollen allergen encoding, DNA replication regulating, and DNA (cytosine-5)-methyltransferase genes in wheat and rye

Three wheat sequences, shown to be homologous to pollen allergen encoding, DNA replication regulating, and DNA (cytosine-5)-methyltransferase genes were localized on chromosomes using nullisomic-tetrasomic wheat ('Chinese Spring') and wheat-rye ('Chinese Spring'/'Imperial') addition lines. Whereas the loci for the pollen allergen encoding sequence (Tri a III) were shown to be located on homoeologous group 4, the DNA replication regulating (Rep) and DNA (cytosine-5)-methyltransferase (Mtase) genes were located to homoeologous groups 1 and 7, respectively, of Triticeae. Chromosomal rearrangements in wheat and rye relative to each other are discussed.