Short Arm Of Chromosome 5D Research Articles

Characterization of a gene conferring resistance to US Russian wheat aphid biotypes in the Iranian wheat landrace PI 625139

AbstractRussian wheat aphid (RWA, Diuraphis noxia Kurdjumov) is a highly invasive and destructive wheat pest evolving rapidly to overcome host resistance. Novel genes conferring resistance to multiple RWA biotypes are needed to sustain wheat production. The Iranian landrace PI 625139 is resistant to all five US RWA biotypes. To map the RWA resistance gene in PI 625139, both F2 and F2:3 populations were developed from cross PI 625139 × Smith's Gold, and the F2:3 population was evaluated for responses to five RWA biotypes, RWA1, RWA2, RWA3/7, RWA6, and RWA8. RWA assays identified a single gene in PI 625139, designated Dn625139, conditioning resistance to all five US RWA biotypes. Selective genotyping of a subset of F2 plants using genotyping‐by‐sequencing (GBS) revealed a set of single‐nucleotide polymorphism (SNP) markers on the short arm of chromosome 7D that are closely associated with RWA resistance. Kompetitive allele‐specific PCR (KASP) markers were developed from selected GBS‐SNPs in 7DS. Genetic analysis using the new KASP and simple sequence repeat (SSR) markers placed Dn625139 to a 2.6 cM interval. Dn625139 was 1.2 cM proximal to the KASP marker Stars‐KASP1007 (169.57 Mb) and 1.4 cM distal to the SSR marker Stars1039 (195.27 Mb) in the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.1 reference sequence, and co‐segregated with the SSR marker Stars1029 (180.82 Mb). Dn625139 is a valuable gene conferring resistance to multiple RWA biotypes, and the molecular markers developed in this study can facilitate its rapid introgression into locally adapted cultivars to enhance wheat RWA resistance.

Rmg10, a Novel Wheat Blast Resistance Gene Derived from Aegilops tauschii.

Wheat blast, caused by Pyricularia oryzae (syn. Magnaporthe oryzae) pathotype Triticum (MoT), is a devastating disease that can result in up to 100% yield loss in affected fields. To find new resistance genes against wheat blast, we screened 199 accessions of Aegilops tauschii, the D genome progenitor of common wheat (Triticum aestivum), by seedling inoculation assays with Brazilian MoT isolate Br48 and found 14 resistant accessions. A synthetic hexaploid wheat line (Ldn/KU-2097) derived from a cross between the T. turgidum 'Langdon' (Ldn) and resistant A. tauschii accession KU-2097 exhibited resistance in seedlings and spikes against Br48. In an F2 population derived from 'Chinese Spring' × Ldn/KU-2097, resistant and susceptible individuals segregated in a 3:1 ratio, suggesting that the resistance from KU-2097 is controlled by a single dominant gene. We designated this gene Rmg10. Genetic mapping using an F2:3 population from the same cross mapped the RMG10 locus to the short arm of chromosome 2D. Rmg10 was ineffective against Bangladesh isolates but effective against Brazilian isolates. Field tests in Bolivia showed increased spike resistance in a synthetic octaploid wheat line produced from a cross between common wheat cultivar 'Gladius' and KU-2097. These results suggest that Rmg10 would be beneficial in farmers' fields in South America.

Mapping of a Recessive Gene for All-Stage Resistance to Stripe Rust in a Wheat Line Derived from Cultivated Einkorn (Triticum monococcum).

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive fungal diseases of wheat. Cultivated einkorn (Triticum monococcum L. ssp. monococcum, 2n = 2x = 14, AmAm), one of the founder crops of agriculture, harbors unexploited genetic sources for wheat improvement. An advanced wheat line, Z15-1949, with 42 chromosomes, selected from the hybrids of Pst-susceptible common wheat cultivar Crocus and resistant T. monococcum accession 10-1, exhibits high resistance to a mixture of the prevalent Chinese Pst races. Genetic analysis on F1, F2, and F2:3 generations of the cross between Z15-1949 and Pst-susceptible common wheat SY95-71 indicated that the resistance of Z15-1949 was conferred by a recessive gene, tentatively designated as YrZ15-1949. This gene was mapped to the short arm of chromosome 7D using the Wheat 55K single nucleotide polymorphism array, flanked by markers KASP-1949-2 and KASP-1949-10 within a 3.3-cM genetic interval corresponding to a 1.12-Mb physical region in the Chinese Spring reference genome V2.0. The gene differs from previously reported Yr genes on 7D based on their physical positions and is probably a novel gene. YrZ15-1949 would be a valuable resource for developing Pst-resistant wheat cultivars, and the linked markers could be used for marker-assisted selection.

Physical mapping of the wheat genes in low-recombination regions: radiation hybrid mapping of the C-locus.

This work reports the physical mapping of an important gene affecting spike compactness located in a low-recombination region of hexaploid wheat. This work paves the way for the eventual isolation and characterization of the factor involved but also opens up possibilities to use this approach to precisely map other wheat genes located on proximal parts of wheat chromosomes that show highly reduced recombination. Mapping wheat genes, in the centromeric and pericentromeric regions (~ 2/3rd of a given chromosome), poses a formidable challenge due to highly suppressed recombination. Using an example of compact spike locus (C-locus), this study provides an approach to precisely map wheat genes in the pericentromeric and centromeric regions that house ~ 30% of wheat genes. In club-wheat, spike compactness is controlled by the dominant C-locus, but previous efforts have failed to localize it, on a particular arm of chromosome 2D. We integrated radiation hybrid (RH) and high-resolution genetic mapping to locate C-locus on the short arm of chromosome 2D. Flanking markers of the C-locus span a physical distance of 11.0Mb (231.0-242Mb interval) and contain only 11 high-confidence annotated genes. This work demonstrates the value of this integrated strategy in mapping dominant genes in the low-recombination regions of the wheat genome. A comparison of the mapping resolutions of the RH and genetic maps using common anchored markers indicated that the RH map provides ~ 9 times better resolution that the genetic map even with much smaller population size. This study provides a broadly applicable approach to fine map wheat genes in regions of suppressed recombination.

Relocation of Sr48 to Chromosome 2D Using an Alternative Mapping Population and Development of a Closely Linked Marker Using Diverse Molecular Technologies.

The Ug99-effective stem rust resistance gene Sr48 was mapped to chromosome 2A based on its repulsion linkage with Yr1 in an Arina/Forno recombinant inbred line (RIL) population. Attempts to identify markers closely linked to Sr48 using available genomic resources were futile. This study used an Arina/Cezanne F5:7 RIL population to identify markers closely linked with Sr48. Using the Arina/Cezanne DArTseq map, Sr48 was mapped on the short arm of chromosome 2D and it co-segregated with 12 markers. These DArTseq marker sequences were used for BlastN search to identify corresponding wheat chromosome survey sequence (CSS) contigs, and PCR-based markers were developed. Two simple sequence repeat (SSR) markers, sun590 and sun592, and two Kompetitive Allele-Specific PCR (KASP) markers were derived from the contig 2DS_5324961 that mapped distal to Sr48. Molecular cytogenetic analysis using sequential fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH) identified a terminal translocation of chromosome 2A in chromosome 2DL of Forno. This translocation would have led to the formation of a quadrivalent involving chromosomes 2A and 2D in the Arina/Forno population, which would have exhibited pseudo-linkage between Sr48 and Yr1 in chromosome 2AL. Polymorphism of the closet marker sunKASP_239 among a set of 178 wheat genotypes suggested that this marker can be used for marker-assisted selection of Sr48.

Validation of a QTL on Chromosome 1DS Showing a Major Effect on Salt Tolerance in Winter Wheat.

Salt stress is one the most destructive abiotic stressors, causing yield losses in wheat worldwide. A prerequisite for improving salt tolerance is the identification of traits for screening genotypes and uncovering causative genes. Two populations of F3 lines developed from crosses between sensitive and tolerant parents were tested for salt tolerance at the seedling stage. Based on their response, the offspring were classified as salt sensitive and tolerant. Under saline conditions, tolerant genotypes showed lower Na+ and proline content but higher K+, higher chlorophyll content, higher K+/Na+ ratio, higher PSII activity levels, and higher photochemical efficiency, and were selected for further molecular analysis. Five stress responsive QTL identified in a previous study were validated in the populations. A QTL on the short arm of chromosome 1D showed large allelic effects in several salt tolerant related traits. An expression analysis of associated candidate genes showed that TraesCS1D02G052200 and TraesCS5B02G368800 had the highest expression in most tissues. Furthermore, qRT-PCR expression analysis revealed that ZIP-7 had higher differential expressions under saline conditions compared to KefC, AtABC8 and 6-SFT. This study provides information on the genetic and molecular basis of salt tolerance that could be useful in development of salt-tolerant wheat varieties.

Genome sequencing-based coverage analyses facilitate high-resolution detection of deletions linked to phenotypes of gamma-irradiated wheat mutants

BackgroundGamma-irradiated mutants of Triticum aestivum L., hexaploid wheat, provide novel and agriculturally important traits and are used as breeding materials. However, the identification of causative genomic regions of mutant phenotypes is challenging because of the large and complicated genome of hexaploid wheat. Recently, the combined use of high-quality reference genome sequences of common wheat and cost-effective resequencing technologies has made it possible to evaluate genome-wide polymorphisms, even in complex genomes.ResultsTo investigate whether the genome sequencing approach can effectively detect structural variations, such as deletions, frequently caused by gamma irradiation, we selected a grain-hardness mutant from the gamma-irradiated population of Japanese elite wheat cultivar “Kitahonami.” The Hardness (Ha) locus, including the puroindoline protein-encoding genes Pina-D1 and Pinb-D1 on the short arm of chromosome 5D, primarily regulates the grain hardness variation in common wheat. We performed short-read genome sequencing of wild-type and grain-hardness mutant plants, and subsequently aligned their short reads to the reference genome of the wheat cultivar “Chinese Spring.” Genome-wide comparisons of depth-of-coverage between wild-type and mutant strains detected ~ 130 Mbp deletion on the short arm of chromosome 5D in the mutant genome. Molecular markers for this deletion were applied to the progeny populations generated by a cross between the wild-type and the mutant. A large deletion in the region including the Ha locus was associated with the mutant phenotype, indicating that the genome sequencing is a powerful and efficient approach for detecting a deletion marker of a gamma-irradiated mutant phenotype. In addition, we investigated a pre-harvest sprouting tolerance mutant and identified a 67.8 Mbp deletion on chromosome 3B where Viviparous-B1 and GRAS family transcription factors are located. Co-dominant markers designed to detect the deletion-polymorphism confirmed the association with low germination rate, leading to pre-harvest sprouting tolerance.ConclusionsShort read-based genome sequencing of gamma-irradiated mutants facilitates the identification of large deletions linked to mutant phenotypes when combined with segregation analyses in progeny populations. This method allows effective application of mutants with agriculturally important traits in breeding using marker-assisted selection.

Mapping of a novel major effect Hessian fly field partial-resistance locus in southern soft red winter wheat line LA03136E71.

Hessian fly resistance has centralized around resistance loci that are biotype specific. We show that field resistance is evident and controlled by a single locus on chromosome 7D. Hessian flies (Mayetiola destructor Say) infest and feed upon wheat (Triticum aestivum L) resulting in significant yield loss. Genetically resistant cultivars are the most effective method of Hessian fly management. Wheat breeders in the southern USA have observed cultivars exhibiting a "field resistance" to Hessian fly that is not detectable by greenhouse assay. The resistant breeding line "LA03136E71" and susceptible cultivar "Shirley" were crossed to develop a population of 200 random F4:5 lines using single seed descent. The population was evaluated in a total of five locations in North Carolina during the 2019, 2020, and 2021 seasons. A subsample of each plot was evaluated for the total number of tillers, number of infested tillers, and total number of larvae/pupae. From these data, the percent infested tillers, number of larvae/pupae per tiller, and the number of larvae/pupae per infested tiller were estimated. In all within and across environment combinations for all traits recorded, the genotype effect was significant (p<0.05). Interval mapping identified a single large effect QTL distally on the short arm of chromosome 7D for all environment-trait combinations. This locus was identified on a chromosome where no other Hessian fly resistance/tolerance QTL has been previously identified. This novel Hessian fly partial-resistance QTL is termed QHft.nc-7D. Fine mapping must be conducted in this region to narrow down the causal agents responsible for this trait, and investigation into the mode of action is highly suggested.

Phenotypic characterization of the glossy1 mutant and fine mapping of GLOSSY1 in common wheat (Triticum aestivum L.).

A novel wax locus GLOSSY1 was finely mapped to an approximately 308.1-kbp genomic interval on chromosome 2DS of wheat. The epicuticular wax, the outermost layer of aerial organs, gives plants their bluish-white (glaucous) appearance. Epicuticular wax is ubiquitous and provides an essential protective function against environmental stresses. In this study, we identified the glossy1 mutant on the basis of its glossy glume from an EMS population in the elite wheat (Triticum aestivum L.) cultivar Jimai22. The mutant had a dramatically different profile in total wax load and composition of individual wax constituents relative to the wild type, resulting in the increased cuticle permeability of glumes. The glossy glume phenotype was controlled by a single, semidominant locus mapping to the short arm of chromosome 2D, within a 308.1-kbp genomic interval that contained ten annotated protein-coding genes. These results pave the way for an in-depth analysis of the underlying genetic basis of wax formation patterns and enrich our understanding of mechanisms regulating wax metabolism.

Lr80: A new and widely effective source of leaf rust resistance of wheat for enhancing diversity of resistance among modern cultivars.

A new leaf rust resistance gene Lr80 was identified and closely linked markers were developed for its successful pyramiding with other marker-tagged genes to achieve durable control of leaf rust. Common wheat landrace Hango-2, collected in 2006 from the Himalayan area of Hango, District Kinnaur, in Himachal Pradesh, exhibited a very low infection type (IT;) at the seedling stage to all Indian Puccinia triticina (Pt) pathotypes, except the pathotype 5R9-7 which produced IT 3+. Genetic analysis based on Agra Local/Hango-2-derived F3 families indicated monogenic control of leaf rust resistance, and the underlying locus was temporarily named LrH2. Bulked segregant analysis using 303 simple sequence repeat (SSR) markers located LrH2 in the short arm of chromosome 2D. An additional set of 10 chromosome 2DS-specific markers showed polymorphism between the parents and these weremapped on the entire Agra Local/Hango-2 F3 population. LrH2 was flanked by markers cau96 (distally) and barc124 (proximally). The 90K Infinium SNP array was used to identify SNP markers linked with LrH2. Markers KASP_17425 and KASP_17148 showed association with LrH2. Comparison of seedling leaf rust response data and marker locations across different maps demonstrated the uniqueness of LrH2 and it was formally named Lr80. The Lr80-linked markers KASP_17425, KASP_17148 and barc124 amplified alleles/products different to Hango-2 in 82 Australian cultivars indicating their robustness for marker-assisted selection of this gene in wheat breeding programs.

The Variability of Puroindoline-Encoding Alleles and Their Influence on Grain Hardness in Modern Wheat Cultivars Cultivated in Poland, Breeding Lines and Polish Old Landraces (Triticum aestivum L.)

Wheat (Triticum aestivum L.) grain hardness is determined mainly by variations in puroindoline genes (Pina-D1 and Pinb-D1), which are located on the short arm of chromosome 5D. This trait has a direct effect on the technological properties of the flour and the final product quality. The objective of the study was to analyze the mutation frequency in both Pin genes and their influence on grain hardness in 118 modern bread wheat cultivars and breeding lines cultivated in Poland, and 80 landraces from Poland. The PCR products containing the Pin gene coding sequences were sequenced by the Sanger method. Based on detected the SNPs (single-nucleotide polymorphisms) we designed CAPS (cleaved amplified polymorphic sequence) markers for the fast screening of Pinb alleles in a large number of genotypes. All analyzed cultivars, breeding lines, and landraces possess the wild-type Pina-D1a allele. Allelic variation was observed within the Pinb gene. The most frequently occurring allele in modern wheat cultivars and breeding lines (over 50%) was Pinb-D1b. The contribution of the remaining alleles (Pinb-D1a, Pinb-D1c, and Pinb-D1d) was much less (approx. 15% each). In landraces, the most frequent allele was Pinb-D1a (over 70%), followed by Pinb-D1b (21% frequency). Pinb-D1c and Pinb-D1g were found in individual varieties. SKCS (single-kernel characterization system) analysis revealed that grain hardness was strictly connected with Pinb gene allelic variation in most tested cultivars. The mean grain hardness values were significantly greater in cultivars with mutant Pinb variants as compared to those with the wild-type Pinb-D1a allele. Based on grain hardness measured by SKCS, we classified the analyzed cultivars and lines into different classes according to a previously proposed classification system.

Characterization and fine mapping of a leaf yellowing mutant in common wheat

Creation of leaf color mutants is the options in the study of photosynthesis, chloroplast development and Chlorophyll biosynthesis. In this study, a leaf color mutant NAU31 was identified from tissue culture of common wheat. In general, the mutant exhibited whole plant yellowing, fewer tillering, dwarfing and interestingly, improved resistance to wheat powdery mildew. Photosynthetic physiological analysis showed that the chloroplast inner structure varied in the mesophyll cells of the mutant, and this may lead to reduced chlorophyll content (chlorophyll “a”, Chlorophyll “b”, total chlorophyll and carotenoid), as well as decreased maximum quantum efficiency of photosystem II (Fv/Fm) and net photosynthetic rate. Transcriptome analysis indicated that the impairing of photosynthesis may be responsible for plant yellowing of NAU31. Inheritance analysis showed that NAU31 was a gain-of-function mutant and the yellowing trait was controlled by a dominant gene, namely Taymg (yellow mutant gene). SSR markers analysis preliminarily mapped Taymg to the distal short arm of chromosome 2D using an F2 population from the cross between NAU31 and W7984, a synthesized wheat. The mapping result was confirmed by BSA using a 55 K wheat SNP array. Through recombinants screening, the Taymg was finely mapped to the terminal region of 2DS, flanked by markers ZH47 and gwm296 and corresponding to a physical interval of 0.76 Mb. The cloning of Taymg will facilitate the dissection of the mechanism involved in chloroplast development of wheat and the coordinating of plant development and disease resistance.

Development and deployment of KASP markers for multiple alleles of Lr34 in wheat

Key messageHeterogeneous Lr34 genes for leaf rust in winter wheat cultivar ‘Duster’ and KASP markers for allelic variation in exon 11 and exon 22 of Lr34.Wheat, Triticum aestivum (2n = 6x = 42, AABBDD), is a hexaploid species, and each of three homoeologous genomes A, B, and D should have one copy for a gene in its ancestral form if the gene has no duplication. Previously reported leaf rust resistance gene Lr34 has one copy on the short arm of chromosome 7D in hexaploid wheat, and allelic variation in Lr34 is in intron 4, exon 11, exon 12, or exon 22. In this study, we discovered that Oklahoma hard red winter wheat cultivar ‘Duster’ (PI 644,016) has two copies of the Lr34 gene, the resistance allele Lr34a and the susceptibility allele Lr34b. Both Lr34a and Lr34b were mapped in the same linkage group on chromosome 7D in a doubled-haploid population generated from a cross between Duster and a winter wheat cultivar ‘Billings’ which carries the susceptibility allele Lr34c. A chromosomal fragment including Lr34 and at least two neighboring genes on its proximal side but excluding genes on its distal side was duplicated in Duster. The Duster Lr34ab allele was associated with tip necrosis and increased resistance against leaf rust at adult plants in the Duster × Billings DH population tested in the field, demonstrating the function of the Duster Lr34ab allele in wheat. We have developed KASP markers for allelic variation in exon 11 and exon 22 of Lr34 in wheat. These markers can be utilized to accelerate the selection of Lr34 in wheat.

Characterization of the Powdery Mildew Resistance Gene in the Elite Wheat Cultivar Jimai 23 and Its Application in Marker-Assisted Selection.

Powdery mildew infection of wheat (Triticum aestivum L.), caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive disease that threatens yield and quality worldwide. The most effective and preferred means for the control of the disease is to identify broad-spectrum resistance genes for breeding, especially the genes derived from elite cultivars that exhibit desirable agronomic traits. Jimai 23 is a Chinese wheat cultivar with superior agronomic performance, high-quality characteristics, and effective resistance to powdery mildew at all growth stages. Genetic analysis indicated that powdery mildew resistance in Jimai 23 was mediated by a single dominant gene, tentatively designated PmJM23. Using bulked segregant RNA-Seq (BSR-Seq), a series of markers was developed and used to map PmJM23. PmJM23 was then located at the Pm2 locus on the short arm of chromosome 5D (5DS). Resistance spectrum analysis demonstrated that PmJM23 provided a broad resistance spectrum different from that of the documented Pm2 alleles, indicating that PmJM23 is most likely a new allele of Pm2. In view of these combined agronomic, quality, and resistance findings, PmJM23 is expected to be a valuable resistance gene in wheat breeding. To efficiently use PmJM23 in breeding, the closely linked markers of PmJM23 were evaluated and confirmed to be applicable for marker-assisted selection (MAS). Using these markers, a series of resistant breeding lines with high resistance and desirable agronomic performance was selected from the crosses involving PmJM23, resulting in improved powdery mildew resistance of these lines.

Aegilops umbellulata introgression carrying leaf rust and stripe rust resistance genes Lr76 and Yr70 located to 9.47-Mb region on 5DS telomeric end through a combination of chromosome sorting and sequencing.

Lr76 and Yr70 have been fine mapped using the sequence of flow-sorted recombinant 5D chromosome from wheat-Ae. umbellulata introgression line. The alien introgression has been delineated to 9.47-Mb region on short arm of wheat chromosome 5D. Leaf rust and stripe rust are among the most damaging diseases of wheat worldwide. Wheat cultivation based on limited number of rust resistance genes deployed over vast areas expedites the emergence of new pathotypes warranting a continuous deployment of new resistance genes. In this paper, fine mapping of Aegilops umbellulata-derived leaf rust and stripe rust resistance genes Lr76 and Yr70 is being reported. We flow sorted and paired-end sequenced 5U chromosome of Ae. umbellulata, recombinant chromosome 5D (5DIL) from wheat-Ae. umbellulata introgression line pau16057 and 5DRP of recurrent parent WL711. Chromosome 5U reads were mapped against the reference Chinese Spring chromosome 5D sequence, and alien-specific SNPs were identified. Chromosome 5DIL and 5DRP sequences were de novo assembled, and alien introgression-specific markers were designed by selecting 5U- and 5D-specific SNPs. Overall, 27 KASP markers were mapped in high-resolution population consisting of 1404 F5 RILs. The mapping population segregated for single gene each for leaf rust and stripe rust resistance. The physical order of the SNPs in pau16057 was defined by projecting the 27 SNPs against the IWGSC RefSeq v1.0 sequence. Based on this physical map, the size of Ae. umbellulata introgression was determined to be 9.47Mb on the distal most end of the short arm of chromosome 5D. This non-recombining alien segment carries six NB-LRR encoding genes based on NLR annotation of assembled chromosome 5DIL sequence and IWGSC RefSeq v1.1 gene models. The presence of SNPs and other sequence variations in these genes between pau16057 and WL711 suggested that they are candidates for Lr76 and Yr70.

Registration of extra‐hard kernel near‐isogenic hexaploid wheat genetic stocks lacking puroindoline genes

AbstractKernel hardness (texture) is a key end‐use quality trait of wheat (Triticum spp.). Two hexaploid wheat (T. aestivum L.) near‐isogenic lines (NILs), WQL18RE5 (Reg. no. GS‐190, PI 691609) and WQL18CS5 (Reg. no. GS‐191, PI 691610), lack the puroindoline genes at the Hardness locus and thus have kernel texture phenotypes more similar to durum wheat [T. turgidum subsp. durum (Desf.) Husn.]. These two genetic stocks were produced in ‘Alpowa’ soft white spring wheat and comprise additions to an ongoing series of NILs in this soft wheat cultivar. Both NILs are advanced generation BC7F2:5 derivatives (Alpowa/donor/7*Alpowa). WQL18RE5 was derived from a Chinese Spring (CS) disomic substitution line, CS (Red Egyptian 5D), and WQL18CS5 was derived from a CS deletion line (CS5DS del.‐2) that lacks the distal portion of the short arm of chromosome 5D. These lines were developed at the USDA‐ARS Western Wheat Quality Laboratory and will be useful to study kernel texture and end‐use quality in hexaploid wheat; they can also serve as parents in developing cultivars with kernel texture equivalent to that of durum wheat.

The development and study of common wheat introgression lines derived from the synthetic form RS7

Synthetic recombination form RS7 (BBAAUS), in which the first two genomes, A and B, originate from common wheat, and the third recombinant genome consists of Aegilops speltoides (S) and Ae. umbellulata (U) chromosomes, was obtained from crossing synthetic forms Avrodes (BBAASS) and Avrolata (BBAAUU). Resistant to leaf rust, yellow rust and powdery mildew, introgression lines have been obtained from backcrosses with the susceptible varieties of common wheat Krasnodarskaya 99, Fisht and Rostislav. PCR analysis showed the presence of amplification fragments with marker SCS421 specific for the Lr28 gene in the line 4991n17. The cytological study (С-banding and FISH) of 14 lines has revealed chromosomal modifications in 12 of them. In most cases, the lines carry translocations from Ae. speltoides, which were identified in chromosomes 1D, 2D, 3D, 2B, 4B, 5B and 7B. Also, lines with the substituted chromosomes 1S (1B), 4D (4S), 5D (5S) and 7D (7S) were identified. Lines that have genetic material from Ae. speltoides and Ae umbellulata at once were revealed. In the line 3379n14, translocations in the short arm of chromosome 7D from Ae. umbellulata and chromosomes 5BL, 1DL, 2DL from Ae. speltoides were revealed. The line 4626p16 presumably has a translocation on the long arm of chromosome 2D from Ae. umbellulata and the T7SS.7SL-7DL translocation from Ae. speltoides. The T1DS.1DL-1SL and T3DS.3DL-3SL translocations from Ae. speltoides, and T2DS.2DL-2UL and T7DL.7DS-7US from Ae. umbellulata have been obtained for the first time. These lines may carry previously unidentified disease resistance genes and, in particular, leaf rust resistance genes from Ae. speltoides and Ae. umbellulata.

Accessing a Russian Wheat Aphid Resistance Gene in Bread Wheat by Long-Read Technologies.

Russian wheat aphid (RWA) ( Kurdjumov) is a serious invasive pest of small-grain cereals and many grass species. An efficient strategy to defy aphid attacks is to identify sources of natural resistance and transfer resistance genes into susceptible crop cultivars. Revealing the genes helps understand plant defense mechanisms and engineer plants with durable resistance to the pest. To date, more than 15 RWA resistance genes have been identified in wheat ( L.) but none of them has been cloned. Previously, we genetically mapped the RWA resistance gene into an interval of 0.83 cM on the short arm of chromosome 7D and spanned it with five bacterial artificial chromosome (BAC) clones. Here, we used a targeted strategy combining traditional approaches toward gene cloning (genetic mapping and sequencing of BAC clones) with novel technologies, including optical mapping and long-read nanopore sequencing. The latter, with reads spanning the entire length of a BAC insert, enabled us to assemble the whole region, a task that was not achievable with short reads. Long-read optical mapping validated the DNA sequence in the interval and revealed a difference in the locus organization between resistant and susceptible genotypes. The complete and accurate sequence of the region facilitated the identification of new markers and precise annotation of the interval, revealing six high-confidence genes. Identification of as the most likely candidate opens an avenue for its validation through functional genomics approaches.

Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.)

Key messageTwo QTL with pleiotropic effects on plant height and spike length linked in coupling phase on chromosome 2DS were dissected, and diagnostic marker for each QTL was developed.Plant height (PHT) is a crucial trait related to plant architecture and yield potential, and dissection of its underlying genetic basis would help to improve the efficiency of designed breeding in wheat. Here, two quantitative trait loci (QTL) linked in coupling phase on the short arm of chromosome 2D with pleiotropic effects on PHT and spike length, QPht/Sl.cau-2D.1 and QPht/Sl.cau-2D.2, were separated and characterized. QPht/Sl.cau-2D.1 is a novel QTL located between SNP makers BS00022234_51 and BobWhite_rep_c63957_1472. QPht/Sl.cau-2D.2 is mapped between two SSR markers, SSR-2062 and Xgwm484, which are located on the same genomic interval as Rht8. Moreover, the diagnostic marker tightly linked with each QTL was developed for the haplotype analysis using diverse panels of wheat accessions. The frequency of the height-reduced allele of QPht/Sl.cau-2D.1 is much lower than that of QPht/Sl.cau-2D.2, suggesting that this novel QTL may be an attractive target for genetic improvement. Consistent with a previous study of Rht8, a significant difference in cell length was observed between the NILs of QPht/Sl.cau-2D.2. By contrast, there was no difference in cell length between NILs of QPht/Sl.cau-2D.1, indicating that the underlying molecular mechanism for these two QTL may be different. Collectively, these data provide a new example of QTL dissection, and the developed diagnostic markers will be useful in marker-assisted pyramiding of QPht/Sl.cau-2D.1 and/or QPht/Sl.cau-2D.2 with the other genes in wheat breeding.

Fine mapping of Aegilops peregrina co-segregating leaf and stripe rust resistance genes to distal-most end of 5DS.

Novel rust resistance genes LrP and YrP from Ae. peregrina identified on chromosome 5D and the linked markers will aid deployment of these genesin combination with other major/minor genes. Aegilops peregrina, a wild tetraploid relative of wheat with genome constitution UUSS, displays genetic variation for resistance to leaf and stripe (yellow) rust. The wheat Ae. peregrina introgression line, IL pau16058, harbouring leaf and stripe rust resistance, was crossed with wheat cv. WL711 to generate an F2:3 mapping population. Inheritance studies on this population indicated the transfer of dominant co-segregating resistance to leaf and stripe rust. Ethyl methane sulphonate mutagenesis of IL pau16058 identified independent loss-of-function mutants for leaf and stripe rust resistance, indicating that the leaf and stripe rust resistance is controlled by independent genes, herein designated LrP and YrP, respectively. A high-resolution genetic map of LrP and YrP was constructed using the Illumina Infinium iSelect 90K wheat array and resistance gene enrichment sequencing (RenSeq) markers. The map spans 4.19cM on the distal-most region of the short arm of chromosome 5D, consisting of eight SNP markers and one microsatellite marker. LrP and YrP co-segregated with markers BS00163889 and 5DS44573_snp and was flanked distally by the SNP marker BS00129707 and proximally by 5DS149010, defining a 15.71Mb region in the RefSeq v1.0 genome assembly.