Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.)

Development of a self-fertile ditelosomic line for the long arm of chromosome 4B and its characterization using SSR markers

The ditelosomic line for the long arm of chromosome 4B (4BL) of Chinese Spring (CS) wheat is not available because it is completely male sterile. Since all deletions in the 4B short arm (4BS) cause male sterility in the homozygous condition, a male-fertility gene should be located in a distal region of 4BS. Among the selfed progeny of a hybrid between a male-sterile 4BS deletion plant (4BS-8) and a Japanese common wheat cultivar Norin 61 (N61), we obtained self-fertile 4BS-8 homozygous deletion plants. We also found fertile nullisomic-4B plants among the selfed progeny of a hybrid between a monosomic line 4B of N61 and CS. This fact suggested that N61 has a novel male-fertility gene on a chromosome other than 4B. We established a self-fertile ditelosomic 4BL line after backcrossing a fertile 4BS-8 plant to CS monotelodisomic 4BL. By cytological observation and PCR analysis using 16 SSR markers, we verified that this ditelosomic line lacked the entire 4BS arm and found that three of the markers were on 4BS. We conducted deletion mapping using three 4BS homozygous deletion lines and three 4BS-specific markers.

Analysis of agronomic and domestication traits in a durum × cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map

Development of a high-density SNP map and evaluation of QTL shed light on domestication events in tetraploid wheat and the potential utility of cultivated emmer wheat for durum wheat improvement. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is tetraploid and considered as one of the eight founder crops that spawned the Agricultural Revolution about 10,000 years ago. Cultivated emmer has non-free-threshing seed and a somewhat fragile rachis, but mutations in genes governing these and other agronomic traits occurred that led to the formation of today's fully domesticated durum wheat (T. turgidum ssp. durum). Here, we evaluated a population of recombinant inbred lines (RILs) derived from a cross between a cultivated emmer accession and a durum wheat variety. A high-density single nucleotide polymorphism (SNP)-based genetic linkage map consisting of 2,593 markers was developed for the identification of quantitative trait loci. The major domestication gene Q had profound effects on spike length and compactness, rachis fragility, and threshability as expected. The cultivated emmer parent contributed increased spikelets per spike, and the durum parent contributed higher kernel weight, which led to the identification of some RILs that had significantly higher grain weight per spike than either parent. Threshability was governed not only by the Q locus, but other loci as well including Tg-B1 on chromosome 2B and a putative Tg-A1 locus on chromosome 2A indicating that mutations in the Tg loci occurred during the transition of cultivated emmer to the fully domesticated tetraploid. These results not only shed light on the events that shaped wheat domestication, but also demonstrate that cultivated emmer is a useful source of genetic variation for the enhancement of durum varieties.

Molecular mapping of genes Yr64 and Yr65 for stripe rust resistance in hexaploid derivatives of durum wheat accessions PI 331260 and PI 480016

This manuscript reports two new genes ( Yr64 and Yr65 ) for effective resistance to stripe rust and usefulness of their flanking SSR markers for marker-assisted selection. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat worldwide and resistance is the best control strategy. Durum wheat accessions PI 331260 and PI 480016 were resistant to all tested Pst races. To transfer the resistance genes to common wheat and map them to wheat chromosomes, both accessions were crossed with the stripe rust-susceptible spring wheat 'Avocet S'. Resistant F3 plants with 42 chromosomes were selected cytologically and by rust phenotype. A single dominant gene for resistance was identified in segregating F4 lines from each cross. F6 populations for each cross were developed from single F5 plants and used for genetic mapping. Different genes from PI 331260 and PI 480016 were mapped to different loci in chromosome 1BS using simple sequence repeat markers. The gene from PI 331260 was flanked by Xgwm413 and Xgdm33 in bin 1BS9-0.84-1.06 at genetic distances of 3.5 and 2.0 cM; and the gene from PI 480016 was flanked by Xgwm18 and Xgwm11 in chromosome bin C-1BS10-0.50 at 1.2 and 2.1 cM, respectively. Chromosomal locations and race and allelism tests indicated that the two genes are different from previously reported stripe rust resistance genes, and therefore are named as Yr64 from PI 331260 and Yr65 from PI 480016. These genes and their flanking markers, and selected common wheat lines with the genes should be valuable for diversifying resistance genes used in breeding wheat cultivars with stripe rust resistance.

QTL mapping of adult-plant resistance to leaf rust in a RIL population derived from a cross of wheat cultivars Shanghai 3/Catbird and Naxos

Six QTL for adult plant resistance to leaf rust, including two QTL effective against additional diseases, were identified in a RIL population derived from a cross between Shanghai 3/Catbird and Naxos. Leaf rust is an important wheat disease and utilization of adult-plant resistance (APR) may be the best approach to achieve long-term protection from the disease. The CIMMYT spring wheat line Shanghai 3/Catbird (SHA3/CBRD) showed a high level of APR to Chinese Puccinia triticina pathotypes in the field. To identify APR genes in this line, a mapping population of 164 recombinant inbred lines (RILs) was developed from a cross of this line and Naxos, a moderately susceptible German cultivar. The RILs were evaluated for final disease severity (FDS) at Baoding, Hebei province, and Zhoukou, Henan province, in the 2010-2011 and 2011-2012 cropping seasons. QTL analysis detected one major QTL derived from SHA3/CBRD on chromosome 2BS explaining from 15 to 37 % of the phenotypic variance across environments. In addition one minor resistance QTL on chromosome 1AL from SHA3/CBRD and four minor QTL from Naxos on chromosomes 2DL, 5B, 7BS, and 7DS were also detected. SHA3/CBRD also possessed seedling resistance gene Lr26, and Naxos contained Lr1 based on gene postulation following tests with an array of P. triticina pathotypes and molecular marker assays. These seedling resistance and APR genes and their closely linked molecular markers are potentially useful for improving leaf rust resistance in wheat breeding programs.

Identification and independent validation of a stable yield and thousand grain weight QTL on chromosome 6A of hexaploid wheat (Triticum aestivum L.)

BACKGROUND

Grain yield in wheat is a polygenic trait that is influenced by environmental and genetic interactions at all stages of the plant's growth. Yield is usually broken down into three components; number of spikes per area, grain number per spike, and grain weight (TGW). In polyploid wheat, studies have identified quantitative trait loci (QTL) which affect TGW, yet few have been validated and fine-mapped using independent germplasm, thereby having limited impact in breeding.

RESULTS

In this study we identified a major QTL for TGW, yield and green canopy duration on wheat chromosome 6A of the Spark x Rialto population, across 12 North European environments. Using independent germplasm in the form of BC2 and BC4 near isogenic lines (NILs), we validated the three QTL effects across environments. In four of the five experiments the Rialto 6A introgression gave significant improvements in yield (5.5%) and TGW (5.1%), with morphometric measurements showing that the increased grain weight was a result of wider grains. The extended green canopy duration associated with the high yielding/TGW Rialto allele was comprised of two independent effects; earlier flowering and delayed final maturity, and was expressed stably across the five environments. The wheat homologue (TaGW2) of a rice gene associated with increased TGW and grain width was mapped within the QTL interval. However, no polymorphisms were identified in the coding sequence between the parents.

CONCLUSION

The discovery and validation through near-isogenic lines of robust QTL which affect yield, green canopy duration, thousand grain weight, and grain width on chromosome 6A of hexaploid wheat provide an important first step to advance our understanding of the genetic mechanisms regulating the complex processes governing grain size and yield in polyploid wheat.

Molecular mapping of an adult plant stem rust resistance gene Sr56 in winter wheat cultivar Arina

This article covers detailed characterization and naming of QSr.sun - 5BL as Sr56 . Molecular markers linked with adult plant stem rust resistance gene Sr56 were identified and validated for marker-assisted selection. The identification of new sources of adult plant resistance (APR) and effective combinations of major and minor genes is well appreciated in breeding for durable rust resistance in wheat. A QTL, QSr.sun-5BL, contributed by winter wheat cultivar Arina providing 12-15 % reduction in stem rust severity, was reported in an Arina/Forno recombinant inbred line (RIL) population. Following the demonstration of monogenic segregation for APR in the Arina/Yitpi RIL population, the resistance locus was formally named Sr56. Saturation mapping of the Sr56 region using STS (from EST and DArT clones), SNP (9 K) and SSR markers from wheat chromosome survey sequences that were ordered based on synteny with Brachypodium distachyon genes in chromosome 1 resulted in the flanking of Sr56 by sun209 (SSR) and sun320 (STS) at 2.6 and 1.2 cM on the proximal and distal ends, respectively. Investigation of conservation of gene order between the Sr56 region in wheat and B. distachyon showed that the syntenic region defined by SSR marker interval sun209-sun215 corresponded to approximately 192 kb in B. distachyon, which contains five predicted genes. Conservation of gene order for the Sr56 region between wheat and Brachypodium, except for two inversions, provides a starting point for future map-based cloning of Sr56. The Arina/Forno RILs carrying both Sr56 and Sr57 exhibited low disease severity compared to those RILs carrying these genes singly. Markers linked with Sr56 would be useful for marker-assisted pyramiding of this gene with other major and APR genes for which closely linked markers are available.

Mapping of Yr62 and a small-effect QTL for high-temperature adult-plant resistance to stripe rust in spring wheat PI 192252

This manuscript reports a new gene (Yr62) and a small-effect QTL for potentially durable resistance to stripe rust and usefulness of Yr62 markers for marker-assisted selection. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating disease of wheat worldwide. Spring wheat germplasm PI 192252 showed a high level of high-temperature adult-plant (HTAP) resistance to stripe rust in germplasm evaluation over 8 years in the State of Washington. To elucidate the genetic basis of resistance, PI 192252 was crossed with 'Avocet susceptible'. A mapping population of 150 F5 recombinant inbred lines was developed using single-seed descent. Stripe rust tests were conducted with selected Pst races in a greenhouse and in field conditions under natural infections. The relative area under the disease progress curve (rAUDPC) data showed continuous distributions, indicating that HTAP resistance of PI 192252 was controlled by quantitative trait loci (QTL). Two QTL were identified in PI 192252, explaining 74.2 % of the total phenotypic variation for rAUDPC. These two QTL were mapped to chromosomes 4BL (QYrPI192252.wgp-4BL) and 5BS (QYrPI192252.wgp-5BS) with SSR and SNP markers and explained 40-60 and 22-27 %, respectively, of the phenotypic variation across the four environments. Because the major-effect QTL on 4BL is different from previously named Yr genes and inherited as a single gene, it is named Yr62. The SSR marker alleles Xgwm192 222 and Xgwm251 133 flanking Yr62 were different from the alleles in various wheat varieties, suggesting that these markers could be useful in marker-assisted selection for incorporating Yr62 into commercial cultivars.

A novel genetic map of wheat: utility for mapping QTL for yield under different nitrogen treatments

Background

Common wheat (Triticum aestivum L.) is one of the most important food crops worldwide. Wheat varieties that maintain yield (YD) under moderate or even intense nitrogen (N) deficiency can adapt to low input management systems. A detailed genetic map is necessary for both wheat molecular breeding and genomics research. In this study, an F_6:7 recombinant inbred line population comprising 188 lines was used to construct a novel genetic map and subsequently to detect quantitative trait loci (QTL) for YD and response to N stress.

Results

A genetic map consisting of 591 loci distributed across 21 wheat chromosomes was constructed. The map spanned 3930.7 cM, with one marker per 6.7 cM on average. Genomic simple sequence repeat (g-SSR), expressed sequence tag-derived microsatellite (e-SSR), diversity arrays technology (DArT), sequence-tagged sites (STS), sequence-related amplified polymorphism (SRAP), and inter-simple sequence repeat (ISSR) molecular markers were included in the map. The linear relationships between loci found in the present map and in previously compiled physical maps were presented, which were generally in accordance. Information on the genetic and physical positions and allele sizes (when possible) of 17 DArT, 50 e-SSR, 44 SRAP, five ISSR, and two morphological markers is reported here for the first time. Seven segregation distortion regions (SDR) were identified on chromosomes 1B, 3BL, 4AL, 6AS, 6AL, 6BL, and 7B. A total of 22 and 12 QTLs for YD and yield difference between the value (YDDV) under HN and the value under LN were identified, respectively. Of these, QYd-4B-2 and QYddv-4B, two major stable QTL, shared support interval with alleles from KN9204 increasing YD in LN and decreasing YDDV. We probe into the use of these QTLs in wheat breeding programs. Moreover, factors affecting the SDR and total map length are discussed in depth.

Conclusions

This novel map may facilitate the use of novel markers in wheat molecular breeding programs and genomics research. Moreover, QTLs for YD and YDDV provide useful markers for wheat molecular breeding programs designed to increase yield potential under N stress.

Fine mapping of LrSV2, a race-specific adult plant leaf rust resistance gene on wheat chromosome 3BS

Fine mapping permits the precise positioning of genes within chromosomes, prerequisite for positional cloning that will allow its rational use and the study of the underlying molecular action mechanism. Three leaf rust resistance genes were identified in the durable leaf rust resistant Argentinean wheat variety Sinvalocho MA: the seedling resistance gene Lr3 on distal 6BL and two adult plant resistance genes, LrSV1 and LrSV2, on chromosomes 2DS and 3BS, respectively. To develop a high-resolution genetic map for LrSV2, 10 markers were genotyped on 343 F2 individuals from a cross between Sinvalocho MA and Gama6. The closest co-dominant markers on both sides of the gene (3 microsatellites and 2 STMs) were analyzed on 965 additional F2s from the same cross. Microsatellite marker cfb5010 cosegregated with LrSV2 whereas flanking markers were found at 1 cM distal and at 0.3 cM proximal to the gene. SSR markers designed from the sequences of cv Chinese Spring BAC clones spanning the LrSV2 genetic interval were tested on the recombinants, allowing the identification of microsatellite swm13 at 0.15 cM distal to LrSV2. This delimited an interval of 0.45 cM around the gene flanked by the SSR markers swm13 and gwm533 at the subtelomeric end of chromosome 3BS.

Molecular and comparative mapping of genes governing spike compactness from wild emmer wheat

The development and morphology of the wheat spike is important because the spike is where reproduction occurs and it holds the grains until harvest. Therefore, genes that influence spike morphology are of interest from both theoretical and practical stand points. When substituted for the native chromosome 2A in the tetraploid Langdon (LDN) durum wheat background, the Triticum turgidum ssp. dicoccoides chromosome 2A from accession IsraelA confers a short, compact spike with fewer spikelets per spike compared to LDN. Molecular mapping and quantitative trait loci (QTL) analysis of these traits in a homozygous recombinant population derived from LDN × the chromosome 2A substitution line (LDNIsA-2A) indicated that the number of spikelets per spike and spike length were controlled by linked, but different, loci on the long arm of 2A. A QTL explaining most of the variation for spike compactness coincided with the QTL for spike length. Comparative mapping indicated that the QTL for number of spikelets per spike overlapped with a previously mapped QTL for Fusarium head blight susceptibility. The genes governing spike length and compactness were not orthologous to either sog or C, genes known to confer compact spikes in diploid and hexaploid wheat, respectively. Mapping and sequence analysis indicated that the gene governing spike length and compactness derived from wild emmer could be an ortholog of the barley Cly1/Zeo gene, which research indicates is an AP2-like gene pleiotropically affecting cleistogamy, flowering time, and rachis internode length. This work provides researchers with knowledge of new genetic loci and associated markers that may be useful for manipulating spike morphology in durum wheat.

Mapping stripe rust resistance in a BrundageXCoda winter wheat recombinant inbred line population

A recombinant inbred line (RIL) mapping population developed from a cross between winter wheat (Triticum aestivum L.) cultivars Coda and Brundage was evaluated for reaction to stripe rust (caused by Puccinia striiformis f. sp. tritici). Two hundred and sixty eight RIL from the population were evaluated in replicated field trials in a total of nine site-year locations in the U.S. Pacific Northwest. Seedling reaction to stripe rust races PST-100, PST-114 and PST-127 was also examined. A linkage map consisting of 2,391 polymorphic DNA markers was developed covering all chromosomes of wheat with the exception of 1D. Two QTL on chromosome 1B were associated with adult plant and seedling reaction and were the most significant QTL detected. Together these QTL reduced adult plant infection type from a score of seven to a score of two reduced disease severity by an average of 25% and provided protection against race PST-100, PST-114 and PST-127 in the seedling stage. The location of these QTL and the race specificity provided by them suggest that observed effects at this locus are due to a complementation of the previously known but defeated resistances of the cultivar Tres combining with that of Madsen (the two parent cultivars of Coda). Two additional QTL on chromosome 3B and one on 5B were associated with adult plant reaction only, and a single QTL on chromosome 5D was associated with seedling reaction to PST-114. Coda has been resistant to stripe rust since its release in 2000, indicating that combining multiple resistance genes for stripe rust provides durable resistance, especially when all-stage resistance genes are combined in a fashion to maximize the number of races they protect against. Identified molecular markers will allow for an efficient transfer of these genes into other cultivars, thereby continuing to provide excellent resistance to stripe rust.

Molecular mapping of stripe rust resistance gene Yr51 in chromosome 4AL of wheat

This manuscript describes the chromosomal location of a new source of stripe rust resistance in wheat. DNA markers closely linked with the resistance locus were identified and validated. A wheat landrace, AUS27858, from the Watkins collection showed high levels of resistance against Australian pathotypes of Puccinia striiformis f. sp. tritici. It was reported to carry two genes for stripe rust resistance, tentatively named YrAW1 and YrAW2. One hundred seeds of an F3 line (HSB#5515; YrAW1yrAW1) that showed monogenic segregation for stripe rust response were sown and harvested individually to generate monogenically segregating population (MSP) #5515. Stripe rust response variation in MSP#5515 conformed to segregation at a single locus. Bulked segregant analysis using high-throughput DArT markers placed YrAW1 in chromosome 4AL. MSP#5515 was advanced to F6 and phenotyped for detailed mapping. Novel wheat genomic resources including chromosome-specific sequence and genome zipper were employed to develop markers specific for the long arm of chromosome 4A. These markers were used for further saturation of the YrAW1 carrying region. YrAW1 was delimited by 3.7 cM between markers owm45F3R3 and sun104. Since there was no other stripe rust resistance gene located in chromosome 4AL, YrAW1 was formally named Yr51. Reference stock for Yr51 was lodged at the Australian Winter Cereal Collection, Tamworth, Australia and it was accessioned as AUS91456. Marker sun104 was genotyped on a set of Australian and Indian wheat cultivars and was shown to lack the resistance-linked sun104-225 bp allele. Marker sun104 is currently being used for marker-assisted backcrossing of Yr51 in Australian and Indian wheat backgrounds.

Genetic mapping and marker development for resistance of wheat against the root lesion nematode Pratylenchus neglectus

BACKGROUND

The Rlnn1 locus, which resides on chromosome 7A of bread wheat (Triticum aestivum L.) confers moderate resistance against the root lesion nematode Pratylenchus neglectus. Prior to this research, the exact linkage relationships of Rlnn1 with other loci on chromosome 7A were not clear and there were no simple codominant markers available for selection of Rlnn1 in wheat breeding. The objectives of the research reported here were to (1) develop an improved genetic map of the Rlnn1 region of chromosome 7A and (2) develop molecular markers that could be used in marker-assisted selection to improve resistance of wheat against P. neglectus.

RESULTS

A large-effect quantitative trait locus (QTL) for resistance against P. neglectus was genetically mapped using a population of Excalibur/Kukri doubled haploid lines. This QTL coincides in position with the rust resistance gene(s) Lr20/Sr15, the phytoene synthase gene Psy-A1 and 10 molecular markers, including five new markers designed using wheat-rice comparative genomics and wheat expressed sequence tags. Two of the new markers are suitable for use as molecular diagnostic tools to distinguish plants that carry Rlnn1 and Lr20/Sr15 from those that do not carry these resistance genes.

CONCLUSIONS

The genomic location of Rlnn1 was confirmed to be in the terminal region of the long arm of chromosome 7A. Molecular markers were developed that provide simple alternatives to costly phenotypic assessment of resistance against P. neglectus in wheat breeding. In Excalibur, genetic recombination seems to be completely suppressed in the Rlnn1 region.

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

Background

The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution.

Results

Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere.

Conclusions

This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.

Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes

Background

The importance of wheat to the world economy, together with progresses in high-throughput next-generation DNA sequencing, have accelerated initiatives of genetic research for wheat improvement. The availability of high density linkage maps is crucial to identify genotype-phenotype associations, but also for anchoring BAC contigs to genetic maps, a strategy followed for sequencing the wheat genome.

Results

Here we report a genetic linkage map in a durum wheat segregating population and the study of mapped DArT markers. The linkage map consists of 126 gSSR, 31 EST-SSR and 351 DArT markers distributed in 24 linkage groups for a total length of 1,272 cM. Through bioinformatic approaches we have analysed 327 DArT clones to reveal their redundancy, syntenic and functional aspects. The DNA sequences of 174 DArT markers were assembled into a non-redundant set of 60 marker clusters. This explained the generation of clusters in very small chromosome regions across genomes. Of these DArT markers, 61 showed highly significant (Expectation < E-10) BLAST similarity to gene sequences in public databases of model species such as Brachypodium and rice. Based on sequence alignments, the analysis revealed a mosaic gene conservation, with 54 and 72 genes present in rice and Brachypodium species, respectively.

Conclusions

In the present manuscript we provide a detailed DArT markers characterization and the basis for future efforts in durum wheat map comparing.

Genetic analysis and detection of the gene MlLX99 on chromosome 2BL conferring resistance to powdery mildew in the wheat cultivar Liangxing 99

The effectiveness of wheat cultivar Liangxing 99 against powdery mildew was shown to be controlled by a single dominant gene located on a new locus of chromosome 2BL in the bin 2BL2-0.35-0.50. Liangxing 99, one of the most widely grown commercial cultivars in the winter wheat (Triticum aestivum) producing regions in northern China, was shown to provide a broad spectrum of resistance to Blumeria graminis f. sp. tritici (Bgt) isolates originating from that region. Using an F2 population and F2:3 lines derived from a cross of Liangxing 99 × Zhongzuo 9504, genetic analysis demonstrated that a single dominant gene, designated MlLX99, was responsible for the resistance of Liangxing 99 to Bgt isolate E09. The results of molecular analysis indicated that this gene is located on chromosome 2BL and flanked by the SSR marker Xgwm120 and EST-STS marker BE604758 at genetic distances of 2.9 and 5.5 cM, respectively. Since the flanking markers of MlLX99 were previously mapped to the bin 2BL2-0.36-0.50, MlLX99 must be located in this chromosomal region. MlLX99 showed a different resistance reaction pattern to 60 Bgt isolates from Pm6, Pm33, and PmJM22, which were all previously mapped on chromosome 2BL, but differed in their positions from MlLX99. Due to its unique position on chromosome 2BL, MlLX99 appears to be a new locus for resistance to powdery mildew. Liangxing 99 has shown superior yield performance and wide adaptation to different agricultural conditions, which has resulted in its extensive use as a wheat cultivar in China. The identification of resistance gene MlLX99 facilitates the use of this cultivar in the protection of wheat from damage caused by powdery mildew.

Molecular characterization of field resistance to Fusarium head blight in two US soft red winter wheat cultivars

In the soft red winter wheat (Triticum aestivum L.) regions of the US, Fusarium head blight (FHB, caused by Fusarium spp.) resistance derived from locally adapted germplasm has been used predominantly. Two soft red winter wheat cultivars, Massey and Ernie, have moderate resistance to FHB. Mapping populations derived from Becker/Massey (B/M) and Ernie/MO 94-317 (E/MO) were evaluated for FHB resistance and other traits in multiple environments. Eight QTL in B/M and five QTL in E/MO were associated with FHB variables including incidence, severity (SEV), index (IND), Fusarium damaged kernels (FDK), deoxynivalenol (DON), and morphological traits flowering time and plant height. Four QTL were common to both populations. Three of them were located at or near known genes: Ppd-D1 on chromosome 2DS, Rht-B1 on 4BS, and Rht-D1 on 4DS. Alleles for dwarf plant height (Rht-B1b and Rht-D1b) and photoperiod insensitivity (Ppd-D1a) had pleiotropic effects in reducing height and increasing FHB susceptibility. The other QTL detected for FHB variables were on 3BL in both populations, 1AS, 1DS, 2BL, and 4DL in B/M, and 5AL (B1) and 6AL in E/MO. The additive effects of FHB variables ranged from 0.4 mg kg(-1) of DON to 6.2 % for greenhouse (GH) SEV in B/M and ranged from 0.3 mg kg(-1) of DON to 8.3 % for GH SEV in E/MO. The 4DS QTL had epistasis with Ppd-D1, Qdon.umc-6AL, and Qht.umc-4BS, and additive × additive × environment interactions with the 4BS QTL for SEV, IND, and FDK in E/MO. Marker-assisted selection might be used to enhance FHB resistance through selection of favorable alleles of significant QTL, taking into account genotypes at Rht-B1b, Rht-D1a and Ppd-D1a.

Cloning and characterization of a critical regulator for preharvest sprouting in wheat

Sprouting of grains in mature spikes before harvest is a major problem in wheat (Triticum aestivum) production worldwide. We cloned and characterized a gene underlying a wheat quantitative trait locus (QTL) on the short arm of chromosome 3A for preharvest sprouting (PHS) resistance in white wheat using comparative mapping and map-based cloning. This gene, designated TaPHS1, is a wheat homolog of a MOTHER OF FLOWERING TIME (TaMFT)-like gene. RNA interference-mediated knockdown of the gene confirmed that TaPHS1 positively regulates PHS resistance. We discovered two causal mutations in TaPHS1 that jointly altered PHS resistance in wheat. One GT-to-AT mutation generates a mis-splicing site, and the other A-to-T mutation creates a premature stop codon that results in a truncated nonfunctional transcript. Association analysis of a set of wheat cultivars validated the role of the two mutations on PHS resistance. The molecular characterization of TaPHS1 is significant for expediting breeding for PHS resistance to protect grain yield and quality in wheat production.

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

BACKGROUND

As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning.

RESULTS

Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome.

CONCLUSIONS

Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.

Quantitative trait loci for leaf chlorophyll fluorescence parameters, chlorophyll and carotenoid contents in relation to biomass and yield in bread wheat and their chromosome deletion bin assignments

Relatively little is known of the genetic control of chlorophyll fluorescence (CF) and pigment traits important in determining efficiency of photosynthesis in wheat and its association with biomass productivity. A doubled haploid population of 94 lines from the wheat cross Chinese Spring × SQ1 was trialled under optimum glasshouse conditions for 4 years to identify quantitative trait loci (QTL) for CF traits including, for the first time in wheat, JIP-test parameters per excited cross section (CS_m): ABS/CS_m, DI_o/CS_m, TR_o/CS_m, RC/CS_m and ET_o/CS_m, key parameters determining efficiency of the photosynthetic apparatus, as well as chlorophyll and carotenoid contents to establish associations with biomass and grain yield. The existing genetic map was extended to 920 loci by adding Diversity Arrays Technology markers. Markers and selected genes for photosynthetic light reactions, pigment metabolism and biomass accumulation were located to chromosome deletion bins. Across all CF traits and years, 116 QTL for CF were located on all chromosomes except 7B, and 39 QTL were identified for pigments on the majority of chromosomes, excluding 1A, 2A, 4A, 3B, 5B, 1D, 2D, 5D, 6D and 7D. Thirty QTL for plant productivity traits were mapped on chromosomes 3A, 5A, 6A, 7A, 1B, 2B, 4B, 6B, 7B, 3D and 4D. A region on chromosome 6B was identified where 14 QTL for CF parameters coincided with QTL for chlorophyll content and grain weight per ear. Thirty-five QTL regions were coincident with candidate genes. The environment was shown to dominate in determining expression of genes for those traits.

QTL mapping of slow-rusting, adult plant resistance to race Ug99 of stem rust fungus in PBW343/Muu RIL population

Races of stem rust fungus pose a major threat to wheat production worldwide. We mapped adult plant resistance (APR) to Ug99 in 141 lines of a PBW343/Muu recombinant inbred lines (RILs) population by phenotyping them for three seasons at Njoro, Kenya in field trials and genotyping them with Diversity Arrays Technology (DArT) markers. Moderately susceptible parent PBW343 and APR parent Muu displayed mean stem rust severities of 66.6 and 5 %, respectively. The mean disease severity of RILs ranged from 1 to 100 %, with an average of 23.3 %. Variance components for stem rust severity were highly significant (p < 0.001) for RILs and seasons and the heritability (h (2)) for the disease ranged between 0.78 and 0.89. Quantitative trait loci (QTL) analysis identified four consistent genomic regions on chromosomes 2BS, 3BS, 5BL, and 7AS; three contributed by Muu (QSr.cim-2BS, QSr.cim-3BS and QSr.cim-7AS) and one (QSr.cim-5BL) derived from PBW343. RILs with flanking markers for these QTLs had significantly lower severities than those lacking the markers, and combinations of QTLs had an additive effect, significantly enhancing APR. The QTL identified on chromosome 3BS mapped to the matching region as the known APR gene Sr2. Four additional QTLs on chromosomes 1D, 3A, 4B, and 6A reduced disease severity significantly at least once in three seasons. Our results show a complex nature of APR to stem rust where Sr2 and other minor slow rusting resistance genes can confer a higher level of resistance when present together.

Identification of the gene Pm47 on chromosome 7BS conferring resistance to powdery mildew in the Chinese wheat landrace Hongyanglazi

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is an important disease that causes substantial yield losses in wheat (Triticum aestivum) in China and other parts of the world. This foliar disease can be effectively managed by host resistance. The Chinese landrace Hongyanglazi from Shaanxi province is highly resistant to many Bgt isolates at the seedling stage. Genetic analysis using an F2:3 population derived from a cross between Hongyanglazi and susceptible cultivar Zhongzuo 9504 indicated that Hongyanglazi carried a single recessive gene (tentatively designated PmHYLZ) conferring its resistance to Bgt isolate E09. PmHYLZ was flanked by EST marker BE606897 and microsatellite marker Xgwm46 on chromosome 7BS at genetic distances of 1.7 and 3.6 cM, respectively. This gene differed from Pm40, also located on 7BS, by origin, linked markers, and reactions to 13 Bgt isolates. Based on these findings, PmHYLZ was permanently designated as Pm47.

Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A

Background

Bread wheat (Triticum aestivum L.) is one of the most important crops worldwide and its production faces pressing challenges, the solution of which demands genome information. However, the large, highly repetitive hexaploid wheat genome has been considered intractable to standard sequencing approaches. Therefore the International Wheat Genome Sequencing Consortium (IWGSC) proposes to map and sequence the genome on a chromosome-by-chromosome basis.

Methodology/Principal Findings

We have constructed a physical map of the long arm of bread wheat chromosome 1A using chromosome-specific BAC libraries by High Information Content Fingerprinting (HICF). Two alternative methods (FPC and LTC) were used to assemble the fingerprints into a high-resolution physical map of the chromosome arm. A total of 365 molecular markers were added to the map, in addition to 1122 putative unique transcripts that were identified by microarray hybridization. The final map consists of 1180 FPC-based or 583 LTC-based contigs.

Conclusions/Significance

The physical map presented here marks an important step forward in mapping of hexaploid bread wheat. The map is orders of magnitude more detailed than previously available maps of this chromosome, and the assignment of over a thousand putative expressed gene sequences to specific map locations will greatly assist future functional studies. This map will be an essential tool for future sequencing of and positional cloning within chromosome 1A.

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species.

Characterization of new loci for Hessian fly resistance in common wheat

The discovery of several new loci for resistance to Hessian fly was reported here. QHf.uga-6AL, the late HR61 was recognized from wheat cultivar 26R61 on the distal end of 6AL with resistance to both biotypes E and vH13. It is the first gene or QTL found on this particular chromosome. QHf.uga-3DL and QHf.uga-1AL, physically assigned to the deletion bins 3DL2-0.27-0.81 and 1AL1-0.17-0.61, respectively, were detected for resistance to biotype vH13. Both QTL should represent new loci for Hessian fly resistance and the latter was detectable only in the late seedling stage when tolerance was evident. In addition, QHf.uga-6DS-C and QHf.uga-1AS had minor effect and were identified from the susceptible parent AGS 2000 for resistance to biotype E and vH13, respectively. QHf.uga-6DS-C is different from the known gene H13 on 6DS and QHf.uga-1AS is different from H9 gene cluster on 1AS. These loci also might be new components of Hessian fly resistance, although their LOD values were not highly significant. The QTL detections were all conducted on a RIL mapping population of 26R61/AGS 2000 with good genome coverage of molecular markers. The strategy used in the current study will serve as a good starting point for the discovery and mapping of resistance genes including tolerance to the pest and the closely linked markers will certainly be useful in selecting or pyramiding of these loci in breeding programs.

PmX: a recessive powdery mildew resistance gene at the Pm4 locus identified in wheat landrace Xiaohongpi

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most devastating foliar diseases of wheat and imposes a constant challenge on wheat breeders. Xiaohongpi, a Chinese landrace of wheat (Triticum aestivum L.), shows resistance to powdery mildew during the entire growth stage in the field and under controlled conditions. The F1 plants from cross of the powdery mildew susceptible cultivar Yangmai158 with Xiaohongpi were susceptible to isolate Bgt19, the locally most prevalent Bgt isolate. In the derived F2 population and F3 progenies, the resistance segregation deviated significantly from the one-gene Mendelian ratio. However, marker analysis indicated that only one recessive gene conferred the resistance, which co-segregated with Xsts-bcd1231 that showed co-segregation with Pm4a in different studies. Allelism test indicated that this recessive resistance gene, designated as pmX, is either allelic or tightly linked to Pm4a. The pmX gene was different from Pm4 alleles in resistance spectrum. Examination of the genotype frequencies at pmX and the linked marker loci in the F2 population showed that a genetic variation favoring the transmission of Xiaohongpi alleles could be the cause of deviated segregation. Mapping of the pmX-linked markers using Chinese Spring deletion lines indicated that it resides in the 0.85-1.00 bin of chromosome 2AL.

Isolation of a wheat (Triticum aestivum L.) mutant in ABA 8'-hydroxylase gene: effect of reduced ABA catabolism on germination inhibition under field condition

Pre-harvest sprouting, the germination of mature seeds on the mother plant under moist condition, is a serious problem in cereals. To investigate the effect of reduced abscisic acid (ABA) catabolism on germination in hexaploid wheat (Triticum aestivum L.), we cloned the wheat ABA 8'-hydroxyase gene which was highly expressed during seed development (TaABA8'OH1) and screened for mutations that lead to reduced ABA catabolism. In a screen for natural variation, one insertion mutation in exon 5 of TaABA8'OH1 on the D genome (TaABA8'OH1-D) was identified in Japanese cultivars including 'Tamaizumi'. However, a single mutation in TaABA8'OH1-D had no clear effect on germination inhibition in double haploid lines. In a screen for a mutation, one deletion mutant lacking the entire TaABA8'OH1 on the A genome (TaABA8'OH1-A), TM1833, was identified from gamma-ray irradiation lines of 'Tamaizumi'. TM1833 (a double mutant in TaABA8'OH1-A and TaABA8'OH1-D) showed lower TaABA8'OH1 expression, higher ABA content in embryos during seed development under field condition and lower germination than those in 'Tamaizumi' (a single mutant in TaABA8'OH1-D). These results indicate that reduced ABA catabolism through mutations in TaABA8'OH1 may be effective in germination inhibition in field-grown wheat.

Development of a multiple bulked segregant analysis (MBSA) method used to locate a new stem rust resistance gene (Sr54) in the winter wheat cultivar Norin 40

An important aspect of studying putative new genes in wheat is determining their position on the wheat genetic map. The primary difficulty in mapping genes is determining which chromosome carries the gene of interest. Several approaches have been developed to address this problem, each with advantages and disadvantages. Here we describe a new approach called multiple bulked segregant analysis (MBSA). A set of 423 simple sequence repeat (SSR) markers were selected based on profile simplicity, frequency of polymorphism, and distribution across the wheat genome. SSR primers were preloaded in 384-well PCR plates with each primer occupying 16 wells. In practice, 14 wells are reserved for "mini-bulks" that are equivalent to four gametes (e.g. two F(2) individuals) comprised of individuals from a segregated population that have a known homozygous genotype for the gene of interest. The remaining two wells are reserved for the parents of the population. Each well containing a mini-bulk can have one of three allele compositions for each SSR: only the allele from one parent, only the allele from the other parent, or both alleles. Simulation experiments were performed to determine the pattern of mini-bulk allele composition that would indicate putative linkage between the SSR in question and the gene of interest. As a test case, MBSA was employed to locate an unidentified stem rust resistance (Sr) gene in the winter wheat cultivar Norin 40. A doubled haploid (DH) population (n = 267) was produced from hybrids of the cross LMPG-6S/Norin 40. The DH population segregated for a single gene (χ (1:1) (2) = 0.093, p = 0.76) for resistance to Puccinia graminis f.sp. tritici race LCBN. Four resistant DH lines were included in each of the 14 mini-bulks for screening. The Sr gene was successfully located to the long arm of chromosome 2D using MBSA. Further mapping confirmed the chromosome location and revealed that the Sr gene was located in a linkage block that may represent an alien translocation. The new Sr gene was designated as Sr54.

SnTox5-Snn5: a novel Stagonospora nodorum effector-wheat gene interaction and its relationship with the SnToxA-Tsn1 and SnTox3-Snn3-B1 interactions

The Stagonospora nodorum-wheat interaction involves multiple pathogen-produced necrotrophic effectors that interact directly or indirectly with specific host gene products to induce the disease Stagonospora nodorum blotch (SNB). Here, we used a tetraploid wheat mapping population to identify and characterize a sixth effector-host gene interaction in the wheat-S. nodorum system. Initial characterization of the effector SnTox5 indicated that it is a proteinaceous necrotrophic effector that induces necrosis on host lines harbouring the Snn5 sensitivity gene, which was mapped to the long arm of wheat chromosome 4B. On the basis of ultrafiltration, SnTox5 is probably in the size range 10-30 kDa. Analysis of SNB development in the mapping population indicated that the SnTox5-Snn5 interaction explains 37%-63% of the variation, demonstrating that this interaction plays a significant role in disease development. When the SnTox5-Snn5 and SnToxA-Tsn1 interactions occurred together, the level of SNB was increased significantly. Similar to several other interactions in this system, the SnTox5-Snn5 interaction is light dependent, suggesting that multiple interactions may exploit the same pathways to cause disease.

A high-density consensus map of A and B wheat genomes

A durum wheat consensus linkage map was developed by combining segregation data from six mapping populations. All of the crosses were derived from durum wheat cultivars, except for one accession of T. ssp. dicoccoides. The consensus map was composed of 1,898 loci arranged into 27 linkage groups covering all 14 chromosomes. The length of the integrated map and the average marker distance were 3,058.6 and 1.6 cM, respectively. The order of the loci was generally in agreement with respect to the individual maps and with previously published maps. When the consensus map was aligned to the deletion bin map, 493 markers were assigned to specific bins. Segregation distortion was found across many durum wheat chromosomes, with a higher frequency for the B genome. This high-density consensus map allowed the scanning of the genome for chromosomal rearrangements occurring during the wheat evolution. Translocations and inversions that were already known in literature were confirmed, and new putative rearrangements are proposed. The consensus map herein described provides a more complete coverage of the durum wheat genome compared with previously developed maps. It also represents a step forward in durum wheat genomics and an essential tool for further research and studies on evolution of the wheat genome.

Endosperm tolerance of paternal aneuploidy allows radiation hybrid mapping of the wheat D-genome and a measure of γ ray-induced chromosome breaks

Physical mapping and genome sequencing are underway for the ≈17 Gb wheat genome. Physical mapping methods independent of meiotic recombination, such as radiation hybrid (RH) mapping, will aid precise anchoring of BAC contigs in the large regions of suppressed recombination in Triticeae genomes. Reports of endosperm development following pollination with irradiated pollen at dosages that cause embryo abortion prompted us to investigate endosperm as a potential source of RH mapping germplasm. Here, we report a novel approach to construct RH based physical maps of all seven D-genome chromosomes of the hexaploid wheat ‘Chinese Spring’, simultaneously. An 81-member subset of endosperm samples derived from 20-Gy irradiated pollen was genotyped for deletions, and 737 markers were mapped on seven D-genome chromosomes. Analysis of well-defined regions of six chromosomes suggested a map resolution of ∼830 kb could be achieved; this estimate was validated with assays of markers from a sequenced contig. We estimate that the panel contains ∼6,000 deletion bins for D-genome chromosomes and will require ∼18,000 markers for high resolution mapping. Map-based deletion estimates revealed a majority of 1–20 Mb interstitial deletions suggesting mutagenic repair of double-strand breaks in pollen provides a useful resource for RH mapping and map based cloning studies.

Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii

BACKGROUND

Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported.

RESULTS

Radiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB), to produce pentaploid RH1s (AABBD), which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH1 plants was obtained, of which 592 plants were generated from the mature RH1 seeds, and 918 plants were rescued through embryo culture due to poor germination (<3%) of mature RH1 seeds. This panel showed a homogenous marker loss (2.1%) after screening with SSR markers uniformly covering all the D-genome chromosomes. Different marker systems mostly detected different lines with deletions. Using markers covering known distances, the mapping resolution of this RH panel was estimated to be <140kb. Analysis of only 16 RH lines carrying deletions on chromosome 2D resulted in a physical map with cM/cR ratio of 1:5.2 and 15 distinct bins. Additionally, with this small set of lines, almost all the tested ESTs could be mapped. A set of 399 most informative RH lines with an average deletion frequency of ~10% were identified for developing high density marker scaffolds of the D-genome.

CONCLUSIONS

The RH panel reported here is the first developed for any wild ancestor of a major cultivated plant species. The results provided insight into various aspects of RH mapping in plants, including the genetically effective cell number for wheat (for the first time) and the potential implementation of this technique in other plant species. This RH panel will be an invaluable resource for mapping gene based markers, developing a complete marker scaffold for the whole genome sequence assembly, fine mapping of markers and functional characterization of genes and gene networks present on the D-genome.

Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii

BACKGROUND

Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported.

RESULTS

Radiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB), to produce pentaploid RH1s (AABBD), which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH1 plants was obtained, of which 592 plants were generated from the mature RH1 seeds, and 918 plants were rescued through embryo culture due to poor germination (<3%) of mature RH1 seeds. This panel showed a homogenous marker loss (2.1%) after screening with SSR markers uniformly covering all the D-genome chromosomes. Different marker systems mostly detected different lines with deletions. Using markers covering known distances, the mapping resolution of this RH panel was estimated to be <140kb. Analysis of only 16 RH lines carrying deletions on chromosome 2D resulted in a physical map with cM/cR ratio of 1:5.2 and 15 distinct bins. Additionally, with this small set of lines, almost all the tested ESTs could be mapped. A set of 399 most informative RH lines with an average deletion frequency of ~10% were identified for developing high density marker scaffolds of the D-genome.

CONCLUSIONS

The RH panel reported here is the first developed for any wild ancestor of a major cultivated plant species. The results provided insight into various aspects of RH mapping in plants, including the genetically effective cell number for wheat (for the first time) and the potential implementation of this technique in other plant species. This RH panel will be an invaluable resource for mapping gene based markers, developing a complete marker scaffold for the whole genome sequence assembly, fine mapping of markers and functional characterization of genes and gene networks present on the D-genome.

Hordeum chilense genome, a useful tool to investigate the endosperm yellow pigment content in the Triticeae

BACKGROUND

The wild barley Hordeum chilense fulfills some requirements for being a useful tool to investigate the endosperm yellow pigment content (YPC) in the Triticeae including its diploid constitution, the availability of genetic resources (addition and deletion stocks and a high density genetic map) and, especially, its high seed YPC not silenced in tritordeums (amphiploids derived from H. chilense and wheat). Thus, the aim of this work was to test the utility of the H. chilense genome for investigating the YPC in the Triticeae.

RESULTS

Twelve genes related to endosperm carotenoid content and/or YPC in grasses (Dxr, Hdr [synonym ispH], Ggpps1, Psy2, Psy3, Pds, Zds, e-Lcy, b-Lcy, Hyd3, Ccd1 and Ppo1) were identified, and mapped in H. chilense using rice genes to identify orthologs from barley, wheat, sorghum and maize. Macrocolinearity studies revealed that gene positions were in agreement in H. vulgare and H. chilense. Additionally, three main regions associated with YPC were identified in chromosomes 2Hch, 3Hch and 7Hch in H. chilense, the former being the most significant one.

CONCLUSIONS

The results obtained are consistent with previous findings in wheat and suggest that Ggpps1, Zds and Hyd3 on chromosome 2Hch may be considered candidate genes in wheat for further studies in YPC improvement. Considering the syntenic location of carotenoid genes in H. chilense, we have concluded that the Hch genome may constitute a valuable tool for YPC studies in the Triticeae.

Molecular mapping of a powdery mildew resistance gene in common wheat landrace Baihulu and its allelism with Pm24

Powdery mildew is one of the most devastating diseases of wheat in areas with cool and maritime climates. Chinese wheat landrace Baihulu confers a high level of resistance against a wide range of Blumeria graminis DC f. sp. tritici (Bgt) races, especially those currently prevailing in Shaanxi. The objectives of this study were to determine the chromosome bin location of the mlbhl gene from Baihulu and its allelism with Pm24. To investigate the inheritance of powdery mildew resistance and detect adjacent molecular markers, we constructed a segregating population of 301 F(2) plants and corresponding F(2:3) families derived from Baihulu/Shaanyou 225. Genetic analysis revealed that a single dominant gene was responsible for seedling stage powdery mildew resistance in Baihulu. A genetic map comprising Xgwm106, Xgwm337, Xgwm1675, Xgwm603, Xgwm789, Xbarc229, Xgpw4503, Xcfd72, Xcfd83, Xcfd59, Xcfd19, and mlbhl spanned 28.2 cM on chromosome 1D. Xgwm603/Xgwm789 and Xbarc229 were flanking markers tightly linked to mlbhl at genetic distances of 1.5 and 1.0 cM, respectively. The mlbhl locus was located in chromosome bin 1DS 0.59-1.00 delimited by the SSR markers Xgwm337 and Xbarc229. When tested with a differential array of 23 Bgt isolates Baihulu displayed a response pattern that was clearly distinguishable from that of Chiyacao and varieties or lines possessing documented Pm genes. Allelism analysis indicated that mlbhl is a new gene, either allelic or closely linked with Pm24. The new gene was designated Pm24b.

Proteomic analysis of albumins and globulins from wheat variety Chinese Spring and its fine deletion line 3BS-8

The relationship between chromosome deletion in wheat and protein expression were investigated using Chinese Spring and fine deletion line 3BS-8. Through 2-DE (2-D electrophoresis) analysis, no differentially expressed proteins (DEPs) were found in leaf samples; however, 47 DEPs showed at least two-fold abundance variation (p < 0.05) in matured wheat grains and 21 spots were identified by tandem MALDI-TOF/TOF-MS. Among the identified spots, four were cultivar-specific, including three (spots B15, B16, and B21) in Chinese Spring and one in 3BS-8 (spot B10). Among variety-different DEPs between Chinese Spring and 3BS-8, most spots showed a higher express profile in CS; only four spots showed up-regulated expression tendency in 3BS-8. An interesting observation was that more than half of the identified protein spots were involved in storage proteins, of which 11 spots were identified as globulins. According to these results, we can presume that the encoded genes of protein spots B15, B16, and B21 were located on the chromosome segment deleted in 3BS-8.

QTL mapping of adult-plant resistances to stripe rust and leaf rust in Chinese wheat cultivar Bainong 64

Stripe rust and leaf rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. and P. triticina, respectively, are devastating fungal diseases of common wheat (Triticum aestivum L.). Chinese wheat cultivar Bainong 64 has maintained acceptable adult-plant resistance (APR) to stripe rust, leaf rust and powdery mildew for more than 10 years. The aim of this study was to identify quantitative trait loci/locus (QTL) for resistance to the two rusts in a population of 179 doubled haploid (DH) lines derived from Bainong 64 × Jingshuang 16. The DH lines were planted in randomized complete blocks with three replicates at four locations. Stripe rust tests were conducted using a mixture of currently prevalent P. striiformis races, and leaf rust tests were performed with P. triticina race THTT. Leaf rust severities were scored two or three times, whereas maximum disease severities (MDS) were recorded for stripe rust. Using bulked segregant analysis (BSA) and simple sequence repeat (SSR) markers, five independent loci for APR to two rusts were detected. The QTL on chromosomes 1BL and 6BS contributed by Bainong 64 conferred resistance to both diseases. The loci identified on chromosomes 7AS and 4DL had minor effects on stripe rust response, whereas another locus, close to the centromere on chromosome 6BS, had a significant effect only on leaf rust response. The loci located on chromosomes 1BL and 4DL also had significant effects on powdery mildew response. These were located at the same positions as the Yr29/Lr46 and Yr46/Lr67 genes, respectively. The multiple disease resistance locus for APR on chromosome 6BS appears to be new. All three genes and their closely linked molecular markers could be used in breeding wheat cultivars with durable resistance to multiple diseases.

Microsatellite mutation rate during allohexaploidization of newly resynthesized wheat

Simple sequence repeats (SSRs, also known as microsatellites) are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and evolutionary dynamics of SSRs in allopolyploids. Three synthesized double haploid (SynDH) populations were made from 241 interspecific F(1 )haploid hybrids between Triticum turgidum L. and Aegilops tauschii (Coss.) through spontaneous chromosome doubling via unreduced gametes. Mutation events were studied at 160 SSR loci in the S(1) generation (the first generation after chromosome doubling) of the three SynDH populations. Of the 148260 SSR alleles investigated in S(1) generation, only one mutation (changed number of repeats) was confirmed with a mutation rate of 6.74 × 10-6. This mutation most likely occurred in the respective F(1) hybrid. In comparison with previously reported data, our results suggested that allohexaploidization of wheat did not increase SSR mutation rate.

QTL mapping of adult-plant resistance to stripe rust in a population derived from common wheat cultivars Naxos and Shanghai 3/Catbird

Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is a severe foliar disease of common wheat (Triticum aestivum L.) worldwide. Use of adult-plant resistance (APR) is an efficient approach to provide long-term protection of crops from the disease. The German spring wheat cultivar Naxos showed a high level of APR to stripe rust in the field. To identify the APR genes in this cultivar, a mapping population of 166 recombinant inbred lines (RILs) was developed from a cross between Naxos and Shanghai 3/Catbird (SHA3/CBRD), a moderately susceptible line developed by CIMMYT. The RILs were evaluated for maximum disease severity (MDS) in Sichuan and Gansu in the 2009-2010 and 2010-2011 cropping seasons. Composite interval mapping (CIM) identified four QTL, QYr.caas-1BL.1RS, QYr.caas-1DS, QYr.caas-5BL.3 and QYr.caas-7BL.1, conferring stable resistance to stripe rust across all environments, each explaining 1.9-27.6, 2.1-5.8, 2.5-7.8 and 3.7-9.1 % of the phenotypic variance, respectively. QYr.caas-1DS flanked by molecular markers XUgwm353-Xgdm33b was likely a new QTL for APR to stripe rust. Because the interval between flanking markers for each QTL was less than 6.5 cM, these QTL and their closely linked markers are potentially useful for improving resistance to stripe rust in wheat breeding.

Genetic analysis and molecular mapping of a new powdery mildew resistant gene Pm46 in common wheat

Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici (Bgt), has become a serious disease and caused severe yield losses in the wheat production worldwide. Resistance gene(s) in wheat cultivars can be quickly overcome by newly evolved pathogen races when these genes are employed for long time or in a large area. It is urgent to search for new sources of resistance to be used in wheat breeding. Tabasco is a German resistant cultivar and a new source of resistance gene(s) to PM. An F(2) population was developed from a cross between Tabasco and a Chinese susceptible cultivar Ningnuo 1. Infection types in 472 F(2) plants and 436 F(2-3) families were evaluated by inoculating plants with isolate Bgt19. Results showed that a single dominant gene, designed Pm46, controlled powdery mildew resistance in Tabasco. This gene was located to the short arm of chromosome 5D (5DS) and flanked by simple sequence repeat markers Xgwm205 and Xcfd81 at 18.9 cM apart. Because another resistance gene Pm2 was also located on 5DS, 15 Bgt isolates were used to inoculate Tabasco and Ulka/8*Cc (Pm2 carrier). The results showed that Tabasco was highly resistant to all of the 15 isolates tested, while Ulka/8*Cc was susceptible to 4 of the isolates, suggesting that Tabasco may carry resistant gene(s) different from Pm2 gene in Ulka/8*Cc. To test the allelism between Pm46 and Pm2, an F(2) population between Tabasco and Ulka/8*Cc was developed. Isolate Bgt2, avirulent to both parents, was used to evaluate the F(2) population and two susceptible plants were identified from 536 progenies with F(2) plants. This result indicated that Pm46 is not allelic to Pm2. Therefore, Pm46 is a new gene for PM resistance identified in this study.

Molecular mapping of stripe rust resistance gene YrSN104 in Chinese wheat line Shaannong 104

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a serious yield-limiting factor for wheat production worldwide. The objective of this study was to identify and map a stripe rust resistance gene in wheat line Shaannong 104 using SSR markers. F(1), F(2) and F(3) populations from Shaannong 104/Mingxian 169 were inoculated with Chinese Pst race CYR32 in a greenhouse. Shaannong 104 carried a single dominant gene, YrSN104. Six potential polymorphic SSR markers identified in bulk segregant analysis were used to genotype F(2) and F(3) families. YrSN104 was closely linked with all six SSR markers on chromosome 1BS with genetic distances of 2.0 cM (Xgwm18, Xgwm273, Xbarc187), 2.6 cM (Xgwm11, Xbarc137) and 5.9 cM (Xbarc240). Pedigree analysis, pathogenicity tests using 26 Pst races, haplotyping of associated markers on isogenic lines carrying known stripe rust resistance genes, and associations with markers suggested that YrSN104 was a new resistance gene or an allele at the Yr24/Yr26 locus on chromosome 1BS. Deployment of YrSN104 singly or in combination to elite genotypes could play an effective role to lessen yield losses caused by stripe rust.

Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome

Background

A synthetic doubled-haploid hexaploid wheat population, SynDH1, derived from the spontaneous chromosome doubling of triploid F₁ hybrid plants obtained from the cross of hybrids Triticum turgidum ssp. durum line Langdon (LDN) and ssp. turgidum line AS313, with Aegilops tauschii ssp. tauschii accession AS60, was previously constructed. SynDH1 is a tetraploidization-hexaploid doubled haploid (DH) population because it contains recombinant A and B chromosomes from two different T. turgidum genotypes, while all the D chromosomes from Ae. tauschii are homogenous across the whole population. This paper reports the construction of a genetic map using this population.

Results

Of the 606 markers used to assemble the genetic map, 588 (97%) were assigned to linkage groups. These included 513 Diversity Arrays Technology (DArT) markers, 72 simple sequence repeat (SSR), one insertion site-based polymorphism (ISBP), and two high-molecular-weight glutenin subunit (HMW-GS) markers. These markers were assigned to the 14 chromosomes, covering 2048.79 cM, with a mean distance of 3.48 cM between adjacent markers. This map showed good coverage of the A and B genome chromosomes, apart from 3A, 5A, 6A, and 4B. Compared with previously reported maps, most shared markers showed highly consistent orders. This map was successfully used to identify five quantitative trait loci (QTL), including two for spikelet number on chromosomes 7A and 5B, two for spike length on 7A and 3B, and one for 1000-grain weight on 4B. However, differences in crossability QTL between the two T. turgidum parents may explain the segregation distortion regions on chromosomes 1A, 3B, and 6B.

Conclusions

A genetic map of T. turgidum including 588 markers was constructed using a synthetic doubled haploid (SynDH) hexaploid wheat population. Five QTLs for three agronomic traits were identified from this population. However, more markers are needed to increase the density and resolution of this map in the future study.

QTL mapping of terminal heat tolerance in hexaploid wheat (T. aestivum L.)

High temperature (>30 °C) at the time of grain filling is one of the major causes of yield reduction in wheat in many parts of the world, especially in tropical countries. To identify quantitative trait loci (QTL) for heat tolerance under terminal heat stress, a set of 148 recombinant inbred lines was developed by crossing a heat-tolerant hexaploid wheat (Triticum aestivum L.) cultivar (NW1014) and a heat-susceptible (HUW468) cultivar. The F(5), F(6), and F(7) generations were evaluated in two different sowing dates under field conditions for 2 years. Using the trait values from controlled and stressed trials, four different traits (1) heat susceptibility index (HSI) of thousand grain weight (HSITGW); (2) HSI of grain fill duration (HSIGFD); (3) HSI of grain yield (HSIYLD); and (4) canopy temperature depression (CTD) were used to determine heat tolerance. Days to maturity was also investigated. A linkage map comprising 160 simple sequence repeat markers was prepared covering the whole genome of wheat. Using composite interval mapping, significant genomic regions on 2B, 7B and 7D were found to be associated with heat tolerance. Of these, two (2B and 7B) were co-localized QTL and explained more than 15 % phenotypic variation for HSITGW, HSIGFD and CTD. In pooled analysis over three trials, QTL explained phenotypic variation ranging from 9.78 to 20.34 %. No QTL × trial interaction was detected for the identified QTL. The three major QTL obtained can be used in marker-assisted selection for heat stress in wheat.

Association mapping for pre-harvest sprouting resistance in white winter wheat

Association mapping identified quantitative trait loci (QTLs) and the markers linked to pre-harvest sprouting (PHS) resistance in an elite association mapping panel of white winter wheat comprising 198 genotypes. A total of 1,166 marker loci including DArT and SSR markers representing all 21 chromosomes of wheat were used in the analysis. General and mixed linear models were used to analyze PHS data collected over 4 years. Association analysis identified eight QTLs linked with 13 markers mapped on seven chromosomes. A QTL was detected on each arm of chromosome 2B and one each on chromosome arms 1BS, 2DS, 4AL, 6DL, 7BS and 7DS. All except the QTL on 7BS are located in a location similar to previous reports and, if verified, the QTL on 7BS is likely to be novel. Principal components and the kinship matrix were used to account for the presence of population structure but had only a minor effect on the results. Although, none of the QTLs was highly significant across all environments, a QTL on the long arm of chromosome 4A was detected in three different environments and also using the best linear unbiased predictions over years. Although previous reports have identified this as a major QTL, its effects were minor in our biparental mapping populations. The results of this study highlight the benefits of association mapping and the value of using elite material in association mapping for plant breeding programs.

Inheritance of resistance to Ug99 stem rust in wheat cultivar Norin 40 and genetic mapping of Sr42

Stem rust, caused by Puccinia graminis f. sp. tritici, is a devastating disease of wheat. The emergence of race TTKSK (Ug99) and new variants in Africa threatens wheat production worldwide. The best method of controlling stem rust is to deploy effective resistance genes in wheat cultivars. Few stem rust resistance (Sr) genes derived from the primary gene pool of wheat confer resistance to TTKSK. Norin 40, which carries Sr42, is resistant to TTKSK and variants TTKST and TTTSK. The goal of this study was to elucidate the inheritance of resistance to Ug99 in Norin 40 and map the Sr gene(s). A doubled haploid (DH) population of LMPG-6/Norin 40 was evaluated for resistance to the race TTKST. Segregation of 248 DH lines fitted a 1:1 ratio (χ (2) 1:1= 0.58, p = 0.45), indicating a single gene in Norin 40 conditioned resistance to Ug99. This was confirmed by an independent F(2:3) population also derived from the cross LMPG-6/Norin 40 where a 1:2:1 ratio (χ (2)1:2:1 = 0.69, p = 0.71) was observed following the inoculation with race TTKSK. Mapping with DNA markers located this gene to chromosome 6DS, the known location of Sr42. PCR marker FSD_RSA co-segregated with Sr42, and simple sequence repeat (SSR) marker BARC183 was closely linked (0.5 cM) to Sr42. A previous study found close linkage between FSD_RSA and SrCad, a temporarily designated gene that also confers resistance to Ug99, thus Sr42 may be the same gene or allelic. Marker FSD_RSA is suitable for marker-assisted selection (MAS) in wheat breeding programs to improve stem rust resistance, including Ug99.