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.
Abstract Developing oat cultivars with partial resistance to crown rust would be beneficial and cost-effective for disease management. Two recombinant inbred line populations were generated by crossing the susceptible cultivar 'Provena' with two partially resistant sources, 'CDC Boyer' and breeding line 94197A1-9-2-2-2-5. A third mapping population was generated by crossing the partially resistant sources to validate the QTL results. The three populations were evaluated for crown rust severity in the field at Louisiana State University (LSU) in 2009 and 2010 and at the Cereal Disease Laboratory (CDL) in St. Paul, Minnesota in 2009, 2010, and 2011. An iSelect platform assays containing 5744 oat single nucleotide polymorphisms was used to genotype the populations. From the 2009 CDL test, linkage analyses revealed two QTL for partial resistance in the Provena/CDC Boyer population on chromosome 19A. One of the 19A QTL was also detected in the 2009 LSU test. Another QTL was detected in on chromosome 12D in the CDL 2009 test. In the Provena/94197A1-9-2-2-2-5 population, only one QTL was detected on chromosome 13A in the CDL 2011 test. The 13A QTL from the Provena/94197A1-9-2-2-2-5 population was validated in CDC Boyer /94197A1-9-2-2-2-5 population in the CDL 2010 and 2011 tests. Comparative analysis of the significant markers sequences with the rice genome database revealed 15 candidate genes for disease resistance on chromosomes 4 and 6 of rice. These genes could be potential targets for cloning from the two resistant parents.
Barley net form net blotch (NFNB), caused by the necrotrophic fungus Pyrenophora teres f. teres, is a destructive foliar disease in barley-growing regions worldwide. Little is known about the genetic and molecular basis of this pathosystem. Here, we identified a small secreted proteinaceous necrotrophic effector (NE), designated PttNE1, from intercellular wash fluids of the susceptible barley line Hector after inoculation with P.?teres f. teres isolate 0-1. Using a barley recombinant inbred line (RIL) population developed from a cross between the sensitive/susceptible line Hector and the insensitive/resistant line NDB 112 (HN population), sensitivity to PttNE1, which we have named SPN1, mapped to a common resistance/susceptibility region on barley chromosome 6H. PttNE1-SPN1 interaction accounted for 31% of the disease variation when the HN population was inoculated with the 0-1 isolate. Strong accumulation of hydrogen peroxide and increased levels of electrolyte leakage were associated with the susceptible reaction, but not the resistant reaction. In addition, the HN RIL population was evaluated for its reactions to 10 geographically diverse P.?teres f. teres isolates. Quantitative trait locus (QTL) mapping led to the identification of at least 10 genomic regions associated with disease, with chromosomes 3H and 6H harbouring major QTLs for resistance/susceptibility. SPN1 was associated with all the 6H QTLs, except one. Collectively, this information indicates that the barley-P.?teres f. teres pathosystem follows, at least partially, an NE-triggered susceptibility (NETS) model that has been described in other necrotrophic fungal disease systems, especially in the Dothideomycete class of fungi.
The domestication of wheat was instrumental in spawning the civilization of humankind, and it occurred through genetic mutations that gave rise to types with non-fragile rachises, soft glumes, and free-threshing seed. Wild emmer (Triticum turgidum ssp. dicoccoides), the tetraploid AB-genome progenitor of domesticated wheat has genes that confer tenacious glumes (Tg) that underwent genetic mutations to give rise to free-threshing wheat. Here, we evaluated disomic substitution lines involving chromosomes 2A and 2B of wild emmer accessions substituted for homologous chromosomes in tetraploid and hexaploid backgrounds. The results suggested that both chromosomes 2A and 2B of wild emmer possess genes that inhibit threshability. A population of recombinant inbred lines derived from the tetraploid durum wheat variety Langdon crossed with a Langdon - T. turgidum ssp. dicoccoides accession PI 481521 chromosome 2B disomic substitution line was used to develop a genetic linkage map of 2B, evaluate the genetics of threshability, and map the gene derived from PI 481521 that inhibited threshability. A 2BS linkage map comprised of 58 markers was developed, and markers delineated the gene to a 2.3 cM interval. Comparative analysis with maps containing the tenacious glume gene Tg-D1 on chromosome arm 2 DS from Aegilops tauschii, the D genome progenitor of hexaploid wheat, revealed that the gene inhibiting threshability in wild emmer was homoeologous to Tg-D1 and therefore designated Tg-B1. Comparative analysis with rice and Brachypodium distachyon indicated a high level of divergence and poorly conserved colinearity, particularly near the Tg-B1 locus. These results provide a foundation for further studies involving Tg-B1, which, together with Tg-D1, had profound influences on wheat domestication.
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.
High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.
Using association and linkage mapping, two SNP markers closely linked to the SBWMV resistance gene on chromosome 5D were identified and can be used to select the gene in breeding. Soil-borne wheat mosaic virus (SBWMV) disease is a serious viral disease of winter wheat growing areas worldwide. SBWMV infection can significantly reduce grain yield up to 80 %. Developing resistant wheat cultivars is the only feasible strategy to reduce the losses. In this study, wheat Infinium iSelect Beadchips with 9 K wheat SNPs were used to genotype an association mapping population of 205 wheat accessions. Six new SNPs from two genes were identified to be significantly associated with the gene for SBWMV resistance on chromosome 5D. The SNPs and Xgwm469, an SSR marker that has been reported to be associated with the gene, were mapped close to the gene using F6-derived recombinant inbred lines from the cross between a resistant parent 'Heyne' and a susceptible parent 'Trego'. Two representative SNPs, wsnp_CAP11_c209_198467 and wsnp_JD_c4438_5568170, from the two linked genes in wheat were converted into KBioscience Competitive Allele-Specific Polymerase assays and can be easily used in marker-assisted selection to improve wheat resistance to SBWMV in breeding.
Wheat stem rust resistance gene SrWeb is an allele at the Sr9 locus that confers resistance to Ug99. Race TTKSK (Ug99) of Puccinia graminis f. sp. tritici, the causal fungus of stem rust, threatens global wheat production because of its broad virulence to current wheat cultivars. A recently identified Ug99 resistance gene from cultivar Webster, temporarily designated as SrWeb, mapped near the stem rust resistance gene locus Sr9. We determined that SrWeb is also present in Ug99 resistant cultivar Gabo 56 by comparative mapping and an allelism test. Analysis of resistance in a population segregating for both Sr9e and SrWeb demonstrated that SrWeb is an allele at the Sr9 locus, which subsequently was designated as Sr9h. Webster and Gabo 56 were susceptible to the Ug99-related race TTKSF+ from South Africa. Race TTKSF+ possesses unique virulence to uncharacterized Ug99 resistance in cultivar Matlabas. This result validated that resistance to Ug99 in Webster and Gabo 56 is conferred by the same gene: Sr9h. The emergence of pathogen virulence to several resistance genes that are effective to the original Ug99 race TTKSK, including Sr9h, suggests that resistance genes should be used in combinations in order to increase resistance durability.
New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections.
Hessian fly (HF), Mayetiola destructor, is an important pest of wheat (Triticum aestivum L.) worldwide. Because it has multiple biotypes that are virulent to different wheat HF resistance genes, pyramiding multiple resistance genes in a cultivar can improve resistance durability, and finding DNA markers tightly linked to these genes is essential to this process. This study identified quantitative trait loci (QTLs) for Hessian fly resistance (HFR) in the wheat cultivar Clark and tightly linked DNA markers for the QTLs. A linkage map was constructed with single nucleotide polymorphism and simple sequence repeat markers using a population of recombinant inbred lines (RILs) derived from the cross Ning7840 × Clark by single-seed descent. Two QTLs associated with resistance to fly biotype GP were identified on chromosomes 6B and 1A, with the resistance alleles contributed from Clark. The QTL on 6B flanked by loci Xsnp921 and Xsnp2745 explained about 37.2 % of the phenotypic variation, and the QTL on 1A was flanked by Xgwm33 and Xsnp5150 and accounted for 13.3 % of phenotypic variation for HFR. The QTL on 6B has not been reported before and represents a novel wheat gene with resistance to HF, thus, it is designated H34. A significant positive epistasis was detected between the two QTLs that accounted for about 9.5 % of the mean phenotypic variation and increased HFR by 0.16. Our results indicated that different QTLs may contribute different degrees of resistance in a cultivar and that epistasis may play an important role in HFR.
This is the first report on genetic analysis and genome mapping of major dominant genes for near non-host resistance to barley crown rust ( Puccinia coronata var. hordei ) in common wheat. Barley crown rust, caused by Puccinia coronata var. hordei, primarily occurs on barley (Hordeum vulgare L.) in the Great Plain regions of the United States. However, a few genotypes of common wheat (Triticum aestivum L.) were susceptible to this pathogen among 750 wheat accessions evaluated. To investigate the genetics of crown rust resistance in wheat, a susceptible winter wheat accession PI 350005 was used in crosses with two resistant wheat varieties, Chinese Spring and Chris. Analysis of F1 plants and F2 populations from these two crosses indicated that crown rust resistance is controlled by one and two dominant genes in Chris and Chinese Spring, respectively. To determine the chromosome location of the resistance gene Cr1 in Chris, a set of 21 monosomic lines derived from Chris was used as female parents to cross with a susceptible spring type selection (SSTS35) derived from the PI 350005/Chris cross. Monosomic analysis indicated that Cr1 is located on chromosome 5D in Chris and one of the crown rust resistance genes is located on chromosome 2D in Chinese Spring. The other gene in Chinese Spring is not on 5D and thus is different from Cr1. Molecular linkage analysis and QTL mapping using a population of 136 doubled haploid lines derived from Chris/PI 350005 further positioned Cr1 between SSR markers Xwmc41-2 and Xgdm63 located on the long arm of chromosome 5D. Our study suggests that near non-host resistance to crown rust in these different common wheat genotypes is simply inherited.
Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat.
A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n?=?6x?=?42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.
Reference populations are valuable resources in genetics studies for determining marker order, marker selection, trait mapping, construction of large-insert libraries, cross-referencing marker platforms, and genome sequencing. Reference populations can be propagated indefinitely, they are polymorphic and have normal segregation. Described are two new reference populations who share the same parents of the original wheat reference population Synthetic W7984 (Altar84/ Aegilops tauschii (219) CIGM86.940) x Opata M85, an F(1)-derived doubled haploid population (SynOpDH) of 215 inbred lines and a recombinant inbred population (SynOpRIL) of 2039 F(6) lines derived by single-plant self-pollinations. A linkage map was constructed for the SynOpDH population using 1446 markers. In addition, a core set of 42 SSR markers was genotyped on SynOpRIL. A new approach to identifying a core set of markers used a step-wise selection protocol based on polymorphism, uniform chromosome distribution, and reliability to create nested sets starting with one marker per chromosome, followed by two, four, and six. It is suggested that researchers use these markers as anchors for all future mapping projects to facilitate cross-referencing markers and chromosome locations. To enhance this public resource, researchers are strongly urged to validate line identities and deposit their data in GrainGenes so that others can benefit from the accumulated information.
Fusarium head blight (FHB) is a devastating disease of wheat worldwide. Novel sources of resistance are critical for improving FHB resistance levels in wheat. From a large-scale evaluation of germplasm for reactions to FHB, we identified one wheat accession (PI 277012) that consistently showed a high level of resistance in both greenhouse and field experiments. To characterize the FHB resistance in this accession, we developed a doubled haploid (DH) mapping population consisting of 130 lines from the cross between PI 277012 and the hard red spring wheat cultivar Grandin. The DH population was then evaluated for reactions to FHB in three greenhouse seasons and five field environments. Based on a linkage map that consisted of 340 SSR markers spanning 2,703 cM of genetic distance, two major quantitative trait loci (QTLs) for FHB resistance were identified on chromosome arms 5AS and 5AL, with each explaining up to 20 and 32% of the variation in FHB severity, respectively. The two QTLs also showed major effects on reducing the percentage of Fusarium damaged kernels (FDK) and deoxynivalenol (DON) accumulation in seeds. FHB resistance has not previously been reported to be associated with this particular genomic region of chromosome arm 5AL, thus indicating the novelty of FHB resistance in PI 277012. Plant maturity was not associated with FHB resistance and the effects of plant height on FHB resistance were minor. Therefore, these results suggest that PI 277012 is an excellent source for improving FHB resistance in wheat. The markers identified in this research are being used for marker-assisted introgression of the QTLs into adapted durum and hard red spring wheat cultivars.
Wheat end product quality is determined by a complex group of traits including dough viscoelastic characteristics and bread-making properties. Quantitative trait loci (QTL) mapping and analysis were conducted for endosperm texture, dough-mixing strength, and bread-making properties in a population of 139 (MN99394 × MN98550) recombinant inbred lines that were evaluated at three environments in 2006. Based on the genetic map of 534 loci, six QTL were identified for endosperm texture, with the main QTL on chromosomes 1A (R(2) = 6.6%-17.3%), 5A (R(2) = 6.1%-17.1%), and 5D (R(2) = 15.8%-22%). Thirty-four QTL were identified for eight dough-mixing strength and bread-making properties. Major QTL clusters were associated with the low-molecular weight glutenin gene Glu-A3, the two high-molecular weight glutenin genes Glu-B1 and Glu-D1, and two regions on chromosome 6D. Alleles at these QTL clusters have previously been proven useful for wheat quality, except one of the QTL clusters on chromosome 6D. A QTL cluster on chromosome 6D is one of the novel chromosome regions influencing dough-mixing strength and bread-making properties. The QTL for endosperm texture on chromosomes 1A, 5A, and 5B also influenced flour ash content (12.4%-23.3%), flour protein content (10.5%-12.5%), and flour colour (7.7%-13.5%), respectively.
A mapping population of 186 recombinant inbred lines developed from a cross between UC1110, an adapted California spring wheat, and PI610750, a synthetic derivative from CIMMYTs Wide Cross Program, was evaluated for its response to current California races of stripe rust (Puccinia striiformis f. sp. tritici) in replicated field trials over four seasons (2007-2010) in the northern Sacramento Valley. A genetic map was constructed consisting of 1,494 polymorphic probes (SSRs, DArTs, and ESTs) mapped to 558 unique loci, and QTL analysis revealed the presence of four stripe rust resistance QTL segregating in this population, two from UC1110 (on chromosomes 3BS and 2BS) and two from PI610750 (5AL and 2AS). The two QTL of largest effects (on 3BS and 5AL) were validated in independent populations and their intervals narrowed to 2.5 and 5.3 cM, respectively. The 3BS QTL was shown, by allelism test and genotype, to carry a gene different from the Yr30/Sr2 complex. Mapped position also suggests that the 3BS QTL is associated with a gene different from either Yrns-B1 or YrRub, two stripe rust resistance genes mapped to this region in other studies. The 5AL QTL carries a previously unreported partial stripe rust resistance gene, designated here as Yr48. This paper discusses the individual contributions to resistance of these four QTL, their epistatic interactions, and their potential in durable resistance breeding strategies based on combinations of partial resistance genes.
Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat.
Chromosome engineering is a useful strategy for transfer of alien genes from wild relatives into modern crops. However, this strategy has not been extensively used for alien gene introgression in most crops due to low efficiency of conventional cytogenetic techniques. Here, we report an improved scheme of chromosome engineering for efficient elimination of a large amount of goatgrass (Aegilops speltoides) chromatin surrounding Sr39, a gene that provides resistance to multiple stem rust races, including Ug99 (TTKSK) in wheat. The wheat ph1b mutation, which promotes meiotic pairing between homoeologous chromosomes, was employed to induce recombination between wheat chromosome 2B and goatgrass 2S chromatin using a backcross scheme favorable for inducing and detecting the homoeologous recombinants with small goatgrass chromosome segments. Forty recombinants with Sr39 with reduced surrounding goatgrass chromatin were quickly identified from 1048 backcross progenies through disease screening and molecular marker analysis. Four of the recombinants carrying Sr39 with a minimal amount of goatgrass chromatin (2.87-9.15% of the translocated chromosomes) were verified using genomic in situ hybridization. Approximately 97% of the goatgrass chromatin was eliminated in one of the recombinants, in which a tiny goatgrass chromosome segment containing Sr39 was retained in the wheat genome. Localization of the goatgrass chromatin in the recombinants led to rapid development of three molecular markers tightly linked to Sr39. The new wheat lines and markers provide useful resources for the ongoing global effort to combat Ug99. This study has demonstrated great potential of chromosome engineering in genome manipulation for plant improvement.
Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico.
Advanced cycle breeding utilizes crosses among elite lines and is a successful method to develop new inbreds. However, it results in a reduction in genetic diversity within the breeding population. The development of malting barley varieties requires the adherence to a narrow malting quality profile and thus the use of advanced cycle breeding strategies. Although attention has been focused on diversity in gene expression and its association with genetic diversity, there are no studies performed in a single breeding program examining the implications that consecutive cycles of breeding have on gene expression variation and identifying the variability still available for future improvement.
Kernel characteristics, particularly kernel weight, kernel size, and grain protein content, are important components of grain yield and quality in wheat. Development of high performing wheat cultivars, with high grain yield and quality, is a major focus in wheat breeding programs worldwide. Here, we report chromosome regions harboring genes that influence kernel weight, kernel diameter, kernel size distribution, grain protein content, and grain yield in hard red spring wheat breeding lines adapted to the Upper Midwest region of the United States. A genetic linkage map composed of 531 SSR and DArT marker loci spanned a distance of 2,505 cM, covering all 21 chromosomes of wheat. Stable QTL clusters influencing kernel weight, kernel diameter, and kernel size distribution were identified on chromosomes 2A, 5B, and 7A. Phenotypic variation explained by individual QTL at these clusters varied from 5 to 20% depending on the trait. A QTL region on chromosome 2B confers an undesirable pleiotropic effect or a repulsion linkage between grain yield (LOD = 6.7; R (2) = 18%) and grain protein content (LOD = 6.2; R (2) = 13.3%). However, several grain protein and grain yield QTL independent of each other were also identified. Because some of the QTL identified in this study were consistent across environments, DNA markers will provide an opportunity for increasing the frequency of desirable alleles through marker-assisted selection.
Wheat stem rust caused by Puccinia graminis f. sp. tritici, can cause significant yield losses. To combat the disease, breeders have deployed resistance genes both individually and in combinations to increase resistance durability. A new race, TTKSK (Ug99), identified in Uganda in 1999 is virulent on most of the resistance genes currently deployed, and is rapidly spreading to other regions of the world. It is therefore important to identify, map, and deploy resistance genes that are still effective against TTKSK. One of these resistance genes, Sr13, was previously assigned to the long arm of chromosome 6A, but its precise map location was not known. In this study, the genome location of Sr13 was determined in four tetraploid wheat (T. turgidum ssp. durum) mapping populations involving the TTKSK resistant varieties Kronos, Kofa, Medora and Sceptre. Our results showed that resistance was linked to common molecular markers in all four populations, suggesting that these durum lines carry the same resistance gene. Based on its chromosome location and infection types against different races of stem rust, this gene is postulated to be Sr13. Sr13 was mapped within a 1.2-2.8 cM interval (depending on the mapping population) between EST markers CD926040 and BE471213, which corresponds to a 285-kb region in rice chromosome 2, and a 3.1-Mb region in Brachypodium chromosome 3. These maps will be the foundation for developing high-density maps, identifying diagnostic markers, and positional cloning of Sr13.
Spot blotch, caused by Cochliobolus sativus, is an important foliar disease of barley. The disease has been controlled for over 40 years through the deployment of cultivars with durable resistance derived from the line NDB112. Pathotypes of C. sativus with virulence for the NDB112 resistance have been detected in Canada; thus, many commercial cultivars are vulnerable to spot blotch epidemics. To increase the diversity of spot blotch resistance in cultivated barley, we evaluated 318 diverse wild barley accessions comprising the Wild Barley Diversity Collection (WBDC) for reaction to C. sativus at the seedling stage and utilized an association mapping (AM) approach to identify and map resistance loci. A high frequency of resistance was found in the WBDC as 95% (302/318) of the accessions exhibited low infection responses. The WBDC was genotyped with 558 Diversity Array Technology (DArT((R))) and 2,878 single nucleotide polymorphism (SNP) markers and subjected to structure analysis before running the AM procedure. Thirteen QTL for spot blotch resistance were identified with DArT and SNP markers. These QTL were found on chromosomes 1H, 2H, 3H, 5H, and 7H and explained from 2.3 to 3.9% of the phenotypic variance. Nearly half of the identified QTL mapped to chromosome bins where spot blotch resistance loci were previously reported, offering some validation for the AM approach. The other QTL mapped to unique genomic regions and may represent new spot blotch resistance loci. This study demonstrates that AM is an effective technique for identifying and mapping QTL for disease resistance in a wild crop progenitor. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-010-9402-8) contains supplementary material, which is available to authorized users.
High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource.
The wheat stem rust resistance gene Sr6, present in several wheat cultivars, confers a high level of resistance against a wide range of races of Puccinia graminis f. sp. tritici. Resistance conferred by Sr6 is influenced by temperature, light intensity, and genetic background of the recipient genotype. Here, we report the identification and validation of molecular markers linked to Sr6 that can be used for the detection of this gene in wheat breeding programs. A mapping population of 136 F2 plants and their F2:3 families derived from a cross between near-isogenic lines, Chinese Spring and ISr6-Ra, were screened for stem rust reaction in the seedling stage. Bulked segregant analysis (BSA) based on seedling tests was used to screen 418 SSR markers that covered the entire genome of wheat. Four markers, Xwmc453, Xcfd43, Xcfd77, and Xgwm484, were mapped within a chromosome region that spanned 9.7 cM from Sr6. The closest markers, Xwmc453 and Xcfd43, were linked to Sr6 at a distance of 1.1 and 1.5 cM, respectively. The markers Xwmc453 and Xcfd43 amplified Sr6-specific marker alleles that were diagnostic for Sr6 in a diverse set of 46 wheat accessions and breeding lines developed and/or collected in Australia, Canada, China, Egypt, Ethiopia, Kenya, Mexico, South Africa, and USA. These markers can now be used for marker-assisted selection of Sr6 and for pyramiding it with other stem rust resistance genes.
Genome-wide association studies (GWAS) provide an opportunity to examine the genetic architecture of quantitatively inherited traits in breeding populations. The objectives of this study were to use GWAS to identify chromosome regions governing traits of importance in six-rowed winter barley (Hordeum vulgare L.) germplasm and to identify single-nucleotide polymorphisms (SNPs) markers that can be implemented in a marker-assisted breeding program. Advanced hulled and hulless lines (329 total) were screened using 3,072 SNPs as a part of the US. Barley Coordinated Agricultural Project (CAP). Phenotypic data collected over 4 years for agronomic and food quality traits and resistance to leaf rust (caused by Puccinia hordei G. Otth), powdery mildew [caused by Blumeria graminis (DC.) E.O. Speer f. sp. hordei Em. Marchal], net blotch (caused by Pyrenophora teres), and spot blotch [caused by Cochliobolus sativus (Ito and Kuribayashi) Drechsler ex Dastur] were analyzed with SNP genotypic data in a GWAS to determine marker-trait associations. Significant SNPs associated with previously described quantitative trait loci (QTL) or genes were identified for heading date on chromosome 3H, test weight on 2H, yield on 7H, grain protein on 5H, polyphenol oxidase activity on 2H and resistance to leaf rust on 2H and 3H, powdery mildew on 1H, 2H and 4H, net blotch on 5H, and spot blotch on 7H. Novel QTL also were identified for agronomic, quality, and disease resistance traits. These SNP-trait associations provide the opportunity to directly select for QTL contributing to multiple traits in breeding programs.
The transfer of alien genes to crop plants using chromosome engineering has been attempted infrequently in tetraploid durum wheat (Triticum turgidum L. subsp. durum). Here, we report a highly efficient approach for the transfer of two genes conferring resistance to stem rust race Pgt-TTKSK (Ug99) from goatgrass (Aegilops speltoides) to tetraploid wheat. The durum line DAS15, carrying the stem rust resistance gene Sr47 derived from Ae. speltoides, was crossed, and backcrossed, to durum 5D(5B) aneuploids to induce homeologous pairing. After a final cross to Rusty durum, allosyndetic recombinants were recovered. The Ae. speltoides chromosomal segment carrying Sr47 was found to have two stem rust resistance genes. One gene conditioning an infection type (IT) 2 was located in the same chromosomal region of 2BS as Sr39 and was assigned the temporary gene symbol SrAes7t. Based on ITs observed on a diverse set of rust races, SrAes7t may be the same as Sr39. The second gene conditioned an IT 0; and was located on chromosome arm 2BL. This gene retained the symbol Sr47 because it had a different IT and map location from other stem rust resistance genes derived from Ae. speltoides. Allosyndetic recombinant lines carrying each gene on minimal alien chromosomal segments were identified as were molecular markers distinguishing each alien segment. This study demonstrated that chromosome engineering of Ae. speltoides segments is feasible in tetraploid wheat. The Sr47 gene confers high-level and broad spectrum resistance to stem rust and should be very useful in efforts to control TTKSK.
Wheat stem rust caused by Puccinia graminis f. sp. tritici can cause devastating yield losses in wheat. Over the past several decades, stem rust has been controlled worldwide through the use of genetic resistance. Stem rust race TTKSK (Ug99), first detected in Uganda in 1998, threatens global wheat production because of its unique virulence combination. As the majority of the currently grown cultivars and advanced breeding lines are susceptible to race TTKSK, sources of resistance need to be identified and characterized to facilitate their use in agriculture. South Dakota breeding line SD 1691 displayed resistance to race TTKSK in the international wheat stem rust nursery in Njoro, Kenya. Seedling screening of progeny derived from SD 1691 crossed to susceptible LMPG-6 indicated that a single resistance gene was present. Allelism and race-specificity tests indicated the stem rust resistance gene in SD 1691 was Sr28. The chromosome arm location of Sr28 was previously demonstrated to be 2BL. We identified molecular markers linked to Sr28 and validated this linkage in two additional populations. Common spring wheat cultivars in the central United States displayed allelic diversity for markers flanking Sr28. These markers could be used to select for Sr28 in breeding populations and for combining Sr28 with other stem rust resistance genes.
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