NORTH DAKOTA
USDA-ARS CEREAL CROPS RESEARCH UNIT
Northern Crop Science Laboratory, North Dakota State University, Fargo, ND 58078, USA.
Zhaohui Liu, James A. Anderson, Jinguo Hu, Timothy L. Friesen, Jack B. Rasmussen, and Justin D. Faris.
Efficient user-friendly methods for mapping plant genomes are highly desirable for the identification of QTL, genotypic profiling, genomic studies, and MAS. SSR (microsatellite) markers are user-friendly and efficient in detecting polymorphism, but they detect few loci. Target region amplification polymorphism (TRAP) is a relatively new PCR-based technique that detects a large number of loci from a single reaction without extensive pre-PCR processing of samples. In this work, we used both SSRs and TRAPs to generate over 700 markers for the construction of a genetic linkage map in a hard red spring wheat intervarietal recombinant inbred population. A framework map consisting of 352 markers accounted for 3,045 cM with an average density of one marker per 8.7 cM. On average, SSRs detected 1.9 polymorphic loci per reaction, whereas TRAPs detected 24. Both marker systems were suitable for assigning linkage groups to chromosomes using wheat aneuploid stocks. We demonstrated the utility of the maps by identifying major QTL for days to heading and reduced plant height on chromosomes 5A and 4B, respectively. This work indicates that TRAPs are highly efficient for genetic mapping in wheat. The maps developed will be useful for the identification of quality and disease resistance QTL that segregate in this population.
Zhaohui Liu, Timothy L. Friesen, Steven W. Meinhardt, Jack B. Rasmussen, and Justin D. Faris.
Stagonospora nodorum blotch (SNB) is an economically important foliar and glume disease in the major wheat growing areas of the world. We previously identified a host-selective toxin (SnTox1) produced by the isolate Sn2000 of S. nodorum and mapped the gene (Snn1) conditioning sensitivity to chromosome 1BS in the International Triticeae Mapping Initiative (ITMI) population. Here, we evaluated SnTox1 sensitivity and resistance to SNB caused by Sn2000 in a population of RILs derived from a cross between Grandin and BR34. In this population, sensitivity to partially purified SnTox1 mapped to the long arm of chromosome 5B and cosegregated with Tsn1, which confers sensitivity to Ptr ToxA produced by the tan spot fungus P. tritici-repentis. The tsn1 locus underlied a major QTL for resistance to SNB and explained 62 % of the phenotypic variation indicating that SnTox1 plays an important role in causing disease. Additional minor QTL were detected on 5BL and 1BS. These results suggest that SnTox1 can recognize multiple host genes to cause necrosis, and that the product of Tsn1 can serve as a target for proteinaceous toxins produced by different pathogenic fungi.
Justin D. Faris and Timothy L. Friesen.
Tan spot, caused by P. tritici-repentis (Ptr), is an economically important foliar disease in the major wheat-growing areas throughout the world. Multiple races of the pathogen have been characterized based on their ability to cause necrosis and/or chlorosis on differential wheat lines. In this research, we evaluated a population of RILs derived from a cross between the common wheat cultivars Grandin and BR34 for reaction to tan spot caused by Ptr races 1, 2, 3, and 5. Composite interval mapping revealed QTL on the short arm of chromosome 1B and the long arm of chromosome 3B significantly associated with resistance to all four races. The effects of the two QTL varied for the different races with the 1B QTL explaining from 13 to 29 percent of the phenotypic variation, whereas the 3B QTL explained from 13 to 41 percent of the variation. With the exception of a minor QTL on the short arm of chromosome 3B associated with resistance to race 3, no other significant QTL were detected. The host-selective toxin Ptr ToxA, which is produced by races 1 and 2, was not a significant factor in the development of disease in this population. The race-nonspecific resistance mechanisms derived from BR34 may preclude the recognition of the gene-for-gene interaction known to be associated with the wheat-tan spot system.
Huangjun Lu and Justin D. Faris.
EST and genome-sequencing data have provided the basis for comparative genomics between wheat and rice. In this study, markers representing expressed sequences within the wheat deletion interval 5BL 0.75-0.76 were used to determine the level of colinearity of this genomic region with rice. A population consisting of 117 recombinant substitution lines (RSLs) derived from the cross 'Chinese Spring (CS)/CS T. turgidum subsp. dicoccoides chromosome 5B substitution line (CS-Dic5B)' was used to develop a genetic map corresponding to the deletion interval. We mapped 35 expressed sequence markers as RFLPs or SSCPs, which resulted in a map of 51.4 cM in length. Of these markers, 19 (54 %) detected homologous sequences in rice genome. Analyses of colinearity using expressed sequences that detected rice homologs indicated a lack of conservation. Small regions of colinearity with rice chromosomes 3 and 9 were found, but multiple breaks, interruptions, and rearrangements exist. These anomalies will make it extremely difficult to use rice as a model for positional cloning of wheat genes in this region due to the lack of conservation.
Huangjun Lu, John P. Fellers, Timothy L. Friesen, Steven W. Meinhardt, Karri M. Haen, and Justin D. Faris.
Tsn1 conditions sensitivity to a host-selective proteinaceous toxin (Ptr ToxA) produced by the pathogenic fungus P. tritici-repentis. A large F2 population consisting of 5,378 gametes was produced to develop a high-resolution map for positional cloning of the gene. Chromosome walking in conjunction with complete sequencing of BACs identified in the Langdon durum BAC library was initiated from two AFLP-derived markers Xfcg17 and Xfcg9 that flank the Tsn1 gene at 0.24 and 0.46 cM, respectively. So far, three BACs on the Xfcg17 side of the gene have been sequenced. The new markers that were developed from these BACs spanning 215 kb cosegregated in the F2 population, suggesting that recombination is greatly suppressed in the vicinity of Xfcg17. On the Xfcg9 side of the gene, a contig of more than 550 kb has been constructed, and we have identified a candidate gene on the end of the contig that cosegregates with Tsn1. Physical to genetic distance ratios in the Tsn1 region ranged from 230 kb/cM to 10 Mb/cM. From the regions that have been sequenced, we have identified about 25 genes, many of which are genes that encode cell wall-associated receptors or kinases and DHHC type zinc finger proteins. The cloning and characterization of Tsn1 will increase our knowledge of the host-pathogen interaction.
Kristin J. Simons, John P. Fellers, Harold N. Trick, Zengcui Zhang, Bikram S. Gill, and Justin D. Faris.
The Q gene is largely responsible for the domestication of wheat because it confers the square spike phenotype and the free-threshing character. Q also pleiotropically influences many other domestication-related traits such as glume shape and tenacity, rachis fragility, spike length, plant height, and ear emergence time. We isolated the Q gene and verified its identity by analysis of knockout mutants and transformation. We found that Q is a floral homeotic gene with similarity to the AP2 class of transcription factors. Ectopic expression analysis allowed us to observe both silencing and overexpression effects of Q. Variation in spike compactness and plant height was directly correlated with the degree of ectopic expression, which verified previous results regarding the dosage effects of Q. Other characters such as rachis fragility, glume shape, and glume tenacity, mimicked the q phenotype in transgenic plants exhibiting silencing of the transgene and the endogenous Q gene. Sequence analysis of the gene in multiple free-threshing and non free-threshing genotypes suggests that Q arose from q through mutation.
Xunfen Chen, Jinguo Hu, Shahryar Kianian, Xiwen Cai, and Justin D. Faris.
The major FHB resistance QTL Qfhs.ndsu-3AS was identified from a wild tetraploid wheat accession T. turgidum subsp. dicoccoides and mapped within a 29.3 cM interval on chromosome 3A. A mapping population of 83 recombinant inbred chromosome lines (RICLs) derived from a cross between the T. turgidum subsp. durum cultivar Langdon (LDN)-T. turdigum subsp. dicoccoides substitution line 3A and LDN has been used for saturation mapping of this QTL region in the present study. To date, we have assigned 30 new molecular markers to the QTL region and located the QTL within a 10.1 cM chromosomal interval, which is about three times smaller than the previous interval (29.3 cM). Comparative mapping suggested that the FHB resistance QTL Qfhs.ndsu-3AS and Qfhs.ndsu-3BS localized on the short arm of chromosome 3A and 3B, respectively, are not homeoloci.
Robert W. Stack and Justin D. Faris.
Fusarium head blight is one of the most devastating diseases of bread and durum wheat. Resistant sources of hexaploid bread wheat have been identified and are currently being employed in breeding programs, but development of resistant tetraploid durum wheat has met with less success. Resistance has been identified in T. turgidum subsp. dicoccoides, a wild tetraploid relative, which readily hybridizes with durum wheat. Evaluation of Langdon durum-T. turgidum subsp. dicoccoides (LDN-DIC) disomic chromosome substitution lines indicated that T. turgidum subsp. dicoccoides chromosome 6B contributed a significant level of resistance. In this work, we evaluated a population of 85 recombinant inbred chromosome lines (RICLs) derived from LDN x LDN-DIC 6B for reaction to FHB, and surveyed markers along the previously constructed chromosome 6B genetic linkage map for associations with FHB resistance. Simple linear regression and composite interval regression analysis indicated the presence of a QTL on the short arm of 6B. This QTL accounted for about 20 percent of the phenotypic variation for resistance to FHB. It will be beneficial to combine this QTL with others to increase the levels of FHB resistance in durum cultivars.
Steven S. Xu, Justin D. Faris, Daryl Klindworth, Xiwen Cai, and Jinguo Hu
Modern molecular marker technologies greatly facilitate the characterization and development of new germ plasm and genetic stocks in crops. During the last 30 years, Dr. L. R. Joppa developed a number of useful germ plasm and genetic stocks in durum and common wheat, including various durum disomic substitutions, translocations, and synthetic hexaploid wheat lines. To provide an efficient means of maintaining these lines, we are extensively characterizing them using DNA markers and gel electrophoresis of seed storage proteins (glutenin subunits and gliadins). Thus far, three sets of Langdon durum-T. turgidum subsp. dicoccoides disomic substitution lines, five durum 1D/1A translocation lines, and 40 synthetic wheat lines have been characterized using TRAP (target region amplification polymorphism) and SSR (simple sequence repeat) markers and seed storage proteins. This research resulted in development of about 800 chromosome-specific TRAP markers, identification of unique alleles for glutenin subunits and gliadins, and mapping of introgressed chromosome segments. The developed TRAP markers are currently being used for wheat genome mapping, chromosome identification, and genetic diversity studies. The glutenin subunits from chromosomes 1A, 1B, and 1D, and gliadins for 6A, 6B, and 6D, have been successfully used in the development of a new set of durum D-genome, chromosome substitution lines and for transferring good bread-making quality from bread wheat to durum wheat cultivars. SSR markers closely flanking Tsn1, which confers sensitivity to a host selective toxin produced by the tan spot fungus, are being used to eliminate the sensitivity locus from commercial cultivars of bread wheat.
R.E. Oliver, S.S. Xu, X. Cai, and R.W. Stack.
Sources of resistance to FHB have been identified and utilized in breeding for FHB resistance in common wheat. However, sources of effective FHB resistance are limited in durum wheat. Attempts to transfer resistance from hexaploid wheat to durum wheat have met with minimal success. In order to identify novel sources of FHB resistance usable for enhancing resistance of durum wheat to FHB, we systematically evaluated 185 accessions of five subspecies under T. turgidum for resistance to spread of FHB infection (type-II resistance) in controlled greenhouse condition. These subspecies include Persian wheat (T. turgidum subsp. carthlicum), cultivated emmer wheat (T. turgidum subsp. dicoccum), Polish wheat (T. turgidum subsp. polonicum), oriental wheat (T. turgidum subsp. turanicum), and poulard wheat (T. turgidum subsp. turgidum). Preliminary results from this study indicated that four accessions of cultivated emmer wheat and six accessions of Persian wheat had a similar level of resistance as Alsen, a Sumai 3-derived HRSW cultivar in North Dakota. Further evaluations are being conducted to confirm FHB resistance of these cultivated tetraploid wheat accessions in the greenhouse and field. These accessions could serve as novel sources of resistance to develop durum wheat cultivars resistant to FHB.