Hard Winter Wheat Genetics Research Unit

Manhattan, KS, United States

Hard Winter Wheat Genetics Research Unit

Manhattan, KS, United States
SEARCH FILTERS
Time filter
Source Type

Cuomo C.A.,The Broad Institute of MIT and Harvard | Bakkeren G.,Agriculture and Agri Food Canada | Khalil H.B.,Agriculture and Agri Food Canada | Panwar V.,Agriculture and Agri Food Canada | And 21 more authors.
G3: Genes, Genomes, Genetics | Year: 2017

Three members of the Puccinia genus, Puccinia triticina (Pt), P. striiformis f.sp. tritici (Pst), and P. graminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi, and basidiomycetes, and to identify genes of significance for infection. Pt had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; in comparison, repeats occupy 31.5% for Pst and 36.5% for Pgt. We find all three genomes are highly heterozygous, with Pst [5.97 single nucleotide polymorphisms (SNPs)/kb] nearly twice the level detected in Pt (2.57 SNPs/kb) and that previously reported for Pgt. Of 1358 predicted effectors in Pt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryotic Puccinia species along with three pheromone receptor (STE3) mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologous Ustilago maydis mating assay and host-induced gene silencing (HIGS) of the HD and STE3 alleles reduced wheat host infection. © 2017 Cuomo et al.


Das M.K.,Oklahoma State University | Das M.K.,Syngenta | Bai G.,Hard Winter Wheat Genetics Research Unit | Mujeeb-Kazi A.,International Maize and Wheat Improvement Center | And 2 more authors.
Genetic Resources and Crop Evolution | Year: 2015

Synthetic hexaploid wheat (SHW) is known to be an excellent vehicle for transferring large genetic variations especially the many useful traits present in the D genome of Aegilops tauschii Coss. (2n = 2x = 14, DD) for improvement of cultivated wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD). The objectives of the present study were to (1) evaluate genetic diversity among 32 selected SHW accessions with resistance to several fungal diseases using Amplified Fragment Length Polymorphism (AFLP) and Simple Sequence Repeat (SSR) markers and (2) identify diverse SHWs for pyramiding genes conferring resistance to different diseases. These SHWs containing different accessional sources of the D genome were identified from about 1000 SHW accessions developed by the Wheat Wide Crosses program at the International Maize and Wheat Improvement Center, Mexico. Of the 32 SHW accessions eight had resistance to Fusarium head blight (Fusarium graminearum Schw.), seven were resistant to leaf rust (Puccinia triticina Eriks.), eight resistant to Helminthosporium spot blotch [Cochliobolus sativus (Ito et Kurib.) Drechsler ex Dastur (syn.: Bipolaris sorokiniana (Sacc.) Shoem., Helminthosporiumsativum Pammel, King et Bakke)], seven resistant to Septoria tritici blotch (Septoria tritici Roberge in Desmaz.), while two were resistant to both Fusarium head blight and leaf rust. Seventeen EcoRI/MseI AFLP primer combinations and 27 highly polymorphic SSR markers including 20 D genome specific markers were screened over all 32 SHW accessions. Among the 703 AFLP fragments scored, 225 were polymorphic across the 32 SHW accessions. Polymorphic information content (PIC) among the SHWs for AFLP ranged from 0.06 to 0.50 with an average PIC of 0.24. Major allelic frequency from SSR analysis ranged from 0.23 to 0.81 with an average of 0.45. Number of alleles per locus for the SSR markers ranged from 3 to 15 with an average allele number of 7.4. Average gene diversity and PIC for the SSR markers was 0.69 and 0.66, respectively, with the highest values being for the D genome specific markers. Cluster analysis showed distinct groups among the SHW accessions studied. Mantel statistics between the distance matrices from AFLP and SSR analyses showed a moderate but significant correlation (r = 0.52**). Our results indicate that the SHW accessions studied possess substantial genetic diversity and are valuable user-friendly pre-breeding materials for breeding improvement of wheat with resistance to Fusarium head blight, leaf rust, Helminthosporium spot blotch, and Septoria tritici blotch. The most diverse SHW accessions can be used for pyramiding resistance genes for different diseases. © 2015 Springer Science+Business Media Dordrecht


Li C.,Northwest Agriculture and Forestry University | Li C.,Kansas State University | Bai G.,Kansas State University | Bai G.,Hard Winter Wheat Genetics Research Unit | And 3 more authors.
Euphytica | Year: 2015

Continuous improvement in grain yield is one of the major challenges for wheat (Triticum aestivum L.) breeding worldwide. This study characterized quantitative trait loci (QTL) underlying wheat grain yield and its components using a high-density genetic linkage map developed from a recombinant inbred line (RIL) population derived from ‘Ning7840’ × ‘Clark’. The map consisted of 594 single nucleotide polymorphism and 404 simple sequence repeat markers covering a genetic distance of 4225.7 cM. The RIL population was evaluated for grain yield (GY), spike number per m2 (SNPM), kernel number per spike (KNPS), and thousand-kernel weight (TKW) in three Oklahoma locations from 2001 to 2003. A total of 29 additive QTL (eight for GY, two for SNPM, five for KNPS, and 14 for TKW) were mapped on 13 chromosomes. Eight pairs of epistatic QTL were detected for different yield components: four for GY, two for KNPS, and two for TKW. Four additive QTL, including two for GY and two for KNPS, showed additive × environment interactions. QTL that were repeatable in multiple environments were identified for all traits except SNPM. Positive alleles were dispersed between the two parents for all traits, with ‘Clark’ contributing slightly more. Seven pleiotropic loci were co-localized for at least two traits. Interestingly, all co-localized loci overlapped for TKW, and four of them overlapped for GY. Thus, selecting QTL for TKW may simultaneously select for or against yield or other yield components in breeding. © 2015 Springer Science+Business Media Dordrecht (outside the USA)


Poland J.A.,Hard Winter Wheat Genetics Research Unit | Poland J.A.,Kansas State University | Brown P.J.,Urbana University | Sorrells M.E.,Cornell University | And 2 more authors.
PLoS ONE | Year: 2012

Advancements in next-generation sequencing technology have enabled whole genome re-sequencing in many species providing unprecedented discovery and characterization of molecular polymorphisms. There are limitations, however, to next-generation sequencing approaches for species with large complex genomes such as barley and wheat. Genotyping-by-sequencing (GBS) has been developed as a tool for association studies and genomics-assisted breeding in a range of species including those with complex genomes. GBS uses restriction enzymes for targeted complexity reduction followed by multiplex sequencing to produce high-quality polymorphism data at a relatively low per sample cost. Here we present a GBS approach for species that currently lack a reference genome sequence. We developed a novel two-enzyme GBS protocol and genotyped bi-parental barley and wheat populations to develop a genetically anchored reference map of identified SNPs and tags. We were able to map over 34,000 SNPs and 240,000 tags onto the Oregon Wolfe Barley reference map, and 20,000 SNPs and 367,000 tags on the Synthetic W9784×Opata85 (SynOpDH) wheat reference map. To further evaluate GBS in wheat, we also constructed a de novo genetic map using only SNP markers from the GBS data. The GBS approach presented here provides a powerful method of developing high-density markers in species without a sequenced genome while providing valuable tools for anchoring and ordering physical maps and whole-genome shotgun sequence. Development of the sequenced reference genome(s) will in turn increase the utility of GBS data enabling physical mapping of genes and haplotype imputation of missing data. Finally, as a result of low per-sample costs, GBS will have broad application in genomics-assisted plant breeding programs.


Elshire R.J.,Cornell University | Glaubitz J.C.,Cornell University | Sun Q.,Cornell University | Poland J.A.,Hard Winter Wheat Genetics Research Unit | And 4 more authors.
PLoS ONE | Year: 2011

Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs). This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM) and barley (Oregon Wolfe Barley) recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.


Xia Y.,Guangzhou University | Xia Y.,South China University of Technology | Li R.,Guangzhou University | Ning Z.,South China University of Technology | And 6 more authors.
PLoS ONE | Year: 2013

Small heat shock protein 17.8 (HSP17.8) is produced abundantly in plant cells under heat and other stress conditions and may play an important role in plant tolerance to stress environments. However, HSP17.8 may be differentially expressed in different accessions of a crop species exposed to identical stress conditions. The ability of different genotypes to adapt to various stress conditions resides in their genetic diversity. Allelic variations are the most common forms of genetic variation in natural populations. In this study, single nucleotide polymorphisms (SNPs) of the HSP17.8 gene were investigated across 210 barley accessions collected from 30 countries using EcoTILLING technology. Eleven SNPs including 10 from the coding region of HSP17.8 were detected, which form nine distinguishable haplotypes in the barley collection. Among the 10 SNPs in the coding region, six are missense mutations and four are synonymous nucleotide changes. Five of the six missense changes are predicted to be deleterious to HSP17.8 function. The accessions from Middle East Asia showed the higher nucleotide diversity of HSP17.8 than those from other regions and wild barley (H. spontaneum) accessions exhibited greater diversity than the cultivated barley (H. vulgare) accessions. Four SNPs in HSP17.8 were found associated with at least one of the agronomic traits evaluated except for spike length, namely number of grains per spike, thousand kernel weight, plant height, flag leaf area and leaf color. The association between SNP and these agronomic traits may provide new insight for study of the gene's potential contribution to drought tolerance of barley. © 2013 Xia et al.


Xia Y.,Guangzhou University | Xia Y.,South China University of Technology | Ning Z.,South China University of Technology | Bai G.,Hard Winter Wheat Genetics Research Unit | And 5 more authors.
PLoS ONE | Year: 2012

Light-harvesting chlorophyll a/b-binding protein (LHCP) is one of the most abundant chloroplast proteins in plants. Its main function is to collect and transfer light energy to photosynthetic reaction centers. However, the roles of different LHCPs in light-harvesting antenna systems remain obscure. Exploration of nucleotide variation in the genes encoding LHCP can facilitate a better understanding of the functions of LHCP. In this study, nucleotide variations in Lhcb1, a LHCP gene in barley, were investigated across 292 barley accessions collected from 35 different countries using EcoTILLING technology, a variation of the Targeting Induced Local Lesions In Genomes (TILLING). A total of 23 nucleotide variations were detected including three insert/deletions (indels) and 20 single nucleotide polymorphisms (SNPs). Among them, 17 SNPs were in the coding region with nine missense changes. Two SNPs with missense changes are predicted to be deleterious to protein function. Seventeen SNP formed 31 distinguishable haplotypes in the barley collection. The levels of nucleotide diversity in the Lhcb1 locus differed markedly with geographic origins and species of accessions. The accessions from Middle East Asia exhibited the highest nucleotide and haplotype diversity. H. spontaneum showed greater nucleotide diversity than H. vulgare. Five SNPs in Lhcb1 were significantly associated with at least one of the six agronomic traits evaluated, namely plant height, spike length, number of grains per spike, thousand grain weight, flag leaf area and leaf color, and these SNPs may be used as potential markers for improvement of these barley traits. © 2012 Xia et al.


Currie Y.,Fayetteville State University | Moch J.,Fayetteville State University | Underwood J.,Fayetteville State University | Kharabsheh H.,Fayetteville State University | And 7 more authors.
Journal of Economic Entomology | Year: 2014

Heat stress exerts a profound impact on the resistance of plants to parasites. In this research, we investigated the impact of an acute transient heat stress on the resistance of the wheat line 'Molly,' which contains the R gene H13, to an avirulent Hessian fly (Mayetiola destructor (Say)) population. We found that a significant portion of Molly seedlings stressed at 40°C for 6 h during or after the initial Hessian fly larval attack became susceptible to otherwise avirulent insects, whereas unstressed control plants remained 100% resistant. Specifically, 77.8,73.3,83.3, and 46.7% of plants heat stressed at 0,6,12, and 24 h, respectively, after the initial larval attack became susceptible. Biochemical analysis revealed that heat stress caused a transient decrease in 12-oxo-phytodienoic acid, but an increase in salicylic acid accumulation in Molly plants. The change in phytohormones after heat stress and Hessian fly infestation was not observed in 'Newton,' a near-isogenic but Hessian fly susceptible wheat line. Instead, heat stress caused a relatively prolonged reduction in palmitoleic acid. The role of phytohormones in heat-induced loss of wheat resistance was discussed. © 2014 Entomological Society of America.


PubMed | Hard Winter Wheat Genetics Research Unit
Type: Journal Article | Journal: PloS one | Year: 2012

Advancements in next-generation sequencing technology have enabled whole genome re-sequencing in many species providing unprecedented discovery and characterization of molecular polymorphisms. There are limitations, however, to next-generation sequencing approaches for species with large complex genomes such as barley and wheat. Genotyping-by-sequencing (GBS) has been developed as a tool for association studies and genomics-assisted breeding in a range of species including those with complex genomes. GBS uses restriction enzymes for targeted complexity reduction followed by multiplex sequencing to produce high-quality polymorphism data at a relatively low per sample cost. Here we present a GBS approach for species that currently lack a reference genome sequence. We developed a novel two-enzyme GBS protocol and genotyped bi-parental barley and wheat populations to develop a genetically anchored reference map of identified SNPs and tags. We were able to map over 34,000 SNPs and 240,000 tags onto the Oregon Wolfe Barley reference map, and 20,000 SNPs and 367,000 tags on the Synthetic W9784 Opata85 (SynOpDH) wheat reference map. To further evaluate GBS in wheat, we also constructed a de novo genetic map using only SNP markers from the GBS data. The GBS approach presented here provides a powerful method of developing high-density markers in species without a sequenced genome while providing valuable tools for anchoring and ordering physical maps and whole-genome shotgun sequence. Development of the sequenced reference genome(s) will in turn increase the utility of GBS data enabling physical mapping of genes and haplotype imputation of missing data. Finally, as a result of low per-sample costs, GBS will have broad application in genomics-assisted plant breeding programs.

Loading Hard Winter Wheat Genetics Research Unit collaborators
Loading Hard Winter Wheat Genetics Research Unit collaborators