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Krasileva KV, Vasquez-Gross HA, Howell T, Bailey P, Paraiso F, Clissold L, Simmonds J, Ramirez-Gonzalez RH, Wang X, Borrill P, Fosker C, Ayling S, Phillips AL, Uauy C, Dubcovsky J. Uncovering hidden variation in polyploid wheat. Proc Natl Acad Sci U S A 2017; 114:E913-E921. [PMID: 28096351 PMCID: PMC5307431 DOI: 10.1073/pnas.1619268114] [Citation(s) in RCA: 313] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mutations. Here we exploited this property to sequence and catalog more than 10 million mutations in the protein-coding regions of 2,735 mutant lines of tetraploid and hexaploid wheat. We detected, on average, 2,705 and 5,351 mutations per tetraploid and hexaploid line, respectively, which resulted in 35-40 mutations per kb in each population. With these mutation densities, we identified an average of 23-24 missense and truncation alleles per gene, with at least one truncation or deleterious missense mutation in more than 90% of the captured wheat genes per population. This public collection of mutant seed stocks and sequence data enables rapid identification of mutations in the different copies of the wheat genes, which can be combined to uncover previously hidden variation. Polyploidy is a central phenomenon in plant evolution, and many crop species have undergone recent genome duplication events. Therefore, the general strategy and methods developed herein can benefit other polyploid crops.
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Affiliation(s)
- Ksenia V Krasileva
- Department of Plant Sciences, University of California, Davis, CA 95616
- The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | | | - Tyson Howell
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Paul Bailey
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | - Francine Paraiso
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Leah Clissold
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | | | - Ricardo H Ramirez-Gonzalez
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
- John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Xiaodong Wang
- Department of Plant Sciences, University of California, Davis, CA 95616
| | | | | | - Sarah Ayling
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | | | | | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616;
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
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Uauy C, Paraiso F, Colasuonno P, Tran RK, Tsai H, Berardi S, Comai L, Dubcovsky J. A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat. BMC Plant Biol 2009; 9:115. [PMID: 19712486 PMCID: PMC2748083 DOI: 10.1186/1471-2229-9-115] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 08/28/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND Wheat (Triticum ssp.) is an important food source for humans in many regions around the world. However, the ability to understand and modify gene function for crop improvement is hindered by the lack of available genomic resources. TILLING is a powerful reverse genetics approach that combines chemical mutagenesis with a high-throughput screen for mutations. Wheat is specially well-suited for TILLING due to the high mutation densities tolerated by polyploids, which allow for very efficient screens. Despite this, few TILLING populations are currently available. In addition, current TILLING screening protocols require high-throughput genotyping platforms, limiting their use. RESULTS We developed mutant populations of pasta and common wheat and organized them for TILLING. To simplify and decrease costs, we developed a non-denaturing polyacrylamide gel set-up that uses ethidium bromide to detect fragments generated by crude celery juice extract digestion of heteroduplexes. This detection method had similar sensitivity as traditional LI-COR screens, suggesting that it represents a valid alternative. We developed genome-specific primers to circumvent the presence of multiple homoeologous copies of our target genes. Each mutant library was characterized by TILLING multiple genes, revealing high mutation densities in both the hexaploid (~1/38 kb) and tetraploid (~1/51 kb) populations for 50% GC targets. These mutation frequencies predict that screening 1,536 lines for an effective target region of 1.3 kb with 50% GC content will result in ~52 hexaploid and ~39 tetraploid mutant alleles. This implies a high probability of obtaining knock-out alleles (P = 0.91 for hexaploid, P = 0.84 for tetraploid), in addition to multiple missense mutations. In total, we identified over 275 novel alleles in eleven targeted gene/genome combinations in hexaploid and tetraploid wheat and have validated the presence of a subset of them in our seed stock. CONCLUSION We have generated reverse genetics TILLING resources for pasta and bread wheat and achieved a high mutation density in both populations. We also developed a modified screening method that will lower barriers to adopt this promising technology. We hope that the use of this reverse genetics resource will enable more researchers to pursue wheat functional genomics and provide novel allelic diversity for wheat improvement.
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Affiliation(s)
- Cristobal Uauy
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- John Innes Centre, Colney, Norwich NR4 7UH, UK
| | - Francine Paraiso
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Pasqualina Colasuonno
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Department of Genetics and Plant Breeding, University of Bari, Italy
| | - Robert K Tran
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
| | - Helen Tsai
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
| | - Steve Berardi
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
| | - Luca Comai
- UC Davis Genome Center, University of California, Davis, CA, 95616, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- John Innes Centre, Colney, Norwich NR4 7UH, UK
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