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Oddy J, Alarcón-Reverte R, Wilkinson M, Ravet K, Raffan S, Minter A, Mead A, Elmore JS, de Almeida IM, Cryer NC, Halford NG, Pearce S. Reduced free asparagine in wheat grain resulting from a natural deletion of TaASN-B2: investigating and exploiting diversity in the asparagine synthetase gene family to improve wheat quality. BMC Plant Biol 2021; 21:302. [PMID: 34187359 PMCID: PMC8240372 DOI: 10.1186/s12870-021-03058-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/17/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND Understanding the determinants of free asparagine concentration in wheat grain is necessary to reduce levels of the processing contaminant acrylamide in baked and toasted wheat products. Although crop management strategies can help reduce asparagine concentrations, breeders have limited options to select for genetic variation underlying this trait. Asparagine synthetase enzymes catalyse a critical step in asparagine biosynthesis in plants and, in wheat, are encoded by five homeologous gene triads that exhibit distinct expression profiles. Within this family, TaASN2 genes are highly expressed during grain development but TaASN-B2 is absent in some varieties. RESULTS Natural genetic diversity in the asparagine synthetase gene family was assessed in different wheat varieties revealing instances of presence/absence variation and other polymorphisms, including some predicted to affect the function of the encoded protein. The presence and absence of TaASN-B2 was determined across a range of UK and global common wheat varieties and related species, showing that the deletion encompassing this gene was already present in some wild emmer wheat genotypes. Expression profiling confirmed that TaASN2 transcripts were only detectable in the grain, while TaASN3.1 genes were highly expressed during the early stages of grain development. TaASN-A2 was the most highly expressed TaASN2 homeologue in most assayed wheat varieties. TaASN-B2 and TaASN-D2 were expressed at similar, lower levels in varieties possessing TaASN-B2. Expression of TaASN-A2 and TaASN-D2 did not increase to compensate for the absence of TaASN-B2, so total TaASN2 expression was lower in varieties lacking TaASN-B2. Consequently, free asparagine concentrations in field-produced grain were, on average, lower in varieties lacking TaASN-B2, although the effect was lost when free asparagine accumulated to very high concentrations as a result of sulphur deficiency. CONCLUSIONS Selecting wheat genotypes lacking the TaASN-B2 gene may be a simple and rapid way for breeders to reduce free asparagine concentrations in commercial wheat grain.
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Affiliation(s)
- Joseph Oddy
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Rocío Alarcón-Reverte
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Mark Wilkinson
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Karl Ravet
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Sarah Raffan
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Andrea Minter
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Andrew Mead
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - J. Stephen Elmore
- Department of Food & Nutritional Sciences, University of Reading, Whiteknights, Reading, RG6 6DZ UK
| | | | - Nicholas C. Cryer
- Mondelēz UK R&D Ltd, Bournville Lane, Bournville, Birmingham, B30 2LU UK
| | - Nigel G. Halford
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
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Cryer NC, Butler DR, Wilkinson MJ. High throughput, high resolution selection of polymorphic microsatellite loci for multiplex analysis. Plant Methods 2005; 1:3. [PMID: 16270924 PMCID: PMC1277016 DOI: 10.1186/1746-4811-1-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Accepted: 08/18/2005] [Indexed: 05/05/2023]
Abstract
BACKGROUND Large-scale genetic profiling, mapping and genetic association studies require access to a series of well-characterised and polymorphic microsatellite markers with distinct and broad allele ranges. Selection of complementary microsatellite markers with non-overlapping allele ranges has historically proved to be a bottleneck in the development of multiplex microsatellite assays. The characterisation process for each microsatellite locus can be laborious and costly given the need for numerous, locus-specific fluorescent primers. RESULTS Here, we describe a simple and inexpensive approach to select useful microsatellite markers. The system is based on the pooling of multiple unlabelled PCR amplicons and their subsequent ligation into a standard cloning vector. A second round of amplification utilising generic labelled primers targeting the vector and unlabelled locus-specific primers targeting the microsatellite flanking region yield allelic profiles that are representative of all individuals contained within the pool. Suitability of various DNA pool sizes was then tested for this purpose. DNA template pools containing between 8 and 96 individuals were assessed for the determination of allele ranges of individual microsatellite markers across a broad population. This helped resolve the balance between using pools that are large enough to allow the detection of many alleles against the risk of including too many individuals in a pool such that rare alleles are over-diluted and so do not appear in the pooled microsatellite profile. Pools of DNA from 12 individuals allowed the reliable detection of all alleles present in the pool. CONCLUSION The use of generic vector-specific fluorescent primers and unlabelled locus-specific primers provides a high resolution, rapid and inexpensive approach for the selection of highly polymorphic microsatellite loci that possess non-overlapping allele ranges for use in large-scale multiplex assays.
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Affiliation(s)
- Nicholas C Cryer
- School of Biological Sciences, University of Reading, Reading, Berkshire, RG6 6AS, UK
| | - David R Butler
- Cocoa Research Unit, The University of West Indies, St. Augustine, Trinidad and Tobago
| | - Mike J Wilkinson
- School of Biological Sciences, University of Reading, Reading, Berkshire, RG6 6AS, UK
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