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Wheat researchers at the John Innes Center are experimenting with a new technique that promises to improve genetic discovery for the world-class crop.
Cultivating crops involves the assembly of desired combinations of traits defined by the underlying genetic variation. Some of this genetic variation often remains the same between generations, with some genes inherited together. These blocks of genes – very rarely broken down in genetic recombination – are called haplotype blocks. These haplotypes are the units that breeders change and select from among plants to create new crop lines.
In the new study appearing in Communications biology John Innes Center researchers led by Professor Cristobal Uauy’s team show that current platforms used by breeders do not provide the resolution needed to distinguish between haplotypes, potentially leading to inaccurate breeding decisions.
They defined blocks of haplotypes shared among the 15 soft wheat cultivars assembled in the 10+ Wheat Genome project, an important international collaboration published today in Nature.
To illustrate the application of this haplotype-driven approach to support crop improvement, they focused on a specific region of the wheat genome on chromosome 6A.
Through detailed genetic studies and extensive field experiments, they have shown that British breeders keep multiple genes as an intact chromosome 6A haplotype to maximize the expression of desirable traits, including flowering time and yield.
Given the low diversity on chromosome 6A, they tested the haplotype approach to discover and introduce new haplotypes from native wheat varieties not subject to modern breeding.
Combining haplotype knowledge, genetics and field studies, they identified three novel haplotypes in native varieties associated with improved productivity traits in UK environments.
Since these haplotypes are not present in modern germplasm, they represent new variants that could be aimed at improving yield in elite cultivars, using modern genomic tools.
Lead author, Dr Jemima Brinton, says, “We used rigorous criteria to distinguish these shared haplotype blocks from nearly identical sequences. We believe this rigidity is essential for crop improvement. The breeding process is intended to undergo an improvement in terms of accuracy and efficiency through haplotype-breeding. “
The knowledge generated in the study directly affects the process of reproduction and discovery allowing scientists to:
- Perform targeted discovery of new haplotypes and use breeding strategies to introduce this genetic diversity into modern germplasm.
- Prioritize research objectives to understand the biological functions of the sequences selected by breeders
- Make more precise selection of parents to maximize genetic gains within breeding programs
- Intentionally assembling optimized haplotype combinations
To make the work more accessible to readers, scientists and breeders, the group has developed a new haplotype display interface at http://www.crop-haplotypes.com.
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Materials provided by John Innes Center. Note: The content can be changed by style and length.
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