A haplotype-led approach to increase the precision of wheat breeding

Crop productivity must increase at unprecedented rates to meet the needs of the growing worldwide population. Exploiting natural variation for the genetic improvement of crops plays a central role in increasing productivity. Although current genomic technologies can be used for high-throughput identification of genetic variation, methods for efficiently exploiting this genetic potential in a targeted, systematic manner are lacking. Here, we developed a haplotype-based approach to identify genetic diversity for crop improvement using genome assemblies from 15 bread wheat (Triticum aestivum) cultivars. We used stringent criteria to identify identical-by-state haplotypes and distinguish these from near-identical sequences (~99.95% identity). We showed that each cultivar shares ~59 % of its genome with other sequenced cultivars and we detected the presence of extended haplotype blocks containing hundreds to thousands of genes across all wheat chromosomes. We found that genic sequence alone was insufficient to fully differentiate between haplotypes, as were commonly used array-based genotyping chips due to their gene centric design. We successfully used this approach for focused discovery of novel haplotypes from a landrace collection and documented their potential for trait improvement in modern bread wheat. This study provides a framework for defining and exploiting haplotypes to increase the efficiency and precision of wheat breeding towards optimising the agronomic performance of this crucial crop.

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  • Name: Brinton, Jemima, Type: Corresponding Author,
  • Name: null, null, Type: Corresponding Author,
  • Name: Ramirez-Gonzalez, Ricardo H., Type: Author,
  • Name: Simmonds, James, Type: Author,
  • Name: Wingen, Luzie, Type: Author,
  • Name: Orford, Simon, Type: Author,
  • Name: Griffiths, Simon, Type: Author,
  • Name: Haberer, Georg, Type: Author,
  • Name: Spannagl, Manuel, Type: Author,
  • Name: Walkowiak, Sean, Type: Author,
  • Name: Pozniak, Curtis, Type: Author,
  • Name: Uauy, Cristobal, Type: Author,
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Article Host Type publisher
Article Is Open Access true
Article License Type cc-by
Article Version Type publishedVersion
Citation Report https://scite.ai/reports/10.1038/s42003-020-01413-2
DFW Organisation JIC
DFW Work Package 3
DOI 10.1038/s42003-020-01413-2
Date Last Updated 2020-11-25T22:44:09.515789
Evidence open (via page says license)
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Journal Is Open Access true
Open Access Status gold
PDF URL https://www.nature.com/articles/s42003-020-01413-2.pdf
Publisher URL https://doi.org/10.1038/s42003-020-01413-2