Genetic characterisation of buckwheat accessions through genome-wide allele frequency fingerprints
Nay et al. describe an approach to genotype buckwheat accessions by reporting population-specific allele-frequencies instead of bi-allelic SNPs. This technique allowed to precisely describe buckwheat breeding material and is an important step to implement molecular plant breeding tools in allogamous buckwheat.
Genomics-assisted breeding of buckwheat (Fagopyrum esculentum Moench) depends on robust genotyping methods. Genotyping by sequencing (GBS) has evolved as a flexible and cost-effective technique frequently used in plant breeding. Several GBS pipelines are available to genetically characterize single genotypes but these are not able to represent the genetic diversity of buckwheat accessions that are maintained as genetically heterogeneous, open-pollinating populations. Here we report the development of a GBS pipeline which, rather than reporting the state of bi-allelic single nucleotide polymorphisms (SNPs), resolves allele frequencies within populations on a genome-wide scale. These genome-wide allele frequency fingerprints (GWAFFs) from 100 pooled individual plants per accession were found to be highly reproducible and revealed the genetic similarity of 20 different buckwheat accessions analysed in our study. The GWAFFs cannot only be used as an efficient tool to precisely describe buckwheat breeding material, they also offer new opportunities to investigate the genetic diversity between different buckwheat accessions and establish variant databases for key material. Furthermore, GWAFFs provide the opportunity to associate allele frequencies to phenotypic traits and quality parameters that are most reliably described on population level. This is the key to practically implement powerful genomics-assisted breeding concepts such as marker-assisted selection and genomic selection in future breeding schemes of allogamous buckwheat.
This work is the result of a fruitful collaboration between the Molecular Plant Breeding from ETH, the Crop Science group from ETH and the Crop Science Department of Tegasac. The article was featured in a special edition of Folia Biologica et Geologica containing the conference proceedings of the International Symposium on Buckwheat 2019.
Citation:
Nay MM, Byrne SL, Pérez EA, Walter A and Studer B (2020) Genetic characterisation of buckwheat accessions through genome-wide allele frequency fingerprints. Folia Biologica et Geologica 61/1:17-23