Extensive allele mining discovers novel genetic diversity in the loci controlling frost tolerance in barley

Davide Guerra, Caterina Morcia, Franz Badeck, Fulvia Rizza, Stefano Delbono, Enrico Francia, Justyna Anna Milc, Istvan Monostori, Gabor Galiba, Luigi Cattivelli & Alessandro Tondelli

Theoretical and Applied Genetics; February 2022; Vol. 135: 553–569

Key message

Exome sequencing-based allele mining for frost tolerance suggests HvCBF14 rather than CNV at Fr-H2 locus is the main responsible of frost tolerance in barley.

Abstract

Wild relatives, landraces and old cultivars of barley represent a reservoir of untapped and potentially important genes for crop improvement, and the recent sequencing technologies provide the opportunity to mine the existing genetic diversity and to identify new genes/alleles for the traits of interest. In the present study, we use frost tolerance and vernalization requirement as case studies to demonstrate the power of allele mining carried out on exome sequencing data generated from > 400 barley accessions. New deletions in the first intron of VRN-H1 were identified and linked to a reduced vernalization requirement, while the allelic diversity of HvCBF2a, HvCBF4b and HvCBF14 was investigated by combining the analysis of SNPs and read counts. This approach has proven very effective to identify gene paralogs and copy number variants of HvCBF2 and the HvCBF4b-HvCBF2a segment. A multiple linear regression model which considers allelic variation at these genes suggests a major involvement of HvCBF14, rather than copy number variation of HvCBF4b-HvCBF2a, in controlling frost tolerance in barley. Overall, the present study provides powerful resource and tools to discover novel alleles at relevant genes in barley.

See: https://link.springer.com/article/10.1007/s00122-021-03985-x

Fig.1: Site frequency spectrum of the alternative allele in the collection. The X axis reports the frequency of the alternative allele; the Y axis reports the number of SNPs in each bin. Each bar is coloured in relation to the proportion of genotypes, in each frequency class, that belong to one of the three categories: cultivar, landrace and wild. The inset is a magnification of bars from frequency class 0.1–0.6