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

Abstract

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.

The genomics of linkage drag in inbred lines of sunflower

“…While certain desirable traits might not be expressed in close relatives, many of the underlying alleles may exist in the primary gene pool, albeit at a lower frequency. If so, there is a growing potential for the use of bioinformatics approaches to identify compatible GenBank germplasm containing the allele(s) of interest ( 73 ). Furthermore, natural introgression from the secondary gene pool into the primary gene pool may provide a source of alleles that have already been purged of deleterious incompatibilities and show reduced linkage drag.…”

The genomics of linkage drag in sunflower

“…While certain desirable traits might not be expressed in close relatives, many of the underlying alleles may exist in the primary gene pool, albeit at a lower frequency. If so, there is a growing potential for the use of bioinformatics approaches to identify compatible genebank germplasm containing the allele(s) of interest (Guerra et al 2022). Furthermore, natural introgression from the secondary gene pool into the primary gene pool may provide a source of alleles that have already been purged of deleterious incompatibilities and show reduced linkage drag.…”

Heritage genetics for adaptation to marginal soils in barley

“…One example of this approach is genome-environment association (GEA) [18], or environmental genome-wide association analysis (envGWAS), which is gaining popularity and has been used to assess barley and wheat for adaptative traits [19]. Specifically, genes involved in frost tolerance in barley have been found through allele mining of exome sequencing data from a population of landrace cultivars [20]. For this reason, locally selected landraces have received renewed interest across all crops [11].…”