Abstract
Key messageExome 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.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.
Highlights
Cultivated barley (Hordeum vulgare ssp. vulgare L.) is the fourth most important cereal crop employed for feed, malt production and, marginally, for preparing foodCommunicated by Kevin Smith.1 3 Vol.:(0123456789)Theoretical and Applied Genetics strategy to increase the diversity available for plant breeding (Brozynska et al 2016; Lopes et al 2015).The systematic research, identification and characterization of new allelic variants for one or multiple genes in large and diverse collections are referred to as “allele mining”
We provide evidence on how the whole-exome sequencing (WES) data generated by Bustos-Korts et al (2019) on a panel of 403 barley accessions organized in the frame of the EU-project WHEALBI can be exploited for extensive allele mining
The co-segregation between Fr-H1 and VRN-H1 highlights the role of growth habit in frost tolerance (Stockinger et al 2007; Akar et al 2009; Visioni et al 2013; Zhu et al 2014) and motivated the exploitation of the allelic diversity detected in the VRN-H1 sequence
Summary
Cultivated barley (Hordeum vulgare ssp. vulgare L.) is the fourth most important cereal crop employed for feed, malt production and, marginally, for preparing foodCommunicated by Kevin Smith.1 3 Vol.:(0123456789)Theoretical and Applied Genetics strategy to increase the diversity available for plant breeding (Brozynska et al 2016; Lopes et al 2015).The systematic research, identification and characterization of new allelic variants for one or multiple genes in large and diverse collections are referred to as “allele mining”. Spontaneum) genotypes (Russell et al 2016) and more recently to elucidate the genetic diversity of a barley collection of 403 accessions including formally bred cultivars, landraces and wild barleys developed in the frame of the European project WHEALBI (Bustos-Kors et al 2019). The exome sequencing approach in barley (Mascher et al 2013) was first used to investigate the environmental adaptation displayed by a collection of 267 landrace and wild relative This germplasm collection includes accessions from 72 different countries covering the geographic range of barley cultivation. In the latter study, the use for the first time of a high-quality reference genome assembly increased the accuracy of variant discovery
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