Disease Resistance Genetics and Genomics in Octoploid Strawberry

Abstract

Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, expression quantitative trait loci (eQTL) analysis and RenSeq analysis in cultivars. Octoploid fruit eQTL were identified for 76 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance toward exploiting variation for strawberry cultivar improvement.

Genetic Analysis of Methyl Anthranilate, Mesifurane, Linalool, and Other Flavor Compounds in Cultivated Strawberry (Fragaria × ananassa)

“…Mature fruits from 61 parents and progeny from the biparental populations 10.113, 13.75, and 13.76 were sequenced via Illumina paired-end RNA-seq (average 65 million, 2 × 100-bp reads) and used for transcript eQTL analysis via the same samples and methodology reported for R-genes ( Barbey et al, 2019 ) and other high-value fruit transcripts ( Barbey C. et al, 2020 ). Briefly, RNA-seq reads were assembled based on the Fragaria × ananassa octoploid “Camarosa” annotated genome, with reads mapping equally well to multiple loci discarded from the analysis.…”

“…Fruit transcript heatmaps were added to the cladogram to show the maximum transcript level detected among the 61 fruit transcriptomes. Genes putatively belonging to published volatile biosynthesis gene families were selected for fruit transcript eQTL analysis, using methods described previously ( Barbey et al, 2019 ; Barbey C. et al, 2020 ). The 200 genes surrounding the most-correlated volatile QTL markers were also analyzed for eQTL and compared for co-segregation with volatile QTL.…”

“…Genes putatively belonging to published volatile biosynthesis gene families were selected for fruit transcript eQTL analysis, using methods described previously (Barbey et al, 2019;. The 200 genes surrounding the most-correlated volatile QTL markers were also analyzed for eQTL and compared for co-segregation with volatile QTL.…”

The Genetics of Differential Gene Expression Related to Fruit Traits in Strawberry (Fragaria ×ananassa)

“…In strawberry, eQTL experiments helped identify the g-decalactone biosynthesis gene in the octoploid mature receptacle even while limited to incomplete de novo and diploid reference-based RNAseq assemblies (Sánchez-Sevilla et al, 2014). Using the recent subgenome-scale octoploid genome for 'Camarosa', 76 mature receptacle-expressed disease resistances genes (R-genes) were identified to be under the control of an eQTL (Barbey et al, 2019).…”

A roadmap for research in octoploid strawberry

“…Only those with direct evidence for involvement in octoploid strawberry ripening are presented here custom-capture libraries and single-molecule resequencing of captured target sequences has been quite effective for identifying causal gene variants 149 . In fact, such a resource has now been developed for cultivated strawberry in the form of a RenSeq library based on the "Camarosa" reference and resequencing of a number of elite cultivars and breeding lines 150 . Combining this resource with mapping and association genetics approaches should help uncover subgenome-specific variants underlying known loci and lead to the cloning of R genes in octoploid strawberry.…”