Identification of resistance to Fusarium basal rot and improved seedling vigour through the creation and characterisation of a novel onion diversity set

Authors: TAYLOR, ANDREW - University Of Warwick; TEAKLE, GRAHAM - University Of Warwick; WALLEY, PETER - University Of Warwick; FINSH-SAVAGE, WILLIAM - University Of Warwick; JACKSON, ALISON - University Of Warwick; JONES, JULIE - University Of Warwick; HAND, PAUL - Harper Adams University College; THOMAS, BRIAN - University Of Warwick; Havey, Michael; PINK, DAVID - University Of Warwick; CLARKSON, JOHN - University Of Warwick

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/24/2019
Publication Date: 9/13/2019
Citation: Taylor, A., Teakle, G.R., Walley, P.G., Finsh-Savage, W., Jackson, A.C., Jones, J.E., Hand, P., Thomas, B., Havey, M.J., Pink, D.A., Clarkson, J.P. 2019. Identification of resistance to Fusarium basal rot and improved seedling vigour through the creation and characterisation of a novel onion diversity set. Frontiers in Plant Science. 132:3245–3264. https://doi.org/10.1007/s00122-019-03422-0.
DOI: https://doi.org/10.1007/s00122-019-03422-0

Interpretive Summary: Conserving biodiversity is critical for safeguarding the future of crop production. Onion is a globally important horticultural crop with a very large (16Gb per 1C) genome which has not been sequenced. Whilst onions are self-fertile, they suffer from severe inbreeding depression and as such are highly heterozygous as a result of out-crossing. Bulb formation is driven by daylength and therefore accessions tend to be adapted to their local photoperiod. For onion production, seed is directly sown in the field and hence seedling establishment is a critical trait. A major constraint to onion production is Fusarium basal rot (FBR), a global problem which is increasing in prevalence. The purpose of this study was to develop a unique onion diversity set, chosen to represent global diversity of the onion crop, and to screen the set for beneficial traits. A diversity set consisting of up to 10 half-sib families for each of 95 accessions was successfully developed and seed stored under long-term storage conditions. deoxyribonucleic acid (DNA) was extracted and the diversity set genotyped using 892 SNP markers, and the underlying population structure and relatedness determined. Moderate heterozygosity was noted, reflecting the outbreeding nature of onion. Using inferred phylogenies, population structure analysis and a principle component analysis, it was found that most accessions grouped according to local daylength conditions. A high level of intra-accession diversity was observed, though this was less than inter-accession diversity. One half-sib family per accession was screened for resistance to FOC and improved seedling vigor leading to the identification of highly resistant and vigorous accessions. This material will be of great benefit for future onion breeding. The phenotype data was then used to explore marker-trait associations leading to the identification of markers linked to the traits of interest. These associations provide crucial preliminary data to aid germplasm selection in future breeding programs and will be further developed when the genome sequence of onion becomes available.

Technical Abstract: Conserving biodiversity is critical for safeguarding the future of crop production. Onion is a globally important horticultural crop with a very large amount of deoxyribonucleic acid (DNA) which has not yet been sequenced. Onion bulb formation is affected by daylength and therefore accessions tend to be adapted to specific photoperiods. Onion seed is directly sown in the field and seedling establishment is a critical trait. A major constraint to onion production is Fusarium basal rot (FBR), a global problem which is increasing in prevalence. The purpose of this study was to develop a unique onion diversity set, chosen to represent global diversity of the onion crop, and to screen the set for beneficial traits. A diversity set consisting of up to 10 half-sib families for each of 95 accessions was successfully developed and seed stored under long-term storage conditions. DNA was extracted and the diversity set genotyped using 892 SNP markers, and the underlying population structure and relatedness determined. A moderate of heterozygosity (mode = 30-35%) was noted, reflecting the outbreeding nature of onion. Using inferred phylogenies, population structure analysis and a principle component analysis, it was found that most accessions grouped according to local daylength conditions. A high level of intra-accession diversity was observed, though this was less than inter-accession diversity. One half-sib family per accession was screened for resistance to FOC and improved seedling vigour leading to the identification of highly resistant and vigorous accessions. This material will be of great benefit for future onion breeding. The phenotype data was then used to explore marker-trait associations leading to the identification of markers linked to the analyzed traits. These associations provide crucial preliminary data to aid germplasm selection in future breeding programmes and will be further developed when the genome sequence of onion becomes available.These results will be of interest to onion breeders for introgression of desirable characteristics into elite cultivars.