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Assembly and characterisation of a unique onion diversity set identifies resistance to Fusarium basal rot and improved seedling vigour
Wednesday, 2019/11/27 | 08:00:39

Andrew Taylor,Graham R. Teakle, Peter G. Walley, William E. Finch-Savage, Alison C. Jackson, Julie E. Jones, Paul Hand, Brian Thomas, Michael J. Havey, David A. C. Pink, John P. Clarkson


Theoretical and Applied Genetics

December 2019, Volume 132, Issue 12pp 3245–3264

Key message

A unique, global onion diversity set was assembled, genotyped and phenotyped for beneficial traits. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers.


Conserving biodiversity is critical for safeguarding future crop production. Onion (Allium cepa L.) is a globally important crop with a very large (16 Gb per 1C) genome which has not been sequenced. While 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 accessions are adapted to the local photoperiod. Onion seed is often directly sown in the field, and hence seedling establishment is a critical trait for production. Furthermore, onion yield losses regularly occur worldwide due to Fusarium basal rot caused by Fusarium oxysporum f. sp. cepae. A globally relevant onion diversity set, consisting of 10 half-sib families for each of 95 accessions, was assembled and genotyping carried out using 892 SNP markers. A moderate level of heterozygosity (30–35%) was observed, reflecting the outbreeding nature of the crop. Using inferred phylogenies, population structure and principal component analyses, most accessions grouped according to local daylength. A high level of intra-accession diversity was observed, but this was less than inter-accession diversity. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers, confirming the utility of the diversity set for discovering beneficial traits. The onion diversity set and associated trait data therefore provide a valuable resource for future germplasm selection and onion breeding.


See https://link.springer.com/article/10.1007/s00122-019-03422-0


Figure 1: Frequency distribution of recorded heterozygous alleles for 94 accessions in the onion diversity set. A total of 765 KASP markers with minor allele frequency < 5%, with 5 or fewer missing data points, and with zero or one inconsistent alleles in the half-sib female parent analysis (Table S4) were used to determine the proportion of heterozygous alleles

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