The cultivated strawberry, Fragaria × ananassa possesses a genetically complex allo-octoploid genome. Advances in genomics research in Fragaria, including the release of a genome sequence for F. vesca, have permitted the development of a high throughput whole genome genotyping array for strawberry, which promises to facilitate genetics and genomics research. In this investigation, we used the Axiom® IStraw90® array for linkage map development, and produced a linkage map containing 8,407 SNP markers spanning 1,820 cM. Whilst the linkage map provides good coverage of the genome of both parental genotypes, the map of ‘Monterey’ contained significantly fewer mapped markers than did that of ‘Darselect’. The array contains a novel marker class known as haploSNPs, which exploit homoeologous sequence variants as probe destabilization sites to effectively reduce marker ploidy. We examined these sites as potential indicators of subgenomic identities by using comparisons to allele states in two ancestral diploids. On this basis, haploSNP loci could be inferred to be derived from F. vesca, F. iinumae, or from an unknown source. When the identity classifications of haploSNPs were considered in conjunction with their respective linkage map positions, it was possible to define two discrete subgenomes, while the remaining homoeologues of each chromosome could not be partitioned into two discrete subgenomic groupings. These findings suggested a novel hypothesis regarding octoploid strawberry subgenome structure and evolutionary origins

Sargent, D.J.; Yang, Y.; Surbanovski, N.; Bianco, L.; Buti, M.; Velasco, R.; Giongo, L.; Davis, T.M. (2016). HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry (Fragaria ×ananassa).. PLANT SCIENCE, 242 (1): 240-250. doi: 10.1016/j.plantsci.2015.07.004 handle: http://hdl.handle.net/10449/27587

HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry (Fragaria ×ananassa).

Sargent, Daniel James;Surbanovski, Nada;Bianco, Luca;Buti, Matteo;Velasco, Riccardo;Giongo, Lara;
2016-01-01

Abstract

The cultivated strawberry, Fragaria × ananassa possesses a genetically complex allo-octoploid genome. Advances in genomics research in Fragaria, including the release of a genome sequence for F. vesca, have permitted the development of a high throughput whole genome genotyping array for strawberry, which promises to facilitate genetics and genomics research. In this investigation, we used the Axiom® IStraw90® array for linkage map development, and produced a linkage map containing 8,407 SNP markers spanning 1,820 cM. Whilst the linkage map provides good coverage of the genome of both parental genotypes, the map of ‘Monterey’ contained significantly fewer mapped markers than did that of ‘Darselect’. The array contains a novel marker class known as haploSNPs, which exploit homoeologous sequence variants as probe destabilization sites to effectively reduce marker ploidy. We examined these sites as potential indicators of subgenomic identities by using comparisons to allele states in two ancestral diploids. On this basis, haploSNP loci could be inferred to be derived from F. vesca, F. iinumae, or from an unknown source. When the identity classifications of haploSNPs were considered in conjunction with their respective linkage map positions, it was possible to define two discrete subgenomes, while the remaining homoeologues of each chromosome could not be partitioned into two discrete subgenomic groupings. These findings suggested a novel hypothesis regarding octoploid strawberry subgenome structure and evolutionary origins
Cultivated strawberry
Whole genome genotyping
SNP array
Genome evolution
Polyploidy
Settore BIO/11 - BIOLOGIA MOLECOLARE
2016
Sargent, D.J.; Yang, Y.; Surbanovski, N.; Bianco, L.; Buti, M.; Velasco, R.; Giongo, L.; Davis, T.M. (2016). HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry (Fragaria ×ananassa).. PLANT SCIENCE, 242 (1): 240-250. doi: 10.1016/j.plantsci.2015.07.004 handle: http://hdl.handle.net/10449/27587
File in questo prodotto:
File Dimensione Formato  
2016 PS Sargent et al.pdf

solo utenti autorizzati

Licenza: Tutti i diritti riservati (All rights reserved)
Dimensione 2.02 MB
Formato Adobe PDF
2.02 MB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10449/27587
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 49
  • ???jsp.display-item.citation.isi??? 50
social impact