Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm
Visualitza/Obre
Autor/a
Verde, Ignazio
Bassil, Nahla
Scalabrin, Simone
Gilmore, Barbara
Lawley, Cynthia T.
Gasic, Ksenija
Micheletti, Diego
Rosyara, Umesh R.
Cattonaro, Federica
Vendramin, Elisa
Main, Dorrie
Aramini, Valeria
Blas, Andrea L.
Mockler, Todd C.
Bryant, Douglas W.
Wilhelm, Larry
Troggio, Michela
Sosinski, Bryon
Iezzoni, Amy
Morgante, Michele
Peace, Cameron
Data de publicació
2012-04-20ISSN
1932-6203
Resum
Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to
enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and markerassisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers,
including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium
(The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in
peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina InfiniumH SNP
genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina
and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs.
Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ,75% of genic
(exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to
arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach
chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of
peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs. The almost 7,000 SNPs
verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies
in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC
peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and
related stone fruit and nut species.
Tipus de document
Article
Versió del document
Versió publicada
Llengua
English
Matèries (CDU)
575 - Genètica general. Citogenètica general. Immunogenètica. Evolució. Filogènia
Pàgines
13
Publicat per
Public Library of Science
Publicat a
PLoS ONE
Citació
Verde, Ignazio, Nahla V. Bassil, Simone Scalabrin, Barbara Gilmore, Cindy Lawley, Ksenija Gašić, Diego Micheletti, et al. 2012. “Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm.” PloS One 7 (4): e35668. doi:10.1371/journal.pone.0035668.
Número de l'acord de la subvenció
EC/FP7/265582/EU/Integrated approach for increasing breeding efficiency in fruit tree crops/FRUIT BREEDOMICS
MICINN/Programa Nacional de Proyectos de Investigación Fundamental/AGL2009-07305/ES/Evaluacion E Introgresion De Nuevas Fuentes De Variabilidad Genetica En Germoplasma De Melocotonero Europeo Y Norte-Americano/
MEC/Programa nacional de medios de transporte/CSD2007-00036/ES/Centro de Genómica Básica y de orientación Agroalimentaria/
Programa
Genòmica i Biotecnologia
Aquest element apareix en la col·lecció o col·leccions següent(s)
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