Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry
- Publication Date
- December 20, 2012
- Journal
- PLOS ONE
- Authors
- Cameron Peace, Nahla Bassil, Dorrie Main, Stephen Ficklin, et al
- Volume
- 7
- Issue
- 12
- Pages
- e48305
- DOI
- https://dx.plos.org/10.1371/journal.pone.0048305
- Publisher URL
- http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0048305
- PubMed
- http://www.ncbi.nlm.nih.gov/pubmed/23284615
- PubMed Central
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527432
- Europe PMC
- http://europepmc.org/abstract/MED/23284615
- Web of Science
- 000312794500005
- Scopus
- 84871449264
- Mendeley
- http://www.mendeley.com/research/development-evaluation-genomewide-6k-snp-array-diploid-sweet-cherry-tetraploid-sour-cherry
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Mendeley | Further Information
{"title"=>"Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry", "type"=>"journal", "authors"=>[{"first_name"=>"Cameron", "last_name"=>"Peace", "scopus_author_id"=>"6603597528"}, {"first_name"=>"Nahla", "last_name"=>"Bassil", "scopus_author_id"=>"6602607415"}, {"first_name"=>"Dorrie", "last_name"=>"Main", "scopus_author_id"=>"7005753580"}, {"first_name"=>"Stephen", "last_name"=>"Ficklin", "scopus_author_id"=>"8207326300"}, {"first_name"=>"Umesh R.", "last_name"=>"Rosyara", "scopus_author_id"=>"16302158300"}, {"first_name"=>"Travis", "last_name"=>"Stegmeir", "scopus_author_id"=>"36570928400"}, {"first_name"=>"Audrey", "last_name"=>"Sebolt", "scopus_author_id"=>"6508310464"}, {"first_name"=>"Barbara", "last_name"=>"Gilmore", "scopus_author_id"=>"55019603800"}, {"first_name"=>"Cindy", "last_name"=>"Lawley", "scopus_author_id"=>"23767892300"}, {"first_name"=>"Todd C.", "last_name"=>"Mockler", "scopus_author_id"=>"6602442579"}, {"first_name"=>"Douglas W.", "last_name"=>"Bryant", "scopus_author_id"=>"35232363500"}, {"first_name"=>"Larry", "last_name"=>"Wilhelm", "scopus_author_id"=>"20735983500"}, {"first_name"=>"Amy", "last_name"=>"Iezzoni", "scopus_author_id"=>"6602159357"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"366319149", "sgr"=>"84871449264", "issn"=>"19326203", "pmid"=>"23284615", "scopus"=>"2-s2.0-84871449264", "doi"=>"10.1371/journal.pone.0048305"}, "id"=>"0fd222b7-8ecf-38c6-a406-5f999e3a44e3", "abstract"=>"High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb) of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome) and P. fruticosa (fruticosa subgenome). Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour cherry genomes. SNPs were developed for each sour cherry subgenome by using minor allele frequency in the sour cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet cherry. The array was evaluated using panels of sweet (n = 269) and sour (n = 330) cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet cherry, 13% of these originally developed for sour cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour cherry, one third of these being originally developed for sweet cherry. This publicly available genomics resource represents a significant advance in cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group.", "link"=>"http://www.mendeley.com/research/development-evaluation-genomewide-6k-snp-array-diploid-sweet-cherry-tetraploid-sour-cherry", "reader_count"=>60, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>19, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>3, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>19, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>3, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>48, "Medicine and Dentistry"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>48}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Netherlands"=>1, "Japan"=>1, "Serbia and Montenegro"=>1, "United Kingdom"=>1, "Germany"=>1}, "group_count"=>0}CrossRef
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Scopus | Further Information
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Relative Metric
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