Targeted Capture of Homoeologous Coding and Noncoding Sequence in Polyploid Cotton

dc.contributor.author Salmon, Armel
dc.contributor.author Udall, Joshua
dc.contributor.author Wendel, Jonathan
dc.contributor.author Jeddeloh, Jeffrey
dc.contributor.author Wendel, Jonathan
dc.contributor.department Ecology, Evolution and Organismal Biology
dc.date 2018-02-17T02:42:08.000
dc.date.accessioned 2020-06-30T02:18:59Z
dc.date.available 2020-06-30T02:18:59Z
dc.date.copyright Sun Jan 01 00:00:00 UTC 2012
dc.date.issued 2012-08-01
dc.description.abstract <p>Targeted sequence capture is a promising technology in many areas in biology. These methods enable efficient and relatively inexpensive sequencing of hundreds to thousands of genes or genomic regions from many more individuals than is practical using whole-genome sequencing approaches. Here, we demonstrate the feasibility of target enrichment using sequence capture in polyploid cotton. To capture and sequence both members of each gene pair (homeologs) of wild and domesticated Gossypium hirsutum, we created custom hybridization probes to target 1000 genes (500 pairs of homeologs) using information from the cotton transcriptome. Two widely divergent samples of G. hirsutum were hybridized to four custom NimbleGen capture arrays containing probes for targeted genes. We show that the two coresident homeologs in the allopolyploid nucleus were efficiently captured with high coverage. The capture efficiency was similar between the two accessions and independent of whether the samples were multiplexed. A significant amount of flanking, nontargeted sequence (untranslated regions and introns) was also captured and sequenced along with the targeted exons. Intraindividual heterozygosity is low in both wild and cultivated Upland cotton, as expected from the high level of inbreeding in natural G. hirsutum and bottlenecks accompanying domestication. In addition, levels of heterozygosity appeared asymmetrical with respect to genome (A(T) or D(T)) in cultivated cotton. The approach used here is general, scalable, and may be adapted for many different research inquiries involving polyploid plant genomes.</p>
dc.description.comments <p>This article is from <em>G3</em> 2 (2012): 921, doi:<a href="http://dx.doi.org/10.1534/g3.112.003392" target="_blank">10.1534/g3.112.003392</a>. Posted with permission.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/eeob_ag_pubs/68/
dc.identifier.articleid 1062
dc.identifier.contextkey 7707423
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath eeob_ag_pubs/68
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/23324
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/eeob_ag_pubs/68/2012_Wendel_TargetdCapture.pdf|||Sat Jan 15 01:28:40 UTC 2022
dc.source.uri 10.1534/g3.112.003392
dc.subject.disciplines Botany
dc.subject.disciplines Ecology and Evolutionary Biology
dc.subject.disciplines Genetics and Genomics
dc.subject.disciplines Plant Breeding and Genetics
dc.subject.keywords Gossypium
dc.subject.keywords allopolyploidy
dc.subject.keywords homoeologs
dc.subject.keywords next-generation sequencing
dc.subject.keywords sequence capture
dc.title Targeted Capture of Homoeologous Coding and Noncoding Sequence in Polyploid Cotton
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication 6d2c458f-b99a-4af5-8869-8b7b2e304592
relation.isOrgUnitOfPublication 6fa4d3a0-d4c9-4940-945f-9e5923aed691
File
Original bundle
Now showing 1 - 1 of 1
Name:
2012_Wendel_TargetdCapture.pdf
Size:
1.73 MB
Format:
Adobe Portable Document Format
Description:
Collections