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Single nucleotide polymorphisms and insertiondeletions for genetic markers and anchoring the maize FingerPrint Contig Physical Map

dc.contributor.authorVroh Bi, Irie
dc.contributor.authorMcMullen, M.
dc.contributor.authorSanchez-Villeda, H.
dc.contributor.authorSchroeder, S.
dc.contributor.authorGardiner, J.
dc.contributor.authorPolacco, M.
dc.contributor.authorSoderlund, C.
dc.contributor.authorWing, R.
dc.contributor.authorFang, Z.
dc.contributor.authorCoe, E.
dc.date.accessioned2019-12-04T11:18:10Z
dc.date.available2019-12-04T11:18:10Z
dc.date.issued2006
dc.identifier.citationVroh Bi, I., McMullen, M., Sanchez-Villeda, H., Schroeder, S., Gardiner, J., Polacco, M., ... & Coe, E. (2006). Single nucleotide polymorphisms and insertion-deletions for genetic markers and anchoring the maize FingerPrint Contig Physical Map. Crop Science, 46(1), 12-26.
dc.identifier.issn0011-183X; 1435-0653
dc.identifier.urihttps://hdl.handle.net/20.500.12478/3089
dc.description.abstractSingle nucleotide polymorphisms (SNPs) and insertion–deletions (InDels) are becoming important genetic markers for major crop species. In this study we demonstrate their utility for locating fingerprint contigs (FPCs) to the genetic map. To derive SNP and InDel markers, we amplified genomic regions corresponding to 3000 unigenes across 12 maize (Zea mays L.) lines, of which 194 unigenes (6.4%) showed size polymorphism InDels between B73 and Mo17 on agarose gels. The analysis of these InDels in 83 diverse inbred lines showed that InDels are often multiallelic markers in maize. Single nucleotide polymorphism discovery conducted on 592 unigenes revealed that 44% of the unigenes contained B73/Mo17 SNPs, while 8% showed no sequence variation among the 12 inbred lines. On average, SNPs and InDels occurred every 73 and 309 bp, respectively. Multiple SNPs within unigenes led to a SNP haplotype genetic diversity of 0.61 among inbreds. The unigenes were previously assigned to maize FPCs by overgo hybridization. From this set of unigenes, 311 (133 SNP and 178 InDel) loci were mapped on the intermated B73 × Mo17 (IBM) high-resolution mapping population. These markers provided unambiguous anchoring of 129 FPCs and orientation for 30 contigs. The FPC anchored map of maize will be useful for map-based cloning, for genome sequencing efforts in maize, and for comparative genomics in grasses. The amplification primers for all mapped InDel and SNP loci, the diversity information for SNPs and InDels, and the corresponding overgoes to anchor bacterial artificial chromosome (BAC) contigs are provided as genetic resources.
dc.description.sponsorshipNational Science Foundation
dc.language.isoen
dc.subjectMolecular
dc.subjectSingle Nucleotide Polymorphism
dc.subjectUnigenes
dc.subjectPhenotype
dc.subjectGenome Sequencing
dc.subjectCloning
dc.titleSingle nucleotide polymorphisms and insertiondeletions for genetic markers and anchoring the maize FingerPrint Contig Physical Map
dc.typeJournal Article
dc.description.versionPeer Review
cg.contributor.affiliationCornell University
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationUniversity of Missouri
cg.contributor.affiliationUnited States Department of Agriculture
cg.contributor.affiliationUniversity of Arizona
cg.coverage.regionAcp
cg.coverage.regionNorth America
cg.coverage.regionSouth America
cg.coverage.countryUnited States
cg.coverage.countryColombia
cg.isijournalISI Journal
cg.authorship.typesCGIAR and advanced research institute
cg.iitasubjectLivelihoods
cg.iitasubjectBioscience
cg.iitasubjectGenetic Improvement
cg.iitasubjectDiseases Control
cg.iitasubjectImpact Assessment
cg.iitasubjectPests Of Plants
cg.iitasubjectPlant Breeding
cg.iitasubjectPlant Genetic Resources
cg.iitasubjectPlant Health
cg.iitasubjectPlant Production
cg.iitasubjectMaize
cg.iitasubjectPlant Diseases
cg.accessibilitystatusLimited Access
local.dspaceid94555
cg.identifier.doihttps://dx.doi.org/10.2135/cropsci2004.0706


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