Construction of a citrus framework genetic map anchored by 708 gene-based markers

Publication Overview
TitleConstruction of a citrus framework genetic map anchored by 708 gene-based markers
AuthorsShimada T, Fujii H, Endo T, Ueda T, Sugiyama A, Nakano M, Kita M, Yoshioka T, Shimizu T, Nesumi H, Ikoma Y, Moriguchi T, Omura M
TypeJournal Article
Journal NameTree genetics & genomes
Volume10
Issue4
Year2014
Page(s)1001-1013
CitationShimada T, Fujii H, Endo T, Ueda T, Sugiyama A, Nakano M, Kita M, Yoshioka T, Shimizu T, Nesumi H, Ikoma Y, Moriguchi T, Omura M. Construction of a citrus framework genetic map anchored by 708 gene-based markers. Tree genetics & genomes. 2014; 10(4):1001-1013.

Abstract

We developed 708 gene-based markers for citrus genome analysis. Sequence-tagged site (STS) primers were designed that were located in conserved exon regions and whose PCR products spanned genomic introns. Of these, 79.7 % comprised cleaved amplified polymorphic sequence markers. The gene-based markers and their annotation and position on Clementine scaffolds ver. 1.0 permitted comparison of the genetic map and the Clementine genome sequence. The 708 gene-based markers were used to construct a genetic map using the 87 progenies (AG population) from the cross between ‘Okitsu 46 gou’ (‘Sweet Spring’ (‘Ueda unshiu’ (Citrus unshiu) × Hassaku (Citrus hassaku Hort. ex Tanaka)) × ‘Trovita’ orange) × ‘Kankitsu Chukanbohon Nou 5 gou’ (‘Lee’ (Citrus clementina × tangelo) × Citrus kinokuni). The markers were integrated using common STSs on different phase maps in cross-pollination mode. The integrated map (AGI map) comprised 706 loci, including two morphological traits, and spanned 990.9 centimorgans (cM) with an average marker distance of 1.40 cM. These markers formed nine linkage groups (LGs) (corresponding to citrus physical chromosomes): LG-01 to LG-09 corresponded to Scaffold_01, Scaffold_07, Scaffold_09, Scaffold_06, Scaffold_03, Scaffold_02, Scaffold_04, Scaffold_08, and Scaffold_05, respectively. LG-08 and LG-09 contained morphological traits controlling embryo color and seedlessness. Eighty-eight loci comprised three or more alleles on the AGI map; 36.4 % of them were related to transcription factors and DNA-binding proteins. The 708 gene-based markers and the AGI map are valuable for integrating various citrus genetic maps, alignment of genomic sequences, chromosome assignment, and understanding the diversity of citrus germplasms.
Featuremaps
This publication contains information about 1 maps:
Map Name
Citrus-Okitsu-46-gou/Kankitsu-Chukanbohon-Nou-5-gou-F2-2014
Stocks
This publication contains information about 3 stocks:
Stock NameUniquenameType
Okitsu-46-gouOkitsu-46-gouaccession
Kankitsu-Chukanbohon-Nou-5-gouKankitsu-Chukanbohon-Nou-5-gouaccession
Citrus-Okitsu-46-gou/Kankitsu-Chukanbohon-Nou-5-gou-F2Citrus-Okitsu-46-gou/Kankitsu-Chukanbohon-Nou-5-gou-F2population
Features
This publication contains information about 710 features:
Feature NameUniquenameType
Cp0100Cp0100genetic_marker
Cp0106Cp0106genetic_marker
Cp0114Cp0114genetic_marker
Cp0160Cp0160genetic_marker
Cp0185Cp0185genetic_marker
Cp0190Cp0190genetic_marker
Cp0214Cp0214genetic_marker
Cp0233Cp0233genetic_marker
Cp0237Cp0237genetic_marker
Cp0249Cp0249genetic_marker
Cp0257Cp0257genetic_marker
Cp0278Cp0278genetic_marker
Cp0297Cp0297genetic_marker
Cp0336Cp0336genetic_marker
Cp0384Cp0384genetic_marker
Cp0415Cp0415genetic_marker
Cp0419Cp0419genetic_marker
Cp0431Cp0431genetic_marker
Cp0452Cp0452genetic_marker
Cp0454Cp0454genetic_marker
Cp0459Cp0459genetic_marker
Cp0506Cp0506genetic_marker
Cp0532Cp0532genetic_marker
Cp0537Cp0537genetic_marker
Cp0540Cp0540genetic_marker

Pages

Properties
Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
Publication Date2014
Published Location|||
Language Abbreng
Publication Model[electronic resource].
URLhttp://dx.doi.org/10.1007/s11295-014-0738-9
KeywordsCitrus clementina, Citrus hassaku, Citrus unshiu, DNA-binding proteins, alleles, clementines, color, cross pollination, exons, germplasm, introns, linkage groups, loci, polymerase chain reaction, seedless varieties, tangelos, transcription factors
Cross References
This publication is also available in the following databases:
DatabaseAccession
AGL: USDA National Agricultural LibraryAGL:4847006