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
AF0004AF0004genetic_marker
Af0015Af0015genetic_marker
Af0016Af0016genetic_marker
Af1003Af1003genetic_marker
Af1017Af1017genetic_marker
Af1031Af1031genetic_marker
Af1036Af1036genetic_marker
Af1037Af1037genetic_marker
Af1042Af1042genetic_marker
Af1043Af1043genetic_marker
Af1047Af1047genetic_marker
Af1052Af1052genetic_marker
Af1056Af1056genetic_marker
Af1059Af1059genetic_marker
Af1060Af1060genetic_marker
Af1062Af1062genetic_marker
Af1068Af1068genetic_marker
Af1084Af1084genetic_marker
Af1086Af1086genetic_marker
Af1087Af1087genetic_marker
Af1091Af1091genetic_marker
Af1094Af1094genetic_marker
Af1096Af1096genetic_marker
Af1100Af1100genetic_marker
Af1109Af1109genetic_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