A BAC-based physical map of the apple genome

被引：41

作者：

Han, Yuepeng

Gasic, Ksenija

Marron, Brandy

Beever, Jonathan E.

Korban, Schuyler S. ^{[1
]}

机构：

[1] Univ Illinois, Dept Nat Resources & Environm Sci, Urbana, IL 61801 USA

[2] Univ Illinois, Dept Anim Sci, Urbana, IL 61801 USA

来源：

GENOMICS | 2007年 / 89卷 / 05期

关键词：

BAC clone fingerprints; Contig map; apple genome; Contig assembly;

D O I：

10.1016/j.ygeno.2006.12.010

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Genome-wide physical mapping is an essential step toward investigating the genetic basis of complex traits as well as pursuing genomics research of virtually all plant and animal species. We have constructed a physical map of the apple genome from a total of 74,281 BAC clones representing similar to 10.5(x) haploid genome equivalents. The physical map consists of 2702 contigs, and it is estimated to span similar to 927 Mb in physical length. The reliability of contig assembly was evaluated by several methods, including assembling comigs using variable stringencies, assembling contigs using fingerprints from individual libraries, checking consensus maps of contigs, and using DNA markers. Altogether, the results demonstrated that the contigs were properly assembled. The apple genome-wide BAC-based physical map represents the first draft genome sequence not only for any member of the large Rosaceae family, but also for all tree species. This map will play a critical role in advanced genomics research for apple and other tree species, including marker development in targeted chromosome regions, fine-mapping and isolation of genes/QTL, conducting comparative genomics analyses of plant chromosomes, and large-scale genomics sequencing. (c) 2007 Elsevier Inc. All rights reserved.

引用

页码：630 / 637

页数：8

共 37 条

[21] A complete BAC-based physical map of the Arabidopsis thaliana genome [J].

Mozo, T ;

Dewar, K ;

Dunn, P ;

Ecker, JR ;

Fischer, S ;

Kloska, S ;

Lehrach, H ;

Marra, M ;

Martienssen, R ;

Meier-Ewert, S ;

Altmann, T .

NATURE GENETICS, 1999, 22 (03) :271-275

[22] Development and linkage mapping of E-STS and RGA markers for functional gene homologues in apple [J].

Naik, Suresh ;

Hampson, Cheryl ;

Gasic, Ksenija ;

Bakkeren, Guus ;

Korban, Schuyler S. .

GENOME, 2006, 49 (08) :959-968

[23] Whole-genome validation of high-information-content fingerprinting [J].

Nelson, WM ;

Bharti, AK ;

Butler, E ;

Wei, FS ;

Fuks, G ;

Kim, H ;

Wing, RA ;

Messing, J ;

Soderlund, C .

PLANT PHYSIOLOGY, 2005, 139 (01) :27-38

[24] Analyses of expressed sequence tags from apple [J].

Newcomb, RD ;

Crowhurst, RN ;

Gleave, AP ;

Rikkerink, EHA ;

Allan, AC ;

Beuning, LL ;

Bowen, JH ;

Gera, E ;

Jamieson, KR ;

Janssen, BJ ;

Laing, WA ;

McArtney, S ;

Nain, B ;

Ross, GS ;

Snowden, KC ;

Souleyre, EJF ;

Walton, EF ;

Yauk, YK .

PLANT PHYSIOLOGY, 2006, 141 (01) :147-166

[25] A BAC-based physical map of the chicken genome [J].

Ren, CW ;

Lee, MK ;

Yan, B ;

Ding, KJ ;

Cox, B ;

Romanov, MN ;

Price, JA ;

Dodgson, JB ;

Zhang, HB .

GENOME RESEARCH, 2003, 13 (12) :2754-2758

[26] Contigs built with fingerprints, markers, and FPCV4.7 [J].

Soderlund, C ;

Humphray, S ;

Dunham, A ;

French, L .

GENOME RESEARCH, 2000, 10 (11) :1772-1787

[27]

Tao QZ, 2001, GENETICS, V158, P1711

[28] Variation in nuclear DNA content in Malus species and cultivated apples [J].

Tatum, TC ;

Stepanovic, S ;

Biradar, DP ;

Rayburn, AL ;

Korban, SS .

GENOME, 2005, 48 (05) :924-930

[29] The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) [J].

Tuskan, G. A. ;

DiFazio, S. ;

Jansson, S. ;

Bohlmann, J. ;

Grigoriev, I. ;

Hellsten, U. ;

Putnam, N. ;

Ralph, S. ;

Rombauts, S. ;

Salamov, A. ;

Schein, J. ;

Sterck, L. ;

Aerts, A. ;

Bhalerao, R. R. ;

Bhalerao, R. P. ;

Blaudez, D. ;

Boerjan, W. ;

Brun, A. ;

Brunner, A. ;

Busov, V. ;

Campbell, M. ;

Carlson, J. ;

Chalot, M. ;

Chapman, J. ;

Chen, G. -L. ;

Cooper, D. ;

Coutinho, P. M. ;

Couturier, J. ;

Covert, S. ;

Cronk, Q. ;

Cunningham, R. ;

Davis, J. ;

Degroeve, S. ;

Dejardin, A. ;

dePamphilis, C. ;

Detter, J. ;

Dirks, B. ;

Dubchak, I. ;

Duplessis, S. ;

Ehlting, J. ;

Ellis, B. ;

Gendler, K. ;

Goodstein, D. ;

Gribskov, M. ;

Grimwood, J. ;

Groover, A. ;

Gunter, L. ;

Hamberger, B. ;

Heinze, B. ;

Helariutta, Y. .

SCIENCE, 2006, 313 (5793) :1596-1604

[30] Repetitive sequences:: cause for variation in genome size and chromosome morphology in the genus Oryza [J].

Uozu, S ;

Ikehashi, H ;

Ohmido, N ;

Ohtsubo, H ;

Ohtsubo, E ;

Fukui, K .

PLANT MOLECULAR BIOLOGY, 1997, 35 (06) :791-799

← 1 2 3 4 →