TY - JOUR
T1 - A BAC-based physical map of the apple genome
AU - Han, Yuepeng
AU - Gasic, Ksenija
AU - Marron, Brandy
AU - Beever, Jonathan Edward
AU - Korban, Schuyler S.
N1 - Funding Information:
This project was supported by the USDA Cooperative State Research, Education and Extension Service–National Research Initiative, Plant Genome Program Grant 2005-35300-15538.
PY - 2007/5
Y1 - 2007/5
N2 - 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 ∼ 10.5× haploid genome equivalents. The physical map consists of 2702 contigs, and it is estimated to span ∼ 927 Mb in physical length. The reliability of contig assembly was evaluated by several methods, including assembling contigs 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.
AB - 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 ∼ 10.5× haploid genome equivalents. The physical map consists of 2702 contigs, and it is estimated to span ∼ 927 Mb in physical length. The reliability of contig assembly was evaluated by several methods, including assembling contigs 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.
KW - Apple genome
KW - BAC clone fingerprints
KW - Contig assembly
KW - Contig map
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U2 - 10.1016/j.ygeno.2006.12.010
DO - 10.1016/j.ygeno.2006.12.010
M3 - Article
C2 - 17270394
AN - SCOPUS:34247098814
SN - 0888-7543
VL - 89
SP - 630
EP - 637
JO - Genomics
JF - Genomics
IS - 5
ER -