Two-dimensional screening of the Wageningen chicken BAC library

Abstract

We have constructed a Bacterial Artificial Chromosome (BAC) library that provides 5.5-fold redundant coverage of the chicken genome. The library was made by cloning partial HindIII-digested high-molecular-weight (HMW) DNA of a female White Leghorn chicken into the HindIII site of the vector pECBAC1. Several modifications of standard protocols were necessary to clone efficiently large partial HindIII DNA fragments. The library consists of 49,920 clones arranged in 130 384-well plates. An average insert size of 134 kb was estimated from the analysis of 152 randomly selected BAC clones. The average number of NotI restriction sites per clone was 0.77. After individual growth, DNA was isolated of the pooled clones of each 384-well plate, and subsequently DNA of each plate was isolated from the individual row and column pools. Screening of the Wageningen chicken BAC library was performed by two-dimensional PCR with 125 microsatellite markers. For 124 markers at least one BAC clone was obtained. FISH experiments of 108 BAC clones revealed chimerism in less than 1%. The number of different BAC clones per marker present in the BAC library was examined for 35 markers which resulted in a total of 167 different BAC clones. Per marker the number of BAC clones varied from 1 to 11, with an average of 4.77. The chicken BAC library constitutes an invaluable tool for positional cloning and for comparative mapping studies.

High-resolution mapping and transcriptional activity analysis of chicken centromere sequences on giant lampbrush chromosomes

“…Additionally, some BAC clones from the Wageningen chicken BAC library (Crooijmans et al 2000, http://www.bioinformatics.nl/gbrowse/cgi-bin/ gbrowse) were used to analyse the transcriptional status of centromeric sequences at the lampbrush stage, to identify the chicken microchromosome 27 and to control the efficiency of Zoo-FISH. The full list of BAC clones used in this study is presented in Table S1.…”

Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions

“…BAC clones from the Wageningen chicken BAC library (Crooijmans et al 2000, http://www.bioinformatics.nl/ gbrowse/cgi-bin/gbrowse) were selected based on the genomic positions assigned for corresponding markers. The selected BAC clones are listed in Table 1.…”

“…A new wave of comparative cytogenetic analysis of chicken and quail karyotypes was initiated when several libraries of chicken genome cloned fragments such as those cloned in bacterial artificial chromosomes (BACs) became available (e.g., Crooijmans et al 2000, reviewed in Schmid et al 2005, and integrated resources for chicken genome assembly were released (http://www.ncbi.nlm.nih.gov/genome/111, http://useast.ensembl.org/Gallus_gallus/Info/Index, http://genome.ucsc.edu). Fluorescent in situ hybridization (FISH) of the chicken-specific probes on chicken and quail metaphase chromosomes first confirmed the predicted pericentric inversions on chromosomes 1, 2, and 4 (Shibusawa et al 2001;Schmid et al 2005;Kayang et al 2006).…”

FISH on avian lampbrush chromosomes produces higher resolution gene mapping

“…Here we have applied chicken BAC clones (Zoorob et al, 1996;Crooijmans et al, 2000) to LBCs of chicken and Japanese quail. This approach allowed us to define the gene order in both chicken and quail genomes more precisely.…”