A large-fragment porcine genomic library resource in a BAC vector

Anderson, Stuart; Lopez-Corrales, Nestor L.; Gorick, B.D.; Archibald, Alan

doi:10.1007/s003350010155

Cited by 51 publications

(29 citation statements)

References 12 publications

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“…For fine mapping, BAC-clones (PigE BAC) from MCR geneservice (www.geneservice.co.uk͞home; ref. 30) were picked up by PCR screening with markers SW2411, SW419, and S0006 located within the disease-associated region on porcine chromosome 16. The selected BAC clones were isolated with the Qiagen plasmid midi kit protocol in accordance with the manufacturer's recommendations.…”

Section: Methodsmentioning

confidence: 99%

An intronic insertion in KPL2 results in aberrant splicing and causes the immotile short-tail sperm defect in the pig

Sironen

Thomsen²,

Andersson

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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The immotile short-tail sperm defect is an autosomal recessive disease within the Finnish Yorkshire pig population. This disease specifically affects the axoneme structure of sperm flagella, whereas cilia in other tissues appear unaffected. Recently, the disease locus was mapped to a 3-cM region on porcine chromosome 16. To facilitate identification of candidate genes, we constructed a porcine-human comparative map, which anchored the disease locus to a region on human chromosome 5p13.2 containing eight annotated genes. Sequence analysis of a candidate gene KPL2 revealed the presence of an inserted retrotransposon within an intron. The insertion affects splicing of the KPL2 transcript in two ways; it either causes skipping of the upstream exon, or causes the inclusion of an intronic sequence as well as part of the insertion in the transcript. Both changes alter the reading frame leading to premature termination of translation. Further work revealed that the aberrantly spliced exon is expressed predominantly in testicular tissue, which explains the tissue-specificity of the immotile short-tail sperm defect. These findings show that the KPL2 gene is important for correct axoneme development and provide insight into abnormal sperm development and infertility disorders.cilia ͉ retrotransposon ͉ spermatogenesis

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Section: Methodsmentioning

confidence: 99%

An intronic insertion in KPL2 results in aberrant splicing and causes the immotile short-tail sperm defect in the pig

Sironen

Thomsen²,

Andersson

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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“…Recently, whole-genome radiation hybrid (WG-RH) panels (7500 and 12 500 rad) have been generated for swine (Hawken et al, 1999;Yerle et al, 2002), resulting in yet another rapid increase in the number of expressed sequences being mapped, facilitating comparative mapping with other species (Rinke et al, 2002). The swine genomics community has also acquired access to resources such as bacterial artificial chromosome (BAC) libraries (Fahrenkrug et al, 2001;Anderson et al, 2000) that provide approximately 35× coverage of the swine genome. These BAC resources have facilitated the production of high-resolution physical maps in specific chromosomal regions (Rogel-Gaillard et al, 1999;Milan et al, 2000) and support the construction of sequence-ready mapping resources for the porcine genome.…”

Section: Background and Discussionmentioning

confidence: 99%

“…A coordinated international effort was initiated to develop a porcine BAC map with two BAC libraries (RPCI-44 and CHORI-242) made by Pieter J. de Jong, one library made at the Roslin Institute (Anderson et al, 2000), and a library produced at INRA (Rogel-Gaillard et al, 1999). Through the exchange of BAC clones, data has been merged to permit a comprehensive analysis.…”

Section: The Swine Genome Sequencing Consortium (Sgsc)mentioning

confidence: 99%

Swine Genome Sequencing Consortium (SGSC): a strategic roadmap for sequencing the pig genome

et al. 2005

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The Swine Genome Sequencing Consortium (SGSC) was formed in September 2003 by academic, government and industry representatives to provide international coordination for sequencing the pig genome. The SGSC's mission is to advance biomedical research for animal production and health by the development of DNAbased tools and products resulting from the sequencing of the swine genome. During the past 2 years, the SGSC has met bi-annually to develop a strategic roadmap for creating the required scientific resources, to integrate existing physical maps, and to create a sequencing strategy that captured international participation and a broad funding base. During the past year, SGSC members have integrated their respective physical mapping data with the goal of creating a minimal tiling path (MTP) that will be used as the sequencing template. During the recent Plant and Animal Genome meeting (January 16, 2005 San Diego, CA), presentations demonstrated that a human-pig comparative map has been completed, BAC fingerprint contigs (FPC) for each of the autosomes and X chromosome have been constructed and that BAC end-sequencing has permitted, through BLAST analysis and RH-mapping, anchoring of the contigs. Thus, significant progress has been made towards the creation of a MTP. In addition, whole-genome (WG) shotgun libraries have been constructed and are currently being sequenced in various laboratories around the globe. Thus, a hybrid sequencing approach in which 3× coverage of BACs comprising the MTP and 3× of the WG-shotgun libraries will be used to develop a draft 6× coverage of the pig genome.

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“…BAC libraries have been constructed for several species of agricultural importance, including cattle (Cai et al, 1995;Zhu et al, 1999;Buitkamp et al, 2000;Warren et al, 2000;Eggen et al, 2001;Fujisaki et al, 2002), goat , horse (Godard et al, 1998), pig (Rogel-Gaillard et al, 1999Anderson et al, 2000;Suzuki et al, 2000;Fahrenkrug et al, 2001;Jeon et al, 2003;Liu et al, 2010), and sheep (Gill et al, 1999;Vaiman et al, 1999). Although large-insert DNA libraries from closely related ruminant species such as cattle, goat, and sheep have been used for in situ hybridization experiments in buffalo (Di Meo et al, 2005Perucatti et al, 2009), a buffalo library is necessary for whole-genome physical mapping and isolation of genes and gene clusters as well as for the identification of regulatory elements.…”

Section: Introductionmentioning

confidence: 99%

Construction and preliminary characterization of a river buffalo bacterial artificial chromosome library

Stafuzza

Abbey²,

Gill

et al. 2012

Genet. Mol. Res.

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ABSTRACT. River buffalo genome analyses have advanced significantly in the last decade, and the genome sequence of Bubalus bubalis will be available shortly. Nonetheless, large-insert DNA library resources such as bacterial artificial chromosomes (BAC) are still required for validation and accurate assembly of the genome sequence. We constructed a river buffalo BAC library containing 52,224 clones with an average insert size of 97 kb, representing 1.7 × coverage of the genome. This genomic resource for river buffalo will facilitate further studies in this economically important species allowing for instance, whole genome physical mapping and isolation of genes and gene clusters, contributing to the elucidation of gene organization and identification of regulatory elements.

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A large-fragment porcine genomic library resource in a BAC vector

Cited by 51 publications

References 12 publications

An intronic insertion in KPL2 results in aberrant splicing and causes the immotile short-tail sperm defect in the pig

An intronic insertion in KPL2 results in aberrant splicing and causes the immotile short-tail sperm defect in the pig

Swine Genome Sequencing Consortium (SGSC): a strategic roadmap for sequencing the pig genome

Construction and preliminary characterization of a river buffalo bacterial artificial chromosome library

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