Advances in BAC-Based Physical Mapping and Map Integration Strategies in Plants

Ariyadasa, Ruvini; Stein, Nils

doi:10.1155/2012/184854

Cited by 33 publications

(33 citation statements)

References 93 publications

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“…Features such as high stability, minimal chimerism and ease of purification of large inserts characterize the BAC vector system as a suitable source of intact DNA fragments for constructing large-scale detailed physical maps of genomic regions. The construction of BAC-based physical maps and their interaction with high-density genetic maps have benefited from next-generation sequencing (NGS) and high-throughput array platforms [Ariyadasa and Stein, 2012]. Although the development of whole-genome shotgun sequence draft maps based on NGS has become costeffective recently, a physical map remains an important component of genome sequencing projects [Nelson and Soderlund, 2009].…”

Section: A Preliminary Genetic Map Inmentioning

confidence: 99%

A Preliminary Genetic Map in Solea senegalensis (Pleuronectiformes, Soleidae) Using BAC-FISH and Next-Generation Sequencing

García-Cegarra¹,

Merlo²,

Ponce³

et al. 2013

Cytogenet Genome Res

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This article presents the first physical mapping carried out in the Senegalese sole (Solea senegalensis), an important marine fish species of Southern Europe. Eight probes were designated to pick up genes of interest in aquaculture (candidate genes) from a bacterial artificial chromosome (BAC) library using a method of rapid screening based on a 4-dimension PCR. Seven known and 3 unknown clones were isolated and labeled. The 10 BAC clones were used as probes to map the karyotype of the species by fluorescence in situ hybridization (FISH). Nine out of the 10 clones were localized in only 1 chromosome pair, whereas the remaining one hybridized on 2 chromosome pairs. The 2-color FISH experiments showed colocation of 4 probes in 2 chromosome pairs. In addition, 2-color FISH was carried out both with 5S rDNA and the BAC containing the lysozyme gene published previously. This first genetic map of the Senegalese sole represents a starting point for future studies of the sole genome. In addition, 7 out of the 10 BAC clones were sequenced using next-generation sequencing, and bioinformatic characterization of the sequences was carried out. Hence the anchoring of the sequences to specific chromosomes or chromosome arms is now possible, leading to an initial scaffold of the Senegalese sole genome.

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Section: A Preliminary Genetic Map Inmentioning

confidence: 99%

A Preliminary Genetic Map in Solea senegalensis (Pleuronectiformes, Soleidae) Using BAC-FISH and Next-Generation Sequencing

García-Cegarra¹,

Merlo²,

Ponce³

et al. 2013

Cytogenet Genome Res

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“…High-quality reference sequences continue to be constructed with the help of physical maps and sequencing single bacterial artificial chromosomes (BACs; Groenen et al, 2012; Amborella Genome Project, 2013). However, this hierarchical shotgun approach entails the laborious and expensive steps of BAC library construction, finger-printing and clone-by-clone sequencing (Ariyadasa and Stein, 2012). …”

Section: Introductionmentioning

confidence: 99%

Genetic anchoring of whole-genome shotgun assemblies

Mascher

Stein

2014

Front. Genet.

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The recent advances in sequencing throughput and genome assembly algorithms have established whole-genome shotgun (WGS) assemblies as the cornerstone of the genomic infrastructure for many species. WGS assemblies can be constructed with comparative ease and give a comprehensive representation of the gene space even of large and complex genomes. One major obstacle in utilizing WGS assemblies for important research applications such as gene isolation or comparative genomics has been the lack of chromosomal positioning and contextualization of short sequence contigs. Assigning chromosomal locations to sequence contigs required the construction and integration of genome-wide physical maps and dense genetic linkage maps as well as synteny to model species. Recently, methods to rapidly construct ultra-dense linkage maps encompassing millions of genetic markers from WGS sequencing data of segregating populations have made possible the direct assignment of genetic positions to short sequence contigs. Here, we review recent developments in the integration of WGS assemblies and sequence-based linkage maps, discuss challenges for further improvement of the methodology and outline possible applications building on genetically anchored WGS assemblies.

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“…Large-insert genomic libraries are usually used in the generation of chromosome contigs in physical mapping, and the isolation of genes by map-based cloning (Ariyadasa and Stein, 2012). To achieve the goal of this study, an O. officinalis genomic TAC library was screened to identify clones that contained stress-related NAC transcription factor genes.…”

Section: Discussionmentioning

confidence: 99%

Drought-tolerant rice germplasm developed from an Oryza officinalis transformation-competent artificial chromosome clone

Liu¹,

Zhang²,

Chen³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Oryza officinalis has proven to be a natural gene reservoir for the improvement of domesticated rice as it carries many desirable traits; however, the transfer of elite genes to cultivated rice by conventional hybridization has been a challenge for rice breeders. In this study, the conserved sequence of plant stress-related NAC transcription factors was selected as a probe to screen the O. officinalis genomic transformation-competent artificial chromosome library by Southern blot; 11 positive transformation-competent artificial chromosome clones were subsequently detected. By Agrobacterium-mediated transformation, an indica rice variety, Huajingxian 74 (HJX74), was transformed with a TAC clone harboring a NAC gene-positive genomic fragment from O. officinalis. Molecular analysis revealed that the O. officinalis genomic fragment was integrated into the genome of HJX74. The transgenic lines exhibited high tolerance to drought stress. Our results demonstrate that the introduction of stress-related transformation-competent artificial chromosome clones, coupled with a transgenic validation approach, is an 13667-13678 (2015) effective method of transferring agronomically important genes from O. officinalis to cultivated rice.

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Advances in BAC-Based Physical Mapping and Map Integration Strategies in Plants

Cited by 33 publications

References 93 publications

A Preliminary Genetic Map in <b><i>Solea senegalensis</i></b> (Pleuronectiformes, Soleidae) Using BAC-FISH and Next-Generation Sequencing

A Preliminary Genetic Map in <b><i>Solea senegalensis</i></b> (Pleuronectiformes, Soleidae) Using BAC-FISH and Next-Generation Sequencing

Genetic anchoring of whole-genome shotgun assemblies

Drought-tolerant rice germplasm developed from an Oryza officinalis transformation-competent artificial chromosome clone

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