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A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L

BACKGROUND: Chickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of...

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Autores principales: Zhang, Xiaojun, Scheuring, Chantel F, Zhang, Meiping, Dong, Jennifer J, Zhang, Yang, Huang, James J, Lee, Mi-Kyung, Abbo, Shahal, Sherman, Amir, Shtienberg, Dani, Chen, Weidong, Muehlbauer, Fred, Zhang, Hong-Bin
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996997/
https://www.ncbi.nlm.nih.gov/pubmed/20849583
http://dx.doi.org/10.1186/1471-2164-11-501
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author Zhang, Xiaojun
Scheuring, Chantel F
Zhang, Meiping
Dong, Jennifer J
Zhang, Yang
Huang, James J
Lee, Mi-Kyung
Abbo, Shahal
Sherman, Amir
Shtienberg, Dani
Chen, Weidong
Muehlbauer, Fred
Zhang, Hong-Bin
author_facet Zhang, Xiaojun
Scheuring, Chantel F
Zhang, Meiping
Dong, Jennifer J
Zhang, Yang
Huang, James J
Lee, Mi-Kyung
Abbo, Shahal
Sherman, Amir
Shtienberg, Dani
Chen, Weidong
Muehlbauer, Fred
Zhang, Hong-Bin
author_sort Zhang, Xiaojun
collection PubMed
description BACKGROUND: Chickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire genome. However, no such a physical map has been developed in chickpea. RESULTS: We present a genome-wide, BAC/BIBAC-based physical map of chickpea developed by fingerprint analysis. Four chickpea BAC and BIBAC libraries, two of which were constructed in this study, were used. A total of 67,584 clones were fingerprinted, and 64,211 (~11.7 ×) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBAC contigs, with each containing an average of 28.3 clones and having an average physical length of 559 kb. The contigs collectively span approximately 1,088 Mb. By using the physical map, we identified the BAC/BIBAC contigs containing or closely linked to QTL4.1 for resistance to Didymella rabiei (RDR) and QTL8 for days to first flower (DTF), thus further verifying the physical map and confirming its utility in fine mapping and cloning of QTL. CONCLUSION: The physical map represents the first genome-wide, BAC/BIBAC-based physical map of chickpea. This map, along with other genomic resources previously developed in the species and the genome sequences of related species (soybean, Medicago and Lotus), will provide a foundation necessary for many areas of advanced genomics research in chickpea and other legume species. The inclusion of transformation-ready BIBACs in the map greatly facilitates its utility in functional analysis of the legume genomes.
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spelling pubmed-29969972010-12-07 A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L Zhang, Xiaojun Scheuring, Chantel F Zhang, Meiping Dong, Jennifer J Zhang, Yang Huang, James J Lee, Mi-Kyung Abbo, Shahal Sherman, Amir Shtienberg, Dani Chen, Weidong Muehlbauer, Fred Zhang, Hong-Bin BMC Genomics Research Article BACKGROUND: Chickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire genome. However, no such a physical map has been developed in chickpea. RESULTS: We present a genome-wide, BAC/BIBAC-based physical map of chickpea developed by fingerprint analysis. Four chickpea BAC and BIBAC libraries, two of which were constructed in this study, were used. A total of 67,584 clones were fingerprinted, and 64,211 (~11.7 ×) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBAC contigs, with each containing an average of 28.3 clones and having an average physical length of 559 kb. The contigs collectively span approximately 1,088 Mb. By using the physical map, we identified the BAC/BIBAC contigs containing or closely linked to QTL4.1 for resistance to Didymella rabiei (RDR) and QTL8 for days to first flower (DTF), thus further verifying the physical map and confirming its utility in fine mapping and cloning of QTL. CONCLUSION: The physical map represents the first genome-wide, BAC/BIBAC-based physical map of chickpea. This map, along with other genomic resources previously developed in the species and the genome sequences of related species (soybean, Medicago and Lotus), will provide a foundation necessary for many areas of advanced genomics research in chickpea and other legume species. The inclusion of transformation-ready BIBACs in the map greatly facilitates its utility in functional analysis of the legume genomes. BioMed Central 2010-09-17 /pmc/articles/PMC2996997/ /pubmed/20849583 http://dx.doi.org/10.1186/1471-2164-11-501 Text en Copyright ©2010 Zhang et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Zhang, Xiaojun
Scheuring, Chantel F
Zhang, Meiping
Dong, Jennifer J
Zhang, Yang
Huang, James J
Lee, Mi-Kyung
Abbo, Shahal
Sherman, Amir
Shtienberg, Dani
Chen, Weidong
Muehlbauer, Fred
Zhang, Hong-Bin
A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L
title A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L
title_full A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L
title_fullStr A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L
title_full_unstemmed A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L
title_short A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L
title_sort bac/bibac-based physical map of chickpea, cicer arietinum l
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996997/
https://www.ncbi.nlm.nih.gov/pubmed/20849583
http://dx.doi.org/10.1186/1471-2164-11-501
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