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Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.).

Varshney RK, Mir RR, Bhatia S, Thudi M, Hu Y, Azam S, Zhang Y, Jaganathan D, You FM, Gao J, Riera-Lizarazu O, Luo MC - Funct. Integr. Genomics (2014)

Bottom Line: The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers.In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea.Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.

View Article: PubMed Central - PubMed

Affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India, r.k.varshney@cgiar.org.

ABSTRACT
Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.

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Related in: MedlinePlus

Insert size estimation of chickpea BAC clones by pulsed field gel electrophoresis (PFGE). A set of 28 clones can be visualized from a CAH0000 library (constructed using HindIII) and b CAE0000 library (constructed using EcoRI). PFG marker can be seen in two lanes on either side of the 28 clones from each library. The insert size of BAC library is ~120 and ~124 kb for CAH0000 and CAE0000 libraries, respectively
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Related In: Results  -  Collection


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Fig1: Insert size estimation of chickpea BAC clones by pulsed field gel electrophoresis (PFGE). A set of 28 clones can be visualized from a CAH0000 library (constructed using HindIII) and b CAE0000 library (constructed using EcoRI). PFG marker can be seen in two lanes on either side of the 28 clones from each library. The insert size of BAC library is ~120 and ~124 kb for CAH0000 and CAE0000 libraries, respectively

Mentions: Two BAC libraries were constructed from genomic DNA of chickpea Desi cultivar “ICC 4958” using HindIII and EcoRI restriction enzymes and were designated as CAH0000 and CAE0000, respectively. From each of these two libraries, 48,384 clones were picked up, and in total, 96,768 clones were obtained. For quality control, four plates were randomly selected from each library, and 24 clones from various quadrants of each plate were picked up. In brief, 96 random clones were selected from both CAE0000 and CAH0000 BAC libraries for quality control analysis. These analyses revealed average insert sizes of 120 kb in CAH0000 library and 124 kb in CAE0000 library and approximately eight-fold coverage of the chickpea haploid genome in each of these two libraries (Fig. 1a, b). It was also observed that ~3 to 4 % of clones in both libraries contained no inserts of chickpea DNA.Fig. 1


Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.).

Varshney RK, Mir RR, Bhatia S, Thudi M, Hu Y, Azam S, Zhang Y, Jaganathan D, You FM, Gao J, Riera-Lizarazu O, Luo MC - Funct. Integr. Genomics (2014)

Insert size estimation of chickpea BAC clones by pulsed field gel electrophoresis (PFGE). A set of 28 clones can be visualized from a CAH0000 library (constructed using HindIII) and b CAE0000 library (constructed using EcoRI). PFG marker can be seen in two lanes on either side of the 28 clones from each library. The insert size of BAC library is ~120 and ~124 kb for CAH0000 and CAE0000 libraries, respectively
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4273598&req=5

Fig1: Insert size estimation of chickpea BAC clones by pulsed field gel electrophoresis (PFGE). A set of 28 clones can be visualized from a CAH0000 library (constructed using HindIII) and b CAE0000 library (constructed using EcoRI). PFG marker can be seen in two lanes on either side of the 28 clones from each library. The insert size of BAC library is ~120 and ~124 kb for CAH0000 and CAE0000 libraries, respectively
Mentions: Two BAC libraries were constructed from genomic DNA of chickpea Desi cultivar “ICC 4958” using HindIII and EcoRI restriction enzymes and were designated as CAH0000 and CAE0000, respectively. From each of these two libraries, 48,384 clones were picked up, and in total, 96,768 clones were obtained. For quality control, four plates were randomly selected from each library, and 24 clones from various quadrants of each plate were picked up. In brief, 96 random clones were selected from both CAE0000 and CAH0000 BAC libraries for quality control analysis. These analyses revealed average insert sizes of 120 kb in CAH0000 library and 124 kb in CAE0000 library and approximately eight-fold coverage of the chickpea haploid genome in each of these two libraries (Fig. 1a, b). It was also observed that ~3 to 4 % of clones in both libraries contained no inserts of chickpea DNA.Fig. 1

Bottom Line: The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers.In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea.Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.

View Article: PubMed Central - PubMed

Affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India, r.k.varshney@cgiar.org.

ABSTRACT
Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.

Show MeSH
Related in: MedlinePlus