Online citations, reference lists, and bibliographies.
← Back to Search

Genetic Structure, Diversity, And Allelic Richness In Composite Collection And Reference Set In Chickpea (Cicer Arietinum L.)

H. Upadhyaya, S. Dwivedi, M. Baum, R. Varshney, S. Udupa, C. L. Gowda, D. Hoisington, S. Singh
Published 2008 · Medicine, Biology

Cite This
Download PDF
Analyze on Scholarcy
Share
BackgroundPlant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions.ResultsThe 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection.ConclusionThe genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s), and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.
This paper references
Quantitative trait loci governing carotenoid concentration and weight in seeds of chickpea
S Abbo (2005)
Abundance of di-, tri-, and tetra-nucleotide tandem repeats in chickpea
P C Sharma (1995)
Isolation and characterization of sequence- tagged mircosatellite sites markers in chickpea (Cicer arietinum L.)
NK Sethy (2003)
10.1093/bioinformatics/bti282
PowerMarker: an integrated analysis environment for genetic marker analysis
Kejun Liu (2005)
10.1007/s00122-004-1849-8
Geographical patterns of genetic variation in the world collections of wild annual Cicer characterized by amplified fragment length polymorphisms
F. Shan (2004)
10.1186/1471-2229-8-55
Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea)
L. M. Cuc (2008)
Mol Genet Genomics
(2001)
10.1023/A:1021210601480
Evaluation of Ethiopian chickpea landraces for tolerance to drought
Y. Anbessa (2004)
10.1071/FP03084
Viewpoint: Evolution of cultivated chickpea: four bottlenecks limit diversity and constrain adaptation.
S. Abbo (2003)
10.1007/s00122-005-1930-y
Quantitative trait loci governing carotenoid concentration and weight in seeds of chickpea (Cicer arietinum L.)
S. Abbo (2005)
10.1139/G98-122
Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.).
B. Huettel (1999)
10.1007/s00122-001-0556-y
A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement
H. Upadhyaya (2001)
10.1007/s00122-007-0556-7
Development of an integrated intraspecific map of chickpea (Cicer arietinum L.) using two recombinant inbred line populations
P. Radhika (2007)
10.1007/978-1-4020-6295-7
Genomics-Assisted Crop Improvement
R. Varshney (2007)
10.1079/PGR2005101
Development of a composite collection for mining germplasm possessing allelic variation for beneficial traits in chickpea
H. Upadhyaya (2006)
10.1007/BF00221000
Abundance and polymorphism of di-, tri-and tetra-nucleotide tandem repeats in chickpea (Cicer arietinum L.)
P. C. Sharma (2004)
10.1007/BF02772596
A high-throughput DNA extraction protocol for tropical molecular breeding programs
E. Mace (2007)
Data analysis methods In Genetic diversity of cultivated tropical plants Edited by
X Perrier
10.1007/s004380051063
Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome
P. Winter (1999)
10.1101/GR.7.11.1104
A simple method for automated allele binning in microsatellite markers.
R. M. Idury (1997)
Research Spillover Benefits and Experiences in Inter-Regional Technology Transfer
B. Shiferaw (2004)
Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L
P Winter (1999)
10.2135/CROPSCI2000.4061606X
Identification and mapping of QTLs conferring resistance to Ascochyta blight in chickpea
D. Santra (2000)
PowerMarker : Integrated analysis environment for genetic marker data
K Liu (2005)
Genomics applications in crops
R. Varshney (2007)
Kence A: Analysis of genetic relationships among perennial and annual Cicer species growing in Turkey using RAPD markers
MA Sudupak (2002)
10.1007/s00438-003-0828-0
Mapping of gene-specific markers on the genetic map of chickpea ( Cicer arietinum L.)
T. Pfaff (2003)
10.1007/s001220051592
A linkage map of the chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinum×C. reticulatum cross: localization of resistance genes for fusarium wilt races 4 and 5
P. Winter (2000)
10.1007/s001220100751
Phylogenetic analysis in the genus Cicer and cultivated chickpea using RAPD and ISSR markers
M. Iruela (2002)
10.1002/9780470650325.CH6
Using Genomics to Exploit Grain Legume Biodiversity in Crop Improvement
S. Dwivedi (2010)
10.1016/0888-7543(89)90076-1
Unequal crossingover between homologous chromosomes is not the major mechanism involved in the generation of new alleles at VNTR loci.
R. Wolff (1989)
10.1023/A:1021567821141
Genetic relationships among annual and perennial wild species of Cicer using inter simple sequence repeat (ISSR) polymorphism
P. N. Rajesh (2004)
Chickpea breeding - progress and prospects.
H. Rheenen (1991)
KHM: Geographical patterns of genetic variation in the world collections of wild annual Cicer characterized by amplified fragment length polymorphisms
F Shan (2005)
10.1007/s00122-002-1060-8
Analysis of genetic relationships among perennial and annual Cicer species growing in Turkey using RAPD markers
M. Sudupak (2002)
10.1007/BF00942142
Allozyme variation and phylogeny in annual species ofCicer (Leguminosae)
K. Kazan (2004)
10.1007/s10681-006-4261-4
Chickpea molecular breeding: New tools and concepts
T. Millan (2006)
10.1007/BF00023889
Genetic diversity and phylogenetic relationships among the annual Cicer species as revealed by isozyme polymorphism
M. Labdi (2004)
10.1023/A:1018683119237
Landraces: A review of definitions and classifications
A. C. Zeven (2004)
10.1046/J.1471-8286.2003.00472.X
Isolation and characterization of sequence‐tagged microsatellite sites markers in chickpea (Cicer arietinum L.)
N. K. Sethy (2003)
10.1007/s00122-002-0993-2
Integration of sequence tagged microsatellite sites to the chickpea genetic map
M. Tekeoglu (2002)
Chickpea breeding
KB Singh (1987)
Chickpea breeding. In The Chickpea
KB Singh (1987)
Abundance of di-, tri-, and tetra-nucleotide tandem repeats in chickpea (Cicer arietinum L.)
PC Sharma (1995)
Origin, history and taxonomy of Chickpea
L. V. D. Maesen (1987)
10.1007/BF02672069
Nuclear DNA content of some important plant species
K. Arumuganathan (2007)
10.2135/CROPSCI1985.0011183X002500030047X
Registration of four short duration Fusarium wilt-resistant kabuli (garbanzo) chickpea germplasms
J. Kumar (1985)
BB: Pulses in New Perspective
S Kumar (2003)
10.1007/s00122-005-0135-8
Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis
N. K. Sethy (2005)
Geograph - ical patterns of genetic variation in the world collections of wild annual Cicer characterized by amplified fragment length polymorphisms
F Shan (2005)
Allozyme variation and phylogeny in annual species of Cicer (Leguminosae). Plant Systematics and Evolution
K Kazan (1991)
10.1093/OXFORDJOURNALS.MOLBEV.A040442
Slipped-strand mispairing: a major mechanism for DNA sequence evolution.
G. Levinson (1987)
10.1139/G89-144
Core collections: a practical approach to genetic resources management
A. D. Brown (1989)
10.1201/9781482280043
Genetic Diversity of Cultivated Tropical Plants
P. Hamon (2003)
10.1007/s001220051187
Potential of DNA markers in detecting divergence and in analysing heterosis in Indian elite chickpea cultivars
V. Sant (1999)
10.1007/s004380100508
High mutation rate and mutational bias at (TAA)n microsatellite loci in chickpea (Cicer arietinum L.)
S. Udupa (2001)
10.1007/s004380050976
Allelic variation at (TAA)n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm
S. Udupa (1999)
SVR: Research spillover benefits and experiences in inter-regional technology transfer: An assessment and synthesis
B Shiferaw (2004)
Muse SV: PowerMarker: Integrated analysis environment for genetic marker data
K Liu (2005)
Extending the repertoire of microsatellite markers for genetic linkage mapping and germplasm screening in chickpea
R. Varshney (2007)
10.1201/b18203-18
Data analysis methods.
E. Hovenga (2002)
Pulses in New Perspective
S Kumar (2003)
10.1007/s00122-003-1199-y
An intraspecific linkage map of the chickpea (Cicer arietinum L.) genome based on sequence tagged microsatellite site and resistance gene analog markers
H. Flandez-Galvez (2003)
10.2135/CROPSCI2001.411206X
Development of a Chickpea Core Subset Using Geographic Distribution and Quantitative Traits
H. D. Upadhyaya (2001)
10.1007/978-1-4020-6297-1_10
MOLECULAR GENETICS AND BREEDING OF GRAIN LEGUME CROPS FOR THE SEMI-ARID TROPICS
R. Varshney (2007)



This paper is referenced by
10.1093/dnares/dst015
Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping
Alice Kujur (2013)
10.1007/s12298-016-0397-4
Genetic variation of a global germplasm collection of chickpea (Cicer arietinum L.) including Italian accessions at risk of genetic erosion
C. De Giovanni (2016)
10.18805/LR.V0IOF.9100
Morpho-molecular characterization of landraces/wild genotypes of Cicer for Biotic/ Abiotic stresses
R. Kumar (2017)
10.5958/0975-6906.2016.00062.6
Genetic options for combating biotic stresses in cool-season food legumes
G. Keneni (2016)
10.1017/S1479262114000458
Enhancement of the use and impact of germplasm in crop improvement
Hari Deo Upadhyaya (2014)
10.3389/fpls.2019.01759
Developing Climate-Resilient Chickpea Involving Physiological and Molecular Approaches With a Focus on Temperature and Drought Stresses
A. Rani (2019)
10.3390/AGRONOMY2030199
Impact of Genomic Technologies on Chickpea Breeding Strategies
P. Gaur (2012)
Specific Germplasm in Chickpea (Cicer arietinum L.) Reference Set
N. Lalitha (2015)
10.1016/j.pbi.2010.01.004
Accessing genetic diversity for crop improvement.
J. C. Glaszmann (2010)
10.3389/978-2-88919-952-5
Natural Diversity in the New Millennium
Joanna M. Cross (2016)
10.1007/s10722-014-0089-2
Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicerarietinum L.) germplasm
Y. Kumar (2014)
10.5504/BBEQ.2013.0070
SSR-Based Genetic Diversity Assessment of Turkish Chickpea Varieties
Mehmet Ali Südüpak (2013)
Assessment of Cowpea Germplasms from Ghana and Mali Using Simple Sequence Repeat (SSR) Markers
I. Doumbia (2014)
Variability, stability and selection response analysis for yield and yield attributing traits in chickpea
H. Santosh (2013)
10.4025/ACTASCIAGRON.V39I3.32520
Genetic diversity between native and improved Cattleya walkeriana Gardner famous clones
E. Tambarussi (2017)
Mini core germplasm collections for infusing genetic diversity in plant breeding programs
H. D. Upadhyaya (2010)
IDENTIFICATION OF MOLECULAR MARKERS ASSOCIATED WITH IRON CONTENT IN GRAINS OF RICE (Oryza sativa L.)
M. Suma (2011)
10.15389/AGROBIOLOGY.2017.5.976ENG
CHICKPEA LANDRACES FROM CENTERS OF THE CROP ORIGIN: DIVERSITY AND DIFFERENCES
Margarita A. Vishnyakova (2017)
10.1007/s12892-017-0119-0
Competency assessment of directed amplified minisatellite DNA and start codon targeted markers for genetic diversity study in accessions of Vigna subterranea (L.) Verdcourt
David Okeh Igwe (2017)
10.3390/AGRICULTURE9050097
Utilization of Molecular Marker Based Genetic Diversity Patterns in Hybrid Parents to Develop Better Forage Quality Multi-Cut Hybrids in Pearl Millet
Govintharaj Ponnaiah (2019)
10.5897/JPBCS2018.0767
Genetic Diversity Analysis of Ethiopian Elite Chickpea (Cicer arietinum L.) Varieties Based on Agronomic Characters
Zerihun Jida (2019)
10.1007/s12298-019-00725-w
Enumerating the phytic acid content in maize germplasm and formulation of reference set to enhance the breeding for low phytic acid
J. L. Pramitha (2019)
10.1007/s11105-016-1021-z
A Genome-Wide mQTL-seq Scan Identifies Potential Molecular Signatures Regulating Plant Height in Chickpea
Swarup Kumar Parida (2016)
10.1071/FP14135
Higher flower and seed number leads to higher yield under water stress conditions imposed during reproduction in chickpea.
R. Pushpavalli (2015)
10.1016/J.FCR.2013.05.022
Partitioning coefficient—A trait that contributes to drought tolerance in chickpea
L. Krishnamurthy (2013)
10.1111/nph.15200
The carboxylate-releasing phosphorus-mobilizing strategy can be proxied by foliar manganese concentration in a large set of chickpea germplasm under low phosphorus supply.
J. Pang (2018)
Molecular diversity of chickpea ('Cicer arietinum' L.) genotypes differing in their Raffinose family Oligosaccharides viz., raffinose and stachyose content as revealed through SSR markers
Sarika Konsam (2014)
10.1007/s00122-020-03584-2
Integrating genomics for chickpea improvement: achievements and opportunities
Manish Roorkiwal (2020)
Freezing for the Future: Conserving crop germplasm for the generations ahead
H. Upadhyaya (2012)
10.1371/journal.pone.0027275
Novel SSR Markers from BAC-End Sequences, DArT Arrays and a Comprehensive Genetic Map with 1,291 Marker Loci for Chickpea (Cicer arietinum L.)
M. Thudi (2011)
10.1002/9781119414735.CH1
Hari Deo Upadhyaya
Sangam Lal Dwivedi (2018)
10.1007/s10681-020-02617-7
The selection of superior plum (Prunus domestica L.) accessions based on morphological and pomological characterizations
Farhad Mirheidari (2020)
See more
Semantic Scholar Logo Some data provided by SemanticScholar