Chickpea (Cicer arietinum)

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The information about Chickpea is by no means final and it is being continuously corrected/ updated.

Genetics:

a) GENERAL
b) INHERITANCE
c) MUTANTS
d) GENETIC MAP
e) MARKERS
f) TRANSPOSABLE ELEMENTS
g) OTHER ELEMENTS
h) REPEATS
i) RELATION WITH PEA AND MEDICAGO

a) GENERAL
Genetics is the study of genes, and tries to explain what they are and how they work.It is a discipline of biology, is the science of heredity and variation in living organisms.The modern science of genetics traces its roots to Gregor Johann Mendel, a German-Czech Augustinian monk and scientist who studied the nature of inheritance in plants.

b) INHERITANCE

Flower color
In Chickpea their are three major and distinct flower colors are identified namely pink, blue and white.About two-thirds of the world germplasm accessions at ICRISAT are pink flowered and nearly one-third have white flower. Those with blue flowers are rare.
Kumar J et al,Inheritance of flower color in chickpea.,J Hered. 2000 Sep-Oct;91(5):416-7. Link

Leaf type
Commonly the chickpea leaf is uni-imparipinnate, having 9-15 leaflets. However, certain variants have been reported; these are available in the chickpea collection at ICRISAT and were re-examined. Based on the lamina differentiation, three major classes of leaf type can be recognized: uni-imparipinnate (normal), multipinnate and simple (leaf). (Certain other leaf forms reported earlier are not classes of leaf type though they are distinct variants). It was determined that the leaf type differences are governed by two genes (mlsl), which show supplementary gene action. The multipinnate leaf is formed when the first gene is dominant (ml+sl/.sl). Whereas the simple leaf occurs when the first gene is recessive and the second gene is in either form (ml./ml.), the normal leaf is expressed when both dominant genes are present (ml+sl+/..).

Normally in chickpea, the first two nodes of the seedling bear small, scale-like structures, and the subsequent leaves are uni-imparipinnate (normal) and alternately placed on the branch . The leaf is differentiated into a rachis 3-7 cm long, which sup- ports 9 to 15 leaflets on an average, inserted on small petiolules . The leaflet arrangement is alter- nate near the base of the rachis, but it becomes almost opposite towards the apex . The leaflet shape is usually elliptic or obtuse, measuring 8- 17 mm long and 5-14 mm wide . However, variants do occur for leaf type . These variants have been characterised by different terms. In the present study, the chickpea leaf variants were re-examined and divided into three different leaf types : normal, multipinnate,and simple .

(R. P. S. Pundir, M. H. Mengesha and K. N. Reddy,Leaf types and their genetics in chickpea (Cicer arietinum L.) , Euphytica.Volume 45, Number 3 / February, 1990)Link

c) MUTANTS
  • Fasciated Mutants(FM)
    • E .J . Knights,Fasciation in chickpea: genetics and evaluation,Euphytica 69 : 163-166,1993.Link

  • Shw1 and COP1 Mutants
    • Shikha Bhatia, Sreeramaiah N. Gangappa, Ritu Kuswaha, Snehangshu Kundu, and Sudip Chattopadhyay,SHORT HYPOCOTYL IN WHITE LIGHT1, a Serine-Arginine-Aspartate-Rich Protein in Arabidopsis, Acts as a Negative Regulator of Photomorphogenic Growth,Plant Physiol. 2008,Link

  • lys-mutant TL28
    • Subrata K. Das et al,Mutation in the lysA gene impairs the symbiotic properties of Mesorhizobium ciceri,Arch Microbiol (2010) 192:69-77Link

  • rpoN gene
    • U.S. Gautam et al,Characterization of an rpoN mutant of Mesorhizobium ciceri,Journal of Applied Microbiology ISSN 1364-5072,Link

  • SerA-mutant (TL68)
    • Subrata K. Das ,Characterization of a symbiotically defective serine auxotroph of Mesorhizobium ciceriLink

  • Mutant TO(52)(Reduction of IAA)
    • Ekta Khare and Naveen Kumar Arora,Effect of Indole-3-Acetic Acid (IAA) Produced by Pseudomonas aeruginosa in Suppression of Charcoal Rot Disease of Chickpea,Curr Microbiol DOI 10.1007/s00284-009-9577-6.Link

  • hog1,can and hog1can Mutants
    • Deepti Jain, Nilanjan Roy, and Debasis Chattopadhyay,CaZF, a Plant Transcription Factor Functions through and Parallel to HOG and Calcineurin Pathways in Saccharomyces cerevisiae to Provide Osmotolerance,PLoS ONE. 2009; 4(4): e5154. Link

    d) GENETIC MAP
    1)An integrated genetic map of chickpea based on recombinant inbred lines of C. arietinum (ICC 4958) x C. reticulatum (PI 489777) contains 521 loci organized into eight linkage groups that span 2,602 cM, with an aver- age inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago.

    Spurthi N. Nayak et al.Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome,Theor Appl Genet DOI 10.1007/s00122-010-1265-1,Link


    2)A composite limkage map was constructed based on two interspecific Chickpea RIL(recombinant inbred line) populations from crosses ILC72 C .arietinum x C. reticulatum and ICCL81001 C .arietinum x C. reticulatum.
    The genetic map is described in 8 LGs(Linkage groups) covering 751 cM.
    Carmen Palomino et al,Integration of new CAPS and dCAPS-RGA markers into a composite chickpea genetic map and their association with disease resistance,Theor Appl Genet (2009) 118:671?682 DOI 10.1007/s00122-008-0928-7. Link


    e) MARKERS
    Joint map of two chickpea RIL populations from crosses ILC72 C .arietinum x C. reticulatum and ICCL81001 C .arietinum x C. reticulatum. The genetic map is described in 8 LGs(Linkage groups) covering 751 cM.This map incorporates 169 markers in which 6 RGAs,10 STMS, 41 RADP )random Amplified Polymorphic DNA),3 ISSR (Inter Simple Sequence Repeats),the flower color locus B/b and 10 RGAs(Resistance gene analogs).
    Carmen Palomino et al,Integration of new CAPS and dCAPS-RGA markers into a composite chickpea genetic map and their association with disease resistance,Theor Appl Genet (2009) 118:671-682 DOI 10.1007/s00122-008-0928-7. Link


    f) TRANSPOSABLE ELEMENTS
    Manoj K Rajput et al,reported a Ty3-gypsy like retrotransposon CARE1 (Cicer arietinum retro-element 1) in chickpea (Accession no. DQ239702). This 5,920-bp AT-rich (63%) element carries 723-bp 50 -LTR and 897-bp 30 -LTR flanking to an internal region of 4,300-bp. The LTRs of CARE1 show 93.9% nucleotide identity to each other and have 4-bp (ACTA) terminal inverted repeats. A 17-bp potential tRNAmet primer binding site downstream to 50 -LTR and a 13-bp polypurine tract upstream to 30 -LTR have been identified.
    Manoj K. Rajput,CARE1, a TY3-gypsy like LTR-retrotransposon in the food legume chickpea (Cicer arietinum L.),Genetica (2009) 136:429-437.Link

    Two satellite repeats (CaSat1 and CaSat2) as well as retrotransposon-like sequences of the Ty3-gypsy type (CaRep1 and CaRep2) were identified in Chickpea. The sequences are genus-specific and contribute to the pericentric heterochromatin of chickpea chro- mosomes. The complete covering of DAPI-positive heterochromatin with CaSat1, CaSat2, CaRep1 and CaRep2 signals in interphase and metaphase nuclei suggests them to be the most abundant repeat elements in the C. arietinum genome.
    Molecular characterization of three repeat families of C. arietinum
    The CaSat1 family
    This is typical of satellite DNA,and the clones are therefore referred to as the CaSat1 (Cicer arietinum Satellite 1) or 168 bp RsaI family. A total of 13 monomers of four different CaSat1 clones were sequenced (AJ005998, AJ005999, AJ00600/1, AJ006004).
    The CaSat2 family
    This new family was designated CaSat2 or 100 bp RsaI repeat family.
    Retrotransposon-like sequences
    Two groups of repetitive sequences called CaRep1 (pCaEr1048) and CaRep2 (pCaEr915, 936) were isolated from the library. pCaEr1048 is 2140 bp long,contains 60% AT residues and shows no homology to CaRep2. pCaEr936 harbours a 956 bp insert with an AT content of 55%. Both CaRep1 and CaRep2 can be regarded as retrotransposon-like sequences of a Ty3-gypsy element or parts of such an element.

    Distribution of the four repetitive sequence classes within species of the genus Cicer and other legumes
    In other annual species except C. cuneatum, the hybridization pattern with monomer unit sizes of 170 bp (CaSat1) and 100 bp (CaSat2), respectively, was conserved. The intensity of the banding pattern varied between the different species. In particular, CaSat1 signals were very strong among members of the first crossability group (C. reticulatum, C. arietinum and C. echinospermum) and even stronger in
    C. chorassanicum
    C. yamashitae revealed a weaker pattern , and in C. bijugum, C. pinnatifidum and C. judaicum (second crossability group) the faintest signals were observed . Bands of lower intensity between the main oligomers were visible in C. echinospermum, C. reticulatum, C. chorassanicum and C. yamashitae and represent a subset of rearranged CaSat1 units, which are complex and less abundant. Differences in hybridization intensities were less pronounced with CaSat2 sequences . The smaller multimer bands in C. chorassanicum were stronger than in C. arietinum from which the probe was derived . A CaSat2 probe revealed similar patterns on DNA from the perennial C. anatolicum and the annual species .

    Neither CaSat1 nor CaSat2 are detectable in any other legume (e.g. Glycine max,Pisum sativum, Phaseolus vulgaris, Pisum sativum,Vicia faba, Medicago sativa) on the level of Southern hybridization. Therefore, we assume these to be specific for the genus Cicer. Since satellite DNA sequences is a rapidly evolving component of the genome, more diverged copies of both families be present in other legumes. Their detection could might nevertheless possibly be improved by PCR.CaRep1 and CaRep2 revealed different bandingpatterns of 1-9 bands each for the first and the second crossability group and for C. cuneatum (CaRep2), re-spectively, indicating a of these elements. Neither CaRep1 nor relatively conserved structure CaRep2 probes detected any homologous sequences in other legumes, suggesting that the retroelements are greatly diverged in these genomes.
    C. Staginnus,Molecular structure and chromosomal localization of major repetitive DNA families in the chickpea (Cicer arietinum L.) genome,Plant Molecular Biology 39: 1037-1050, 1999.Link

    g) OTHER ELEMENTS

    h) REPEATS ( SSRs etc.)
    There are six types of micrstellites (SSRs) in Chickpea and these are distributed in two classes,Class I and Class II.These are the features of SSRs identified in the chickpea unigenes

    Total number of sequences examined          9,569
    Total size of examined sequences (bp)         5,269,104
    Total number of identified SSRs                   3,728
    Number of SSR containing sequences         2,029
    Number of sequences containing more than one SSR        581
    Number of SSRs present in compound formation               1,354
    Frequency of SSR                                         1/700 bp

    Distribution of SSRs

    Number of mononucleotide repeats      1,793
    Number of di-nucleotide repeats           126
    Number of tri-nucleotide repeats          110
    Number of tetra-nucleotide repeats       7
    Number of penta-nucleotide repeats      8
    Number of hexa-nucleotide repeats       5
    Rajeev K Varshney,A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.),BMC Genomics. 2009; 10: 523,Link

    i) RELATION WITH P.sativam AND Medicago
    Relation with P.sativam

    Study done by Carmen Palomino et al 2009 for Integration of new CAPS and dCAPS-RGA markers into a composite chickpea genetic map and their association with disease resistance revealed that the two RGAs were 100% identical to previously published Pisum sativum and Lens culinaris RGAs : RGA08 to AF123703 (RGA-G3A) and RGA09 to AJ516062 (2K1) and AJ516060 (3K3). Thus, six out of ten RGA classes used in this study (RGA01, RGA02, RGA03, RGA04, RGA06 and RGA07)were novel sequences.

    Relation with Medicago

    Chickpea is a close relative of the model legume system Medicago truncatula.
    1) A Comparative map of Medicago and chickpea is introduced. Gene-based SNP markers were used as the anchor markers in comparative analysis of chickpea and Medicago genome. The resistance gene homologs (RGH) are their homologs in Medicago are shown in this map. The macrosynteny observed across chickpea and Medicago with respect to 71 gene-based markers.
    Spurthi N. Nayak et al.Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome.
    Theor Appl Genet DOI 10.1007/s00122-010-1265-1Link


    2) Carmen Palomino et al 2009 studies revealed that in the genetic map of C.arietinum , the RGA( Resistance gene analogs) markers RGA01 and RGA02 exhibited high similarity to several Medicago truncatula ESTs.Two RGA sequences were 100% identical to previously reported C. arietinum and Medicago sativa RGAs : RGA05 to AF186624 (CP2) and RGA10 to AJ307992 (RGA-G) and AF487949. Classes RGA05 to RGA10 showed similarity with M. truncatula ESTs that are expressed under pathogenic infections or induced by methyl jasmonate, suggesting that these RGAs are putative candidates involved in resistance mechanisms of Cicer.