Genetic marker discovery, intraspecific linkage map construction and quantitative trait locus analysis of ascochyta blight resistance in chickpea (Cicer arietinum L.)

Molecular Breeding

Volumn 33, Issue 2, 2014, Pages 297-313

  Stephens, Amber ^a   Lombardi, Maria ^a   Cogan, Noel O I ^a   Forster, John W ^a,d   Hobson, Kristy ^b,c   Materne, Michael ^b   Kaur, Sukhjiwan ^a  

^a LA TROBE UNIVERSITY   (Australia)

^b Biosciences Research Division   (Australia)

^c NSW DEPARTMENT OF PRIMARY INDUSTRIES   (Australia)

^d LA TROBE UNIVERSITY   (Australia)

Author keywords

Comparative genomics; Disease resistance; Grain legume; Molecular breeding; Transcriptome

Indexed keywords

BIOMARKERS; DNA SEQUENCES; MAPPING; PLANTS (BOTANY);

ASCOCHYTA BLIGHT RESISTANCE; CHICKPEA (CICER ARIETINUM L.); COMPARATIVE GENOMICS; DISEASE RESISTANCE; GENETIC MARKERS; GRAIN LEGUME; LINKAGE MAP; MOLECULAR BREEDING; QUANTITATIVE TRAIT LOCUS; TRANSCRIPTOMES;

GENES;

EID: 84890872120     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-013-9950-9     Document Type: Article

References (58)

1. Agarwal G, Jhanwar S, Priya P, Singh VK, Saxena MS et al (2012) Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS ONE 7(12): e52443. doi: 10. 1371/journal. pone. 0052443.
2. Anbessa Y, Taran B, Warkentin TD, Tullu A, Vandenberg A (2009) Genetic analyses and conservation of QTL for ascochyta blight resistance in chickpea (Cicer arietinum L.). Theor Appl Genet 119(4): 757-765.
3. Barbara T, Palma-Silva C, Paggi GM, Bered F, Fay MF, Lexer C (2007) Cross-species transfer of nuclear microsatellite markers: potential and limitations. Mol Ecol 16(18): 3759-3767.
4. Bertioli DJ, Moretzsohn MC, Madsen LH, Sandal N, Leal-Bertioli SC, Guimaraes PM, Hougaard BK, Fredslund J, Schauser L, Nielsen AM et al (2009) An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes. BMC Genomics 5: 16.
5. Buhariwalla HK, Jayashree B, Eshwar K, Crouch JH (2005) Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus. BMC Plant Biol 5: 16.
6. Chabane K, Ablett GA, Cordeiro GM, Valkoun J, Henry RJ (2005) EST versus genomic derived microsatellites for genotyping wild and cultivated barley. Genet Res Crop Evol 52: 903-909.
7. Choi HK, Kim DJ, Uhm T, Limpens E, Lim H, Mun JH, Kalo P, Penmesta RV, Seres A, Kulikova O et al (2004) A sequence based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics 166: 1463-1502.
8. Choi I-Y, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon M-S, Hwang E-Y, Yi S-I et al (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176: 685-696.
9. Choudhary S, Sethy NK, Shokeen B, Bhatia S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 118(3): 591-608.
10. Choudhary S, Gaur R, Gupta S (2012a) EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea. Theor Appl Genet 124(8): 1449-1462.
11. Choudhary P, Khanna SM, Jain PK, Bharadwaj C, Kumar J, Lakhera PC, Srinivasan R (2012b) Genetic structure and diversity analysis of the primary gene pool of chickpea using SSR markers. Genet Mol Res 11(2): 891-905.
12. Cogan NOI, Ponting RC, Vecchies A, Drayton MC, George J, Dracatos PM, Dobrowlski M, Sawbridge TI et al (2006) Gene-associated single nucleotide polymorphism discovery in perennial ryegrass (Lolium perenne L.). Mol Gen Genet 276: 101-112.
13. Cong B, Liu JP, Tanksley SD (2002) Natural alleles at a tomato fruit size quantitative trait locus differ by heterochronic regulatory mutations. Proc Natl Acad Sci USA 99(21): 13606-13611.
14. Flandez-Galvez H, Ford R, Pang EC, Taylor PW (2003a) An intraspecific linkage map of the chickpea (Cicer arietinum L.) genome based on sequence ged microsatellite site and resistance gene analog markers. Theor Appl Genet 106(8): 1447-1456. doi: 10. 1007/s00122-003-1199-y.
15. Flandez-Galvez H, Ades PK, Ford R, Pang ECK, Taylor PWJ (2003b) QTL analysis for ascochyta blight resistance in an intraspecific population of chickpea (Cicer arietinum L.). Theor Appl Genet 107: 1257-1265.
16. Galeano CH, Fernandez AC, Franco-Herrera N, Cichy KA, McLean PE, Vanderleyden J, Blair MW (2011) Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean. PLoS ONE 6: e28135.
17. Garg R, Patel RK, Tyagi AK, Jain M (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18(1): 53-63.
18. Gaur R, Sethy NK, Choudhary S, Shokeen B, Gupta V, Bhatia S (2011) Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.). BMC Genomics 12: 117.
19. Gaur R, Azam S, Jeena G, Khan AW, Choudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S (2012) High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res 19(5): 357-373.
20. Gore MA, Wright MH, Ersoz ES, Bouffard P, Szekeres ES, Jarvie TP, Hurwitz BL, Narechania A, Harkins TT, Grills GS et al (2009) Large-scale discovery of gene-enriched SNPs. Plant Genome 2: 121-133.
21. Gujaria N, Kumar A, Dauthal P, Dubey A, Hiremath P, Prakash AB, Farmer A, Bhide M, Shah T, Gaur PM, Upadhyaya HD, Bhatia S, Cook DR, May GD, Varshney RK (2011) Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). Theor Appl Genet 122(8): 1577-1589.
22. Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Kumar A, Bhanuprakash A, Mulaosmanovic B, Gujaria N, Krishnamurthy L, Gaur PM, Kavikishor PB, Shah T, Srinivasan R, Lohse M, Xiao Y, Town CD, Cook DR, May GD, Varshney RK (2011) Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnol J 9(8): 922-931.
23. Hiremath PJ, Kumar A, Penmetsa RV, Farmer A, Schlueter JA, Chamarthi SK, Whaley AM, Carrasquilla-Garcia N, Gaur PM, Upadhyaya HD, Kavi Kishor PB, Shah TM, Cook DR, Varshney RK (2012) Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnol J 10(6): 716-732.
24. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, Ren Y, Zhu H, Li J, Lin K, Jin W, Fei Z, Li G, Staub J, Kilian A, van der Vossen EAG, Wu Y, Guo J, He J, Jia Z, Ren Y, Tian G, Lu Y, Ruan J, Qian W, Wang M, Huang Q, Li B, Xuan Z, Cao J, Asan WuZ, Zhang J, Cai Q, Bai Y, Zhao B, Han Y, Li Y, Li X, Wang S, Shi Q, Liu S, Cho WK, Kim J-Y, Xu Y, Heller-Uszynska K, Miao H, Cheng Z, Zhang S, Wu J, Yang Y, Kang H, Li M, Liang H, Ren X, Shi Z, Wen M, Jian M, Yang H, Zhang G, Yang Z, Chen R, Liu S, Li J, Ma L, Liu H, Zhou Y, Zhao J, Fang X, Li G, Fang L, Li Y, Liu D, Zheng H, Zhang Y, Qin N, Li Z, Yang G, Yang S, Bolund L, Kristiansen K, Zheng H, Li S, Zhang X, Yang H, Wang J, Sun R, Zhang B, Jiang S, Wang J, Du Y, Li S (2009) The genome of the cucumber Cucumis sativus L. Nat Genet 41(12): 1275-1281.
25. Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11: 38.
26. Iruela M, Castro P, Rubio J, Cubero JI, Jacinto C, Millan T, Gil J (2007) Validation of a QTL for resistance to ascochyta blight linked to resistance to fusarium wilt race 5 in chickpea (Cicer arietinum L.). Eur J Plant Pathol 119: 29-37.
27. Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M, Adam-Blondon A-F, Weissenbach J, Quetier F, Wincker P, French-Italian P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161): 463-467.
28. Jain M, Misra G, Patel RK, Priya P, Jhanwar S, Khan AW, Shah N, Singh VK, Garg R, Jeena G, Yadav M, Kant C et al (2013) A draft genome sequence of the pulse crop species chickpea (Cicer arietinum L.). Plant J 74(5): 715-729. doi: 10. 1111/tpj. 12173.
29. Jayakumar P, Gan PY, Gossen BD, Warkentin TD, Banniza S (2005) Ascochyta blight of chickpea: infection and host resistance mechanisms. Can J Plant Pathol 27: 499-509.
30. Jhanwar S, Priya P, Garg R, Parida SK, Tyagi AK, Jain M (2012) Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol J 10(6): 690-702.
31. Jones ES, Mahoney NL, Hayward MD, Armstead IP, Jones JG, Humphreys MO, King IP, Kishida T, Yamada T et al (2002) An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes. Genome 45: 282-295.
32. Kaur S, Cogan NOI, Pembleton LW, Shinozuka M, Savin KW, Materne M, Forster JW (2011) Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics 12: 265.
33. Kaur S, Pembleton L, Cogan N, Savin K, Leonforte T, Paull J, Materne M, Forster J (2012) Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers. BMC Genomics 13(1): 104.
34. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12: 172-175.
35. Kulheim C, Yeoh SH, Maintz J, Foley WJ, Moran GF (2009) Comparative SNP diversity among four Eucalyptus species for genes from secondary metabolite biosynthetic pathways. BMC Genomics 24: 452.
36. Labdi M, Robertson LD, Singh KB, Charrier A (1996) Genetic diversity and phylogenetic relationships among the annual Cicer species as revealed by isozyme polymorphism. Euphytica 88(3): 181-188.
37. Lichtenzveig J, BonWl DJ, Zhang HB, Shtienberg D, Abbo S (2006) Mapping quantitative trait loci in chickpea associated with time to Xowering and resistance to Didymella rabiei the causal agent of ascochyta blight. Theor Appl Genet 113: 1357-1369.
38. Madrid E, Rajesh PN, Rubio J, Gil J, Millan T, Chen W (2012) Characterization and genetic analysis of an EIN4-like sequence (CaETR-1) located in QTL(AR1) implicated in ascochyta blight resistance in chickpea. Plant Cell Rep 31: 1033-1042.
39. Madrid E, Chen W, Rajesh PN, Castro P, Millan T, Gil J (2013) Allele-specific amplification for the detection of ascochyta blight resistance in chickpea. Euphytica 189: 183-190.
40. Manly KF, Cudmore RH, Meer JM (2001) Map manager QTX, cross-platform software for genetic mapping. Mamm Genome 12: 930-932.
41. Mattioni C, Cherubini M, Taurchini D, Villani F, Martin MA (2010) Evaluation of genomic SSRs and EST-SSRs markers in genetic diversity studies in European chestnut populations. Acta Hort 866: 151-156.
42. McLean P, Mamidi S, McConnell M, Chikara S, Lee R (2010) Synteny mapping between common bean and soybean reveals extensive blocks of shared loci. BMC Genomics 11: 184.
43. Moreno MT, Cubero JI (1978) Variation in Cicer arietinum L. Euphytica 27: 465-485.
44. Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamrker S, Pottorff M, Hearne S, Cisse N, Fatokun C, Ehlers JD, Roberts PA, Close TJ (2009) A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proc Natl Acad Sci USA 106: 18159-18164.
45. Nayak SN, Zhu H, Varghese N, Datta S, Choi HK, Horres R, Jungling R, Singh J, Kishor PB, Sivaramakrishnan S, Hoisington DA, Kahl G, Winter P, Cook DR, Varshney RK (2010) 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 120: 1415-1441.
46. Radhika P, Gowda SJ, Kadoo NY, Mhase LB, Jamadagni BM, Sainani MN, Chandra S, Gupta VS (2007) Development of an integrated intraspecific map of chickpea (Cicer arietinum L.) using two recombinant inbred line populations. Theor Appl Genet 115: 209-216.
47. Ren Y, Zhao H, Kou Q, Jiang J, Guo S, Zhang H, Hou W, Zou X, Sun H, Gong G, Levi A, Xu Y (2012) A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome. PLoS ONE 7: e29453.
48. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18: 233-234.
49. Sefera T, Abebie B, Gaur PM, Assefa K, Varshney RK (2011) Characterisation and genetic diversity analysis of selected chickpea cultivars of nine countries using simple sequence repeat (SSR) markers. Crop Pasture Sci 62: 177-187.
50. Singh KB, Hawtin GC, Nene YL, Reddy MV (1981) Resistance in chickpeas to Ascochyta rabiei. Plant Dis 65: 586-587.
51. Subbaiyan GK, Waters DLE, Katiyar SK, Sadananda AR, Vaddadi S, Henry RJ (2012) Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing. Plant Biotechnol J 10: 623-634.
52. Thudi M, Bohra A, Nayak SN, Varghese N, Shah TM, Penmetsa RV, Thirunavukkarasu N, Gudipati S, Gaur PM, Kulwal PL, Upadhyaya HD, Kavikishor PB, Winter P, Kahl G, Town CD, Kilian A, Cook DR, Varshney RK (2011) Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1, 291 marker loci for chickpea (Cicer arietinum L.). PLoS ONE 6: e27275.
53. Udupa SM, Baum M (2003) Genetic dissection of pathotype-specific resistance to ascochyta blight disease in chickpea (Cicer arietinum L.) using microsatellite markers. Theor Appl Genet 106: 1196-1202.
54. van der Knaap E, Tanksley SD (2003) The making of a bell pepper-shaped tomato fruit: identification of loci controlling fruit morphology in yellow stuffer tomato. Theor Appl Genet 107: 139-147.
55. Varshney RK, Hiremath PJ, Lekha P, Kashiwagi J, Balaji J, Deokar AA, Vadez V, Xiao Y, Srinivasan R, Gaur PM, Siddique KHM, Town CD, Hoisington DA (2009) A comprehensive resource of drought- and salinity-responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics 10: 523.
56. Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Taran B et al (2013) Draft genome sequence of chickpea (Cicer arietinum L.) provides a resource for trait improvement. Nat Biotechnol 31: 240-248.
57. Voorips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: 77-78.
58. Wang S, Basten CJ, Zeng Z-B (2012) Windows QTL Cartographer 2. 5. Department of Statistics, North Carolina State University, Raleigh, NC. (http://statgen. ncsu. edu/qtlcart/WQTLCart. htm).