Skip to main content

Molecular Genetics and Breeding of Grain Legume Crops for the Semi-Arid Tropics

  • Chapter
Genomics-Assisted Crop Improvement

Abstract

Grain legumes are important crops for providing key components in the diets of resource-poor people of the semi-arid tropic (SAT) regions of the world. Although there are several grain legume crops grown in SAT, the present chapter deals with three important legumes i.e. groundnut or peanut (Arachis hypogaea), chickpea (Cicer arietinum) and pigeonpea (Cajanus cajan). Production of these legume crops are challenged by serious abiotic stresses e.g. drought, salinity as well as several fungal, viral and nematode diseases. To tackle these constraints through molecular breeding, some efforts have been initiated to develop genomic resources e.g. molecular markers, molecular genetic maps, expressed sequence tags (ESTs), macro-/micro- arrays, bacterial artificial chromosomes (BACs), etc. These genomic resources together with recently developed genetic and genomics strategies e.g. functional molecular markers, linkage-disequilibrium (LD) based association mapping, functional and comparative genomics offer the possibility of accelerating molecular breeding for abiotic and biotic stress tolerances in the legume crops. However, low level of polymorphism present in the cultivated genepools of these legume crops, imprecise phenotyping of the germplasm and the higher costs of development and application of genomic tools are critical factors in utilizing genomics in breeding of these legume crops.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Abbo S, Molina C, Jungmann R, Grusak MA, Berkovitch Z, Reifen R, Kahl G, Winter P, Reifen R (2005) QTL governing carotenoid concentration and weight in seeds of chickpea (Cicer arietinum L.). Theor Appl Genet 111:185–195

    PubMed  CAS  Google Scholar 

  • Amirul Islam FM, Beebe S, Muñoz M, Tohme J, Redden RJ, Basford KE (2004) Using molecular markers to assess the effect of introgression on quantitative attributes of common bean in the Andean gene pool. Theor Appl Genet 108:243–252

    CAS  Google Scholar 

  • Azhaguvel P, Vidya Saraswathi D, Sharma A, Varshney RK (2006) Methodological advancement in molecular markers to delimit the gene(s) for crop improvement. In: Teixera da Silva J. (ed) Floriculture, ornamental and plant biotechnology: Advances and topical issues, Global Science Books, London, UK, pp 460–499

    Google Scholar 

  • Banerjee H, Pai RA, Sharma RP (1999) Restriction fragment length polymorphism and random amplified polymorphic DNA analysis of chickpea accessions. Biol Plant 42:197–199

    CAS  Google Scholar 

  • Beer SC, Siripoonwiwat W, O’Donoughue LS, Souza E, Matthews D, Sorrells ME (1997) Association between molecular markers and quantitative traits in an oat germplasm pool: can we infer linkages. Jour Agr Genom 3 (http://wheat.pw.usda.gov/jag/papers97/paper197/jqtl1997–01.html)

    Google Scholar 

  • Benko-Iseppon AM, Winter P, Huettel B, Staginnus C, Muehlbauer FJ, Kahl G (2003) Molecular markers closely linked to Fusarium resistance genes in chickpea show significant alignments to pathogenesis-related genes located on Arabidopsis chromosomes 1 and 5. Theor Appl Genet 107:379–386

    PubMed  CAS  Google Scholar 

  • Botstein D, White DL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    PubMed  CAS  Google Scholar 

  • Bretting PK, Widrlechner MP (1995) Genetic markers and plant genetic resource management. Plant Breed Rev 31:11–86

    Google Scholar 

  • Brown AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31:818–824

    Google Scholar 

  • Brown SM, Kresovich S (1996) Molecular characterization for plant genetic resources conservation. In: Paterson AH (ed) Genome mapping of plants. Academic Press, San Diego, pp 85–93

    Google Scholar 

  • Buhariwalla HK, Jayashree B, Eshwar K, Crouch JH (2005) ESTs from chickpea roots with putative roles in drought tolerance. BMC Plant Biol 5:16

    PubMed  Google Scholar 

  • Burns MJ, Edwards KJ, Newbury HJ, Ford-Lloyd BV, Baggott CD (2001) Development of simple sequence repeat (SSR) markers for the assessment of gene flow and genetic diversity in pigeonpea (Cajanus cajan). Mol Ecol Notes 1:283–285

    CAS  Google Scholar 

  • Burow MD, Starr JL, Simpson CE, Paterson AH (1996) Identification of RAPD markers in peanut (Arachis hypogaea L.) associated with root-knot nematode resistance derived from A. cardenasii. Mol Breed 2:307–319

    Google Scholar 

  • Burrow MD, Simpson CE, Paterson AH, Starr JL (1996) Identification of peanut (Arachis hypogaea L.) RAPD markers diagnostic of root-knot nematode (Meloidogyne arenaria (Neal) Chitwood) resistance. Mol Breed 2:369–379

    Google Scholar 

  • Burrow MD, Simpson CE, Starr JL, Paterson AH (2001) Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.): broadening the gene pool of a monophyletic polyploid species. Genetics 159:823–837

    Google Scholar 

  • Chandra S, Buhariwalla HK, Kashiwagi J, Harikrishna S, Rupa Sridevi K, Krishnamurthy L, Serraj R, Crouch JC (2004) Identifying QTL-linked markers in marker-deficient crops. In new directions for a diverse plant: Proceedings of the 4th international crop science congress brisbane, Australia, 26 September–1 October bibitem

    Google Scholar 

  • Cho S, Chen W, Muehlbauer FJ (2004) Pathotype-specific genetic factors in chickpea (Cicer arietinum L.) for quantitative resistance to ascochyta blight. Theor Appl Genet 109:733–739

    PubMed  Google Scholar 

  • Choi HK, Mun JH, Kim DJ, Zhu H, Baek JM, Mudge J, Roe B, Ellis N, Doyle J, Kiss GB, Young ND, Cook DR (2004) Estimating genome conservation between crop and model legume species. Proc Nat Acad Sci 101:15289–15294

    PubMed  CAS  Google Scholar 

  • Choi HK, Luckow MA, Doyle J, Cook DR (2006) Development of nuclear gene-derived molecular markers linked to legume genetic maps. Mol Gen Genome 276:56–70

    CAS  Google Scholar 

  • Choudhary S, Sethy NK, Shokeen B, Bhatia S (2006) Development of sequence tagged microsatellite site markers for chickpea (Cicer arietinum L.). Mol Ecol Notes 6:3–95

    Google Scholar 

  • Clarke H, Siddique KHM (2003) Chilling tolerance in chickpea – novel methods for crop improvement. In: Sharma RN, Yasin M, Swami SL, Khan MA, William AJ (ed) International Chickpea Conference, Indira Gandhi Agricultural University, Raipur, India, pp 5–12

    Google Scholar 

  • Cobos MJ, Fernandez MJ, Rubio J, Kharrat M, Moreno MT, Gil J, Millan T (2005) A linkage map of chickpea (Cicer arietinum L.) based on populations from Kabuli × Desi crosses: location of genes for resistance to fusarium wilt race 0. Theor Appl Genet 110:1347–1353

    PubMed  CAS  Google Scholar 

  • Collard BCY, Pang ECK, Ades PK, Taylor PWJ (2003) Preliminary investigation of QTLs associated with seedling resistance to ascochyta blight from Cicer echinospermum, a wild relative of chickpea. Theor Appl Genet 107:719–729

    PubMed  CAS  Google Scholar 

  • Coram TE, Pang ECK (2005a) Isolation and analysis of candidate ascochyta blight defence genes in chickpea. Part I. Generation and analysis of an expressed sequence tag (EST) library. Physiol Mol Plant Pathol 66:192–200

    CAS  Google Scholar 

  • Coram TE, Pang ECK (2005b) Isolation and analysis of candidate ascochyta blight defence genes in chickpea. Part II. Microarray expression analysis of putative defence-related ESTs. Physiol Mol Plant Path 66:201–210

    CAS  Google Scholar 

  • Coram TE, Pang ECK (2006) Expression profiling of chickpea genes differentially regulated during a resistance response to Ascochyta rabiei. J Plant Biotechnol 4:647–666

    CAS  Google Scholar 

  • De Koning DJ, Haley CS (2005) Genetical genomics in humans and model organisms. Trends Genet 21:377–381

    PubMed  Google Scholar 

  • Desbrosses GG, Kopka J, Udvardi MK (2005) Lotus japonicus metabolic profiling. Development of gas chromatography-mass spectrometry resources for the study of plant–microbe interactions. Plant Physiol 137:1302–1318

    PubMed  CAS  Google Scholar 

  • Dixon RA, Sumner LW (2003) Legume natural products: understanding and manipulating complex pathways for human and animal health. Plant Physiol 131:878–885

    PubMed  CAS  Google Scholar 

  • Duranti M, Gius C (1997) Legume seeds: protein content and nutritional value. Field Crops Res 53:31–45

    Google Scholar 

  • Dwivedi SL, Gurtu S, Chandra S, Yuejin W, Nigam SN (2001) Assessment of genetic diversity among selected groundnut germplasm. I: RAPD analysis. Plant Breed 120:345–349

    CAS  Google Scholar 

  • Dwivedi SL, Blair MW, Upadhyaya HD, Serraj R, Balaji J, Buhariwalla HK, Ortiz R, Crouch JH (2006) Using genomics to exploit grain biodiversity in crop improvement. Plant Breed Rev 26:171–310

    CAS  Google Scholar 

  • Ersoz ES, Yu J, Buckler ES (2007) Applications of linkage disequillibrium and association mapping in crop plants. In: Varshney RK, Tuberosa R (eds) Genomics assisted crop improvement Vol 1: Genomics approaches and platforms, Springer, The Netherlands, pp 97–120

    Google Scholar 

  • Ferguson ME, Burrow M, Schulze S, Bramel PJ, Paterson A, Kresovich S, Mitchell S (2004) Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet 108:1064–1070

    PubMed  CAS  Google Scholar 

  • Flandez-Galvez H, Ford R, Pang ECK, Taylor PWJ (2003a) An intraspecific linkage map of the chickpea (Cicer arietinum L.) genome based on sequence tagged based microsatellite site and resistance gene analog markers. Theor Appl Genet 106:1447–1453

    CAS  Google Scholar 

  • Flandez-Galvez H, Ford R, Taylor PWJ (2003b) Mapping QTLs governing resistance to ascochyta blight in chickpea. Theor Appl Genet 107:1257–1265

    CAS  Google Scholar 

  • Forster BP, Russell JR, Ellis RP, Handley LL, Robinson D, Hackett CA, Nevo E, Waugh R, Gordon DC, Keith R, Powell W (1997) Locating genotypes and genes for abiotic stress tolerance in barley: a strategy using maps, markers and the wild species. New Physiol 137:141–147

    Google Scholar 

  • Fredslund J, Schauser L, Madsen LH, Sandal N, Stougaard J (2005) PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs. Nucl Acids Res 33: W516–W520

    PubMed  CAS  Google Scholar 

  • Fredslund J, Madsen LH, Hougaard BK, Nielsen AM, Bertioli D, Sandal N, Stougaard J, Schauser L (2006a) A general pipeline for the development of anchor markers for comparative genomics in plants. BMC Genome 7:207

    Google Scholar 

  • Fredslund J, Madsen LH, Hougaard BK, Sandal N, Stougaard J, Bertioli D, Schauser L (2006b) GeMprospector – Online design of cross-species genetic marker candidates in legumes, grasses. Nucl Acids Res 34:W630–W640

    Google Scholar 

  • Garcia GM, Stalker HT, Kochert G (1995) Introgression analysis of an interspecific hybrid population in peanuts (Arachis hypogaea L.) using RFLP and RAPD markers. Genome 38:166–176

    PubMed  CAS  Google Scholar 

  • Garcia GM, Stalker HT, Shroeder E, Kochert GA (1996) Identification of RAPD, SCAR and RFLP markers tightly linked to nematode resistance genes introgressed from Arachis cardenasii to A. hypogaea. Genome 39:836–845

    PubMed  CAS  Google Scholar 

  • Gaur PM, Slinkard AE (1990a) Genetic control and linkage relations of additional isozymes markers in chickpea. Theor Appl Genet 80:648–653

    CAS  Google Scholar 

  • Gaur PM, Slinkard AE (1990b) Inheritance and linkage of isozyme coding genes in chickpea. J Hered 81:455–459

    CAS  Google Scholar 

  • Gepts P, Beavis WD, Brummer EC, Shoemaker RC, Stalker HT, Weeden NF, Young ND (2005) Legumes as a model plant family. Genomics for food and feed report of the cross-legume advances through genomics conference. Plant Physiol 137:1228–1235

    PubMed  CAS  Google Scholar 

  • Ghassemi F, Jackman AJ, Nix HA (1995) Salinization of land and water resources. CAB international, Wallingford, UK, p 526

    Google Scholar 

  • Gobbi A, Teixeira C, Moretzsohn M, Guimaraes P, Leal-Bertioli S, Bertioli D, Lopes CR, Gimenes M (2006) Development of a linkage map to species of B genome related to the peanut (Arachis hypogaea – AABB). Plant and animal genomes XIV conference, San Diego, CA, USA, P 679 (http://www.intl-pag.org/14/abstracts/PAG14_P679.html)

    Google Scholar 

  • Goff SA, Salmeron JM (2004) Back to the future of cereals. Sci Am 291:42–48

    PubMed  CAS  Google Scholar 

  • Grusak, MA (2002) Enhancing mineral content in plant food products. J Am Coll Nutr 21:178S–183S

    Google Scholar 

  • Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185

    CAS  Google Scholar 

  • Gupta PK, Varshney RK (2004) Cereal genomics. Kluwer Academic Publishers, Dordrecht, The Netherlands

    Google Scholar 

  • Gutierrez MV, Vaz Patto MC, Huguet T, Cubero JI, Moreno MT, Torres AM (2005) Cross-species amplification of Medicago truncatula microsatellites across three major pulse crops. Theor Appl Genet 110:1210–1217

    PubMed  CAS  Google Scholar 

  • Halward TM, Stalker HT, Kochert G (1993) Development of an RFLP linkage map in diploid peanut species. Theor Appl Genet 87:379–384

    CAS  Google Scholar 

  • Halward TM, Stalker HT, LaRue E, Kochert G (1992) Use of single-primer DNA amplifications in genetic studies of peanut (Arachis hypogaea L.). Plant Mol Biol 18:315–325

    PubMed  CAS  Google Scholar 

  • Hannan RM, Kaiser WJ, Muehlbauer FJ (1994) Development and utilization of the USDA chickpea germplasm core collection. Agron Abstr, ASA, Madison, WI, p 217

    Google Scholar 

  • Hansen M, Kraft T, Ganestam S, Sall T, Nilsson NO (2001) Linkage disequilibrium mapping of the bolting gene in sea beet using AFLP markers. Genet Res 77:61–66

    PubMed  CAS  Google Scholar 

  • He G, Prakash CS (1997) Identification of polymorphic DNA markers in cultivated peanut (Arachis hypogaea L.). Euphytica 97:143–149

    CAS  Google Scholar 

  • He G, Meng R, Newman M, Gao G, Pittman RN, Prakash CS (2003) Microsatellites as DNA markers in cultivated peanut (A. hypogaea L.). BMC Plant Biol 3:3

    PubMed  Google Scholar 

  • Herselman L, Thwaites R, Kimmins FM, Courtois B, van der Merwe PJA, Seal SE (2004) Identification and mapping of AFLP markers linked to peanut (Arachis hypogaea L.) resistance to the aphid vector of groundnut rosette disease. Theor Appl Genet 109:1426–1433

    PubMed  CAS  Google Scholar 

  • Hill WG, Weir BS (1994) Maximum-likelihood estimation of gene location by linkage disequilibrium. Am J. Hum Genet 54:705–714

    PubMed  CAS  Google Scholar 

  • Hirschhorn JN, Daly MJ (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6:95–108

    PubMed  CAS  Google Scholar 

  • Holbrook CC, Anderson WF, Pittman RN (1993) Selection of a core collection from the US germplasm collection of peanut. Crop Sci 33: 859–861

    Google Scholar 

  • Hopkins MS, Casa AM, Wang T, Mitchell SE, Dean RE, Kochert GD, Kresovich S (1999) Discovery and characterization of polymorphic simple sequence repeats (SSRs) in peanut. Crop Sci 39: 1243–1247

    CAS  Google Scholar 

  • Hovav R, Upadhyaya KC, Beharav A, Abbo S (2003) Major flowering time gene and polygene effects on chickpea seed weight. Plant Breed 122:539–541

    Google Scholar 

  • Huettel B, Winter P, Weising K, Choumane W, Weigand F, Kahl G (1999) Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Genome 42:210–217

    Google Scholar 

  • Igartua E, Casas AM, Ciudad F, Montoya JL, Romagosa I (1999) RFLP markers associated with major genes controlling heading date evaluated in a barley germplasm pool. Heredity 83:551–559

    PubMed  Google Scholar 

  • Iruela M, Rubio J, Barro F, Cubero JI, Millan T, Gil J (2006) Detection of two quantitative trait loci for resistance to ascochyta blight in an intra-specific cross of chickpea (Cicer arietinum L.): development of SCAR markers associated with resistance. Theor Appl Genet 112:278–287

    PubMed  CAS  Google Scholar 

  • Ivandic V, Thomas WTB, Nevo E, Zhang Z, Forster BP (2003) Associations of simple sequence repeats with quantitative trait variation including biotic and abiotic stress tolerance in Hordeum spontaneum. Plant Breed 122:300–304

    CAS  Google Scholar 

  • Ivandic V, Hackett CA, Nevo E, Keith R, Thomas WTB, Forster BP (2002) Analysis of simple sequence repeats (SSRs) in wild barley from the fertile crescent: associations with ecology, geography, and flowering time. Plant Mol Biol 48:511–527

    PubMed  CAS  Google Scholar 

  • Jain SM, Brar DS, Ahloowalia BS (2002) Molecular techniques in crop improvement. Kluwer Academic Publishers, Dordrecht, The Netherlands

    Google Scholar 

  • Jansen RC, Nap JP (2001) Genetical genomics: the added value from segregation. Trends Genet 17: 388–391

    PubMed  CAS  Google Scholar 

  • Jesubatham AM, Burrow MD (2006) Peanut Map: an online genome database for comparative molecular maps of peanut. BMC Bioinformatics 7:375

    PubMed  Google Scholar 

  • Jones N, Ougham H, Thomas H (1997) Markers and mapping: we are all geneticists now. New Phytol 137:165–177

    Google Scholar 

  • Kashiwagi J, Krishnamurthy L, Upadhyaya HD, Krishna H, Chandra S, Vadez V, Serraj R (2004) Genetic variability of drought-avoidance root traits in the mini-core germplasm collection of chickpea (Cicer arietinum L.). Euphytica 146:213–222

    Google Scholar 

  • Kashiwagi J, Krishnamurthy L, Crouch JH, Serraj R (2006) Variability of root length density and its contributions to seed yield in chickpea (Cicer arietinum L.) under terminal drought stress. Fields Crop Res 95:171–181

    Google Scholar 

  • Katam R, Vasanthaiah HKN, Basha SM (2006) Differential expression of mRNA transcripts and proteins in leaf tissue of peanut genotypes to water stress. In: Plant and animal genome XIV conference, San Diego, CA, USA, P446 (www.intl-pag.org/14/abstracts/PAG14_P446.html)

    Google Scholar 

  • Kazan K, Muehlbauer FJ, Weeden NE, Ladizinsky G (1993) Inheritance and linkage relationships of morphological and isozyme loci in chickpea (Cicer arietinum L.). Theor Appl Genet 86: 417–426

    CAS  Google Scholar 

  • Killian A, Huttner E, Wenzl P, Jaccoud D, Carling J, Caig V, Evers M, Heller-Uszynska K, Uszynski G, Cayla C, Patarapuwadol S, Xia L, Yang S, Thomson B (2005) The fast and the cheap: SNP and DArT – based whole genome profiling for crop improvement. In: Proceedings of the international congress, ‘In the wake of double helix: from the green revolution to the gene revolution’, 27–31 May 2003, Bologna, Italy, pp 443–461

    Google Scholar 

  • Kirst M, Yu Q (2007) Genetical genomics: successes and prospects in plants. In: Varshney RK, Tuberosa R (eds) Genomics assisted crop improvement Vol 1: genomic approaches and platforms, springer, The Netherlands, pp 245–265

    Google Scholar 

  • Kochert G, Halward T, Branch WD, Simpson CE (1991) RFLP variability in peanut (Arachis hypogaea L.) cultivars and wild species. Theor Appl Genet 81:565–570

    Google Scholar 

  • Koebner RMD (2004) Marker assisted selection in the cereals: the dream and the reality. In: Gupta PK, Varshney RK (eds) Cereal genomics. Kluwer Academic Publishers, Netherlands, pp 199–252

    Google Scholar 

  • Koebner RMD, Varshney RK (2006) The development and application of genomic models for large crop plant genomes. In: Varshney RK, Koebner RMD (eds) Model plants and crop improvement CRC Press, FL pp 1–10

    Google Scholar 

  • Kotresh H, Fakrudin B, Punnuri S, Rajkumar B, Thudi M, Paramesh H, Lohithswa H, Kuruvinashetti M (2006) Identification of two RAPD markers genetically linked to a recessive allele of a Fusarium wilt resistance gene in pigeonpea (Cajanus cajan (L.) Millsp.). Euphytica 149:113–120

    CAS  Google Scholar 

  • Krapovikas A, Gregory WC (1994) Taxonomy of genus Arachis (Legumonisae). Bonplandia 8:1–186

    Google Scholar 

  • Krishnamurthy L, Kashiwagi J, Upadhyaya HD, Serraj R (2003) Genetic diversity of drought avoidance root traits in the mini core germplasm collection of chickpea. Intl Chickpea Pigeonpea Newsl 10:21–24

    Google Scholar 

  • Kumar J, Van Rheenen HA (2000) A major gene for time of flowering in chickpea. J Hered 91:67–68

    PubMed  CAS  Google Scholar 

  • Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang HB (2005) Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea (Cicer arietinum L.). Theor Appl Genet 110:492–510

    PubMed  CAS  Google Scholar 

  • Lodwig EM, Hosie AH, Bourdes A, Findlay K, Allaway D, Karunakaran R, Downie JA, Poole PS (2003) Amino-acid cycling drives nitrogen fixation in the legume–Rhizobium symbiosis. Nature 422:672–674

    Google Scholar 

  • Luo M, Dang P, Guo BZ, He G, Holbrook CC, Bausher MG, Lee RD (2005) Generation of expressed sequence tags (ESTs) for gene discovery and marker development in cultivate peanut. Crop Sci 45:346–353

    CAS  Google Scholar 

  • Luo M, Dang P, Guo BZ, Holbrook CC, Bausher M (2003) Application of EST technology in functional genomics of Arachis hypogaea L. Phytopathology 94:S55

    Google Scholar 

  • Melchinger AE (1990) Use of molecular markers in breeding for oligogenic disease resistance. Plant Breed 104:1–19

    Google Scholar 

  • Milla SR (2003) Relationships and utiligation of Arachis germplasm in peanut improvement. PhD Thesis, North Carolina State University, USA, pp 1–150

    Google Scholar 

  • Milla SR, Isleib TG, Stalker HT (2005) Taxonomic relationships among Arachis sect. Arachis species as revealed by AFLP markers. Genome 48:1–11

    PubMed  CAS  Google Scholar 

  • Millan T, Rubio J, Iruela M (2003) Markers associated with Ascochyta blight resistance in chickpea and their potential in marker-assisted selection. Field Crops Res 84:373–384

    Google Scholar 

  • Millan T, Clarke HJ, Siddique KHM, Buhariwalla HK, Gaur PM, Kumar J, Gil J, Kahl G, Winter P (2006) Chickpea molecular breeding: new tools and concepts. Euphytica 147:81–103

    Google Scholar 

  • Moretzsohn MC, Hopkins MS, Mitchell SE, Resovich SK, Valls JFM, Ferreira ME (2004) Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biol 4:11

    Google Scholar 

  • Moretzsohn MC, Leoi L, Proite K, Guimara PM, Leal-Bertioli SCM, Gimenes MA, Martins WS, Valls JFM, Grattapaglia D, Bertioli DAJ (2005) Microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae). Theor Appl Genet 111:1060–1071

    PubMed  CAS  Google Scholar 

  • Morgante M, Salamini F (2003) From plant genomics to breeding practice. Curr Opin Biotech 14: 214–219

    PubMed  CAS  Google Scholar 

  • Nadimpalli RG, Jarret RL, Phatak SC, Kochert G (1994) Phylogenetic relationships of the pigeon pea (Cajanus cajan L.) based on nuclear restriction fragment length polymorphism. Genome 36:216–223

    Google Scholar 

  • Nobile PM, Lopes CR, Barata T, Barsalobres C, Guimaraes P, Leal-Bertioli S, Gimenes M (2006) Identification and characterization of peanut (Arachis hypogaea L.) ESTs regulated during interaction with Cercosporidium personatum (Berk and Curt) Deighton In: XIV international plant and animal genome conference, San Diego, CA, USA, P680 (wwwintl-pagorg/14/abstracts/PAG14_P680html)

    Google Scholar 

  • Odeny DA, Jayashree B, Ferguson M, Hoisington D, Crouch J, Gebhardt C (2007) Development, characterization and utilization of microsatellite markers in pigeonpea. Plant Breed 126:130–136

    CAS  Google Scholar 

  • Or E, Hovav R, Abbo S (1999) A major gene for flowering time in chickpea. Crop Sci 39:315–322

    Google Scholar 

  • Paik-Ro OG, Smith RL, Knauft DA (1992) Restriction fragment length polymorphism evaluation of six peanut species within the Arachis section. Theor Appl Genet 84:201–208

    CAS  Google Scholar 

  • Pakniyat H, Powell W, Baired E, Handley LL, Robinson D, Scrimgeour CM, Novo E, Hackett CA, Caligari PDS, Foster BP (1997) AFLP variation in wild barley (Hordeum spontaneum C Koch) with reference to salt tolerance and associated ecogeography. Genome 40:332–341

    CAS  Google Scholar 

  • Palmieri DA, Bechara MD, Curi RA, Gimenes MA, Lopes CR (2005) Novel polymorphic microsatellite markers in section Caulorrhizae (Arachis, Fabaceae). Mol Ecol Notes 5:77–79

    CAS  Google Scholar 

  • Paran I, Mitchelmore RW (1993) Development of reliable PCR-based markers linked to downy mildew resistance gene in lettuce. Theor Appl Genet 85:985–993

    CAS  Google Scholar 

  • Passioura J (1977) Grain yield, harvest index and water use of wheat. J Aust Inst Agric Sci 43:117–120

    Google Scholar 

  • Pereira MG, de Sousa MMT, Duarte IM (2001) Status of European Cicer database In: Magioni L, Ambrose M, Schachl R, Duc G, Lipman E (compilers) Report of a working group on grain legumes. Third Meeting, 5–7 July 2001, Krakow, Poland IPGRI, Rome, Italy, pp 45–46

    Google Scholar 

  • Pfaff T, Kahl G (2003) Mapping of gene-specific markers on the genetic map of chickpea (Cicer arietinum L). Mol Gen Genomics 269:243–251

    CAS  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotyping data. Genetics 155:945–959

    PubMed  CAS  Google Scholar 

  • Punguluri SK, Janaiah K, Govil JN, Kumar PA, Sharma PC (2006) AFLP fingerprinting in pigeonpea (Cajanus cajan (L.) Millsp) and its wild relatives. Genet Resour Crop Evol 53:523–531

    Google Scholar 

  • Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100

    PubMed  CAS  Google Scholar 

  • Raina SN, Rani V, Kojima T, OgiharaY, Singh KP (2001) RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification, and phylogenetic relationships in peanut (Arachis hypogaea L.) cultivars and wild species. Genome 44:763–772

    PubMed  CAS  Google Scholar 

  • Rajesh PN, Tullu A, Gil J, Gupta VS, Ranjekar PK, Muehlbauer FJ (2002) Identification of an STMS marker for the double-podding gene in chickpea. Theor Appl Genet 105:604–607

    PubMed  CAS  Google Scholar 

  • Rajesh PN, Coyne C, Meksem K, Sharma KD, Gupta V, Muehlbauer FJ (2004) Construction of a Hind III bacterial artificial chromosome library and its use in identification of clones associated with disease resistance in chickpea. Theor Appl Genet 108:663–669

    PubMed  CAS  Google Scholar 

  • Ratnaparkhe MB, Gupta VS, Ven Murthy MR, Ranjekar PK (1995) Genetic fingerprinting of pigeonpea [Cajanus cajan (L.) Millsp] and its wild relatives using RAPD markers. Theor Appl Genet 91:893–898

    CAS  Google Scholar 

  • Reddy LJ, Upadhyaya HD, Gowda CLL, Singh S (2005) Development of core collection in pigeonpea (Cajanus cajan (L.) Millasp). Genet Resour Crop Evol 52:1049–1056

    Google Scholar 

  • Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 25: 11479–11484

    Google Scholar 

  • Ryan JG, Spencer DC (2001) Future challenges and opportunities for agricultural R&D in the semi-arid tropics, International crops research institute for the semi-arid tropics, Patancheru 502 324, Andhra Pradesh, India, p 83

    Google Scholar 

  • Santra DK, Tekeoglu M, Ratnaparkhe MB, Gupta VS, Ranjekar PK, Muehlbauer FJ (2000) Identification and mapping of QTLs conferring resistance to Ascochyta blight in chickpea. Crop Sci 40: 1606–1612

    CAS  Google Scholar 

  • Saxena NP (1984) Chickpea in the physiology of tropical field crops. In: Goldworthy PR, Fisher NM (eds) Wiley, New York, pp 419–452

    Google Scholar 

  • Saxena KB, Singh L, Ariyanagam RP (1993) Role of partially cleistogamy in maintaining genetic purity of pigeonpea. Euphytica 66:225–229

    Google Scholar 

  • Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff T G, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422:297–301

    PubMed  CAS  Google Scholar 

  • Schultze M, Kondorosi A (1998) Regulation of symbiotic root nodule development. Annu Rev Genet 32:33–57

    PubMed  CAS  Google Scholar 

  • Septiningsih EM, Trijatmiko KR, Moeljopawiro S, McCouch SR (2003) Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O rufipogon. Theor Appl Genet 107:1433–1441

    PubMed  CAS  Google Scholar 

  • Serraj R (2004) Symbiotic nitrogen fixation:challenges and future prospects for application in tropical agroecosystems. Oxford & IBH, New Delhi, India

    Google Scholar 

  • Serraj R, Krishnamurthy L, Upadhyaya HD (2004) Screening chickpea mini-core germplasm for tolerance to salinity. Intl Chickpea Pigeonpea Newsl 11:29–32

    Google Scholar 

  • Sethy NK, Shokeen B, Bhatia S (2003) Isolation and characterization of sequence-tagged microsatellite sites markers in chickpea (Cicer aeritinum L.). Mol Ecol Notes 3:428–430

    CAS  Google Scholar 

  • Sethy NK, Choudhary S, Shokeen B, Bhatia S (2006a) Identification of microsatellite markers from Cicer reticulatum:molecular variation and phylogenetic analysis. Theor Appl Genet 112:347–357

    CAS  Google Scholar 

  • Sethy NK, Shokeen B, Edwards KJ, Bhatia S (2006b) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor Appl Genet 112:1416–1428

    CAS  Google Scholar 

  • Sharma HC (2001) Cytoplasmic male-sterility and source of pollen influence the expression of resistance to sorghum midge, Stenodiplosis sorghicola. Euphytica 122:391–395

    Google Scholar 

  • Sharma KK, Lavanya M (2002) Recent developments in transgenics for abiotic stress in legumes of the semi-arid tropics In: Ivanaga M (ed) Genetic engineering of crop plants for abiotic stress, JIRCAS Working Report No 23:61–73 Tsukuba, Japan

    Google Scholar 

  • Sharma KD, Winter P, Kahl G, Muehlbauer FJ (2004) Molecular mapping of Fusarium oxysporum f.sp. ciceris race 3 resistance gene in chickpea. Theor Appl Genet 108:1243–1248

    PubMed  CAS  Google Scholar 

  • Sharma PC, Matsumura H, Terauchi R (2007) Use of serial analysis of gene expression (SAGE) for transcript analysis. In: Varshney RK, Tuberosa R (eds) Genomics assisted crop improvement Vol I: genomics approaches and platforms, Springer, the Netherlands, pp 227–244

    Google Scholar 

  • Simko I, Costanzo S, Haynes KG, Christ BJ, Jones RW (2004) Linkage disequilibrium mapping of a Verticillium dahliae resistance quantitative trait locus in tetraploid potato (Solanum tuberosum) through a candidate gene approach. Theor Appl Genet 108:217–224

    PubMed  CAS  Google Scholar 

  • Simon CJ, Muehlbauer FJ (1997) Construction of a chickpea linkage map and its comparison with maps of pea and lentil. J Hered 88:115–119

    CAS  Google Scholar 

  • Simpson CE, Nelson SC, Starr JL, Woodard KE, Smith OD (1993) Registration of TxAg-6 and TxAg-7 peanut germplasm lines. Crop Sci 33:1418

    Google Scholar 

  • Singh KB, Kumar J, Haware MP, Lateef SS (1990) Disease and pest resistance breeding: which way to go in the nineties. In Chickpea in the nineties: Proceeding of the second international workshop on Chickpea improvement, 4–8 December 1989, International crops research institute for the semi-arid tropics, Patancheru 502 324, Andhra Pradesh, India, pp 223–238

    Google Scholar 

  • Sivaramakrishnan S, Seetha K, Nageshwar Rao A, Singh L (1997) RFLP analysis of cytoplasmic male-sterile lines of pigeonpea [Cajanus cajan (L.) Millsp] developed by interspecific crosses. Euphytica 93:307–312

    CAS  Google Scholar 

  • Skot L, Hamilton NRS, Mizen S, Chorlton KH, Thomas ID (2002) Molecular genecology of temperature response in Lolium perenne: 2 Association of AFLP markers with ecogeography. Mol Ecol 11: 1865–1876

    PubMed  CAS  Google Scholar 

  • Stalker HT, Mozingo LG (2001) Molecular markers of Arachis and marker assisted selection. Peanut Sci 28:117–123

    CAS  Google Scholar 

  • Subramanian V, Gurtu S, Nageswara Rao RC, Nigam SN (2000) Identification of DNA polymorphism in cultivated groundnut using random amplified polymorphic DNA (RAPD) assay. Genome 43:656–660

    PubMed  CAS  Google Scholar 

  • Sun GL, William M, Liu J, Kasha KJ, Pauls KP (2001) Microsatellite and RAPD polymorphisms in Ontario corn hybrids are related to the commercial sources and maturity ratings. Mol Breed 7:13–24

    CAS  Google Scholar 

  • Sun G, Bond M, Nass H, Martin R, Dong Z (2003) RAPD polymorphisms in spring wheat cultivars and lines with different level of Fusarium resistance. Theor Appl Genet 106:1059–1067

    PubMed  CAS  Google Scholar 

  • Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066

    PubMed  CAS  Google Scholar 

  • Tanksley SD, Nelson JC (1996) Advance backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTL from unadapted germplasm to the elite breeding lines. Theor Appl Genet 92:191–203

    Google Scholar 

  • Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Biotechnology 7:257–264

    CAS  Google Scholar 

  • Tautz D (1989) Hypervariablity of simple sequences as a general source of polymorphic DNA markers. Nucl Acids Res 17:6463–6471

    PubMed  CAS  Google Scholar 

  • Tekeoglu M, Rajesh PN, Muehlbauer FJ (2002) Integration of sequence tagged microsatellite sites to the chickpea genetic map. Theor Appl Genet 105:847–854

    PubMed  CAS  Google Scholar 

  • Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler IV ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nature Genet 28:286–289

    PubMed  CAS  Google Scholar 

  • Thro AM, Parrott W, Udall JA, Beavis WD (2004) Genomics and plant breeding: the experience of the initiative for future agricultural and food systems. Crop Sci 44:1893–1919

    Google Scholar 

  • Till BJ, Comai L, Henikoff S (2007) TILLING and EcoTILLING for crop improvement. In: Varshney RK, Tuberosa R (eds) Genomics assisted crop improvement Vol I: Genomics Approaches and Platforms, Springer, The Netherlands, pp 333–350

    Google Scholar 

  • Tohme J, Gonzalez OD, Beebe S, Duque MC (1996) AFLP analysis of gene pools of a wild bean core collection. Crop Sci 36:1375–1384

    CAS  Google Scholar 

  • Turpeinen T, Tenhola T, Manninen O, Nevo E, Nissila E (2001) Microsatellite diversity associated with ecological factors in Hordeum spontaneum populations in Israel. Mol Ecol 10:1577–1591

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Udupa SM, Sharma A, Sharma AP, Pai RA (1993) Narrow genetic variability in Cicer arietinum L. as revealed by RFLP analysis. J. Plant Biochem Biotechnol 2:83–86

    CAS  Google Scholar 

  • Upadhyaya HD, Ortiz R (2001) A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources. Theor Appl Genet 102:1292–1298

    Google Scholar 

  • Upadhyaya HD, Bramel PJ, Singh S (2001a) Development of a chickpea core subset using geographic distribution and quantitative traits. Crop Sci 41:206–210

    Google Scholar 

  • Upadhyaya HD, Nigam SN, Singh S (2001b) Evaluation of groundnut core collection to identify sources of tolerance to low temperature at germination. Indian J Plant Genet Resour 14:165–167

    Google Scholar 

  • Upadhyaya HD, Bramel PJ, Ortiz R, Singh S (2002) Developing a mini core of peanut for utilization of genetic resources. Crop Sci 42:2150–2156

    Google Scholar 

  • Upadhyaya HD, Ortiz R, Bramel PJ, Singh S (2003) Development of a groundnut core collection using taxonomical, geographical and morphological descriptors. Genet Resour Crop Evol 50:139–148

    CAS  Google Scholar 

  • Upadhyaya HD, Gowda CLL, Buhariwalla HK, Crouch JH (2006a) Efficient use of crop germplasm resources: Identifying useful germplasm for crop improvement through core and mini-core collections and molecular marker approaches. Plant Genet Resour 4:25–35

    CAS  Google Scholar 

  • Upadhyaya HD, Reddy LJ, Gowda CLL, Reddy KN, Singh S (2006b) Development of a mini core subset for enhanced and diversified utilization of pigeonpea germplasm resources. Crop Sci 46:2127–2132

    Google Scholar 

  • Vadez V, Krishnamurthy L, Gaur PM, Upadhyaya HD, Hoisington DA, Varshney RK, Turner NC, Siddique KHM (2006) Tapping the large genetic variability for salinity tolerance in chickpea. Proceeding of the Australian society of agronomy meeting, 10–14 September 2006 (http://wwwregionalorgau/au/asa/2006/ concurrent/environment/4561_vadezhtm)

    Google Scholar 

  • Van der Maesen, LJG (1987) Origin, history, and taxonomy of chickpea. In: Saxena MC, Singh KB (eds) The Chickpea, CABI/ICARDA, Wallingford, UK, pp 11–43

    Google Scholar 

  • van Treuren R, van Soest LJM, van Hintum ThJL (2001) Marker-assisted rationalization of genetic resource collections: a case study in flax using AFLPs. Theor Appl Genet 103:144–152

    Google Scholar 

  • Vance CP, Graham PH, Allan DL (2000) Biological nitrogen fixation phosphorus: a critical future need In: Pedrosa FO, Hungria M, Yates MG, Newton WE (eds) Nitrogen fixation: from molecules to crop productivity. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 506–514

    Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630

    PubMed  CAS  Google Scholar 

  • Varshney RK, Hoisington D, Tyagi AK (2006) Advances in cereal genomics and applications in crop breeding. Trends Biotechnol 24:490–499

    PubMed  CAS  Google Scholar 

  • Velculescu VE, Hang LZ, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484–487

    PubMed  CAS  Google Scholar 

  • Virk PS, Newbury HJ, Jackson MT, Ford-Lloyd BV (1995) The identification of duplicate accessions within a rice germplasm collection using RAPD analysis. Theor Appl Genet 90:1049–1055

    CAS  Google Scholar 

  • Virk PS, Ford-Lloyd BV, Jackson MT, Pooni HS, Clemeno TP, Newbury HJ (1996) Predicting quantitative variation within rice germplasm using molecular markers. Heredity 76:296–304

    Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, Lee T van de, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M (1995) AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23:4407–4414

    PubMed  CAS  Google Scholar 

  • Wang D, Graef GL, Procopiuk AM, Diers BW (2004a) Identification of putative QTL that underlie yield in interspecific soybean backcross populations. Theor Appl Genet 108:458–467

    CAS  Google Scholar 

  • Wang ML, Gillaspie AG, Newman ML, Dean RE, Pittman RN, Morris JB, Pederson GA (2004b) Transfer of simple sequence repeat (SSR) markers across the legume family for germplasm characterization and evaluation. Plant Genet Resour 2:107–119

    CAS  Google Scholar 

  • Williams JGK, Kubelik ARK, Livak JL, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by random primers are useful as genetic markers. Nucl Acids Res 18:6531–6535

    PubMed  CAS  Google Scholar 

  • Winter P, Pfaff T, Udupa SM, Huttel B, Sharma PC, Sahi S, Arreguin-Espinoza R, Weigand F, Muehlbauer FJ, Kahl G (1999) Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol Gen Genet 262:90–101

    PubMed  CAS  Google Scholar 

  • Winter P, Benko-Iseppon AM, Huttel B, Ratnaparkhe M, Tullu A, Sonnante G, Pfaff T, Tekeoglu M, Santra D, Sant VJ, Rajesh PN, Kahl G, Muehlbauer FJ (2000) A linkage map of 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. Theor Appl Genet 101:1155–1168

    Google Scholar 

  • Yang S, Pang W, Ash G, Harper J, Carling J, Wenzl P, Huttner E, Zong X, Kilian A (2006) Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology. Theor Appl Genet 113:585–595

    PubMed  CAS  Google Scholar 

  • Young ND, Mudge J, Ellis THN (2003) Legume genomes: more than peas in a nod. Curr Opin Plant Biol 6:199–204

    PubMed  CAS  Google Scholar 

  • Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S (2005) Sequencing the genespaces of Medicago truncatula and Lotus japonicus. Plant Physiol 137:1174–1181

    PubMed  CAS  Google Scholar 

  • Yu J, Buckler IV ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160

    PubMed  CAS  Google Scholar 

  • Yu J, Pressoir G, Briggs WH, Vroh BI, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208

    PubMed  CAS  Google Scholar 

  • Yüksel B, Paterson AH (2005) Construction and characterization of a peanut HindIII BAC library. Theor Appl Genet 111:630–639

    PubMed  Google Scholar 

  • Yüksel B, Bowers JE, Estill J, Goff L, Lemke C, Paterson AH (2005) Exploratory integration of peanut genetic and physical maps and possible contributions from Arabidopsis. Theor Appl Genet 111:87–94

    PubMed  Google Scholar 

  • Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer

About this chapter

Cite this chapter

Varshney, R.K. et al. (2007). Molecular Genetics and Breeding of Grain Legume Crops for the Semi-Arid Tropics. In: Varshney, R.K., Tuberosa, R. (eds) Genomics-Assisted Crop Improvement. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6297-1_10

Download citation

Publish with us

Policies and ethics