Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan)

Frontiers in Plant Science

Volumn 6, Issue FEB, 2015, Pages

  Pazhamala, Lekha ^a   Saxena, Rachit K ^a   Singh, Vikas K ^a   Sameerkumar, C V ^a   Kumar, Vinay ^a   Sinha, Pallavi ^a   Patel, Kishan ^a   Obala, Jimmy ^a,b   Kaoneka, Seleman R ^a,b   Tongoona, P ^b   Shimelis, Hussein A ^b   Gangarao, N V P R ^c   Odeny, Damaris ^c   Rathore, Abhishek ^a   Dharmaraj, P S ^d   Yamini, K N ^e   Varshney, Rajeev K ^a,f  

^a INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

^b UNIVERSITY OF KWAZULU NATAL   (South Africa)

^c International Crops Research Institute for the Semi Arid Tropics   (Kenya)

^d AGRICULTURAL RESEARCH STATION   (India)

^e ACHARYA N G RANGA AGRICULTURAL UNIVERSITY   (India)

^f UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

Genetic variability; Genomic resources; Genomic selection; Genomics assisted breeding; Marker assisted selection; Pigeonpea

Indexed keywords

EID: 84923238601     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2015.00050     Document Type: Review

References (115)

1. Akinola, J. O., and Whiteman, P. C. (1975). Agronomic studies on pigeon pea (Cajanus cajan (L.) Millsp.). I. field responses to sowing time. Aust. J. Agric. Res. 26, 43-56.
2. Ariyanayagam, R. P., Rao, A. N., and Zaveri, P. P. (1993). Gene-cytoplasmic male-sterility in pigeonpea. Int. Pigeonpea Newsl. 18, 7-11.
3. Ariyanayagam, R. P., Rao, A. N., and Zaveri, P. P. (1995). Cytoplasmic genic male-sterility in interspecific matings of Cajanus. Crop Sci. 35, 981-985. doi: 10.2135/cropsci1995.0011183X003500040008x
4. Aruna, R., Rao, D. M., Sivaramakrishnan, S., Reddy, J. L., Bramel, P., and Upadhyaya, H. (2008). Efficiency of three DNA markers in revealing genetic variation among wild Cajanus species. Plant Genet. Resour. 7, 113-121. doi: 10.1017/S1479262108061479
5. Bohra, A., Dubey, A., Saxena, R. K., Penmetsa, R. V., Poornima, K. N., Kumar, N., et al. (2011). Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.). BMC Plant Biol. 11:56. doi: 10.1186/1471-2229-11-56
6. Bohra, A., Mallikarjuna, N., Saxena, K. B., Upadhyaya, H., Vales, I., and Varshney, R. K. (2010). Harnessing the potential of crop wild relatives through genomics tools for pigeonpea improvement. J. Plant Biol. 37, 83-98.
7. Bohra, A., Saxena, R. K., Gnanesh, B. N., Saxena, K. B., Byregowda, M., Rathore, A., et al. (2012). An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L.) Millspaugh] derived from six mapping populations. Theor. Appl. Genet. 125, 1325-1338. doi: 10.1007/s00122-012-1916-5
8. Bohra, A., Saxena, R. K., Saxena, K. B., Sameerkumar, C. V., and Varshney, R. K. (2014a). "Advances in pigeonpea genomics," in Legumes in the Omic Era, eds S. Gupta, N. Nadarajan, and D. Sen Gupta (New York; Heidelberg; Dordrecht; London: Springer), 95-110.
9. Bohra, A., Singh, I. P., Yadav, A. K., Pathak, A., Soren, K. R., Chaturvedi, S. K., et al. (2014b). Utility of informative SSR markers in the molecular characterization of cytoplasmic genetic male sterility-based hybrid and its parents in pigeonpea. Natl. Acad. Sci. Lett. 38, 13-19. doi: 10.1007/s40009-014-0288-6
10. Choudhury, R. P., Singh, I. P., Shulabhi, V., Singh, N. P., and Kumar, S. (2008). RAPD markers for identification of cytoplasmic genic male sterile, maintainer and restorer lines of pigeonpea. J. Food Legumes 21, 218-221.
11. Dalvi, V. A., Saxena, K. B., and Madrap, I. A. (2008). Fertility restoration in cytoplasmic-nuclear male-sterile lines derived from 3 wild relatives of pigeonpea. J. Hered. 99, 671-673. doi: 10.1093/jhered/esn034
12. Deeplanaik, N., Kumaran, R. C., Venkatarangaiah, K., Shivashankar, S. K. H., Doddamani, D., and Telkar, S. (2013). Expression of drought responsive genes in pigeonpea and in silico comparison with soybean cDNA library. J. Crop Sci. Biotech. 16, 243-251. doi: 10.1007/s12892-013-0069-7
13. Deschamps, S., Llaca, V., and May, G. D. (2012). Genotyping-by-sequencing in plants. Biology 1, 460-483. doi: 10.3390/biology1030460
14. Dhanasekar, P., Dhumal, K. H., and Reddy, K. S. (2010). Identification of RAPD marker linked to plant type gene in pigeonpea. Indian J. Biotechnol. 9, 58-63.
15. Dubey, A., Farmer, A., Schlueter, J., Cannon, S. B., Abernathy, B., Tuteja, R., et al. (2011). Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.). DNA Res. 18, 153-164. doi: 10.1093/dnares/dsr007
16. Dutta, S., Kumawat, G., Singh, B. P., Gupta, D. K., Singh, S., Dogra, V., et al. (2011). Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]. BMC Plant Biol. 11:17. doi: 10.1186/1471-2229-11-17
17. Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S., et al. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379. doi: 10.1371/journal.pone.0019379
18. FAOSTAT. (2012). FAOSTAT Database. Available online at: http://faostat.fao.org/site
19. Gnanesh, B. N., Bohra, A., Sharma, M., Byregowda, M., Pande, S., Wesley, V., et al. (2011). Genetic mapping and quantitative trait locus analysis of resistance to sterility mosaic disease in pigeonpea [Cajanus cajan (L.) Millsp.].Field Crops Res. 123, 56-61. doi: 10.1016/j.fcr.2011.04.011
20. Gowda, C. L. L., Upadhyaya, H. D., Sharma, S., Varshney, R. K., and Dwivedi, S. L. (2013). Exploiting genomic resources for efficient conservation and use of chickpea, groundnut, and pigeonpea collections for crop improvement. Plant Genome 6, 1-11. doi: 10.3835/plantgenome2013.05.0016
21. Heffner, E. L., Sorrells, M. E., and Jannink, J. L. (2009). Genomic selection for crop improvement. Crop Sci. 49, 1-12. doi: 10.2135/cropsci2008.08.0512
22. Holloway, B., and Li, B. (2010). Expression QTLs: applications for crop improvement. Mol. Breed. 26, 381-391. doi: 10.1007/s11032-010-9396-2
23. Jadhav, D. R., Mallikarjuna, N., Sharma, H. C., and Saxena, K. B. (2012). Introgression of Helicoverpa armigeraresistance from Cajanus acutifolius-a wild relative from secondary gene pool of pigeon pea (Cajanus cajan). Asian J. Agric. Sci. 4, 242-248.
24. Kassa, M. T., Penmetsa, R. V., Carrasquilla-Garcia, N., Sarma, B. K., Datta, S., Upadhyaya, H. D., et al. (2012). Genetic patterns of domestication in pigeonpea (Cajanus cajan (L.) Millsp.) and wild Cajanus relatives. PLoS ONE7:e39563. doi: 10.1371/journal.pone.0039563
25. Kotresh, H., Fakrudin, B., Punnuri, S., Rajkumar, B., Thudi, M., Paramesh, H., et al. (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. doi: 10.1007/s10681-005-9059-2
26. Krishnamurthy, L., Upadhyaya, H. D., Saxena, K. B., and Vadez, V. (2012). Variation for temporary water logging response within the mini core pigeonpea germplasm. J. Agric. Sci. 150, 357-364. doi: 10.1017/S0021859611000682
27. Kudapa, H., Bharti, A. K., Cannon, S. B., Farmer, A. D., Mulaosmanovic, B., Kramer, R., et al. (2012). A comprehensive transcriptome assembly of pigeonpea (Cajanus cajan L.) using Sanger and second-generation sequencing platforms. Mol. Plant 5, 1020-1028. doi: 10.1093/mp/ssr111
28. Kulkarni, N. K., Reddy, A. S., Kumar, P. L., Vijaynarasimha, J., Rangaswamy, K. T., Muniyappa, V., et al. (2003). Broad-based resistance to pigeonpea sterility mosaic disease in accessions of Cajanus scarabaeoides (L.) Benth.Indian J. Plant Prot. 31, 6-11.
29. Kumar, A., Priyanka, V. L., Lall, V., and Lal, D. (2011). Abiotic factors and pigeonpea pod fly, Melanagromyza Obtusa (Malloch). Indian J. Entomol. 73, 59-62.
30. Kumawat, G., Raje, R. S., Bhutani, S., Pal, J. K., Mithra, S. V. C. R., Gaikwad, K., et al. (2012). Molecular mapping of QTLs for plant type and earliness traits in pigeonpea (Cajanus cajan L. Millsp.). BMC Genet. 13:84. doi: 10.1186/1471-2156-13-84
31. Lakshmi, M. P., Senthilkumar, P., Parani, M., Jithesh, M. N., and Parida, A. K. (2000). PCR-RFLP analysis of chloroplast gene regions in Cajanus (Leguminosae) and allied genera. Euphytica 116, 243-250. doi: 10.1023/A:1004030207084
32. Lohithaswa, H. C., Hittalmani, S., Shashidhar, H. E., and Dhanaraj, P. S. (2003). Assessment of genetic variability in some pigeonpea [Cajanus cajan (L.) Millsp.] genotypes using RAPD markers. Indian J. Genet. 63, 329-330.
33. Ma, H. (2013). A battle between genomes in plant male fertility. Nat Genet. 45, 472-473. doi: 10.1038/ng.2618
34. Majumder, N. D., and Singh, F. (2005). "Pigeonpea improvement in India," in Souvenir 4th International Food Legume Research Conference, 18-22 October, 2005 (New Delhi), 53-66.
35. Mallikarjuna, N. (2003). "Wide hybridization in important food legumes," in Improvement Strategies for Leguminosae Biotechnology, eds P. K. Jaiwal and R. P. Singh (Dordrecht: Kluwer Academic Publishers), 155-171.
36. Mallikarjuna, N. (2007). Production of fertile progeny from interspecific incompatible cross Cajanus platycarpus ×C. cajan. J. SAT Agric. Res. 3, 1.
37. Mallikarjuna, N., and Moss, J. P. (1995). Production of hybrids between Cajanus platycarpus and Cajanus cajan. Euphytica 83, 43-46. doi: 10.1007/BF01677859
38. Mallikarjuna, N., and Saxena, K. B. (2005). A new cytoplasmic nuclear male-sterility system derived from cultivated pigeonpea cytoplasm. Euphytica 142, 143-148. doi: 10.1007/s10681-005-1199-x
39. Mallikarjuna, N., Jadhav, D., and Reddy, P. (2006). Introgression of Cajanus platycarpus genome into cultivated pigeonpea genome. Euphytica 149, 161-167. doi: 10.1007/s10681-005-9063-6
40. Mallikarjuna, N., Jadhav, D., Reddy, M. V., and Dutta-Tawar, U. (2005). Introgression of phytophthora blight disease resistance from Cajanus platycarpus into short duration pigeonpeas. Indian J. Genet. 65, 261-264.
41. Mallikarjuna, N., Senthilvel, S., Jadhav, D. R., Saxena, K. B., Sharma, H. C., Upadhyaya, H. D., et al. (2011). Progress in the utilization of Cajanus platycarpus (Benth.) Maesen in pigeonpea improvement. Plant Breed. 130, 507-514. doi: 10.1111/j.1439-0523.2011.01870.x
42. Mallikarjuna, N., Sharma, H. C., and Upadhyaya, H. D. (2007). Exploitation of wild relatives of pigeonpea and chickpea for resistance to Helicoverpa armigera. J. SAT Agric. Res. 3, 4.
43. Malviya, N., and Yadav, D. (2010). RAPD analysis among pigeonpea [Cajanus cajan (L.) Millsp.] cultivars for their genetic diversity. Genet. Eng. Biotechnol. J. 1, 1-9.
44. Mir, R. R., Kudapa, H., Srikanth, S., Saxena, R. K., Sharma, A., Azam, S., et al. (2014). Candidate gene analysis for determinacy in pigeonpea (Cajanus spp.). Theor. Appl. Genet. 127, 2663-2678. doi: 10.1007/s00122-014-2406-8
45. Mir, R. R., Saxena, R. K., Saxena, K. B., Upadhyaya, H. D., Kilian, A., Cook, D. R., et al. (2013). Whole-genome scanning for mapping determinacy in pigeonpea (Cajanus spp.). Plant Breed. 132, 472-478. doi: 10.1111/j.1439-0523.2012.02009.x
46. Moose, S. P., and Mumm, R. H. (2008). Molecular plant breeding as the foundation for 21st century crop improvement. Plant Physiol. 147, 969-977. doi: 10.1104/pp.108.118232
47. Nadimpalli, R. G., Jarret, J. L., Pathak, S. C., and Kochert, G. (1993). Phylogenetic relationships of pigeonpea (Cajanus cajan) based on nuclear restriction fragment length polymorphism. Genome 36, 216-223. doi: 10.1139/g93-030
48. Narina, S. S., Bhardwaj, H. L., Hamama, A. A., Burke, J. J., Pathak, S. C., and Xu, Y. (2014). Seed protein and starch qualities of drought tolerant pigeonpea and native tepary beans. J. Agric. Sci. 6:247. doi: 10.5539/jas.v6n11p247
49. Odeny, D. A., Jayashree, B., Ferguson, M., Hoisington, D., Cry, L. J., and Gebhardt, C. (2007). Development, characterization and utilization of microsatellite markers in pigeonpea. Plant Breed. 126, 130-136. doi: 10.1111/j.1439-0523.2007.01324.x
50. Panguluri, S. K., Janaiah, J., Govil, J. N., Kumar, P. A., and Sharma, P. C. (2005). AFLP fingerprinting in pigeonpea (Cajanus cajan L. Millsp.) and its wild relatives. Genet. Res. Crop. Evol. 53, 523-531. doi: 10.1007/s10722-004-2031-5
51. Prasanthi, L., Reddy, B. V. B., Rekha Rani, K., and Naidu, P. H. (2009). Molecular marker for screening Fusariumwilt resistance in pigeonpea [Cajanus cajan (L.) Millspaugh]. Legume Res. 32, 19-24.
52. Priyanka, B., Sekhar, K., Sunita, T., Reddy, V. D., and Rao, K. V. (2010). Characterization of expressed sequence tags (ESTs) of pigeonpea (Cajanus cajan L.) and functional validation of selected genes for abiotic stress tolerance inArabidopsis thaliana. Mol. Genet. Genomics 283, 273-287. doi: 10.1007/s00438-010-0516-9
53. Raju, N. L., Gnanesh, N., Lekha, P., Jayashree, B., Pande, S., Hiremath, P. J., et al. (2010). The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.). BMC Plant Biol. 10:45. doi: 10.1186/1471-2229-10-45
54. Rao, S. C., Phillips, W. A., Mayeux, H. S., and Phatak, S. C. (2003). Potential grain and forage production of early maturing pigeonpea in the southern Great Plains. Crop Sci. 43, 2212-2217. doi: 10.2135/cropsci2003.2212
55. Ratnaparkhe, M. B., Gupta, V. S., Ven Murthy, M. R., and Ranjekar, P. K. (1995). Genetic fingerprinting of pigeonpea (Cajanus cajan (L.) Millsp) and its wild relatives using RAPD markers. Theor. Appl. Genet. 91, 893-898. doi: 10.1007/BF00223897
56. Reddy, L. J., and Faris, D. J. (1981). A cytoplasmic-genetic male sterile line in pigeonpea. Int. Pigeonpea Newsl. 1, 16-17.
57. Reddy, L. J., Upadhyaya, H. D., Gowda, C. L. L., and Singh, S. (2005). Development of core collection in pigeonpea [Cajanus cajan (L.) Millsp.] using geographic and qualitative morphological descriptors. Genet. Resour. Crop Evol. 52, 1049-1056. doi: 10.1007/s10722-004-6152-7
58. Saxena, K. B. (2008). Genetic improvement of pigeonpea- a review. Trop. Plant Biol. 1, 159-178. doi: 10.1007/s12042-008-9014-1
59. Saxena, K. B. (2014). Temperature-sensitive male-sterility system in pigeonpea. Curr Sci. 107, 277-281.
60. Saxena, K. B., Ariyanyagam, R. P., and Reddy, L. J. (1992). Genetics of a high-selfing trait in pigeon pea. Euphytica59, 125-127. doi: 10.1007/BF00041263
61. Saxena, K. B., and Kumar, R. V. (2003). Development of a cytoplasmic nuclear male-sterility system in pigeonpea using C. scarabaeoides (L.) Thouars. Indian J. Genet. Plant Breed. 63, 225-229.
62. Saxena, K. B., Kumar, R. V., and Rao, P. V. (2002). Pigeonpea nutrition and its improvement. Int. J. Plant Prod. 5, 227-260.
63. Saxena, K. B., Kumar, R. V., Srivastava, N., and Shiying, B. (2005). A cytoplasmic nuclear male-sterility system derived from a cross between Cajanus cajanifolius and C. cajan. Euphytica 145, 291-296. doi: 10.1007/s10681-005-1647-7
64. Saxena, K. B., and Nadarajan, N. (2010). Prospects of pigeonpea hybrids in Indian agriculture. Electron. J. Plant Breed. 1, 1107-1117.
65. Saxena, K. B., and Sawargaonkar, S. L. (2014). First information on heterotic groups in pigeonpea [Cajanus cajan(L.) Millsp.]. Euphytica 200, 187-196. doi: 10.1007/s10681-014-1142-0
66. Saxena, K. B., and Sharma, D. (1990). "Pigeonpea: genetics," in The Pigeonpea, eds Y. L. Nene, S. D. Hall, and V. K. Sheila (Wallingford: CAB International), 137-157.
67. Saxena, K. B., Sultana, R., Mallikarjuna, N., Saxena, R. K., Sawargaonkar, S. L., and Varshney, R. K. (2010a). Male-sterility systems in pigeonpea and their role in enhancing yield. Plant Breed. 129, 125-134. doi: 10.1111/j.1439-0523.2009.01752.x
68. Saxena, R. K., Cui, X., Thakur, V., Walter, B., Close, T. J., and Varshney, R. K. (2011). Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.). Funct. Integr. Genomics 11, 651-657. doi: 10.1007/s10142-011-0227-2
69. Saxena, R. K., Penmetsa, R. V., Upadhyaya, H. D., Kumar, A., Carrasquilla-Garcia, N., Schlueter, J. A., et al. (2012). Large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes. DNA Res. 19, 449-461. doi: 10.1093/dnares/dss025
70. Saxena, R. K., Prathima, C., Hoisington, D. A., Singh, N. K., and Varshney, R. K. (2010b). Novel SSR markers for polymorphism detection in pigeonpea (Cajanus spp.). Plant Breed. 129, 142-148. doi: 10.1111/j.1439-0523.2009.01680.x
71. Saxena, R. K., Saxena, K. B., Kumar, R. V., Hoisington, D. A., and Varshney, R. K. (2010c). Simple sequence repeat-based diversity in elite pigeonpea genotypes for developing mapping populations to map resistance to Fusariumwilt and sterility mosaic disease. Plant Breed. 129, 135-141. doi: 10.1111/j.1439-0523.2009.01698.x
72. Saxena, R. K., von Wettberg, E., Upadhyaya, H. D., Sanchez, V., Songok, S., Saxena, K. B., et al. (2014). Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs. PLoS ONE 9:e88568. doi: 10.1371/journal.pone.0088568
73. Sekhar, K., Priyanka, B., Reddy, V. D., and Rao, K. V. (2010). Isolation and characterization of a pigeonpea cyclophilin (CcCYP) gene, and its overexpression in Arabidopsis confers multiple abiotic stress tolerance. Plant Cell Environ. 33, 1324-1338. doi: 10.1111/j.1365-3040.2010.02151.x
74. Sekhar, K., Priyanka, B., Reddy, V. D., and Rao, K. V. (2011). Metallothionein 1 (CcMT1) of pigeonpea (Cajanus cajan, L.) confers enhanced tolerance to copper and cadmium in Escherichia coli and Arabidopsis thaliana. Environ. Exp. Bot. 72, 131-139. doi: 10.1016/j.envexpbot.2011.02.017
75. Sharma, D., Kannaiyan, J., and Saxena, K. B. (1987). Sources and inheritance of resistance to Alternaria blight in pigeonpea. SABRAO J. 19, 109-114.
76. Sharma, H. C., Pampapathy, G., and Reddy, L. J. (2003). Wild relatives of pigeonpea as a source of resistance to the pod fly (Melanagromyza obtusa Malloch) and pod wasp (Tanaostigmodes cajaninae La Salle). Genet. Resour. Crop. Evol. 50, 817-824. doi: 10.1023/A:1025967528757
77. Sharma, H. C., Sujana, G., and Rao, D. M. (2009). Morphological and chemical components of resistance to pod borer, Helicoverpa armigera in wild relatives of pigeonpea. Arthropod-Plant Interact. 3, 151-161. doi: 10.1007/s11829-009-9068-5
78. Sharma, M., Rathore, A., Mangala, U. N., Ghosh, R., Sharma, S., Upadhyay, H. D., et al. (2012). New sources of resistance to Fusarium wilt and sterility mosaic disease in a mini-core collection of pigeonpea germplasm. Eur. J. Plant Pathol. 133, 707-714. doi: 10.1007/s10658-012-9949-9
79. Sharma, S., Upadhyaya, H. D., Varshney, R. K., and Gowda, C. L. L. (2013). Pre-breeding for diversification of primary gene pool and genetic enhancement of grain legumes. Front. Plant Sci. 4:309. doi: 10.3389/fpls.2013.00309
80. Sharma, S. B. (1995). Resistance to Rotylenchulus reniformis, Heterodera cajani, and Meloidogyne javanica in accessions of Cajanus platycarpus. Plant Dis. 79, 1033-1035. doi: 10.1094/PD-79-1033
81. Singh, M., Gautam, N. K., Rana, M. K., Dahiya, O. P., Dutta, M., and Bansal, K. C. (2014). Pigeon pea genetic resources and its utilization in India, current status and future prospects. J. Plant Sci. Res. 1, 107.
82. Singh, N., Tyagi, R. K., and Pandey, C. (2013). Genetic Resources of Pigeonpea: Conservation for Use. New Delhi: National Bureau of Plant Genetic Resources (NBPGR), 1-49.
83. Singh, N. B., Singh, I. P., and Singh, B. B. (2005). "Pigeonpea breeding," in Advances in Pigeonpea Research, eds M. Ali and S. Kumar (Kanpur: Indian Institute of Pulses Research), 67-95.
84. Singh, S., Singh, K. N., Kant, R., Mehfooz, S., and Dutta, S. (2008). Assessment of genetic diversity among pigeonpea genotypes using SSR markers. Indian J. Genet. 68, 255-260.
85. Sivaramakrishnan, S., Seetha, K., Rao, A. N., and Singh, L. (1997). RFLP analysis of cytoplasmic male sterile lines in pigeonpea (Cajanus cajan L. Millsp.). Euphytica 126, 293-299.
86. Sivaramakrishnan, S., Seetha, K., and Reddy, L. J. (2002). Diversity in selected wild and cultivated species of pigeonpea using RFLP of mtDNA. Euphytica 125, 21-28. doi: 10.1023/A:1015759318497
87. Songok, S., Ferguson, M., Muigai, A. W., and Silim, S. (2010). Genetic diversity in pigeonpea [Cajanus cajan (L.) Millsp.] landraces as revealed by simple sequence repeat markers. Afr. J. Biotech. 9, 3231-3241.
88. Srikanth, S., Rao, M. V., and Mallikarjuna, N. (2014). Inter-specific hybridization between Cajanus cajan (L.) Millsp. and C. lanceolatus (WV Fitgz) van der Maesen. Plant Genet. Resour. 12, 255-258. doi: 10.1017/S1479262113000361
89. Srivastava, N., Vadez, V., Upadhyaya, H. D., and Saxena, K. B. (2006). Screening for intra and inter-specific variability for salinity tolerance in pigeonpea (Cajanus cajan L.Millsp.) and its related wild species. J. SAT Agric. Res. 2, 1.
90. Subbarao, G. V., Johansen, C., Jana, M. K., and Rao, J. V. D. K. (1991). Comparative salinity responses among pigeonpea genotypes and their wild relatives. Crop Sci. 31, 415-418. doi: 10.2135/cropsci1991.0011183X003100020037x
91. 1 hybrids of pigeonpea and a tolerant wild relative. Crop Sci. 30, 785-788. doi: 10.2135/cropsci1990.0011183X003000040005x
92. Sujana, G., Sharma, H. C., and Manohar, R. D. (2008). Antixenosis and antibiosis components of resistance to pod borer, Helicoverpa armigera in wild relatives of pigeonpea. Int. J. Trop. Insect Sci. 28, 191-200.
93. Tamirisa, S., Vudem, D. R., and Khareedu, V. R. (2014). Overexpression of pigeonpea stress-induced cold and drought regulatory gene (CcCDR) confers drought, salt, and cold tolerance in Arabidopsis. J Exp Bot. 65, 4769-4781. doi: 10.1093/jxb/eru224
94. Tanksley, S. D., and Nelson, J. C. (1996). Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor. Appl. Genet. 92, 191-203. doi: 10.1007/BF00223376
95. Tikka, S. B. S., Parmer, L. D., and Chauhan, R. M. (1997). First record of cytoplasmic genetic male sterility in pigeonpea (Cajanus cajan (L.) Millsp.) through wide hybridization. Gujarat Agric. Univ. Res. J. 22, 60-162.
96. Tuteja, R., Saxena, R. K., Davila, J., Shah, T., Chen, W., Xiao, Y. L., et al. (2013). Cytoplasmic male sterility-associated chimeric open reading frames identified by mitochondrial genome sequencing of four Cajanusgenotypes. DNA Res. 20, 485-495. doi: 10.1093/dnares/dst025
97. Upadhyaya, H. D., Reddy, K. N., Shivali, S., Varshney, R. K., Bhattacharjee, R., Singh, S., et al. (2011). Pigeonpea composite collection for enhanced utilization of germplasm in crop improvement programs. Plant Genet. Resour. 9, 97-108. doi: 10.1017/S1479262110000419
98. Upadhyaya, H. D., Reddy, L. J., Gowda, C. L. L., Reddy, K. N., and Singh, S. (2006). Development of a mini core subset for enhanced and diversified utilization of pigeonpea germplasm resources. Crop Sci. 46, 2127-2132. doi: 10.2135/cropsci2006.01.0032
99. Upadhyaya, H. D., Sharma, S., Reddy, K. N., Saxena, R., Varshney, R. K., and Gowda, C. L. L. (2013). "Pigeonpea," inGenetic and Genomic Resources of Grain Legume Improvement, eds M. Singh, H. D. Upadhyaya, and I. S. Bisht (London, UK: Elsevier), 181-202.
100. van der Maesen, L. J. G. (1990). "Pigeonpea: origin, history, evolution and taxonomy," in The Pigeonpea, eds Y. L. Nene, S. D. Hall, and V. K. Sheila (Wallingford: CAB International), 15-46.
101. Varshney, R. K., Kudapa, H., Roorkiwal, M., Thudi, M., Pandey, M. K., Saxena, R. K., et al. (2012b). Advances in genomics research and molecular breeding applications in SAT legume crops by using next generation sequencing and high-throughput genotyping technologies. J. Biosci. 37, 811-820. doi: 10.1007/s12038-012-9228-0
102. Varshney, R. K., Chen, W., Li, Y., Bharti, A. K., Saxena, R. K., Schlueter, J. A., et al. (2012a). Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30, 83-89. doi: 10.1038/nbt.2022
103. Varshney, R. K., Graner, A., and Sorrells, M. E. (2005). Genomics-assisted breeding for crop improvement. Trends Plant Sci. 10, 621-630. doi: 10.1016/j.tplants.2005.10.004
104. Varshney, R. K., Mohan, S. M., Gaur, P. M., Chamarthi, S. K., Singh, V. K., Srinivasan, S., et al. (2014c). Marker-assisted backcrossing to introgress resistance to Fusarium wilt (FW) race 1 and Ascochyta blight (AB) in C 214, an elite cultivar of chickpea. Plant Genome 7, 1-11. doi: 10.3835/plantgenome2013.10.0035
105. Varshney, R. K., Murali Mohan, S., Gaur, P. M., Gangarao, N. V. P. R., Pandey, M. K., Bohra, A., et al. (2013). Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics.Biotechnol. Adv. 31, 1120-1134. doi: 10.1016/j.biotechadv.2013.01.001
106. Varshney, R. K., Nayak, S. N., May, G. D., and Jackson, S. A. (2009). Next generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol. 27, 522-530. doi: 10.1016/j.tibtech.2009.05.006
107. Varshney, R. K., Pandey, M. K., Janila, P., Nigam, S. N., Sudhini, H., Gowda, M. V. C., et al. (2014d). Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.). Theor. Appl. Genet. 127, 1771-1781. doi: 10.1007/s00122-014-2338-3
108. Varshney, R. K., Penmetsa, R. V., Dutta, S., Kulwal, P. L., Saxena, R. K., Datta, S., et al. (2010). Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.). Mol Breed. 26, 393-408. doi: 10.1007/s11032-009-9327-2
109. Varshney, R. K., Terauchi, R., and McCouch, S. R. (2014a). Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol. 2:e1001883. doi: 10.1371/journal.pbio.1001883
110. Varshney, R. K., Thudi, M., Nayak, S. N., Gaur, P. M., Kashiwagi, J., Krishnamurthy, L., et al. (2014b). Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theor. Appl. Genet. 127, 445-462. doi: 10.1007/s00122-013-2230-6
111. Wanjari, K. B., Patil, A. N., Manapure, P., Manjayya, J. G., and Patel, M. (1999). Cytoplasmic male sterility in pigeonpea with cytoplasm from Cajanus volubilis. Ann. Plant Physiol. 13, 170-174.
112. Wanjari, K. B., Patil, A. N., Patel, M. C., and Manjaya, J. C. (2000). Male-sterility derived from Cajanus sericeus ×Cajanus cajan: confusion of cytoplasmic male-sterility with dominant genic male-sterility. Euphytica 115, 59-64. doi: 10.1023/A:1003974005782
113. Wasike, S., Okori, P., and Rubaihayo, P. R. (2005). Genetic variability and relatedness of the Asian and African pigeon pea as revealed by AFLP. Afr. J. Biotechnol. 4, 1228-1233.
114. Yang, S., Pang, W., Harper, J., Carling, J., Wenzl, P., Huttner, E., et al. (2006). Low level of genetic diversity in cultivated pigeonpea compared to its wild relatives is revealed by diversity arrays technology (DArT). Theor. Appl. Genet. 113, 585-595. doi: 10.1007/s00122-006-0317-z
115. Yang, S., Saxena, R. K., Kulwal, P. L., Ash, G. J., Dubey, A., Harper, J. D., et al. (2011). First genetic map of pigeonpea based on diversity array technology (DArT) markers. J. Genet. 90, 103-109. doi: 10.1007/s12041-011-0050-5