Genomics of crop wild relatives: Expanding the gene pool for crop improvement

Plant Biotechnology Journal

Volumn 14, Issue 4, 2016, Pages 1070-1085

  Brozynska, Marta ^a   Furtado, Agnelo ^a   Henry, Robert J ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Crop wild relatives; Genomics; Plant genetic resources

Indexed keywords

ADAPTATION; BIODIVERSITY; CATERING SERVICE; CROP; GENE POOL; GENETIC VARIATION; GENETICS; GENOMICS; PLANT BREEDING; PLANT GENOME; PROCEDURES;

ADAPTATION, PHYSIOLOGICAL; BIODIVERSITY; CROPS, AGRICULTURAL; FOOD SUPPLY; GENE POOL; GENETIC VARIATION; GENOME, PLANT; GENOMICS; PLANT BREEDING;

EID: 84961210276     PISSN: 14677644     EISSN: 14677652     Source Type: Journal    
DOI: 10.1111/pbi.12454     Document Type: Review

References (193)

1. Amborella Genome Project. (2013) The amborella genome and the evolution of flowering plants. Science, 342, 1241089.
2. Amiri, R., Bahraminejad, S., Sasani, S., Jalali-Honarmand, S. and Fakhri, R. (2015) Bread wheat genetic variation for grain's protein, iron and zinc concentrations as uptake by their genetic ability. Eur. J. Agron. 67, 20-26.
3. Arisa, T. and Pires, C.J. (2012) A fully resolved chloroplast phylogeny of the brassica crops and wild relatives (Brassicaceae: Brassiceae): novel clades and potential taxonomic implications. Taxon, 61, 980-988.
4. Bally, I.S.E., Graham, G.C. and Henry, R.J. (1996) Genetic diversity of Kensington mango in Australia. Aust. J. Exp. Agric. 36, 243-247.
5. Bao, Y., Xu, S., Jing, X., Meng, L. and Qin, Z. (2015) De novo assembly and characterization of Oryza officinalis leaf transcriptome by using RNA-Seq. Biomed Res. Int. 2015, 982065.
6. Batchu, A.K., Zimmermann, D., Schulze-Lefert, P. and Koprek, T. (2006) Correlation between hordatine accumulation, environmental factors and genetic diversity in wild barley (Hordeum spontaneum C. Koch) accessions from the Near East Fertile Crescent. Genetica, 127, 87-99.
7. Bedada, G., Westerbergh, A., Muller, T., Galkin, E., Bdolach, E., Moshelion, M., Fridman, E. and Schmid, K. (2014) Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts. BMC Genom. 15, 995.
8. Berkman, P.J., Bundock, P.C., Casu, R.E., Henry, R.J., Rae, A.L. and Aitken, K.S. (2014) A survey sequence comparison of Saccharum genotypes reveals allelic diversity differences. Trop. Plant Biol. 7, 71-83.
9. Birky, C. (2001) The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and models. Annu. Rev. Genet. 35, 125.
10. Biselli, C., Urso, S., Bernardo, L., Tondelli, A., Tacconi, G., Martino, V., Grando, S. and Valè, G. (2010) Identification and mapping of the leaf stripe resistance gene Rdg1a in Hordeum spontaneum. Theor. Appl. Genet. 120, 1207-1218.
11. Blair, M.W., Iriarte, G. and Beebe, S. (2006) QTL analysis of yield traits in an advanced backcross population derived from a cultivated Andean × wild common bean (Phaseolus vulgaris L.) cross. Theor. Appl. Genet. 112, 1149-1163.
12. Bolger, A., Scossa, F., Bolger, M.E., Lanz, C., Maumus, F., Tohge, T., Quesneville, H., Alseekh, S., Sorensen, I., Lichtenstein, G., Fich, E.A., Conte, M., Keller, H., Schneeberger, K., Schwacke, R., Ofner, I., Vrebalov, J., Xu, Y., Osorio, S., Aflitos, S.A., Schijlen, E., Jimenez-Gomez, J.M., Ryngajllo, M., Kimura, S., Kumar, R., Koenig, D., Headland, L.R., Maloof, J.N., Sinha, N., van Ham, R.C.H.J., Lankhorst, R.K., Mao, L., Vogel, A., Arsova, B., Panstruga, R., Fei, Z., Rose, J.K.C., Zamir, D., Carrari, F., Giovannoni, J.J., Weigel, D., Usadel, B. and Fernie, A.R. (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat. Genet. 46, 1034-1038.
13. Bouyioukos, C., Moscou, M.J., Champouret, N., Hernández-Pinzón, I., Ward, E.R. and Wulff, B.B.H. (2013) Characterisation and analysis of the Aegilops sharonensis transcriptome, a wild relative of wheat in the sitopsis section. PLoS ONE, 8, e72782.
14. Brozynska, M., Omar, E.S., Furtado, A., Crayn, D., Simon, B., Ishikawa, R. and Henry, R.J. (2014) Chloroplast genome of novel rice germplasm identified in northern Australia. Trop. Plant Biol. 7, 111-120.
15. Ceccarelli, S. (2014) Plant genetic resources and climate change. In Drought (Jackson, M., Ford-Lloyd, B. and Parry, M., eds), pp. 221-235. Wallingford, UK: CAB International.
16. Chaw, S.M., Chang, C.C., Chen, H.L. and Li, W.H. (2004) Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J. Mol. Evol. 58, 424-441.
17. Chen, G., Liu, Y., Ma, J., Zheng, Z., Wei, Y., McIntyre, C.L., Zheng, Y.L. and Liu, C. (2013a) A novel and major quantitative trait locus for fusarium crown rot resistance in a genotype of wild barley (Hordeum spontaneum L.). PLoS ONE, 8, e58040.
18. Chen, J., Huang, Q., Gao, D., Wang, J., Lang, Y., Liu, T., Li, B., Bai, Z., Luis Goicoechea, J., Liang, C., Chen, C., Zhang, W., Sun, S., Liao, Y., Zhang, X., Yang, L., Song, C., Wang, M., Shi, J., Liu, G., Liu, J., Zhou, H., Zhou, W., Yu, Q., An, N., Chen, Y., Cai, Q., Wang, B., Liu, B., Min, J., Huang, Y., Wu, H., Li, Z., Zhang, Y., Yin, Y., Song, W., Jiang, J., Jackson, S.A., Wing, R.A., Wang, J. and Chen, M. (2013b) Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat. Commun. 4, 1595.
19. Chen, X., Xia, J., Xia, Z., Zhang, H., Zeng, C., Lu, C., Zhang, W. and Wang, W. (2015) Potential functions of microRNAs in starch metabolism and development revealed by miRNA transcriptome profiling of cassava cultivars and their wild progenitor. BMC Plant Biol. 15, 33-33.
20. Chitwood, D.H., Maloof, J.N. and Sinha, N.R. (2013) Dynamic transcriptomic profiles between tomato and a wild relative reflect distinct developmental architectures. Plant Physiol. 162, 537-552.
21. Chung, W.H., Jeong, N., Kim, J., Lee, W.K., Lee, Y.G., Lee, S.H., Yoon, W., Kim, J.H., Choi, I.Y., Choi, H.K., Moon, J.K., Kim, N. and Jeong, S.C. (2014) Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes. DNA Res. 21, 153-167.
22. Concibido, V., La Vallee, B., McLaird, P., Pineda, N., Meyer, J., Hummel, L., Yang, J., Wu, K. and Delannay, X. (2003) Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars. Theor. Appl. Genet. 106, 575-582.
23. Cronin, J.K., Bundock, P.C., Henry, R.J. and Nevo, E. (2007) Adaptive climatic molecular evolution in wild barley at the Isa defense locus. Proc. Natl Acad. Sci. USA, 104, 2773-2778.
24. Davey, M., Gudimella, R., Harikrishna, J.A., Sin, L.W., Khalid, N. and Keulemans, J. (2013) A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids. BMC Genom. 14, 683.
25. Dempewolf, H., Rieseberg, L. and Cronk, Q. (2008) Crop domestication in the Compositae: a family-wide trait assessment. Genet. Resour. Crop Evol. 55, 1141-1157.
26. Dempewolf, H., Eastwood, R.J., Guarino, L., Khoury, C.K., Müller, J.V. and Toll, J. (2014) Adapting agriculture to climate change: a global initiative to collect, conserve, and use crop wild relatives. Agroecol. Sust. Food, 38, 369-377.
27. Denoeud, F., Carretero-Paulet, L., Dereeper, A., Droc, G., Guyot, R., Pietrella, M., Zheng, C., Alberti, A., Anthony, F., Aprea, G., Aury, J.M., Bento, P., Bernard, M., Bocs, S., Campa, C., Cenci, A., Combes, M.C., Crouzillat, D., Da Silva, C., Daddiego, L., De Bellis, F., Dussert, S., Garsmeur, O., Gayraud, T., Guignon, V., Jahn, K., Jamilloux, V., Joët, T., Labadie, K., Lan, T., Leclerc, J., Lepelley, M., Leroy, T., Li, L.T., Librado, P., Lopez, L., Muñoz, A., Noel, B., Pallavicini, A., Perrotta, G., Poncet, V., Pot, D., Priyono, Rigoreau, M., Rouard, M., Rozas, J., Tranchant-Dubreuil, C., VanBuren, R., Zhang, Q., Andrade, A.C., Argout, X., Bertrand, B., de Kochko, A., Graziosi, G., Henry, R.J., Jayarama, Ming, R., Nagai, C., Rounsley, S., Sankoff, D., Giuliano, G., Albert, V.A., Wincker, P. and Lashermes, P. (2014) The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science, 345, 1181-1184.
28. D'Hont, A., Denoeud, F., Aury, J.M., Baurens, F.C., Carreel, F., Garsmeur, O., Noel, B., Bocs, S., Droc, G., Rouard, M., Da Silva, C., Jabbari, K., Cardi, C., Poulain, J., Souquet, M., Labadie, K., Jourda, C., Lengelle, J., Rodier-Goud, M., Alberti, A., Bernard, M., Correa, M., Ayyampalayam, S., McKain, M.R., Leebens-Mack, J., Burgess, D., Freeling, M., Mbeguie-A-Mbeguie, D., Chabannes, M., Wicker, T., Panaud, O., Barbosa, J., Hribova, E., Heslop-Harrison, P., Habas, R., Rivallan, R., Francois, P., Poiron, C., Kilian, A., Burthia, D., Jenny, C., Bakry, F., Brown, S., Guignon, V., Kema, G., Dita, M., Waalwijk, C., Joseph, S., Dievart, A., Jaillon, O., Leclercq, J., Argout, X., Lyons, E., Almeida, A., Jeridi, M., Dolezel, J., Roux, N., Risterucci, A.M., Weissenbach, J., Ruiz, M., Glaszmann, J.C., Quetier, F., Yahiaoui, N. and Wincker, P. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488, 213-217.
29. Dillon, S.L., Lawrence, P.K., Henry, R.J., Ross, L., Price, H.J. and Johnston, J.S. (2004) Sorghum laxiflorum and S. macrospermum, the Australian native species most closely related to the cultivated S. bicolor based on ITS1 and ndhF sequence analysis of 25 Sorghum species. Plant Syst. Evol. 249, 233-246.
30. Dillon, S.L., Lawrence, P.K., Henry, R.J., Ross, L. and Price, H.J. (2007a) Sorghum resolved as a distinct genus based on combined ITS1, ndhF and Adh1 analyses. Plant Syst. Evol. 268, 29-43.
31. Dillon, S.L., Shapter, F.M., Henry, R.J., Cordeiro, G., Izquierdo, L. and Lee, L.S. (2007b) Domestication to crop improvement: genetic resources for Sorghum and Saccharum (Andropogoneae). Ann. Bot. 100, 975-989.
32. Edwards, M.A. and Henry, R.J. (2011) DNA sequencing methods contributing to new directions in cereal research. J. Cereal Sci. 54, 395-400.
33. Ellstrand, C.N. (2003) Dangerous Liaisons? When Cultivated Plants Mate with their Wild Relatives. Baltimore, MD: John Hopkins University Press.
34. Eshed, Y. and Zamir, D. (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics, 141, 1147-1162.
35. FAO (2015) Biodiversity. Available at: http://www.fao.org/biodiversity/components/plants/en/accessed (Last accessed 15 May 2015).
36. Feng, F., Xu, X., Du, X., Tong, H., Luo, L. and Mei, H. (2012) Assessment of drought resistance among wild rice accessions using a protocol based on single-tiller propagation and PVC-tube cultivation. Aust. J. Crop Sci. 6, 1204-1211.
37. Fitzgerald, H. (2013) The National Crop Wild Relative Strategy Report for Finland. MTT Report. Jokioinen, Finland: EU Seventh Framework Programme.
38. Fitzgerald, T.L., Shapter, F.M., McDonald, S., Waters, D.L.E., Chivers, I.H., Drenth, A., Nevo, E. and Henry, R.J. (2011) Genome diversity in wild grasses under environmental stress. Proc. Natl Acad. Sci. USA, 108, 21139-21144.
39. Fox, S.E., Preece, J., Kimbrel, J.A., Marchini, G.L., Sage, A., Youens-Clark, K., Cruzan, M.B. and Jaiswal, P. (2013) Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae). Appl. Plant Sci. 1, apps 120001.
40. Friedt, W., Horsley, R.D., Harvey, B.L., Poulsen, D.M.E., Lance, R.C.M., Ceccarelli, S., Grando, S. and Capettini, F. (2010) Barley breeding history, progress, objectives, and technology. In Barley (Ullrich, S.E., ed.), pp. 160-220. Hoboken, NJ, USA: Wiley-Blackwell.
41. Fu, Q., Zhang, P., Tan, L., Zhu, Z., Ma, D., Fu, Y., Zhan, X., Cai, H. and Sun, C. (2010) Analysis of QTLs for yield-related traits in Yuanjiang common wild rice (Oryza rufipogon Griff.). J. Genet. Genomics, 37, 147-157.
42. Gaikwad, K.B., Singh, N., Bhatia, D., Kaur, R., Bains, N.S., Bharaj, T.S. and Singh, K. (2014) Yield-enhancing heterotic QTL Transferred from wild species to cultivated rice Oryza sativa L. PLoS ONE, 9, e96939.
43. Ganie, S., Karmakar, J., Roychowdhury, R., Mondal, T. and Dey, N. (2014) Assessment of genetic diversity in salt-tolerant rice and its wild relatives for ten SSR loci and one allele mining primer of salT gene located on 1st chromosome. Plant Sys. Evol. 300, 1741-1747.
44. Garg, R., Verma, M., Agrawal, S., Shankar, R., Majee, M. and Jain, M. (2014) Deep transcriptome sequencing of wild halophyte rice, Porteresia coarctata, provides novel insights into the salinity and submergence tolerance factors. DNA Res. 21, 69-84.
45. Gill, S.S., Gill, R., Kumar, G., Pareek, A., Sharma, P.C., Anjum, N.A. and Tuteja, N. (2012) Mustard: approaches for crop improvement and abiotic stress tolerance. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R, eds), pp. 1351-1368. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
46. Gill-Langarica, H.R., Muruaga-Martínez, J.S., Vargas-Vázquez, M.L.P., Rosales-Serna, R. and Mayek-Pérez, N. (2011) Genetic diversity analysis of common beans based on molecular markers. Genet. Mol. Biol. 34, 595-605.
47. Gothandam, K.M. (2012) Rice: improving cold stress tolerance. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R., eds), pp. 733-750. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
48. Guimarães, P., Brasileiro, A., Morgante, C., Martins, A., Pappas, G., Silva, O., Togawa, R., Leal-Bertioli, S., Araujo, A., Moretzsohn, M. and Bertioli, D. (2012) Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection. BMC Genom. 13, 387.
49. Hajjar, R. and Hodgkin, T. (2007) The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica, 156, 1-13.
50. Hamon, P. (2015) The International Coffea Genome 13 Project: A Way to Understand the Evolutionary History of Coffea Genomes and Unlock the Potential Use of Wild Species in Breeding? XXIII Plant and Animal Genome (PAG) Meeting, San Diego, California, January 9-15, 2015.
51. Harlan, J.R. and de Wet, J.M.J. (1971) Toward a rational classification of cultivated plants. Taxon, 20, 509-517.
52. Henry, R.J. (2010) Plant Resources for Food, Fuel and Conservation. London, UK: Earthscan. pp. 200.
53. Henry, R.J. (2012) Next generation sequencing for understanding and accelerating crop domestication. Brief. Funct. Genomics, 11, 51-56.
54. Henry, R.J. (2014a) Sequencing crop wild relatives to support the conservation and utilization of plant genetic resources. Plant Genet. Resour. C, 12, S9-S11.
55. Henry, R.J. (2014b) Genomics strategies for germplasm characterization and the development of climate resilient crops. Front. Plant Sci. 5, 68.
56. Henry, R.J. and Nevo, E. (2014) Exploring natural selection to guide breeding for agriculture. Plant Biotechnol. 12, 655-662.
57. Henry, R.J., Rice, N., Waters, D.L.E., Kasem, S., Ishikawa, R., Dillon, S.L., Crayn, D., Wing, R. and Vaughan, D. (2010) Australian Oryza: utility and conservation. Rice, 3, 235-241.
58. Heywood, V., Casas, A., Ford-Lloyd, B., Kell, S. and Maxted, N. (2007) Conservation and sustainable use of crop wild relatives. Agric. Ecosyst. Environ. 121, 245-255.
59. Hill, H., Lee, L.S. and Henry, R.J. (2012) Variation in sorghum starch synthesis genes associated with differences in starch phenotype. Food Chem. 131, 175-183.
60. Hirakawa, H., Shirasawa, K., Kosugi, S., Tashiro, K., Nakayama, S., Yamada, M., Kohara, M., Watanabe, A., Kishida, Y., Fujishiro, T., Tsuruoka, H., Minami, C., Sasamoto, S., Kato, M., Nanri, K., Komaki, A., Yanagi, T., Guoxin, Q., Maeda, F., Ishikawa, M., Kuhara, S., Sato, S., Tabata, S. and Isobe, S.N. (2014) Dissection of the Octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. DNA Res. 21, 169-181.
61. Hirosawa, S., Takumi, S., Ishii, T., Kawahara, T., Nakamura, C. and Mori, N. (2004) Chloroplast and nuclear DNA variation in common wheat: insight into the origin and evolution of common wheat. Genes Genet. Syst. 79, 271-282.
62. Hodgins, K.A., Lai, Z., Oliveira, L.O., Still, D.W., Scascitelli, M., Barker, M.S., Kane, N.C., Dempewolf, H., Kozik, A., Kesseli, R.V., Burke, J.M., Michelmore, R.W. and Rieseberg, L.H. (2014) Genomics of compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives. Mol. Ecol. Resour. 14, 166-177.
63. Honnay, O., Jacquemyn, H. and Aerts, R. (2012) Crop wild relatives: more common ground for breeders and ecologists. Front. Ecol. Environ. 10, 121-121.
64. Honsdorf, N., March, T.J., Berger, B., Tester, M. and Pillen, K. (2014) High-throughput phenotyping to detect drought tolerance QTL in wild barley introgression lines. PLoS ONE, 9, e97047.
65. Huang, X., Kurata, N., Wei, X., Wang, Z.X., Wang, A., Zhao, Q., Zhao, Y., Liu, K., Lu, H., Li, W., Guo, Y., Lu, Y., Zhou, C., Fan, D., Weng, Q., Zhu, C., Huang, T., Zhang, L., Wang, Y., Feng, L., Furuumi, H., Kubo, T., Miyabayashi, T., Yuan, X., Xu, Q., Dong, G., Zhan, Q., Li, C., Fujiyama, A., Toyoda, A., Lu, T., Feng, Q., Qian, Q., Li, J. and Han, B. (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature, 490, 497-501.
66. Hufford, M.B., Xu, X., van Heerwaarden, J., Pyhajarvi, T., Chia, J.M., Cartwright, R.A., Elshire, R.J., Glaubitz, J.C., Guill, K.E., Kaeppler, S.M., Lai, J., Morrell, P.L., Shannon, L.M., Song, C., Springer, N.M., Swanson-Wagner, R.A., Tiffin, P., Wang, J., Zhang, G., Doebley, J., McMullen, M.D., Ware, D., Buckler, E.S., Yang, S. and Ross-Ibarra, J. (2012) Comparative population genomics of maize domestication and improvement. Nat. Genet. 44, 808-811.
67. Iehisa, J.C.M., Shimizu, A., Sato, K., Nasuda, S. and Takumi, S. (2012) Discovery of high-confidence single nucleotide polymorphisms from large-scale de novo analysis of leaf transcripts of Aegilops tauschii, a wild wheat progenitor. DNA Res. 19, 487-497.
68. Iehisa, J., Shimizu, A., Sato, K., Nishijima, R., Sakaguchi, K., Matsuda, R., Nasuda, S. and Takumi, S. (2014) Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii. Theor. Appl. Genet. 127, 261-271.
69. Ilut, D.C., Coate, J.E., Luciano, A.K., Owens, T.G., May, G.D., Farmer, A. and Doyle, J.J. (2012) A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species. Am. J. Bot. 99, 383-396.
70. Jacquemin, J., Bhatia, D., Singh, K. and Wing, R.A. (2013) The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Curr. Opin. Plant Biol. 16, 1-10.
71. Jena, K.K. (1994) Production of intergeneric hybrid between Oryza sativa L. and Porteresia coarctata. Curr. Sci. 67, 9-10.
72. Jhanwar, S., Priya, P., Garg, R., Parida, S.K., Tyagi, A.K. and Jain, M. (2012) Transcriptome sequencing of wild chickpea as a rich resource for marker development. Plant Biotechnol. J., 10, 690-702.
73. Jia, J., Zhao, S., Kong, X., Li, Y., Zhao, G., He, W., Appels, R., Pfeifer, M., Tao, Y., Zhang, X., Jing, R., Zhang, C., Ma, Y., Gao, L., Gao, C., Spannagl, M., Mayer, K.F.X., Li, D., Pan, S., Zheng, F., Hu, Q., Xia, X., Li, J., Liang, Q., Chen, J., Wicker, T., Gou, C., Kuang, H., He, G., Luo, Y., Keller, B., Xia, Q., Lu, P., Wang, J., Zou, H., Zhang, R., Xu, J., Gao, J., Middleton, C., Quan, Z., Liu, G., Wang, J., Yang, H., Liu, X., He, Z., Mao, L. and Wang, J. (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature, 496, 91-95.
74. Jilal, A., Grando, S., Henry, R.J., Lee, L.S., Rice, N., Hill, H., Baum, M. and Ceccarelli, S. (2008) Genetic diversity of ICARDA's worldwide barley landrace collection. Genet. Resour. Crop Evol., 55, 1221-1230.
75. Jobin-Décor, M.P., Graham, G.C., Henry, R.J. and Drew, R. (1997) RAPD and isozyme analysis of genetic relationships between Carica papaya and wild relatives. Genet. Resour. Crop Evol., 44, 471-477.
76. Jun, Y., Fang, W., Haibo, Q., Guoxiong, C., Eviatar, N., Fahima, T. and Jianping, C. (2011) Natural variation in grain selenium concentration of wild barley, Hordeum spontaneum, populations from Israel. Biol. Trace Elem. Res. 142, 773-786.
77. Kalladan, R., Worch, S., Rolletschek, H., Harshavardhan, V., Kuntze, L., Seiler, C., Sreenivasulu, N. and Röder, M. (2013) Identification of quantitative trait loci contributing to yield and seed quality parameters under terminal drought in barley advanced backcross lines. Mol. Breeding, 32, 71-90.
78. Kane, N.C. and Cronk, Q. (2008) Botany without borders: barcoding in focus. Mol. Ecol. 17, 5175-5176.
79. Kane, N., Sveinsson, S., Dempewolf, H., Yang, J.Y., Zhang, D., Engels, J.M. and Cronk, Q. (2012) Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA. Am. J. Bot. 99, 320-329.
80. Kasem, S., Waters, D.L.E., Rice, N., Shapter, F.M. and Henry, R.J. (2010) Whole grain morphology of Australian rice species. Plant Genet. Resour. C, 8, 74-81.
81. Kasem, S., Waters, D.L.E., Rice, N., Shapter, F.M. and Henry, R.J. (2011) The endosperm morphology of rice and its wild relatives as observed by scanning electron microscopy. Rice, 4, 12-13.
82. Kell, S. (2012) Crop wild relative. In Novel Characterization of Crop Wild Relative and Landrace Resources as a Basis for Improved Crop Breeding (Kell, S. and Maxted, N., eds), pp. 4-7. PGR Secure-EU Seventh Framework Programme, THEME KBBE.2010.1.1-03, GA 266394.
83. Kell, S., Qin, H., Chen, B., Ford-Lloyd, B., Wei, W., Kang, D. and Maxted, N. (2015) China's crop wild relatives: diversity for agriculture and food security. Agric. Ecosyst. Environ. 209, 138-154.
84. Kharabian-Masouleh, A., Waters, D.L.E., Reinke, R.F. and Henry, R.J. (2011) Discovery of polymorphisms in starch related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing. Plant Biotechnol. J. 9, 1074-1085.
85. Kharabian-Masouleh, A., Waters, D.L.E., Reinke, R.F., Ward, R. and Henry, R.J. (2012) SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Sci. Rep. 2, 557.
86. Khoury, C.K., Greene, S., Wiersema, J., Maxted, N., Jarvis, A. and Struik, P.C. (2013) An inventory of crop wild relatives of the United States. Crop Sci. 53, 1496-1508.
87. Kim, M.Y., Lee, S., Van, K., Kim, T.H., Jeong, S.C., Choi, I.Y., Kim, D.S., Lee, Y.S., Park, D., Ma, J., Kim, W.Y., Kim, B.C., Park, S., Lee, K.A., Kim, D.H., Kim, K.H., Shin, J.H., Jang, Y.E., Kim, K.D., Liu, W.X., Chaisan, T., Kang, Y.J., Lee, Y.H., Kim, K.H., Moon, J.K., Schmutz, J., Jackson, S.A., Bhak, J. and Lee, S.H. (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc. Natl Acad. Sci. USA, 107, 22032-22037.
88. Koch, A.M. and Karol, M. (2012) Phylogeny and systematics of Brassicaceae-introduction. Taxon, 61, 929-930.
89. Koenig, D., Jiménez-Gómez, J.M., Kimura, S., Fulop, D., Chitwood, D.H., Headland, L.R., Kumar, R., Covington, M.F., Devisetty, U.K., Tat, A.V., Tohge, T., Bolger, A., Schneeberger, K., Ossowski, S., Lanz, C., Xiong, G., Taylor-Teeples, M., Brady, S.M., Pauly, M., Weigel, D., Usadel, B., Fernie, A.R., Peng, J., Sinha, N.R. and Maloof, J.N. (2013) Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc. Natl Acad. Sci. USA, 110, E2655-E2662.
90. Kole, C. (2011) Wild Crop Relatives: Genomic and Breeding Resources. Berlin, Heidelberg, New York: Springer.
91. Korff, M.V., Wang, H., Léon, J. and Pillen, K. (2006) AB-QTL analysis in spring barley: II. Detection of favourable exotic alleles for agronomic traits introgressed from wild barley (H. vulgare ssp. spontaneum). Theor. Appl. Genet. 112, 1221-1231.
92. Krishnan, S., Waters, D.L.E., Katiyar, S.K., Sadananda, A.R., Satyadev, V. and Henry, R. (2012) Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing. Plant Biotechnol. J. 10, 623-634.
93. Krishnan, S., Waters, D.L.E. and Henry, R.J. (2014) Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome. PLoS ONE, 9, e98843.
94. Kunchge, N., Kumar, K. and Firke, P. (2012) Vegetable crops (chili pepper and onion): approaches to improve crop productivity and abiotic stress tolerance. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R., eds), pp. 951-978. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
95. Lai, Z., Kane, N.C., Kozik, A., Hodgins, K.A., Dlugosch, K.M., Barker, M.S., Matvienko, M., Yu, Q., Turner, K.G., Pearl, S.A., Bell, G.D.M., Zou, Y., Grassa, C., Guggisberg, A., Adams, K.L., Anderson, J.V., Horvath, D.P., Kesseli, R.V., Burke, J.M., Michelmore, R.W. and Rieseberg, L.H. (2012) Genomics of compositae weeds: EST libraries, microarrays, and evidence of introgression. Am. J. Bot. 99, 209-218.
96. Lakew, B., Eglinton, J., Henry, R.J., Baum, M., Grando, S. and Ceccarelli, S. (2011) The potential contribution of wild barley (Hordeum vulgare ssp. spontaneum) germplasm to drought tolerance of cultivated barley (H. vulgare ssp. vulgare). Field Crops Res. 120, 161-168.
97. Lakew, B., Henry, R.J., Eglinton, J., Baum, M., Ceccarelli, S. and Grando, S. (2013) SSR analysis of introgression of drought tolerance from the genome of Hordeum spontaneum into cultivated barley (Hordeum vulgare ssp vulgare). Euphytica, 191, 231-243.
98. Lakhanpaul, S., Singh, V., Kumar, S., Bhardwaj, D. and Bhat, K.V. (2012) Sesame: overcoming the abiotic stresses in the queen of oilseed crops. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R., eds), pp. 1251-1283. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
99. Lam, H.M., Xu, X., Liu, X., Chen, W., Yang, G., Wong, F.L., Li, M.W., He, W., Qin, N., Wang, B., Li, J., Jian, M., Wang, J., Shao, G., Wang, J., Sun, S.S.M. and Zhang, G. (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat. Genet. 42, 1053-1059.
100. Li, D., Pfeiffer, T.W. and Cornelius, P.L. (2008) Soybean QTL for yield and yield components associated with Glycine soja alleles. Crop Sci. 48, 571-581.
101. Li, W.T., Huang, X., Wang, J.R., Chen, G.Y., Nevo, E., Zheng, Y.L. and Wei, Y.M. (2010) Genetic analysis and ecological association of Hina genes based on single nucleotide polymorphisms (SNPs) in wild barley, Hordeum spontaneum. Hereditas, 147, 18-26.
102. Li, Y.H., Zhao, S.C., Ma, J.X., Li, D., Yan, L., Li, J., Qi, X.T., Guo, X.S., Zhang, L., He, W.M., Chang, R.Z., Liang, Q.S., Guo, Y., Ye, C., Wang, X.B., Tao, Y., Guan, R.X., Wang, J.Y., Liu, Y.L., Jin, L.G., Zhang, X.Q., Liu, Z.X., Zhang, L.J., Chen, J., Wang, K.J., Nielsen, R., Li, R.Q., Chen, P.Y., Li, W.B., Reif, J., Purugganan, M., Wang, J., Zhang, M.C., Wang, J. and Qiu, L.J. (2013) Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genom. 14, 579.
103. Li, Y.H., Zhou, G., Ma, J., Jiang, W., Jin, L.G., Zhang, Z., Guo, Y., Zhang, J., Sui, Y., Zheng, L., Zhang, S.S., Zuo, Q., Shi, X.H., Li, Y.F., Zhang, W.K., Hu, Y., Kong, G., Hong, H.L., Tan, B., Song, J., Liu, Z.X., Wang, Y., Ruan, H., Yeung, C.K.L., Liu, J., Wang, H., Zhang, L.J., Guan, R.X., Wang, K.J., Li, W.B., Chen, S.Y., Chang, R.Z., Jiang, Z., Jackson, S.A., Li, R. and Qiu, L.J. (2014) De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat. Biotechnol. 32, 1045-1052.
104. Li, X., Yang, Y., Henry, R.J., Rossetto, M., Wang, Y. and Chen, S. (2015) Plant DNA barcoding: from gene to genome. Biol. Rev. 90, 157-166.
105. Lin, T., Zhu, G., Zhang, J., Xu, X., Yu, Q., Zheng, Z., Zhang, Z., Lun, Y., Li, S., Wang, X., Huang, Z., Li, J., Zhang, C., Wang, T., Zhang, Y., Wang, A., Zhang, Y., Lin, K., Li, C., Xiong, G., Xue, Y., Mazzucato, A., Causse, M., Fei, Z., Giovannoni, J.J., Chetelat, R.T., Zamir, D., Stadler, T., Li, J., Ye, Z., Du, Y. and Huang, S. (2014) Genomic analyses provide insights into the history of tomato breeding. Nat. Genet. 46, 1220-1226.
106. Ling, H.Q., Zhao, S., Liu, D., Wang, J., Sun, H., Zhang, C., Fan, H., Li, D., Dong, L., Tao, Y., Gao, C., Wu, H., Li, Y., Cui, Y., Guo, X., Zheng, S., Wang, B., Yu, K., Liang, Q., Yang, W., Lou, X., Chen, J., Feng, M., Jian, J., Zhang, X., Luo, G., Jiang, Y., Liu, J., Wang, Z., Sha, Y., Zhang, B., Wu, H., Tang, D., Shen, Q., Xue, P., Zou, S., Wang, X., Liu, X., Wang, F., Yang, Y., An, X., Dong, Z., Zhang, K., Zhang, X., Luo, M.C., Dvorak, J., Tong, Y., Wang, J., Yang, H., Li, Z., Wang, D., Zhang, A. and Wang, J. (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature, 496, 87-90.
107. Liu, T., Tang, S., Zhu, S., Tang, Q. and Zheng, X. (2014a) Transcriptome comparison reveals the patterns of selection in domesticated and wild ramie (Boehmeria nivea L. Gaud). Plant Mol. Biol. 86, 85-92.
108. Liu, Y.X., Wang, J.R., Liu, Z.H., Wang, Y., Chen, X., Henry, R.J., Wei, Y.M., Nevo, E. and Zheng, Y.L. (2014b) Adaptive evolution of alpha-amylase genes in wild barley (Hordeum spontaneum) on micro and macro scales. J. Syst. Evol. 52, 765-778.
109. Luo, X., Wu, S., Tian, F., Xin, X., Zha, X., Dong, X., Fu, Y., Wang, X., Yang, J. and Sun, C. (2011) Identification of heterotic loci associated with yield-related traits in Chinese common wild rice (Oryza rufipogon Griff.). Plant Sci. 181, 14-22.
110. Malory, S., Shapter, F.M., Elphinstone, M.S., Chivers, I.H. and Henry, R.J. (2011) Characterizing homologues of crop domestication genes in poorly described wild relatives by high-throughput sequencing of whole genomes. Plant Biotechnol. J. 9, 1131-1140.
111. Mandel, J.R., Dechaine, J.M., Marek, L.F. and Burke, J.M. (2011) Genetic diversity and population structure in cultivated sunflower and a comparison to its wild progenitor, Helianthus annuus L. Theor. Appl. Genet. 123, 693-704.
112. Maxted, N. and Kell, S. (2009) Crop wild relative. In Conserving Plant Genetic Diversity for Use now and in the Future (Maxted, N. and Dulloo, E., eds), pp. 7-8. Birmingham: University of Birmingham, Crop Wild Relative Specialist Group.
113. Maxted, N., Kell, S., Ford-Lloyd, B., Dulloo, E. and Toledo, Á. (2012) Toward the systematic conservation of global crop wild relative diversity. Crop Sci. 52, 774-785.
114. McPherson, H., van der Merwe, M., Delaney, S.K., Edwards, M.A., Henry, R.J., McIntosh, E., Rymer, P.D., Milner, M.L., Siow, J. and Rossetto, M. (2013) Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree. BMC Ecol. 13, 8.
115. Michael, T.P. and VanBuren, R. (2015) Progress, challenges and the future of crop genomes. Curr. Opin. Plant Biol. 24, 71-81.
116. Mickelbart, M.V., Hasegawa, P.M. and Bailey-Serres, J. (2015) Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat. Rev. Genet. 16, 237-251.
117. Middleton, C.P., Senerchia, N., Stein, N., Akhunov, E.D., Keller, B., Wicker, T. and Kilian, B. (2014) Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS ONE, 9, e85761.
118. Moghe, G.D., Hufnagel, D.E., Tang, H., Xiao, Y., Dworkin, I., Town, C.D., Conner, J.K. and Shiua, S.H. (2014) Consequences of whole-genome triplication as revealed by comparative genomic analyses of the wild radish Raphanus raphanistrum and three other Brassicaceae species. Plant Cell, 26, 1925-1937.
119. Morrell, P. and Clegg, M. (2011) Hordeum. In Wild Crop Relatives: Genomic and Breeding Resources(Kole, C., ed), pp. 309-319. Berlin, Heidelberg: Springer.
120. Nath, P., Sane, V.A., Asif, M.H., Sane, A.P. and Trivedi, P.K. (2012) Fruit crops: omic approaches toward elucidation of abiotic stress tolerance. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R., eds), pp. 1033-1048. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
121. Naz, A.A., Arifuzzaman, M., Muzammil, S., Pillen, K. and Leon, J. (2014) Wild barley introgression lines revealed novel QTL alleles for root and related shoot traits in the cultivated barley (Hordeum vulgare L.). BMC Genet. 15, 107.
122. Nevo, E. and Chen, G. (2010) Drought and salt tolerances in wild relatives for wheat and barley improvement. Plant, Cell Environ. 33, 670-685.
123. Ngu, M., Thomson, M., Bhuiyan, M., Ho, C. and Wickneswari, R. (2014) Fine mapping of a grain weight quantitative trait locus, qGW6, using near isogenic lines derived from Oryza rufipogon IRGC105491 and Oryza sativa cultivar MR219. Genet. Mol. Res. 13, 9477-9488.
124. Nikiforova, S.V., Cavalieri, D., Velasco, R. and Goremykin, V. (2013) Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line. Mol. Biol. Evol. 30, 1751-1760.
125. Nock, C., Waters, D.L.E., Edwards, M.A., Bowen, S., Rice, N., Cordeiro, G.M. and Henry, R.J. (2011) Chloroplast genome sequence from total DNA for plant identification. Plant Biotechnol. J. 9, 328-333.
126. Pakniyat, H. and Namayandeh, A. (2007) Salt tolerance associations with RAPD markers in Hordeum vulgare L. and H. spontaneum C. Koch. Pak. J. Biol. Sci. 10, 1317-1320.
127. Palmer, C.D., Keller, W., Singh, J. and Datla, R. (2012) Brassica crop species: improving water use efficiency: challenges and opportunities. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R., eds), pp. 1301-1314. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
128. Phillips, J., Kyratzis, A., Christoudoulou, C., Kell, S. and Maxted, N. (2014) Development of a national crop wild relative conservation strategy for Cyprus. Genet. Resour. Crop Evol. 61, 817-827.
129. Pickering, R.A., Steeffenson, B.J., Hill, A.M. and Borovkova, I. (1998) Association of leaf rust and powdery mildew resistance in a recombinant derived from a Hordeum vulgare × Hordeum bulbosum hybrid. Plant Breed. 117, 83-84.
130. Pickering, R., Ruge-Wehling, B., Johnston, P.A., Schweizer, G., Ackermann, P. and Wehling, P. (2006) The transfer of a gene conferring resistance to scald (Rhynchosporium secalis) from Hordeum bulbosum into H. vulgare chromosome 4HS. Plant Breed. 125, 576-579.
131. Pimentel, D., Wilson, C., McCullum, C., Huang, R., Dwen, P., Flack, J., Tran, Q., Saltman, T. and Cliff, B. (1997) Economic and environmental benefits of biodiversity. Bioscience, 47, 747-757.
132. Pineda, B., García-Abellán, J.O., Antón, T., Pérez, F., Moyano, E., García Sogo, B., Campos, J.F., Angosto, T., Morales, B. and Capel, J., Moreno, V., Lozano, R., Bolarín, M.C. and Atarés, A. (2012) Tomato: genomic approaches for salt and drought stress tolerance. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R., eds), pp. 1085-1120. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
133. Poiré, R., Chochois, V., Sirault, X.R.R., Vogel, J.P., Watt, M. and Furbank, R.T. (2014) Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon. J. Integr. Plant Biol. 56, 781-796.
134. Prescott-Allen, C. and Prescott-Allen, R. (1987) The first resource: wild species in the North American economy. Brittonia, 39, 427-427.
135. Prescott-Allen, R. and Prescott-Allen, C. (1988) Genes from the Wild: Using Wild Genetic Resources for Food and Raw Materials (Natural Resource Management Set). London, UK: Earthscan.
136. Prince, S.J., Song, L., Qiu, D., Maldonado dos Santos, J.V., Chai, C., Joshi, T., Patil, G., Valliyodan, B., Vuong, T.D., Murphy, M., Krampis, K., Tucker, D.M., Biyashev, R., Dorrance, A.E., Maroof, M.A.S., Xu, D., Shannon, J.G. and Nguyen, H.T. (2015) Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean. BMC Genom. 16, 132.
137. Qi, J., Liu, X., Shen, D., Miao, H., Xie, B., Li, X., Zeng, P., Wang, S., Shang, Y., Gu, X., Du, Y., Li, Y., Lin, T., Yuan, J., Yang, X., Chen, J., Chen, H., Xiong, X., Huang, K., Fei, Z., Mao, L., Tian, L., Stadler, T., Renner, S.S., Kamoun, S., Lucas, W.J., Zhang, Z. and Huang, S. (2013) A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat. Genet. 45, 1510-1515.
138. Qi, X., Li, M.W., Xie, M., Liu, X., Ni, M., Shao, G., Song, C., Kay-Yuen Yim, A., Tao, Y., Wong, F.L., Isobe, S., Wong, C.F., Wong, K.S., Xu, C., Li, C., Wang, Y., Guan, R., Sun, F., Fan, G., Xiao, Z., Zhou, F., Phang, T.H., Liu, X., Tong, S.W., Chan, T.F., Yiu, S.M., Tabata, S., Wang, J., Xu, X. and Lam, H.M. (2014) Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat. Commun. 5, 4340.
139. Qin, C., Yu, C., Shen, Y., Fang, X., Chen, L., Min, J., Cheng, J., Zhao, S., Xu, M., Luo, Y., Yang, Y., Wu, Z., Mao, L., Wu, H., Ling-Hu, C., Zhou, H., Lin, H., González-Morales, S., Trejo-Saavedra, D.L., Tian, H., Tang, X., Zhao, M., Huang, Z., Zhou, A., Yao, X., Cui, J., Li, W., Chen, Z., Feng, Y., Niu, Y., Bi, S., Yang, X., Li, W., Cai, H., Luo, X., Montes-Hernández, S., Leyva-González, M.A., Xiong, Z., He, X., Bai, L., Tan, S., Tang, X., Liu, D., Liu, J., Zhang, S., Chen, M., Zhang, L., Zhang, L., Zhang, Y., Liao, W., Zhang, Y., Wang, M., Lv, X., Wen, B., Liu, H., Luan, H., Zhang, Y., Yang, S., Wang, X., Xu, J., Li, X., Li, S., Wang, J., Palloix, A., Bosland, P.W., Li, Y., Krogh, A., Rivera-Bustamante, R.F., Herrera-Estrella, L., Yin, Y., Yu, J., Hu, K. and Zhang, Z. (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc. Natl Acad. Sci. USA, 111, 5135-5140.
140. Qiu, J., Wang, Y., Wu, S., Wang, Y.Y., Ye, C.Y., Bai, X., Li, Z., Yan, C., Wang, W., Wang, Z., Shu, Q., Xie, J., Lee, S.H. and Fan, L. (2014) Genome re-sequencing of semi-wild soybean reveals a Complex Soja population structure and deep introgression. PLoS ONE, 9, e108479.
141. Rao, G.U., Ben Chaim, A., Borovsky, Y. and Paran, I. (2003) Mapping of yield-related QTLs in pepper in an interspecific cross of Capsicum annuum and C. frutescens. Theor. Appl. Genet. 106, 1457-1466.
142. Redden, R. (2015) Wild relatives for the crop improvement challenges of climate change: the adaptation range of crops. In Crop Wild Relatives and Climate Change (Redden, R., Yadav, S.S., Maxted, N., Dulloo, M.E., Guarino, L. and Smith, P., eds), pp. 61-76. New Jersey, USA: John Wiley & Sons.
143. Reddy, D.S., Bhatnagar-Mathur, P., Vadez, V. and Sharma, K.K. (2012) Grain legumes (soybean, chickpea, and peanut): omics approaches to enhance abiotic stress tolerance. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R., eds), pp. 995-1032. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
144. Renaut, S., Grassa, C.J., Yeaman, S., Moyers, B.T., Lai, Z., Kane, N.C., Bowers, J.E., Burke, J.M. and Rieseberg, L.H. (2013) Genomic islands of divergence are not affected by geography of speciation in sunflowers. Nat. Commun. 4, 1827.
145. Robinson, S.J. and Parkin, I.A.P. (2012) Brassica crops: improving abiotic stress tolerance-current status and prospects. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R., eds), pp. 1315-1349. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
146. Rossetto, M. and Henry, R.J. (2014) Escape from the laboratory: new horizons for plant genetics. Trends Plant Sci. 19, 554-555.
147. Rossetto, M., Jackes, B.R., Scott, K.D. and Henry, R.J. (2001) Intergeneric relations in the Vitaceae: new evidence from cpDNA analysis. Genet. Resour. Crop Evol. 48, 307-314.
148. Rubio Teso, M.L., Torres, M.E., Parra-Quijano, M. and Iriondo, J.M. (2012) Prioritization of crop wild relatives in Spain. Crop Wild Relatives, 8, 18-21.
149. Sala, C.A., Bulos, M., Altieri, E. and Ramos, M.L. (2012) Sunflower: improving crop productivity and abiotic stress tolerance. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R., eds), pp. 1203-1249. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
150. Saski, C., Lee, S.B., Fjellheim, S., Guda, C., Jansen, R.K., Luo, H., Tomkins, J., Rognli, O.A., Daniell, H. and Clarke, J.L. (2007) Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. Theor. Appl. Genet. 115, 571-590.
151. Schmalenbach, I., Körber, N. and Pillen, K. (2008) Selecting a set of wild barley introgression lines and verification of QTL effects for resistance to powdery mildew and leaf rust. Theor. Appl. Genet. 117, 1093-1106.
152. Sehgal, D., Rajpal, V.R. and Raina, S.N. (2008) Chloroplast DNA diversity reveals the contribution of two wild species to the origin and evolution of diploid safflower (Carthamus tinctorius L.). Genome, 51, 638-643.
153. Septiningsih, E., Trijamiko, K., Moeljopawiro, S. and Mccouch, S. (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.
154. Shapter, F.M., Fitzgerald, T.L., Waters, D.L.E., McDonald, S., Chivers, I.H. and Henry, R.J. (2012) Analysis of adaptive ribosomal gene diversity in wild plant populations from contrasting climatic environments. Plant Signal. Behav. 7, 1-3.
155. Shapter, F.M., Cross, M., Ablett, G., Malory, S., Chivers, I.H., King, G.J. and Henry, R.J. (2013) High-throughput sequencing and mutagenesis to accelerate the domestication of Microlaena stipoides as a new food crop. PLoS ONE, 8, e82641.
156. Shavrukov, Y., Gupta, N., Miyazaki, J., Baho, M., Chalmers, K., Tester, M., Langridge, P. and Collins, N. (2010) HvNax3-a locus controlling shoot sodium exclusion derived from wild barley (Hordeum vulgare ssp. spontaneum). Funct. Integr. Genomics, 10, 277-291.
157. Sherman-Broyles, S., Bombarely, A., Grimwood, J., Schmutz, J. and Doyle, J. (2014) Complete plastome sequences from glycine syndetika and six additional perennial wild relatives of soybean. G3 Genes Genom. Genet. 4, 2023-2033.
158. Shrivastava, A.K. and Srivastava, S. (2012) Sugarcane: physiological and molecular approaches for improving abiotic stress tolerance and sustaining crop productivity. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R., eds), pp. 885-921. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
159. Singh, K. and Ocampo, B. (1993) Interspecific hybridization in annual Cicer species. J. Genet. Breed. 47, 199-194.
160. Singh, K. and Ocampo, B. (1997) Exploitation of wild Cicer species for yield improvement in chickpea. Theor. Appl. Genet. 95, 418-423.
161. Singh, K., Chugh, V., Sahi, G.K. and Chhuneja, P. (2012a) Wheat: mechanisms and genetic means for improving heat tolerance. In Improving Crop Resistance to Abiotic Stressvol. 1 and 2 (Tuteja, N. Singh, S. G. Tiburcio, A. F. and Tuteja, R., eds), pp. 657-694. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
162. Singh, I., Nepolean, T., Rajendran, R.A. and Shono, M. (2012b) Maize: physiological and molecular approaches for improving drought tolerance. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R., eds), pp. 751-778. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
163. Snow, A. (2003) Genetic engineering: unnatural selection. Nature, 424, 619-619.
164. Sotowa, M., Ootsuka, K., Kobayashi, Y., Hao, Y., Tanaka, K., Ichitani, K., Flowers, J.M., Purugganan, M.D., Nakamura, I., Sato, Y.I., Sato, T., Crayn, D., Simon, B., Waters, D.L.E., Henry, R.J. and Ishikawa, R. (2013) Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms. Rice, 6, 26.
165. Souza, G.M., Berges, H., Bocs, S., Casu, R., D'Hont, A., Ferreira, J.E., Henry, R., Ming, R., Potier, B., Van Sluys, M.A., Vincentz, M. and Paterson, A.H. (2011) The sugarcane genome challenges: strategies for sequencing a highly complex genome. Trop. Plant Biol. 4, 145-156.
166. Suszkiw, J. (2014) National inventory takes stock of crops' wild relatives. Agricultural Research, 62, 16-17.
167. Swamy, B.P.M. and Sarla, N. (2008) Yield-enhancing quantitative trait loci (QTLs) from wild species. Biotechnol. Adv. 26, 106-120.
168. Swamy, B., Kaladhar, K., Reddy, G., Viraktamath, B. and Sarla, N. (2014) Mapping and introgression of QTL for yield and related traits in two backcross populations derived from Oryza sativa cv. Swarna and two accessions of O. nivara. J. Genet. 93, 643-654.
169. Swarbreck, S.M., Lindquist, E.A., Ackerly, D.D. and Andersen, G.L. (2011) Analysis of leaf and root transcriptomes of soil-grown Avena barbata plants. Plant Cell Physiol. 52, 317-332.
170. Tai, A.P.K., Martin, M.V. and Heald, C.L. (2014) Threat to future global food security from climate change and ozone air pollution. Nat. Clim. Change, 4, 817-821.
171. Thalapati, S., Batchu, A., Neelamraju, S. and Ramanan, R. (2012) Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice. Funct. Integr. Genomics, 12, 277-289.
172. The 100 Tomato Genome Sequencing Consortium, Aflitos, S., Schijlen, E., de Jong, H., de Ridder, D., Smit, S., Finkers, R., Wang, J., Zhang, G., Li, N., Mao, L., Bakker, F., Dirks, R., Breit, T., Gravendeel, B., Huits, H., Struss, D., Swanson-Wagner, R., van Leeuwen, H., van Ham, R.C.H.J., Fito, L., Guignier, L., Sevilla, M., Ellul, P., Ganko, E., Kapur, A., Reclus, E., de Geus, B., van de Geest, H., Te Lintel Hekkert, B., van Haarst, J., Smits, L., Koops, A., Sanchez-Perez, G., van Heusden, A.W., Visser, R., Quan, Z., Min, J., Liao, L., Wang, X., Wang, G., Yue, Z., Yang, X., Xu, N., Schranz, E., Smets, E., Vos, R., Rauwerda, J., Ursem, R., Schuit, C., Kerns, M., van den Berg, J., Vriezen, W., Janssen, A., Datema, E., Jahrman, T., Moquet, F., Bonnet, J. and Peters, S. (2014) Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J. 80, 136-148.
173. The International Brachypodium Initiative. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463, 763-768.
174. Verulkar, S.B., Mandal, N.P., Dwivedi, J.L., Singh, B.N., Sinha, P.K., Mahato, R.N., Dongre, P., Singh, O.N., Bose, L.K., Swain, P., Robin, S., Chandrababu, R., Senthil, S., Jain, A., Shashidhar, H.E., Hittalmani, S., Vera Cruz, C., Paris, T., Raman, A., Haefele, S., Serraj, R., Atlin, G. and Kumar, A. (2010) Breeding resilient and productive genotypes adapted to drought-prone rainfed ecosystem of India. Field Crops Res. 117, 197-208.
175. Vincent, H., Wiersema, J., Kell, S., Fielder, H., Dobbie, S., Castañeda-Álvarez, N.P., Guarino, L., Eastwood, R., León, B. and Maxted, N. (2013) A prioritized crop wild relative inventory to help underpin global food security. Biol. Conserv. 167, 265-275.
176. Wambugu, P., Furtado, A., Waters, D., Nyamongo, D. and Henry, R. (2013) Conservation and utilization of African Oryza genetic resources. Rice, 6, 29.
177. Wang, W., Feng, B., Xiao, J., Xia, Z., Zhou, X., Li, P., Zhang, W., Wang, Y., Møller, B.L., Zhang, P., Luo, M.C., Xiao, G., Liu, J., Yang, J., Chen, S., Rabinowicz, P.D., Chen, X., Zhang, H.-B., Ceballos, H., Lou, Q., Zou, M., Carvalho, L.J.C.B., Zeng, C., Xia, J., Sun, S., Fu, Y., Wang, H., Lu, C., Ruan, M., Zhou, S., Wu, Z., Liu, H., Kannangara, R.M., Jørgensen, K., Neale, R.L., Bonde, M., Heinz, N., Zhu, W., Wang, S., Zhang, Y., Pan, K., Wen, M., Ma, P.A., Li, Z., Hu, M., Liao, W., Hu, W., Zhang, S., Pei, J., Guo, A., Guo, J., Zhang, J., Zhang, Z., Ye, J., Ou, W., Ma, Y., Liu, X., Tallon, L.J., Galens, K., Ott, S., Huang, J., Xue, J., An, F., Yao, Q., Lu, X., Fregene, M., López-Lavalle, L.A.B., Wu, J., You, F.M., Chen, M., Hu, S., Wu, G., Zhong, S., Ling, P., Chen, Y., Wang, Q., Liu, G., Liu, B., Li, K. and Peng, M. (2014b) Cassava genome from a wild ancestor to cultivated varieties. Nat. Commun. 5, 6110.
178. Wang-Pruski, G. and Schofield, A. (2012) Potato: improving crop productivity and abiotic stress tolerance. In Improving Crop Resistance to Abiotic Stress (Tuteja, N., Singh Gill, S., Tiburcio, A.F. and Tuteja, R., eds), pp. 1121-1153. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.
179. Warschefsky, E., Penmetsa, R.V., Cook, D.R. and von Wettberg, E.J.B. (2014) Back to the wilds: tapping evolutionary adaptations for resilient crops through systematic hybridization with crop wild relatives. Am. J. Bot. 101, 1791-1800.
180. Waters, D.L.E., Nock, C.J., Ishikawa, R., Rice, N. and Henry, R.J. (2012) Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice. Ecol. Evol. 2, 211-217.
181. Wu, G.A., Prochnik, S., Jenkins, J., Salse, J., Hellsten, U., Murat, F., Perrier, X., Ruiz, M., Scalabrin, S., Terol, J., Takita, M.A., Labadie, K., Poulain, J., Couloux, A., Jabbari, K., Cattonaro, F., Del Fabbro, C., Pinosio, S., Zuccolo, A., Chapman, J., Grimwood, J., Tadeo, F.R., Estornell, L.H., Munoz-Sanz, J.V., Ibanez, V., Herrero-Ortega, A., Aleza, P., Perez-Perez, J., Ramon, D., Brunel, D., Luro, F., Chen, C., Farmerie, W.G., Desany, B., Kodira, C., Mohiuddin, M., Harkins, T., Fredrikson, K., Burns, P., Lomsadze, A., Borodovsky, M., Reforgiato, G., Freitas-Astua, J., Quetier, F., Navarro, L., Roose, M., Wincker, P., Schmutz, J., Morgante, M., Machado, M.A., Talon, M., Jaillon, O., Ollitrault, P., Gmitter, F. and Rokhsar, D. (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat. Biotechnol. 32, 656-662.
182. Xiao, J., Grandillo, S., Ahn, S.N., McCouch, S.R., Tanksley, S.D., Li, J. and Yuan, L. (1996) Genes from wild rice improve yield. Nature, 384, 223-224.
183. Xiao, J., Li, J., Grandillo, S., Ahn, S.N., Yuan, L., Tanksley, S.D. and McCouch, S.R. (1998) Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics, 150, 899-909.
184. Xin, H., Zhu, W., Wang, L., Xiang, Y., Fang, L., Li, J., Sun, X., Wang, N., Londo, J.P. and Li, S. (2013) Genome wide transcriptional profile analysis of Vitis amurensis and Vitis vinifera in response to cold stress. PLoS ONE, 8, e58740.
185. Xu, X., Liu, X., Ge, S., Jensen, J.D., Hu, F., Li, X., Dong, Y., Gutenkunst, R.N., Fang, L., Huang, L., Li, J., He, W., Zhang, G., Zheng, X., Zhang, F., Li, Y., Yu, C., Kristiansen, K., Zhang, X., Wang, J., Wright, M., McCouch, S., Nielsen, R., Wang, J. and Wang, W. (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat. Biotechnol. 30, 105-111.
186. Xu, W., Li, R., Zhang, N., Ma, F., Jiao, Y. and Wang, Z. (2014) Transcriptome profiling of Vitis amurensis, an extremely cold-tolerant Chinese wild Vitis species, reveals candidate genes and events that potentially connected to cold stress. Plant Mol. Biol. 86, 527-541.
187. Yang, H., Hu, L., Hurek, T. and Reinhold-Hurek, B. (2010) Global characterization of the root transcriptome of a wild species of rice, Oryza longistaminata, by deep sequencing. BMC Genom. 11, 705.
188. Zeng, J., He, X., Wu, D., Zhu, B., Cai, S., Nadira, U.A., Jabeen, Z. and Zhang, G. (2014) Comparative transcriptome profiling of two Tibetan wild barley genotypes in responses to low potassium. PLoS ONE, 9, e100567.
189. Zhang, Q.J., Zhu, T., Xia, E.H., Shi, C., Liu, Y.L., Zhang, Y., Liu, Y., Jiang, W.K., Zhao, Y.J., Mao, S.Y., Zhang, L.P., Huang, H., Jiao, J.Y., Xu, P.Z., Yao, Q.Y., Zeng, F.C., Yang, L.L., Gao, J., Tao, D.Y., Wang, Y.J., Bennetzen, J.L. and Gao, L.Z. (2014a) Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proc. Natl Acad. Sci. USA, 111, E4954-E4962.
190. Zhang, T., Zhao, X., Wang, W., Huang, L., Liu, X., Zong, Y., Zhu, L., Yang, D., Fu, B. and Li, Z. (2014b) Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum. Plant Mol. Biol. 84, 315-327.
191. Zhang, X., Lu, G., Long, W., Zou, X., Li, F. and Nishio, T. (2014c) Recent progress in drought and salt tolerance studies in Brassica crops. Breed Sci., 64, 60-73.
192. Zhou, Z., Jiang, Y., Wang, Z., Gou, Z., Lyu, J., Li, W., Yu, Y., Shu, L., Zhao, Y., Ma, Y., Fang, C., Shen, Y., Liu, T., Li, C., Li, Q., Wu, M., Wang, M., Wu, Y., Dong, Y., Wan, W., Wang, X., Ding, Z., Gao, Y., Xiang, H., Zhu, B., Lee, S.H., Wang, W. and Tian, Z. (2015) Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol. 33, 408-414.
193. Zohary, D., Hopf, M., Weiss, E. and Ebooks, C. (2012) Domestication of Plants in the Old World: The Origin and Spread of Domesticated Plants in Southwest Asia, Europe, and the Mediterranean Basin. Oxford: OUP Oxford.