Molecular Marker Technology for Genetic Improvement of Underutilised Crops

  • Acga Cheng
  • Hui Hui Chai
  • Wai Kuan Ho
  • Aliyu Siise Abdullah Bamba
  • Aryo Feldman
  • Presidor Kendabie
  • Razlin Azman Halim
  • Alberto Tanzi
  • Sean Mayes
  • Festo Massawe


A subset of underutilised crops copes comparatively better in marginal soils and under less favourable environmental conditions than their major crop equivalents. Hence, developing the subset further for future agriculture makes a suitable and complementary approach to the continued use of major crops. This is particularly true given the expected negative impact of climate change on current major crop production systems and the gap between the current rate of genetic improvement of most major crops and the higher rates required to be able to feed the predicted nine billion in 2050. One such promising crop is bambara groundnut (Vigna subterranea (L.) Verdc.), an indigenous African legume which thrives in hot climates and is well suited to poor, infertile soils where other crops fail to produce reasonable yields. Another is winged bean (Psophocarpus tetragonolobus), a multi-purpose legume in which all parts of the plant, except the stem, are edible and nutritious. Nevertheless, there are a number of constraints to expanding the use of underutilised crops, one of which is erratic yields. The use of molecular markers could facilitate the genetic improvement of underutilised crops, including achieving higher and more stable yields. In this chapter, we first discuss the types of molecular markers commonly used in plant studies, followed by a detailed discussion on the different uses of markers. In addition to the generation of specific data within species, cross-species approaches and, in particular, translating knowledge and resources derived from closely related model and major plant species is a pragmatic approach to develop, given that limiting resources are often one of the major bottlenecks in programmes to develop underutilised crops.


Climate change Food and nutrition security Genetic improvement Molecular markers Underutilised species 


  1. Abdullah Bamba SA, Massawe F (2013) Microsatellites based marker molecular analysis of Ghanaian bambara groundnut (Vigna subterranean (L.) Verdc.) landraces alongside morphological characterization. Genet Resour Crop Evol 60:777–787CrossRefGoogle Scholar
  2. Abdullah Bamba SA, Massawe F, Mayes S (2015a) Beyond landraces: developing improved germplasm resources for underutilized species—a case for Bambara groundnut. Biotechnol Genet Eng Rev 30:37–41. doi: 10.1080/02648725.2014.992625 Google Scholar
  3. Abdullah Bamba SA, Massawe F, Mayes S (2015b) Beyond landraces: developing improved germplasm resources for underutilized species—a case for Bambara groundnut. Biotechnol Genet Eng Rev 1-2:37–41Google Scholar
  4. Abraham B, Araya H, Berhe T, Edwards S, Gujja B, Khadka RB, Sen D, Koma Y, Sharif A, Styger E, Uphoff N, Verma A (2014) The system of crop intensification: reports from the field on improving agricultural production, food security, and resilience to climate change for multiple crops. Agric Food Sci 3:1–12CrossRefGoogle Scholar
  5. Ahmad SA, Redjeki ES, Ho WK, Aliyu S, Mayes K, Massawe F, Kilian A, Mayes S (2016) Construction of a genetic linkage map and QTL analysis in bambara groundnut. Gen 59:459–472. doi: 10.1139/gen-2015-0153 Google Scholar
  6. Arias RS, Borrone JW, Tondo CL, Kuhn DN, Irish BM, Schnell RJ (2012) Genomics of tropical fruit tree crops. In: Schnell RJ, Priyadarshan PM (eds) Genomics of tree crops. Springer Science, New York, pp 209–239CrossRefGoogle Scholar
  7. Arif IA, Bakir MA, Khan HA, Al Farhan AH, Al Homaidan AA, Bahkali AH et al (2010) A brief review of molecular techniques to assess plant diversity. Int J Mol Sci 11(5):2079–2096PubMedPubMedCentralCrossRefGoogle Scholar
  8. Babu BK, Dinesh P, Agrawal PK, Sood S, Chandrashekara C, Bhatt JC, Kumar A (2014) Comparative genomics and association mapping approaches for blast resistant genes in finger millet using SSRs. PLoS One 9(6):e99182PubMedPubMedCentralCrossRefGoogle Scholar
  9. Bardakci F (2000) Random amplified polymorphic DNA (RAPD) markers. Turk J Biol 25:185–196Google Scholar
  10. Basu S, Roberts JA, Azam-Ali SN, Mayes S (2007) Development of microsatellite markers for bambara groundnut (Vigna subterranea L. Verdc.)—an underutilized African legume crop species. Mol Ecol Notes 7:1326–1328CrossRefGoogle Scholar
  11. Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep P, Feng L, Vaughn JN et al (2012) Reference genome sequence of the model plant Setaria. Nat Biotechnol 30(6):555–561PubMedCrossRefGoogle Scholar
  12. Bisen PS (2014) Laboratory protocols in applied life sciences. CRC Press, Boca RatonCrossRefGoogle Scholar
  13. Bohra A, Pandey MK, Jha UC, Singh B, Singh IP, Datta D, Chaturvedi SK, Nadarajan N, Varshney RK (2014) Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects. Theor Appl Genet 127(6):1263–1291PubMedPubMedCentralCrossRefGoogle Scholar
  14. Chen X, Sullivan PF (2003) Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics J 3:77–96PubMedCrossRefGoogle Scholar
  15. Chen H, Chen X, Tian J, Yang Y, Liu Z, Hao X et al (2015) Development of gene-based SSR markers in rice bean (Vigna umbellata L.) based on transcriptome data. PLoS One 11(3):e0151040CrossRefGoogle Scholar
  16. Chen HL, Chen X, Tian J, Yang Y, Liu Z, Hao X et al (2016) Development of gene-based SSR markers in rice bean (Vigna umbellata L.) based on transcriptome data. PLoS One 11(3):e0151040PubMedPubMedCentralCrossRefGoogle Scholar
  17. Cheng A, Ismanizan I, Mohamad O, Habibuddin H (2012) Simple and rapid molecular techniques for identification of amylose levels in rice varieties. Int J Mol Sci 13:6156–6166PubMedPubMedCentralCrossRefGoogle Scholar
  18. Cheng A, Mayes S, Dalle G, Demissew S, Massawe F (2015) Diversifying crops for food and nutrition security—a case of teff. Biol Rev 92:188–198PubMedCrossRefGoogle Scholar
  19. Christensen SA, Pratt DB, Pratt C, Nelson PT, Stevens MR, Jellen EN et al (2007) Assessment of genetic diversity in the USDA and CIP-FAO international nursery collections of quinoa (Chenopodium quinoa Willd.) using microsatellite markers. Plant Gen Res 5:82–95CrossRefGoogle Scholar
  20. Coles ND, Coleman CE, Christensen SA, Jellen EN, Stevens MR, Bonifacio A, Rojas-Beltran JA, Fairbanks DJ, Maughan PJ (2005) Development and use of an expressed sequenced tag library in quinoa (Chenopodium quinoa Willd.) for the discovery of single nucleotide polymorphisms. Plant Sci 168(2):439–447CrossRefGoogle Scholar
  21. Cruz VMV, Kilian A, Dierig DA (2013) Development of DArT marker platforms and genetic diversity assessment of the U.S. collection of the new oilseed crop Lesquerella and related species. PLoS One 8:e64062PubMedPubMedCentralCrossRefGoogle Scholar
  22. Dane F, Liu J, Zhang C (2006) Phylogeography of the bitter apple, Citrullus colocynthis. Genet Resour Crop Evol 54:327–336CrossRefGoogle Scholar
  23. Dansi A, Mignouna HD, Zoudjihekpon J, Sangare A, Asiedu R, Ahoussou N (2000) Identification of some Benin Republic’s Guinea yam cultivars using randomly amplified polymorphic DNA. Genet Resourc Crop Evol 47:619–662CrossRefGoogle Scholar
  24. Das AK, Anjaneluyu ASR, Gadekar YP, Singh RP, Pragati H (2008) Effect of full-fat soy paste and textured soy granules on quality and shelf-life of goat meat nuggets in frozen storage. Meat Sci 80:607–614PubMedCrossRefGoogle Scholar
  25. Dawson IK, Guarino L, Jaenicke H (2007) Underutilised plant species: impacts of promotion on biodiversity. Position Paper No. 2. ICUC, Colombo, Sri LankaGoogle Scholar
  26. De La Fuente GN, Frei UK, Lubberstedt T (2013) Accelerating plant breeding. Trends Plant Sci 18:667–672CrossRefGoogle Scholar
  27. Dhanasekar P, Dhumal KN, Reddy KS (2010) Identification of RAPD markers linked to plant type gene in pigeonpea. Indian J Biotechnol 9:58–63Google Scholar
  28. Ebert AW (2014) Potential of underutilized traditional vegetables and legume crops to contribute to food and nutritional security, income and more sustainable production systems. Sustainability 6:319–335CrossRefGoogle Scholar
  29. Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20:758–760PubMedGoogle Scholar
  30. Ellis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125–132PubMedCrossRefGoogle Scholar
  31. Francia E, Tacconi G, Crosatti C, Barabaschi D, Bulgarelli D, Dall’Aglio E, Valè G (2005) Marker assisted selection in crop plants. Plant Cell Tissue Org 82:317–342CrossRefGoogle Scholar
  32. Fu D, Ma B, Mason A, An Z (2013) MicroRNA-based molecular markers: a novel PCR-based genotyping technique in brassica species. Plant Breed 132(4):75–81CrossRefGoogle Scholar
  33. Ganal MW, Altmann T, Röder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12:211–217PubMedCrossRefGoogle Scholar
  34. Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G et al (2012) The genome of melon (Cucumis melo L.) Proc Natl Acad Sci U S A 109(29):11872–11877PubMedPubMedCentralCrossRefGoogle Scholar
  35. Gonthier P, Sillo F, Lagostina E, Roccotelli A, Cacciola OS, Stenlid J, Garbelotto M (2015) Selection processes in simple sequence repeats suggest a correlation with their genomic location: insights from a fungal model system. BMC Genomics 16:1107PubMedPubMedCentralCrossRefGoogle Scholar
  36. Govindaraj M, Vetriventhan M, Srinivasan M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int 2015:431–487Google Scholar
  37. Gupta PK, Kumar J, Mir RR, Kumar A (2010) Marker assisted selection as a component of conventional plant breeding. Plant Breed Rev 33:145–217Google Scholar
  38. Harel-Beja R, Tzuri G, Portnoy V, Lotan-Pompan M, Lev S et al (2010) A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes. Theor Appl Genet 121(3):511–533PubMedCrossRefGoogle Scholar
  39. Ho WK, Muchugi A, Muthemba S, Kariba R, Mavenkeni BO, Hendre P, Song B, Deynze V, Massawe F, Mayes S (2016) Use of microsatellite markers for the assessment of bambara groundnut breeding system and varietal purity before genome sequencing. Genome 59(6):427–431PubMedCrossRefGoogle Scholar
  40. Huang CW, Lin YT, Ding ST, Lo LL, Wang PH, Lin EC, Liu FW, Lu YW (2015) Efficient SNP discovery by combining microarray and lab-on-a-chip data for animal breeding and selection. Microarrays 4:570–595PubMedPubMedCentralCrossRefGoogle Scholar
  41. Hunt HV, Campana MG, Lawes MC, Park Y-J, Bower MA, Howe CJ et al (2011) Genetic diversity and phylogeography of broomcorn millet (Panicum miliaceum L.) across Eurasia. Mol Ecol 20:4756–4771PubMedPubMedCentralCrossRefGoogle Scholar
  42. Hwang J, Ang JK, Son B, Kim K, Park Y (2011) Genetic diversity in watermelon cultivars and related species based on AFLPs and EST-SSRs. Notulae Botanicae Horti Agrobotanici Cluj-Napoca 39(2):285Google Scholar
  43. Iranjo P, Nabati Ahmadi D, Sorkheh K, Memeari HR, Ercisli S (2016) Genetic diversity and phylogenetic relationships between and within wild Pistacia species populations and implications for its conservation. J Forestry Res 27(3):685–697CrossRefGoogle Scholar
  44. Jaccoud DK, Peng D, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29(4):e25PubMedPubMedCentralCrossRefGoogle Scholar
  45. Jarvis DE, Kopp OR, Jellen EN, Mallory MA, Pattee J, Bonifacio A, Coleman CE, Stevens MR, Fairbanks DJ, Maughan PJ (2008) Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.) J Genet 87:39–51PubMedCrossRefGoogle Scholar
  46. Jarvis DE, Ho YS, Lightfoot DJ, Schmockel SM, Li B et al (2017) The genome of Chenopodium quinoa. Nature 542(7641):307–312PubMedCrossRefGoogle Scholar
  47. Ji Q, Xu X, Wang K (2013) Genetic transformation of major cereal crops. Int J Dev Biol 57:495–508PubMedCrossRefGoogle Scholar
  48. Jia J, Zhou S, Kong X et al (2013) Aegilops tauschiidraft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496(7443):91–95PubMedCrossRefGoogle Scholar
  49. Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F et al (1997) Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breed 3:381–390CrossRefGoogle Scholar
  50. Joshi SP, Ranjekar PK, Gupta VS (1999) Molecular markers in plant genome analysis. Crop Sci 16:102–105Google Scholar
  51. Kesawat MS, Kumar BD (2009) Molecular markers: it’s application in crop improvement. J Crop Sci Biotechnol 12:169–181CrossRefGoogle Scholar
  52. Khoury CK, Bjorkman AD, Dempewolf H, Ramirez-villegas J, Guarino L, Jarvis A, Rieseberg LH, Struik PC (2014) Increasing homogeneity in global food supplies and the implications for food security. Proc Natl Acad Sci U S A 111:4001–4006PubMedPubMedCentralCrossRefGoogle Scholar
  53. Kumar P, Gupta VK, Misra AK, Modi DR, Pandey BK (2009) Potential of molecular markers in plant biotechnology. Plant Omics J 2(4):141–162Google Scholar
  54. Kumar J, Choudhary AK, Solanki RK, Pratap A (2011) Towards marker-assisted selection in pulses: a review. Plant Breed 130:297–313CrossRefGoogle Scholar
  55. Kumar S, Banks TW, Cloutier S (2012) SNP discovery through next-generation sequencing and its applications. Int J Plant Genomics 2012:831460. doi: 10.1155/2012/831460 PubMedPubMedCentralGoogle Scholar
  56. Kumari K, Pande A (2010) Study of genetic diversity in finger millet (Eleusine coracana L. Gaertn) using RAPD markers. Afr J Biotechnol 9(29):4542–4549Google Scholar
  57. Kumpatla SP, Buyyarapu R, Abdurakhmonov IY, Mammadov JA (2012) Genomics-assisted plant breeding in the 21st century: technological advances and progress. Plant Breed:131–184Google Scholar
  58. Lai PS, Ho WS, Pang SL (2013) Development, characterization and cross-species transferability of expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from kelampayan tree transcriptome. Biotechnology 12:225–235CrossRefGoogle Scholar
  59. Levi A, Thomas CE, Keinath AP, Wehner TC (2001) Genetic diversity among watermelon (Citrullus lanatus and Citrullus colocynthis) accessions. Gen Res Crop Evol 48:559CrossRefGoogle Scholar
  60. Lin WH, Kussell E (2012) Evolutionary pressures on simple sequence repeats in prokaryotic coding regions. Nucleic Acids Res 40(6):2399–2413PubMedCrossRefGoogle Scholar
  61. Lin J, Kuo J, Ma J (1996) A PCR-based DNA fingerprinting technique: AFLP for molecular typing of bacteria. Nucleic Acids Res 24(18):3649–3650PubMedPubMedCentralCrossRefGoogle Scholar
  62. Liu P, Yang YS, Hao CY, Guo WD (2007a) Ecological risk assessment using RAPD and distribution pattern of a rare and endangered species. Chemosphere 68:1497–1505PubMedCrossRefGoogle Scholar
  63. Liu S, Banik M, Yu K, Park SJ, Poysa V, Guan Y (2007b) Marker-assisted election (MAS) in major cereal and legume crop breeding: current progress and future directions. Int J Plant Breed 1:74–88Google Scholar
  64. Ma JQ, Yao MZ, Ma CL, Wang XC, Jin JQ, Wang XM, Chen L (2014) Construction of a SSR-based genetic map and identification of QTLs for Catechins content in tea plant (Camellia sinensis). PLoS One 9(3):e93131PubMedPubMedCentralCrossRefGoogle Scholar
  65. Massawe FJ, Dickinson M, Roberts JA, Azam-Ali SN (2002) Genetic diversity in bambara groundnut landraces (Vigna subterranea (L.) Verdc) revealed by AFLP markers. Gen 45:1175–1180Google Scholar
  66. Massawe FJ, Roberts JA, Azam-Ali SN, Davey MR (2003) Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces assessed by random amplified polymorphic DNA (RAPD) markers. Genet Resour Crop Evol 50:737–741CrossRefGoogle Scholar
  67. Massawe F, Mwale SS, Azam-Ali SN, Roberts JA (2005) Breeding in bambara groundnut (Vigna subterranea (L.) Verdc.): strategic considerations. Afr J Biotechnol 4(6):463–471Google Scholar
  68. Massawe F, Mayes S, Cheng A (2016) Crop diversity: an unexploited treasure trove for food security. Trends Plant Sci 21(5):365–368PubMedCrossRefGoogle Scholar
  69. Masters WA (2010) Africa’s turnaround: from crisis to opportunity in African agriculture. In: Food and financial crises: impacts on Sub-Saharan Africa. CAB International, WallingfordGoogle Scholar
  70. Maughan PJ, Bonifacio A, Jellen EN, Stevens MR, Coleman CE, Ricks M et al (2004) A genetic linkage map of quinoa (Chenopodium Quinoa) based on AFLP, RAPD, and SSR markers. Theor Appl Genet 109(6):1188–1195PubMedCrossRefGoogle Scholar
  71. Maughan PJ, Yourstone SM, Jellen EN, Udall JA (2009) SNP discovery via genomic reduction, barcoding and 454-pyro-sequencing in amaranth. Plant Gen 2:260–270CrossRefGoogle Scholar
  72. Maughan PJ, Smith SM, Jellen EN, Fairbanks D (2011) Development, characterization and linkage mapping of single nucleotide polymorphisms in the grain amaranths (Amaranthus sp.) Plant Gen 4:1–10CrossRefGoogle Scholar
  73. Maughan PJ, Smith SM, Rojas-Beltran JA, Elzinga D, Raney JA, Jellen EN, Bonifacio A, Udall JA, Fairbanks DJ (2012) Single nucleotide polymorphism identification, characterization, and linkage mapping in quinoa. Plant Genome 5:114–125CrossRefGoogle Scholar
  74. Mayes S, Massawe F, Anderson PG, Roberts JA, Azam-Ali SN, Hermann M (2011) The potential of underutilized crops to improve security of food production. J Exp Bot 63:1075–1079PubMedCrossRefGoogle Scholar
  75. Mba C, Tohme J (2005) Use of AFLP markers in surveys of plant diversity. Methods Enzymol 395:177–201PubMedCrossRefGoogle Scholar
  76. Meksem K, Ruben E, Hyten D, Triwitayakorn K, Lightfoot DA (2001) Conversion of AFLP bands into high-throughput DNA markers. Mol Genet Genomics 265(2):207–214PubMedCrossRefGoogle Scholar
  77. Melo ATO, Bartaula R, Hale L (2016) GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data. BMC Bioinformatics 17:29PubMedPubMedCentralCrossRefGoogle Scholar
  78. Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Islam KN, Latif MA (2013) A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. Int J Mol Sci 14(11):22499–22528PubMedPubMedCentralCrossRefGoogle Scholar
  79. Mignouna HD, Abang Asiedu R (2007) Advances in yam (Dioscorea spp.) genetics and genomics proceedings of the 13th ISTRC symposium, pp 72–81Google Scholar
  80. Mignouna HD, Ellis NTH, Asiedu R, Ng QN (1998) Analysis of genetic diversity in Guinea yams (Dioscorea spp) using AFLP fingerprinting. Trop Agric (Trinidad) 75:224–229Google Scholar
  81. Mignouna HD, Mank RA, Ellis THN, van den Bosch N et al (2002a) A genetic linkage map of water yam (Dioscorea alata L.) based on AFLP markers and QTL analysis for anthracnose resistance. Theor Appl Genet 105:726–735PubMedCrossRefGoogle Scholar
  82. Mignouna HD, Mank RA, Ellis THN et al (2002b) A genetic linkage map of Guinea yam (Dioscorea rotundata L.) based on AFLP markers. Theor Appl Genet 105:716–725PubMedCrossRefGoogle Scholar
  83. Mignouna HD, Abang MM, Fagbemi SA (2003) A comparative assessment of molecular marker assays (AFLP, RAPD and SSR) for white yam (Dioscorea rotundata Poir.) germplasm characterisation. Ann Appl Biol 142:269–276CrossRefGoogle Scholar
  84. Mochida K, Shinozaki K (2013) Unlocking Triticeae genomics to sustainably feed the future. Plant Cell Physiol 54(12):1931–1950PubMedPubMedCentralCrossRefGoogle Scholar
  85. Moe KT, Gwag JG, Park YJ (2012) Trends in genomics and molecular marker systems for the development of some underutilized crops. Gen Genom 34(5):451–466CrossRefGoogle Scholar
  86. Molosiwa OO, Aliyu S, Stadler F, Mayes K, Massawe F, Kilian A, Mayes S (2015) SSR marker development, genetic diversity and population structure analysis of Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces. Gen Res Crop Evol 62(8):1225–1243CrossRefGoogle Scholar
  87. Narina SS, Buyyarapu R, Kottapalli KR, Sartie AM, Ali MI, Robert A et al (2011) Generation and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.) BMC Genomics 12:100PubMedPubMedCentralCrossRefGoogle Scholar
  88. Naylor RL, Falcon WP, Goodman RM, Jahn MM, Sengooba T, Tefera H, Nelson RJ (2004) Biotechnology in the developing world: a case for increased investments in orphan crops. Food Policy 29:15–44CrossRefGoogle Scholar
  89. Ngwira AR, Thierfelder C, Lambert DM (2012) Conservation agriculture systems for Malawian smallholder farmers: longterm effects on crop productivity, profitability and soil quality. Renew Agric Food Syst 28(4):350–363CrossRefGoogle Scholar
  90. Nimmakayala P, Tomason YR, Jeong J, Ponniah SK, Karunathilake A, Levi A, Perumal R, Levi UK (2010) Genetic reticulation and interrelationships among citrullus species as revealed by joint analysis of shared AFLPs and species-specific SSR alleles. Plant Gen Res 8(1):16–25CrossRefGoogle Scholar
  91. Ojiewo C, Tenkouano A, Oluoch M, Yang R (2010) The role of AVRDC—the world vegetable centre in vegetable value chains. Afr J Hort Sci 3:1–23Google Scholar
  92. Padulosi S, Hoeschle-Zeledon I (2004) Underutilized plant species: what are they? LEISA 20(1):56Google Scholar
  93. Petro D, Onyeka TJ, Etienne S, Rubens S (2011) An intraspecific genetic map of water yam (Dioscorea alata L.) based on AFLP markers and QTL analysis for anthracnose resistance. Euphytica 179:405–416CrossRefGoogle Scholar
  94. Phung NTP, Mai CD, Mournet P, Frouin J, Droc G, Ta NK, Jouannic S, Lê LT, Do VN, Gantet P, Courtois B (2014) Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes. BMC Plant Biol 14:371PubMedPubMedCentralCrossRefGoogle Scholar
  95. Pingali PL (2012) Green revolution: impacts, limits, and the path ahead. Proc Natl Acad Sci U S A 109:12302–12308PubMedPubMedCentralCrossRefGoogle Scholar
  96. Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1(7):215–222CrossRefGoogle Scholar
  97. Rahman MM, Aminul MI, Sofian MA, Amru NB (2014) Tropical legume crop rotation and nitrogen fertilizer effects on agronomic and nitrogen efficiency of rice. Sci World J. doi: 10.1155/2014/490841
  98. Ranamukhaarachchi DG, Kane ME, Guy CL, Li QB (2000) Modified AFLP technique for rapid genetic characterization in plants. Biotechniques 29(4):858–859PubMedGoogle Scholar
  99. Raney JA, Reynolds DJ, Elzinga DB, Page J, Udall JA, Jellen EN, Bonfacio A, Fairbanks D, Maughan PJ (2014) Transcriptome analysis of drought induced stress in Chenopodium quinoa. Am J Plant Sci 5:338–357CrossRefGoogle Scholar
  100. Raveendar S, Lee GA, Jeon YA, Lee YJ, Lee JR, Cho GT, Cho JH, Park JH, Ma KH, Chung JW (2015) Cross-amplification of Vicia sativa subsp. sativa microsatellites across 22 other Vicia species. Molecules 20(1):1543–1550PubMedCrossRefGoogle Scholar
  101. Ray DK, Mueller ND, West PC, Foley JA (2013) Yield trends are insufficient to double global crop production by 2050. PLoS One 8:1–8Google Scholar
  102. Ren X, Wang J, Liu L, Sun G, Li C, Luo H, Sun D (2016) SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley. Sci Rep 6:31741. doi: 10.1038/srep31741 PubMedPubMedCentralCrossRefGoogle Scholar
  103. Roberts RJ, Vincze T, Posfai J, Macelis D (2003) REBASE: restriction enzymes and methyltransferases. Nucleic Acids Res 31(1):418–420PubMedPubMedCentralCrossRefGoogle Scholar
  104. Rubinstein M, Katzenellenbogen M, Eshed R, Rozen A, Katzir N, Colle M et al (2015) Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array. PLoS One 10(4):e0124101PubMedPubMedCentralCrossRefGoogle Scholar
  105. Saeed B, Baranwal VK, Khurana P (2016) Comparative transcriptomics and comprehensive marker resource development in mulberry. BMC Genomics 17:98PubMedPubMedCentralCrossRefGoogle Scholar
  106. Sánchez-Sevilla JF, Horvath A, Botella MA, Gaston A, Folta K, Kilian A, Denoyes B, Amaya I (2015) Diversity arrays technology (DArT) marker platforms for diversity analysis and linkage mapping in a complex crop, the octoploid cultivated strawberry (Fragaria × ananassa). PLoS One 10(12):e0144960PubMedPubMedCentralCrossRefGoogle Scholar
  107. Sansaloni C, Petroli C, Jaccoud D, Carling J, Detering F, Grattapaglia D, Kilian A (2011) Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. BMC Proc 5(Suppl 7):54CrossRefGoogle Scholar
  108. Saski CA, Bhattacharjee R, Scheffler BE, Asiedu R (2015) Genomic resources for water yam (Dioscorea alata L.): analyses of EST-sequences, de novo sequencing and GBS libraries. PLoS One 10(7):e0134031PubMedPubMedCentralCrossRefGoogle Scholar
  109. Schlotterer C (2004) The evolution of molecular markers—just a matter of fashion? Nat Rev Genet 5:63–69PubMedCrossRefGoogle Scholar
  110. Semagn K, Bjørnstad A, Ndjiondjop MN (2006) An overview of molecular marker methods for plants. Afr J Biotechnol 5(25):2540–2568Google Scholar
  111. Shi W, Tao F (2014) Vulnerability of African maize yield to climate change and variability during 1961–2010. Food Secur 6:471–481CrossRefGoogle Scholar
  112. Si Y, Zhang C, Meng S, Dane F (2009) Gene expression changes in response to drought stress in Citrullus colocynthis. Plant Cell Rep 28:997–1009PubMedCrossRefGoogle Scholar
  113. Suresh S, Chung JW, Cho GT, Sung JS, Park JH, Gwag JG, Baek HJ (2014) Analysis of molecular genetic diversity and population structure in Amaranthus germplasm using SSR markers. Plant Biosyst 148(4):635–644CrossRefGoogle Scholar
  114. Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Nat Biotechnol 7:257–264CrossRefGoogle Scholar
  115. Tártara SMC, Manifesto MM, Bramardi SJ, Bertero HD (2012) Genetic structure in cultivated quinoa (Chenopodium quinoa Willd.), a reflection of landscape structure in Northwest Argentina. Conserv Genet 13:1027-1038CrossRefGoogle Scholar
  116. Thies E (2000) Promising and underutilized species, crops and breeds. GTZ, Eschborn, GermanyGoogle Scholar
  117. Tomar RS (2010) Molecular markers and plant biotechnology. New India Publishing, New DelhiGoogle Scholar
  118. Troconis-Torres IG, Rojas-López M, Hernández-Rodríguez C, Villa-Tanaca L, Maldonado-Mendoza IE et al (2002) Biochemical and molecular analysis of some commercial samples of chilli peppers from Mexico. J Biomed Biotechnol 2012:873090Google Scholar
  119. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55PubMedCrossRefGoogle Scholar
  120. Varshney RK, Chen W, Li Y et al (2012) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30(1):83–89CrossRefGoogle Scholar
  121. Vatanparast M, Shetty P, Chopra R, Doyle JJ, Sathyanarayana N, Egan AN (2016) Transcriptome sequencing and marker development in winged bean (Psophocarpus tetragonolobus; Leguminosae). Sci Rep 6:29070. doi: 10.1038/srep29070 PubMedPubMedCentralCrossRefGoogle Scholar
  122. Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F et al (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45(5):487–494PubMedCrossRefGoogle Scholar
  123. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedPubMedCentralCrossRefGoogle Scholar
  124. Wang Z, Hu H, Goertzen LR, McElroy JS, Dane F (2014) Analysis of the Citrullus colocynthis transcriptome during water deficit stress. PLoS One 9(8):e104657PubMedPubMedCentralCrossRefGoogle Scholar
  125. Weising K, Nybom H, Pfenninger M, Wolff K, Meyer W (1994) DNA fingerprinting in plants and fungi. CRC Press, Boca RatonGoogle Scholar
  126. Williams JT, Haq N (2002) Global research on underutilized crops. An assessment of current activities and proposals for enhanced cooperation. ICUC, SouthamptonGoogle Scholar
  127. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535PubMedPubMedCentralCrossRefGoogle Scholar
  128. Wong QN, Massawe F, Mayes K, Blythe M (2016) Molecular genetic tools to support genetic improvement of winged bean (Psophocarpus tetragonolobus) for food and nutrition security. Acta Hortic 1110:1–6CrossRefGoogle Scholar
  129. Wong QN, Tanzi AS, Ho WK, Malla S, Blythe M et al (2017) Development of gene based SSR markers in winged bean (Psophocarpus tetragonolobus (L.) DC.) for diver-sity assessment. Genes 8(3):100PubMedCentralCrossRefGoogle Scholar
  130. Yu H, Li Q (2007) Development of EST-SSRs in the Mediterranean blue mussel, Mytilus galloprovincialis. Mol Ecol Notes 7(6):1308–1310CrossRefGoogle Scholar
  131. Zeid M, Belay G, Mulkey S, Poland J, Sorrells ME (2011) QTL mapping for yield and lodging resistance in an enhanced SSR-based map for tef. Theor Appl Genet 122:77–93PubMedCrossRefGoogle Scholar
  132. Zeid M, Assefa K, Haddis A, Chanyalew S, Sorrells ME (2012) Genetic diversity in tef (Eragrostis tef) germplasm using SSR markers. Field Crop Res 127:64–70CrossRefGoogle Scholar
  133. Zhao Y, Williams R, Prakash CS, He G (2012) Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.) BMC Plant Biol 12:237PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Acga Cheng
    • 1
    • 2
  • Hui Hui Chai
    • 1
  • Wai Kuan Ho
    • 1
    • 3
  • Aliyu Siise Abdullah Bamba
    • 1
    • 3
    • 4
  • Aryo Feldman
    • 3
  • Presidor Kendabie
    • 5
  • Razlin Azman Halim
    • 3
  • Alberto Tanzi
    • 1
    • 3
  • Sean Mayes
    • 3
    • 5
  • Festo Massawe
    • 1
    • 3
  1. 1.Biotechnology Research Centre, School of BiosciencesThe University of Nottingham Malaysia CampusSemenyihMalaysia
  2. 2.Institute of Biological Sciences, Faculty of ScienceUniversity of MalayaKuala LumpurMalaysia
  3. 3.Crops For the Future, Jalan BrogaSemenyihMalaysia
  4. 4.CSIR-Savannah Agricultural Research InstituteNyankpalaGhana
  5. 5.Plant and Crop SciencesSchool of Biosciences, The University of NottinghamLoughboroughUK

Personalised recommendations