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Bringing the Benefits of Sorghum Genomics to Africa

  • Segenet KelemuEmail author
  • Brhane Gebrekidan
  • Jagger Harvey
Chapter
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 11)

Abstract

Sorghum was the first indigenous African crop to have a completed genome sequence. This provides an invaluable tool for understanding sorghum traits genetically and identifying useful molecular markers. The challenge is to extract relevant information to improve the diverse complex traits of sorghum including drought tolerance, disease and pest resistance, and overall yield. The promise of sorghum to improve food security and help lift millions of Africans out of poverty provides a moral imperative for investing in its improvement. Therefore, we must critically and objectively assess all available resources and coordinate our efforts for the benefit of Africans.

Keywords

Sorghum Genomics Africa National Agricultural Research Systems (NARS) Crop improvement Biotic stress Abiotic stress Molecular breeding Capacity building 

References

  1. Africa Harvest Biotech Foundation International (AHBFI) (2007) A global vision with an African focus to fight poor nutrition with nutrient-rich crops. The Africa Biofortified Sorghum Project: Mid-Term Report, December 2007. Nairobi, Kenya; Johannesburg, South Africa; Washington DC, USA, p 40Google Scholar
  2. Bennetzen J (2002) The rice genome. Opening the door to comparative plant biology. Science 296:60–63PubMedCrossRefGoogle Scholar
  3. Bruce WB, Edmeades GO, Barker TC (2002) Molecular and physiological approaches to maize improvement for drought tolerance. J Exp Bot 53:13–25PubMedCrossRefGoogle Scholar
  4. Casas AM, Kononowicz AK, Zehr UB, Tomes DT, Axtell JD, Butler LG, Bressan RA, Hasegawa PM (1993) Transgenic sorghum plants via microprojectile bombardment. Proc Natl Acad Sci U S A 90:11212–11216PubMedCrossRefGoogle Scholar
  5. Casas AM, Kononowicz AK, Haan TG, Zhang L, Tomes DT, Bressan RA, Hasegawa PM (1997) Transgenic sorghum plants obtained after microprojectile bombardment of immature inflorescences. In Vitro Cell Dev Biol Plant 33:92–100Google Scholar
  6. Cheung F, Haas BJ, Goldberg SM, May GD, Xiao Y, Town CD (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7:272PubMedCrossRefGoogle Scholar
  7. Cook D, Rimando AM, Clemente TE, Schroder J, Dayan FE, Nanayakkara NP, Pan Z, Noonan BP, Fishbein M, Abe I, Duke SO, Baerson SR (2010) Alkylresorcinol synthases expressed in Sorghum bicolor root hairs play an essential role in the biosynthesis of the allelopathic benzoquinone sorgoleone. Plant Cell 22:867–887PubMedCrossRefGoogle Scholar
  8. Doggett H (1988) Sorghum, 2nd edn. Longman Scientific and Technical, Harlow, UKGoogle Scholar
  9. Eathington SR, Crosbie TM, Edwards MD, Reiter RS, Bull JK (2007) Molecular markers in a commercial breeding program. Crop Sci 47(S3):S154–S163Google Scholar
  10. Ejeta G, Gressel J (2007) Integrating new technologies for Striga control: towards ending the witch-hunt. World Scientific, LondonCrossRefGoogle Scholar
  11. Food and Agriculture Organization of the United Nations (2007) Marker-assisted selection—current status and future perspectives in crops, livestock, forestry and fish. FAO, RomeGoogle Scholar
  12. Food and Agriculture Organization of the United Nations/the International Crops Research Institute for the Semi-Arid Tropics (1996) The world sorghum and millet economies: facts, trends and outlook. FAO/ICRISAT, Rome/IndiaGoogle Scholar
  13. Gale MD, Devos KM (1998) Plant comparative genetics after 10 years. Science 282:656–659PubMedCrossRefGoogle Scholar
  14. Gebrekidan B (1979) Sorghum genetic resources in Africa. Eth J Agri Sci 1:108–115Google Scholar
  15. Gebrekidan B (1987) Sorghum improvement and production in Eastern Africa. In: Menyonga JM, Bezuneh T, Youdeowei A (eds) Food grain production in semi-arid Africa. OAU/STRC-SAFGRAD, Ouagadougou, Burkina Faso, pp 141–154Google Scholar
  16. Gebrekidan B (2009) Linking science to product development: focusing on sorghum. Paper presented in the BecA-Syngenta Foundation for Sustainable Agriculture Foundation conference held on April 29, 2009 at the BecA-ILRI Hub, Nairobi, KenyaGoogle Scholar
  17. Gebrekidan B, Gebre-Hiwot B (1981) Sorghum injera preparations and its quality parameters, Proc. of the Intl. Symp. on Sorghum Grain Quality. ICRISAT, Hyderabad, IndiaGoogle Scholar
  18. Girijashankar V, Sharma HC, Sharma KK, Swathisree V, Prasad LS, Bhat BV, Royer M, Secundo BS, Narasu ML, Altosaar I, Seetharama N (2005) Development of transgenic sorghum for insect resistance against the spotted stem borer (Chilo partellus). Plant Cell Rep 24:513–522PubMedCrossRefGoogle Scholar
  19. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100PubMedCrossRefGoogle Scholar
  20. Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES (2009) A first-generation haplotype map of maize. Science 326:1115–1117PubMedCrossRefGoogle Scholar
  21. Grenier C, Ibrahim Y, Haussmann B, Kiambi D, Ejeta G (2007) Marker-assisted selection for Striga resistance in sorghum. In: Ejeta G, Gressel J (eds) Integrating new technologies for Striga control: towards ending the witch-hunt. World Scientific, LondonGoogle Scholar
  22. Gupta PK, Kumar J, Mir RR, Kumar A (2010) Marker-assisted selection as a component of plant breeding. In: Janick J (ed) Plant breeding reviews, vol 33. Wiley, New Jersey, pp 145–205CrossRefGoogle Scholar
  23. Hallauer AR (2007) History, contribution, and future of quantitative genetics in plant breeding: lessons from maize. Crop Sci 47(S3):S4–S19Google Scholar
  24. Haussmann BI, Mahalakshmi V, Reddy BV, Seetharama N, Hash CT, Geiger HH (2002) QTL mapping of stay-green in two sorghum recombinant inbred populations. Theor Appl Genet 106:133–142PubMedGoogle Scholar
  25. Heffner EL, Sorrels ME, Jannink J-L (2009) Genomic selection for crop improvement. Crop Sci 49:1–12CrossRefGoogle Scholar
  26. Howe A, Sato S, Dweikat I, Fromm M, Clemente T (2006) Rapid and reproducible Agrobacterium-mediated transformation of sorghum. Plant Cell Rep 25:784–791PubMedCrossRefGoogle Scholar
  27. Iyer-Pascuzzi AS, Symonova O, Mileyko Y, Hao Y, Belcher H, Harer J, Weitz JS, Benfey PN (2010) Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems. Plant Physiol 152:1148–1157PubMedCrossRefGoogle Scholar
  28. James C (2010) Global status of commercialized Biotech/GM Crops: 2009, ISAAA Brief 41. ISAAA, Ithaca, New YorkGoogle Scholar
  29. Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomic Proteomic 9:166–177Google Scholar
  30. Kelemu S, Mahuku G, Fregene M, Pachico P, Johnson N, Calvert L, Rao I, Buruchara R, Amede T, Kimani P, Kirkby P, Kaaria S, Ampofo K (2003) Harmonizing the agricultural biotechnology debate for the benefit of African farmers. Afr J Biotechnol 2(11):394–416Google Scholar
  31. Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung CW, Wei X, Yap I, Youens-Clark K, Ware D, Stein L (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Res 36:D947–D953PubMedCrossRefGoogle Scholar
  32. Mahalakshmi V, Bidinger FR (2002) Evaluation of stay-green sorghum germplasm lines at ICRISAT. Crop Sci 42:965–974CrossRefGoogle Scholar
  33. Mayor PJ, Bernardo R (2009) Genomewide selection and marker-assisted recurrent selection in double haploid versus F2 populations. Crop Sci 49:1719–1725CrossRefGoogle Scholar
  34. McBee GG (1984) Relation of senescence, nonsenescence, and kernel maturity to carbohydrate metabolism in sorghum. In: Mughogho LK (ed.) Sorghum root and stalk rots: a critical Review. Proc. Consult. Group Discussion on Research Needs and Strategies for Control of Sorghum Root and Stalk Rot Diseases, Bellagio, Italy. 27 Nov–2 Dec 1983. ICRISAT, Patancheru, India, pp 119–129Google Scholar
  35. Morris M, Dreher K, Ribaut J-M, Khairallah M (2003) Money matters (II): costs of maize inbred line conversion schemes at CIMMYT using conventional and marker-assisted selection. Mol Breed 11:235–247CrossRefGoogle Scholar
  36. Mugabe J, Ambali A (2006) Africa’s science and technology consolidated plan of action. The NEPAD Office of Science and Technology, Pretoria, South AfricaGoogle Scholar
  37. Mughogho LK, Pande S (1984) Charcoal rot of sorghum. In: Mughogho LK (ed) Sorghum root and stalk rots: a critical Review. Proc. Consult. Group discussion on research needs and strategies for control of sorghum root and stalk rot diseases, Bellagio, Italy. 27 Nov–2 Dec 1983. ICRISAT, Patancheru, India, pp 11–24Google Scholar
  38. Nelson DE, Repetti PP, Adams TR, Creelman RA, Wu J, Warner DC, Anstrom DC, Bensen RJ, Castiglioni PP, Donnarummo MG, Hinchey BS, Kumimoto RW, Maszle DR, Canales RD, Krolikowski KA, Dotson SB, Gutterson N, Ratcliffe OJ, Heard JE (2007) Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improved corn yields on water-limited acres. Proc Natl Acad Sci U S A 104:16450–16455PubMedCrossRefGoogle Scholar
  39. Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18:2024–2033PubMedCrossRefGoogle Scholar
  40. Pardey PG, Alston JM, Piggott RR (2006) Agricultural R&D in the developing world: too little, too late? International Food Policy Research Institute, Washington, DC, USAGoogle Scholar
  41. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboobur R, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556PubMedCrossRefGoogle Scholar
  42. Ragot M, Lee M (2007) Marker-assisted selection in maize: current status, potential, limitations and perspectives from the private and public sectors. In: Guimarães E, Ruane J, Scherf B, Sonnino A, Dargie JD (eds) Marker-assisted selection: current status and future perspectives in crops, livestock, forestry and fish. Food and Agriculture Organization of the United Nations, RomeGoogle Scholar
  43. Rosenow DT, Clark LE (1981) Drought tolerance in sorghum. In: Loden HD, Wilkinson D (eds) Proc 36th Annu. Corn and Sorghum Industry Res Conf Chicago, IL 9–11 Dec. 1981. Am. Seed Trade Assoc, Washington, DC, pp 18–31Google Scholar
  44. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115PubMedCrossRefGoogle Scholar
  45. Septiningsih EM, Pamplona AM, Sanchez DL, Neeraja CN, Vergara GV, Heuer S, Ismail AM, Mackill DJ (2009) Development of submergence-tolerant rice cultivars: the Sub1 locus and beyond. Ann Bot 103:151–160PubMedCrossRefGoogle Scholar
  46. Tester M, Langridge P (2010) Breeding technologies to increase crop production in a changing world. Science 327:818–822PubMedCrossRefGoogle Scholar
  47. The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768CrossRefGoogle Scholar
  48. Till BJ, Comai L, Henikoff S (2007) TILLING and EcoTILLING for crop improvement. In: Varshney RK, Tuberosa R (eds) Genomic assisted crop improvement: genomics approaches and platforms. Springer, Dordrecht, The Netherlands, pp 333–349CrossRefGoogle Scholar
  49. Varshney RK, Hoisington DA, Tyagi AK (2006) Advances in cereal genomics and applications in crop breeding. Trends Biotechnol 24:490–499PubMedCrossRefGoogle Scholar
  50. Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB (2007) Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol 144:32–42PubMedCrossRefGoogle Scholar
  51. World Bank (2008) World development report 2008: agriculture for development. The World Bank, Washington, DCGoogle Scholar
  52. Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708PubMedCrossRefGoogle Scholar
  53. Yan J, Kandianis CB, Harjes CE, Bai L, Kim EH, Yang X, Skinner DJ, Fu Z, Mitchell S, Li Q, Fernandez MG, Zaharieva M, Babu R, Fu Y, Palacios N, Li J, Dellapenna D, Brutnell T, Buckler ES, Warburton ML, Rocheford T (2010) Rare genetic variation at Zea mays crtRB1 increases beta-carotene in maize grain. Nat Genet 42:322–327PubMedCrossRefGoogle Scholar
  54. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Li J, Liu Z, Qi Q, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Zhao W, Li P, Chen W, Zhang Y, Hu J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Tao M, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Segenet Kelemu
    • 1
    Email author
  • Brhane Gebrekidan
    • 2
  • Jagger Harvey
    • 1
  1. 1.Biosciences eastern and central Africa-International Livestock Research Institute Hub (BecA-ILRI Hub)NairobiKenya
  2. 2.Agriculture Working GroupEthiopian Academy of SciencesAddis AbabaEthiopia

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