Skip to main content
SpringerLink
Log in

Genomic Tools and Strategies for Breeding Climate Resilient Cereals

  • Chapter
  • First Online:
Genomics and Breeding for Climate-Resilient Crops

Abstract

Cereal crops are vital for meeting the food, feed and nutritional demands of the world. However, long-term production growth of cereals could be severely affected by the changing climate, which is already exacerbating existing challenges such as drought and heat stresses, insect pests and diseases, and soil degradation, especially in the tropics. While adaptation to climate change would require convergence of appropriate technologies, policies and institutional innovations, the focus of this chapter is on some of the promising genomic tools and strategies that can enhance time- and cost-effectiveness of breeding for climate-resilient cereals. For this, we use maize as a case study, considering the availability of genomic resources, the significance of maize as the number one cereal crop in the world at present in terms of total area and production, the vulnerability of sub-Saharan Africa (where maize is the most important staple food crop) and South Asia (where maize plays a significant role as food and feed) to the changing climates. CIMMYT’s experiences and initiatives with regard to designing and implementing modern breeding strategies for developing climate-resilient maize varieties, including high-density genotyping, whole genome resequencing, high-throughput and precise phenotyping, doubled haploids (DH), genomics-assisted breeding (e.g., genome-wide association studies, breeder-ready marker development, rapid-cycle genomic selection, marker-assisted recurrent selection), and crop modeling are particularly highlighted here. The key challenges to the international scientific community are (a) to generate high-quality phenotypic data in breeding programs, and integrating the same with modern tools and technologies for accelerated development of climate-resilient germplasm; (b) to better understand the effects of climate change on diversity of cropping systems in different regions; and (c) to effectively monitor the patterns of change both temporally and spatially, coupled with appropriate policies and actions at the farm level.

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

Access this chapter

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

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • ADB (2009) Climate change threatens water and food security of 1.6 billion South Asians. NewsRelease, 2 Sept 2009

    Google Scholar 

  • Araus JL, Slafer GA, Royo C, Serret MD (2008) Breeding for yield potential and stress adaptation in cereals. Crit Rev Plant Sci 27:1–36

    Article  Google Scholar 

  • Araus JL, Sanchez C, Edmeades GO (2011) Phenotyping maize for adaptation to drought. In: Monneveux P, Ribaut J-M (eds) Drought phenotyping in crops: from theory to practice. Generation Challenge Program, Texcoco, Mexico, pp 259–282

    Google Scholar 

  • Babu R, Nair SK, Vivek BS, San Vicente F, Prasanna BM (2012) Integrating marker-assisted selection in the DH-based breeding pipeline for rapid development and delivery of superior parental lines and cultivars. In: Prasanna BM, Chaikam V, Mahuku G (eds) Doubled haploid technology in maize breeding: theory and practice. CIMMYT, Mexico DF, pp 39–44

    Google Scholar 

  • Barnabás B, Jäger K, Fehér A (2008) The effect of drought and heat stress on reproductive processes in cereals. Plant Cell Environ 31:11–38

    PubMed  Google Scholar 

  • Barrière Y, Thomas J, Denoue D (2008) QTL mapping for lignin content, lignin monomeric composition, p-hydroxycinnamate content, and cell wall digestibility in the maize recombinant inbred line progeny F838 X F286. Plant Sci 175:585–595

    Article  CAS  Google Scholar 

  • Bernardo R, Yu J (2007) Prospects for genomewide selection for quantitative traits in maize. Crop Sci 47:1082–1090

    Article  Google Scholar 

  • Blum A (2011) Plant breeding for water-limited environments. Springer, New York, 255 p

    Book  Google Scholar 

  • Boote KJ, Kropff MJ, Bindraban PS (2001) Physiology and modelling of traits in crop plants: implications for genetic improvement. Agric Syst 70:395–420

    Article  Google Scholar 

  • Bouchez A, Gallais A (2000) Efficiency of the use of doubled haploids in recurrent selection for combining ability. Crop Sci 40:23–29

    Article  Google Scholar 

  • Burke MB, Lobell DB, Guarino L (2009) Shifts in African crop climates by 2050, and the implications for crop improvements and genetic resources conservation. Glob Environ Change 19:317–325

    Article  Google Scholar 

  • Cabrera-Bosquet L, Crossa J, von Zitzewitz J, Serret MD, Araus JL (2012) High-throughput phenotyping and genomic selection: the frontiers of crop breeding converge. J Integr Plant Biol 54:312–320

    Article  PubMed  Google Scholar 

  • Cairns JE, Impa SM, O’Toole JV, Jagadish SVK, Price AH (2011) Influence of the soil physical environment on rice (Oryza sativa L.) response to drought stress and its implications for drought research. Field Crops Res 121:303–310

    Article  Google Scholar 

  • Cairns JE, Crossa J, Zaidi PH, Grudloyma P, Sanchez C, Araus JL, Thaitad S, Makumbi D, Magorokosho C, Bänziger M, Menkir A, Hearne S, Atlin GN (2012a) Identification of drought, heat and combined drought and heat tolerance donors in maize. Crop Sci (In Press)

    Google Scholar 

  • Cairns JE, Sanchez C, Vargas M, Ordoñez RA, Araus JL (2012b) Dissecting maize productivity: ideotypes associated with grain yield under drought stress and well-watered conditions. J Integr Plant Biol. doi:10.1111/j.1744-7909.2012.01156.x

    Google Scholar 

  • Campos H, Heard JE, Ibañez M, Luethy MH, Peters TJ, Warner DC (2011) Effective and efficient platforms for crop phenotype characterisation under drought. In: Monneveux P, Ribaut JM (eds) Drought phenotyping in crops: from theory to practice. CGIAR Generation Challenge Programme, Texcoco, Mexico, pp 39–47

    Google Scholar 

  • Chang MT, Coe EH (2009) Doubled haploids. In: Kriz AL, Larkins BA (eds) Biotechnology in agriculture and forestry, vol 63, Molecular genetic approaches to maize improvement. Springer, Berlin, pp 127–142

    Google Scholar 

  • Chen S, Li L, Li H (2009) Maize doubled haploid breeding [in Chinese]. China Agricultural University Press, Beijing

    Google Scholar 

  • Chia J-M, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut G, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna BM, Pyhäjärvi T, Rong T, Sekhon RS, Sun Q, Tenaillon MI, Tian F, Wang J, Xu X, Zhang Z, Kaeppler SM, Ross-Ibarra J, McMullen MD, Buckler ES, Zhang G, Xu Y, Ware D (2012) Maize HapMap 2 identifies extant variation from a genome in flux. Nature Genetics 44:803–807

    Article  PubMed  CAS  Google Scholar 

  • Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein A, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szûcs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582

    Article  PubMed  CAS  Google Scholar 

  • Collins NC, Tardieu F, Tuberosa R (2008) QTL approaches for improving crop performance under abiotic stress conditions: where do we stand? Plant Physiol 147:469–486

    Article  PubMed  CAS  Google Scholar 

  • Crafts-Brander SJ, Salvucci ME (2002) Sensitivity of photosynthesis in a C4 plant, maize, to heat stress. Plant Physiol 129:1773–1780

    Article  CAS  Google Scholar 

  • DePauw RM, Townley-Smith TF, Humphreys G, Knox RE, Clarke FR, Clarke JM (2005) Lillian hard red spring wheat. Can J Plant Sci 85:397–401

    Article  Google Scholar 

  • DePauw RM, Knox RE, Thomas JB, Smith M, Clarke JM, Clarke FR, McCaig TN, Fernandez MR (2009) Goodeve hard red spring wheat. Can J Plant Sci 89:937–944

    Article  Google Scholar 

  • Dwivedi SL, Crouch JH, Mackill DJ, Xu Y, Blair MW, Ragot M, Upadhyaya HD, Ortiz R (2007) The molecularization of public sector crop breeding: progress, problems and prospects. Adv Agron 95:163–318

    Article  CAS  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379

    Article  PubMed  CAS  Google Scholar 

  • Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics, 4th edn. Longman, Essex

    Google Scholar 

  • Finkel E (2009) With “phenomics”, plant scientists hope to shift breeding into overdrive. Science 325:380–381

    Article  PubMed  CAS  Google Scholar 

  • Forster BP, Heberle-Bors E, Kasha KJ, Touraev A (2007) The resurgence of haploids in higher plants. Trends Plant Sci 12:368–375

    Article  PubMed  CAS  Google Scholar 

  • Geiger HH, Gordillo GA (2009) Doubled haploids in hybrid maize breeding. Maydica 54:485–499

    Google Scholar 

  • George MLC, Prasanna BM, Rathore RS, Setty TAS, Kasim F, Azrai M, Vasal S, Balla O, Hautea D, Canama A, Regalado E, Vargas M, Khairallah M, Jeffers D, Hoisington D (2003) Identification of QTLs conferring resistance to downy mildews of maize in Asia. Theor Appl Genet 107:544–551

    Article  PubMed  CAS  Google Scholar 

  • Goodman MM (2005) Broadening the U.S. maize germplasm base. Maydica 50:203–214

    Google Scholar 

  • Goodman MM, Brown WL (1988) Races of corn. In: Sprague GF, Dudley JW (eds) Corn and corn improvement. American Society of Agronomy, Madison, WI, pp 33–79

    Google Scholar 

  • 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 326:1115–1117

    Article  PubMed  CAS  Google Scholar 

  • Gregory PJ, Johnson SN, Newton AC, Ingram JSI (2009) Integrating pests and pathogens into the climate change/food security debate. J Exp Bot 60:2827–2838

    Article  PubMed  CAS  Google Scholar 

  • Grewal TS, Rossnagel BG, Scoles GJ (2010) Validation of molecular markers associated with net blotch resistance and their utilization in barley breeding. Crop Sci 50:177–184

    Article  Google Scholar 

  • Gupta PK, Langridge P, Mir RR (2010) Marker-assisted wheat breeding: present status and future possibilities. Mol Breed 26:145–161

    Article  Google Scholar 

  • Hao X, Thelen K, Gao J (2010) Effects of soil and topographic properties on spatial variability of corn grain ethanol yield. Agron J 102:998–1006

    Article  CAS  Google Scholar 

  • Harjes CE, Rocheford TR, Bai L, Brutnell TP, Kandianis CB, Sowinski SG, Stapleton AE, Vallabhaneni R, Williams M, Wurtzel ET, Yan J, Buckler ES (2008) Natural genetic variation in Lycopene Epsilon Cyclase tapped for maize biofortification. Science 319:330–333

    Article  PubMed  CAS  Google Scholar 

  • Hash CT (2005) Opportunities for application of molecular markers for sustainable crop production in stress environments: sorghum and pearl millet. In: International conference on sustainable crop production in stress environments: management and genetic options. Jawaharlal Nehru Krishi VishwaVidyalaya, Jabalpur, India, p 113 (abstr)

    Google Scholar 

  • Heffner EL, Lorenz AJ, Jannink JL, Sorrells ME (2010) Plant breeding with genomic selection: gain per unit time and cost. Crop Sci 50:1681–1690

    Article  Google Scholar 

  • Heyne EG, Brunson AM (1940) Genetic studies of heat and drought tolerance in maize. J Am Soc Agron 32:803–814

    Article  Google Scholar 

  • IPCC (2007) Fourth assessment report: synthesis. Published online 17 Nov 2007. http://www.ipcc.ch/pdf/assessment-report/ar4/syr/ar4_syr.pdf

  • Jagadish SVK, Septiningsih EM, Kohil A, Thomson MJ, Ye C, Redona E, Kumar A, Gregorio GB, Wassman R, Ismail AM, Sinigh EK (2012) Genetic advances in adapting rice to a rapidly changing climate. J Agron Crop Sci. doi:10.1111/j.1439-037X.2012.00525

    Google Scholar 

  • Jannink J-L, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166–177

    Article  PubMed  CAS  Google Scholar 

  • Jones PG, Thornton PK (2003) The potential impacts of climate change on maize production in Africa and Latin America in 2055. Glob Environ Change 13:51–59

    Article  Google Scholar 

  • Kumar J, Mir RR, Kumar N, Kumar A, Mohan A, Prabhu KV, Balyan HS, Gupta PK (2010) Marker assisted selection for pre-harvest sprouting tolerance and leaf rust resistance in bread wheat. Plant Breed 12:617–621

    Article  CAS  Google Scholar 

  • Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, Belcher AR, Oropeza-Rosas MA, Zwonitzer JC, Kresovich S, McMullen MD, Ware D, Balint-Kurti PJ, Holland JB (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43:163–168

    Article  PubMed  CAS  Google Scholar 

  • Lane A, Jarvis A (2007) Changes in climate will modify the geography of crop suitability: agricultural biodiversity can help with adaptation. In: Paper presented at ICRISAT/CGIAR 35th anniversary symposium, climate-proofing innovation for poverty reduction and food security, ICRISAT, Patancheru, India, 22–24 Nov 2007, 12 p. http://www.icrisat.org/Journal/SpecialProject/sp2.pdf. Accessed 8 Mar 2010

  • Li Y (1998) Development and germplasm base of maize hybrids in China. Maydica 43:259–269

    Google Scholar 

  • Li Y, Wang JK, Qiu LJ, Ma YZ, Li XH, Wan JM (2010) Crop molecular breeding in China: current status and perspectives. Acta Agron Sin 36:1425–1430

    CAS  Google Scholar 

  • Lobell B, Burke MB (2010) On the use of statistical models to predict crop yield responses to climate change. Agric For Meteorol 150:1443–1452

    Article  Google Scholar 

  • Lobell DB, Burke MB, Tebaldi C, Mastrandrea MD, Falcon WP, Naylor RL (2008) Prioritizing climate change adaptation and needs for food security in 2030. Science 319:607–610

    Article  PubMed  CAS  Google Scholar 

  • Lobell DB, Bänziger M, Magorokosho C, Vivek B (2011) Nonlinear heat effects on African maize as evidenced by historical yield trials. Nat Clim Change 1:42–45

    Article  Google Scholar 

  • Lorenzana RE, Bernardo R (2009) Accuracy of genetic value predictions for marker-based selection in biparental plant populations. Theor Appl Genet 120:151–161

    Article  PubMed  Google Scholar 

  • Lu Y, Zhang SH, Shah T, Xie C, Hao Z, Li X, Farkhari M, Ribaut JM, Cao M, Rong T, Xu Y (2010) Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize. Proc Natl Acad Sci USA 107:19585–19590

    Article  PubMed  CAS  Google Scholar 

  • Masuka B, Araus JL, Das B, Sonder K, Cairns JE (2012) Phenotyping for abiotic stress tolerance in maize. J Integr Plant Biol 54:238–249

    Article  PubMed  CAS  Google Scholar 

  • Mayor PJ, Bernardo R (2009) Genomewide selection and marker-assisted recurrent selection in doubled haploid versus F2 populations. Crop Sci 49:1719–1725

    Article  Google Scholar 

  • McCouch SR, Zhao K, Wright M, Tung CW, Ebana K, Thomson M, Reynolds A, Wang D, DeClerck G, Ali ML, McClung A, Eizenga G, Bustamante C (2010) Development of genome-wide SNP assays for rice. Breed Sci 60:524–535

    Article  Google Scholar 

  • McNally K, Childs K, Bohnert R, Davidson R, Zhao K, Ulat V, Zeller G, Clark R, Hoen D, Bureau T, Stokowski R, Ballinger D, Frazer K, Cox D, Padhukasahasram B, Bustamante C, Weigel D, Mackill D, Bruskiewich R, Rätsch G, Buell C, Leung H, Leach J (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci USA 106:12273–12278

    Article  PubMed  CAS  Google Scholar 

  • Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829

    PubMed  CAS  Google Scholar 

  • Mittler R (2006) Abiotic stress, the field environment and stress combination. Trends Plant Sci 11:15–19

    Article  PubMed  CAS  Google Scholar 

  • Miura K, Ashikari M, Matsuoka M (2012) The role of QTLs in the breeding of high-yielding rice. Trends Plant Sci 17:129–138

    Article  CAS  Google Scholar 

  • Montes JM, Technow F, Dhillon BS, Mauch F, Melchinger AE (2011) High-throughput non-destructive biomass determination during early plant development in maize under field conditions. Field Crops Res 121:268–273

    Article  Google Scholar 

  • Muchow TR, Sinclair TR, Bennett JM (1990) Temperature and solar radiation effects on potential maize yield across locations. Agron J 82:338–343

    Article  Google Scholar 

  • Nair SK, Prasanna BM, Garg A, Rathore RS, Setty TAS, Singh NN (2005) Identification and validation of QTLs conferring resistance to sorghum downy mildew (Peronosclerospora sorghi) and Rajasthan downy mildew (P. heteropogoni) in maize. Theor Appl Genet 110:1384–1392

    Article  PubMed  CAS  Google Scholar 

  • Ortiz R, Sayre KD, Govarets B, Gupta R, Subbarao GV, Ban T, Hodson D, Dixon JM, Ortiz-Monasterio I, Reynolds M (2008) Climate change: can wheat beat the heat? Agric Ecosyst Environ 126:46–58

    Article  Google Scholar 

  • Paulsen GM (1994) High temperature responses of crop plants. In: Boote KJ, Bennett JM, Sinclair TR, Paulsen GM (eds) Physiology and determination of crop yield. American Society of Agronomy, Madison, WI, pp 365–389

    Google Scholar 

  • Phillips RL (2009) Mobilizing science to break yield barriers. Crop Sci 50:S99–S108

    Google Scholar 

  • Prasad PVV, Boote KJ, Allen LH, Sheehy JE, Thomas JMG (2006) Species, ecotypes and cultivar differences in spikelet fertility and harvest index of rice in response to high temperature stress. Field Crops Res 95:398–411

    Article  Google Scholar 

  • Prasanna BM, Pixley K, Warburton ML, Xie CX (2010) Molecular marker-assisted breeding options for maize improvement in Asia. Mol Breed 26:339–356

    Article  CAS  Google Scholar 

  • Prasanna BM, Araus JL, Crossa J, Cairns JE, Palacios N, Das B, Magorokosho C (2012a) High-throughput and precision phenotyping for cereal breeding programs. In: Gupta PK, Varshney RK (eds) Cereal genomics-II. Springer, Heidelberg

    Google Scholar 

  • Prasanna BM, Chaikam V, Mahuku G (eds) (2012b) Doubled haploid technology in maize breeding: theory and practice. CIMMYT, Mexico DF, 50 p

    Google Scholar 

  • Prigge V, Sanchez C, Dhillon BS, Schipprack W, Araus JL, Bänziger M, Melchinger AE (2011) Doubled haploids in tropical maize: 1. Effects of inducers and source germplasm on in vivo haploid induction rate. Crop Sci 51:1498–1506

    Article  Google Scholar 

  • Prigge V, Schipprack W, Mahuku G, Atlin GN, Melchinger AE (2012a) Development of in vivo haploid inducers for tropical maize breeding programs. Euphytica 185:481–490

    Article  Google Scholar 

  • Prigge V, Babu R, Das B, Rodriguez MH, Atlin GN, Melchinger AE (2012b) Doubled haploids in tropical maize: II. Quantitative genetic parameters for testcross performance. Euphytica 185:453–463

    Article  Google Scholar 

  • Qiu LJ, Guo Y, Li Y, Wang XB, Zhou GA, Liu ZX, Zhou SR, Li XH, Ma YZ, Wang JK, Wan JM (2011) Novel gene discovery of crops in China: status, challenges, and perspective. Acta Agron Sin 37:1–17

    Article  CAS  Google Scholar 

  • Ribaut JM, de Vicente MC, Delannay X (2010) Molecular breeding in developing countries: challenges and perspectives. Curr Opin Plant Biol 13:213–218

    Article  PubMed  Google Scholar 

  • Rizhsky L, Hongjian L, Mittler R (2002) The combined effect of drought stress and heat shock on gene expression in tobacco. Plant Physiol 130:1143–1151

    Article  PubMed  CAS  Google Scholar 

  • Rizhsky L, Liang H, Shuman J, Shulaev V, Davletova S, Mittler R (2004) When defence pathways collide: the response of Arabidopsis to a combination of drought and heat stress. Plant Physiol 134:1683–1696

    Article  PubMed  CAS  Google Scholar 

  • Robertson M, Carberry PS (2010) The evolving role of crop modelling in agronomy research. In: Proceedings of 15th Australian agronomy conference. Australian Society of Agronomy/The Regional Institute, Gosford, NSW

    Google Scholar 

  • Rowhani P, Lobell DB, Linderman M, Ramankutty N (2011) Climate variability and crop production in Tanzania. Agric For Meteorol 151:449–460

    Article  Google Scholar 

  • Roy SJ, Tucker EJ, Tester M (2011) Genetic analysis of abiotic stress tolerance in crops. Curr Opin Plant Biol 14:1–8

    Article  CAS  Google Scholar 

  • Rutkoski JE, Heffner EL, Sorrells ME (2011) Genomic selection for durable stem rust resistance in wheat. Euphytica 179:161–173

    Article  Google Scholar 

  • Schmidt W (2003) Hybrid maize breeding at KWS SAAT AG. In: Bericht über die Arbeitstagung der Vereinigung der Pflanzenz üchter und Saatgutkaufleute Österreichs, Gumpenstein, Österreich, 25–27 November, pp 1–6

    Google Scholar 

  • Schnable PS, Ware D, Fulton RS, Stein JC, Wei F et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115

    Article  PubMed  CAS  Google Scholar 

  • Schoper JB, Lambert RJ, Vasilas BL (1987a) Pollen viability, pollen shedding and combining ability for tassel heat tolerance in maize. Crop Sci 27:27–31

    Article  Google Scholar 

  • Schoper JB, Lambert RJ, Vasilas BL, Westgate ME (1987b) Plant factors controlling seed set in maize: the influence of silk, pollen and ear-leaf water status and tassel heat treatment at pollination. Plant Physiol 83:121–125

    Article  PubMed  CAS  Google Scholar 

  • Seitz G (2005) The use of doubled haploids in corn breeding. In: Proceedings of 41st annual Illinois Corn Breeders’ School 2005. Urbana-Champaign, IL, pp 1–7

    Google Scholar 

  • Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145

    Article  PubMed  CAS  Google Scholar 

  • Shiferaw B, Prasanna BM, Hellin J, Bänziger M (2011) Crops that feed the world. Past successes and future challenges to the role played by maize in global food security. Food Secur 3:307–327

    Article  Google Scholar 

  • Siangliw M, Toojinda T, Tragoonrung S, Vanavichit A (2003) Thai Jasmine rice carrying QTLch9 (SubQTL) is submergence tolerant. Ann Bot 91:255–261

    Article  PubMed  CAS  Google Scholar 

  • Smith JSC, Hussain T, Jones ES, Graham G, Podlich D, Wall S, Williams M (2008) Use of doubled haploids in maize breeding: implications for intellectual property protection and genetic diversity in hybrid crops. Mol Breed 22:51–59

    Article  Google Scholar 

  • Stone P (2001) The effects of heat stress on cereal yield and quality. In: Basara AS (ed) Crop responses and adaptations to temperature stress. Food Products, Binghamton, NY, pp 243–291

    Google Scholar 

  • Tardieu F, Tuberosa R (2010) Dissection and modelling of abiotic stress tolerance in plants. Curr Opin Plant Biol 13:206–212

    Article  PubMed  Google Scholar 

  • Tester M, Langridge P (2010) Breeding technologies to increase crop production in a changing world. Science 327:818–822

    Article  PubMed  CAS  Google Scholar 

  • Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43:159–162

    Article  PubMed  CAS  Google Scholar 

  • Trebbi D, Maccaferri M, de Heer P, Sørensen A, Giuliani S, Salvi S, Sanguineti MC, Massi A, van der Vossen EAG, Tuberosa R (2011) High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.). Theor Appl Genet 123:555–569

    Article  PubMed  Google Scholar 

  • Truntzler M, Barrière Y, Sawkins MC, Lespinasse D, Betran J, Charcosset A, Moreau L (2010) Meta-analysis of QTL involved in silage quality of maize and comparison with the position of candidate genes. Theor Appl Genet 121:1465–1482

    Article  PubMed  CAS  Google Scholar 

  • Vielle-Calzada J-P, de la Vega OM, Hernández-Guzmán G et al (2010) The Palomero genome suggests metal effects on maize domestication. Science 326:1078

    Article  CAS  Google Scholar 

  • Voesenik LACJ, Pierik R (2008) Plant stress profiles. Science 320:880–881

    Article  Google Scholar 

  • Wang J (2011) Simulation modelling in plant breeding. J Indian Soc Agric Stat 65:225–235

    Google Scholar 

  • Wang CL, Zhang YD, Zhu Z, Chen T, Zhao L, Lin J, Zhou LH (2009) Development of a new japonica rice variety Nanjing 46 with good eating quality by marker assisted selection. Mol Plant Breed 7:1070–1076

    CAS  Google Scholar 

  • Wang C, Chen S, Yu S (2011a) Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice. Theor Appl Genet 122:905–913

    Article  PubMed  Google Scholar 

  • Wang L, Wang A, Huang X, Zhao Q, Dong G, Qian Q, Sang T, Han B (2011b) Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines. Theor Appl Genet 122:327–340

    Article  PubMed  Google Scholar 

  • Wassman R, Jagadish SVK, Sumfleth K, Pathak H, Howell G, Ismail A, Serraj R, Redona E, Singh RK, Heuer S (2009) Regional vulnerability of climate change impacts on Asian rice production and scope for adaptation. Adv Agron 102:91–133

    Article  Google Scholar 

  • Weber VS, Atlin GN, Crossa J, Hickey JM, Jannick J-L, Sorrels M, Ramen B, Cairns JE, Tarekegne A, Semagn K, Beyene Y, Grudloyma P, Technow F, Riedelsheimer C, Melchinger AE (2012) Effectiveness of genomic prediction of maize hybrid performance in different breeding populations and environments. Gen Genet Genomics 2:1427–1436

    Google Scholar 

  • Wedzony M, Forester BP, Izur I, Golemiec E, Szechynska-Heba M, Dubas E, Gotebiowska G (2008) Progress in doubled haploid technology in higher plants. In: Touraev A, Forester BP, Jain SM (eds) Advances in haploid production in higher plants. Springer, New York, pp 1–34

    Google Scholar 

  • Wei X, Jin LLL, Xu JF, Jiang L, Zhang WW, Wang JK, Zhai HQ, Wan JM (2009) Breeding strategies for optimum heading date using genotypic information in rice. Mol Breed 25:287–298

    Article  CAS  Google Scholar 

  • White JW, Andrare-Sanchez P, Gore MA, Bronson KF, Coffelt TA, Conleya MM, Feldmann KA, French AN, Heun JT, Hunsaker TA, Jenks MA, Kimball BA, Roth RL, Strand RJ, Thorp KR, Wall GW, Wang G (2012) Field-based phenomics for plant genetics research. Field Crops Res 133:101–112

    Article  Google Scholar 

  • Xu Y (2010) Molecular plant breeding. CAB International, Wallingford, 734 p

    Google Scholar 

  • Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407

    Article  Google Scholar 

  • Xu K, Xia X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AI, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene response factor-like gene that confers submergence tolerance to rice. Nature 442:705–708

    Article  PubMed  CAS  Google Scholar 

  • Xu X, Xin Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, 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, Wang W (2012a) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30:105–111

    Article  CAS  Google Scholar 

  • Xu Y, Lu Y, Xie C, Gao S, Wan J, Prasanna BM (2012b) Whole genome strategies for marker-assisted plant breeding. Mol Breed 29:833–854

    Article  CAS  Google Scholar 

  • Xu Y, Wan J, He Z, Prasanna BM (2012c) Marker-assisted selection: strategies and examples from cereals. In: Gupta PK, Varshney RK (eds) Cereal Genomics-II. Springer, Heidelberg

    Google Scholar 

  • Yamamoto T, Nagasaki H, Yonemaru J, Ebana K, Nakajima M, Shibaya T, Yano M (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genomics 11:267

    Article  PubMed  CAS  Google Scholar 

  • Yan J, Shah T, Warburton ML, Buckler ES, McMullen MD, Crouch J (2009) Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoS One 4:e8451

    Article  PubMed  CAS  Google Scholar 

  • Yan J, Yang X, Shah T, Sánchez-Villeda H, Li J, Warburton M, Zhou Y, Crouch JH, Xu Y (2010a) High-throughput SNP genotyping with the GoldenGate assay in maize. Mol Breed 25:441–451

    Article  CAS  Google Scholar 

  • Yan J, Kandianis CB, Harjes CE, Bai L, Kim E, Yang X, Skinner D, Fu Z, Mitchell S, Li Q, Fernandez MGS, Zaharieva M, Babu R, Fu Y, Palacios N, Li J, DellaPenna D, Brutnell T, Buckler ES, Warburton ML, Rocheford T (2010b) Rare genetic variation at Zea mays crtRB1 increases β-carotene in maize grain. Nat Genet 42:322–327

    Article  PubMed  CAS  Google Scholar 

  • Yin XY, Stam P, Kropff MJ, Schapendonk A (2003) Crop modelling, QTL mapping, and their complementary role in plant breeding. Agron J 95:90–98

    Article  CAS  Google Scholar 

  • Yu Y, Wang R, Shi Y, Song Y, Wang T, Li Y (2007) Genetic diversity and structure of the core collection for maize inbred lines in China. Maydica 52:181–194

    Google Scholar 

  • Yu J, Hollan JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–551

    Article  PubMed  Google Scholar 

  • Zaidi PH, Cairns JE (2011) Enhancing climate-resilience in tropical maize. In: Zaidi PH, Babu R, Cairns J, Kha LQ et al (eds) Addressing climate change effects and meeting maize demand for Asia. Book of extended summaries of the 11th Asian maize conference, Nanning, China, 7–11 Nov 2011. CIMMYT, Mexico DF, pp 13–16

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. CIMMYT (International Maize and Wheat Improvement Center), ICRAF House, United Nations Avenue, Gigiri, Nairobi, 00621, Kenya

    B. M. Prasanna

  2. CIMMYT, MP 163, Mount Pleasant, Harare, Zimbabwe

    Jill Cairns

  3. CIMMYT, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Yunbi Xu

Authors
  1. B. M. Prasanna
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jill Cairns
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yunbi Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to B. M. Prasanna .

Editor information

Editors and Affiliations

  1. Bidhan Chandra Krishi Viswavidyalaya (BC, Nadia, Mohanpur, 741252, West Bengal, India

    Chittaranjan Kole

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Prasanna, B.M., Cairns, J., Xu, Y. (2013). Genomic Tools and Strategies for Breeding Climate Resilient Cereals. In: Kole, C. (eds) Genomics and Breeding for Climate-Resilient Crops. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37045-8_5

Download citation

Publish with us

Policies and ethics

Search

Navigation