Skip to main content
SpringerLink
Log in

Emerging Concepts and Strategies for Genomics and Breeding

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

  • 1718 Accesses

Abstract

To feed the ever-increasing population on earth, production of food crops must increase at an unprecedented pace with limited inputs and little or no harm to the environment. The target is more challenging in the face of a changing climate scenario. The main focus should be on developing technologies and crop genotypes suitable for the input-poor and low-yielding areas that represent the lion’s share of the cultivable areas of the world. Plant breeding is evolving; more so with the advancement of molecular biological sciences. Emerging concepts of structural and functional genomics, transcriptomics, proteomics, and metabolomics approaches contribute towards identification of target genes and eQTL (expression-quantitative trait loci) for effective deployment. The genome editing technologies creating site-directed mutation can facilitate development of nontransgenic designer crop genotypes having wider adaptation. Plant breeding approaches should focus on the natural resources to identify and deploy useful gene(s)/alleles to develop genotypes with enhanced yield potential, better stress tolerance and, quality end products. Improvement in mapping efforts like genomic selection (GS), marker-assisted recurrent selection (MARS), and next-generation mapping, viz. NAM (nested association mapping), MAGIC (multiparent advanced generation intercross) would accelerate breeding progress with improved genotyping and phenotyping facilities. Plant biotechnology and genetic engineering techniques would continue to play a pivotal role in making a crop widely adaptable to the changed climate. Improving crop efficiencies in utilization of solar radiation, inorganic nitrogen, water and other inputs would render crops suitable for climate-resilient agriculture. Policies should be in place to make technologies accessible and affordable by all sections of users globally.

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

  • Allard RW (1960) Principles of plant breeding. Wiley, New York, NY

    Google Scholar 

  • Allard RW, Kahler AL, Weir BS (1972) The effect of selection on esterase allozymes in a barley population. Genetics 72:489–503

    PubMed  CAS  Google Scholar 

  • Ardlie K, Kruglyak L, Seielstad M (2002) Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 3:299–309

    Article  PubMed  CAS  Google Scholar 

  • Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T et al (2005) Cytokinin oxidase regulates rice grain production. Science 309:741–745

    Article  PubMed  CAS  Google Scholar 

  • Atwell S, Yu S, Huang, Bjarni J, Vilhjálmsson, Willems G et al (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:631–637

    Article  CAS  Google Scholar 

  • Backes G, Graner A, Foroughi-Wehr B, Fischbeck G, Wenzel G, Jahoor A (1995) Localization of quantitative trait loci (QTL) for agronomic important characters by the use of a RFLP map in barley (Hordeum vulgare L.). Theor Appl Genet 90:294–302

    Article  CAS  Google Scholar 

  • Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376

    Article  PubMed  CAS  Google Scholar 

  • Baldwin D, Crane V, Rice D (1999) A comparison of gel-based, nylon filter and microarray techniques to detect differential RNA expression in plants. Curr Opin Plant Biol 2:96–103

    Article  PubMed  CAS  Google Scholar 

  • Basten CJ, Weir BS, Zeng ZB (1994) QTL Cartographer. Department of Statistics, North Carolina State University, Raleigh, NC

    Google Scholar 

  • Baulcombe DC (1999) Fast forward genetics based on virus-induced gene silencing. Curr Opin Plant Biol 2:109–113

    Article  PubMed  CAS  Google Scholar 

  • Bernacchi D, Beck-Bunn T, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley S (1998) Advanced backcross QTL analysis in tomato. I. Identification of QTLs for traits of agronomic importance from Lycopersicon hirsutum. Theor Appl Genet 97:381–397

    Article  CAS  Google Scholar 

  • Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48:1649–1664

    Article  Google Scholar 

  • Bernardo R, Charcosset A (2006) Usefulness of gene information in marker-assisted recurrent selection: a simulation appraisal. Crop Sci 46:614–621

    Article  Google Scholar 

  • Bernier J, Kumar A, Serraj R, Spaner D, Atlin G (2008) Review: Breeding upland rice for drought resistance. J Sci Food Agric 88:927–939

    Article  CAS  Google Scholar 

  • Beumer KJ, Trautman JK, Bozas A, Liu JL, Rutter J, Gall JG, Carroll D (2008) Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases. Proc Natl Acad Sci USA 105:19821–19826

    Article  PubMed  CAS  Google Scholar 

  • Bhushan D, Pandey A, Choudhary MK, Datta A, Chakraborty S, Chakraborty N (2007) Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress. Mol Cell Proteomics 6:1868–1884

    Article  PubMed  CAS  Google Scholar 

  • Bibikova M, Carroll D, Segal DJ, Trautman JK, Smith J et al (2001) Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol 21:289–297

    Article  PubMed  CAS  Google Scholar 

  • Bibikova M, Golic M, Golic KG, Carroll D (2002) Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161:1169–1175

    PubMed  CAS  Google Scholar 

  • Bibikova M, Beumer K, Trautman JK, Carroll D (2003) Enhancing gene targeting with designed zinc finger nucleases. Science 300:764

    Article  PubMed  CAS  Google Scholar 

  • Bishop GJ, Harrison K, Jones JDG (1996) The tomato Dwarf gene isolated by heterologous transposon tagging encodes the first member of a new cytochrome P450 family. Plant Cell 8:959–969

    PubMed  CAS  Google Scholar 

  • Bogdanove AJ, Voytas DF (2011) TAS effectors: customizable proteins for DNA targeting. Science 333:1843–1846

    Article  PubMed  CAS  Google Scholar 

  • Bozas A, Beumer KJ, Trautman JK, Carroll D (2009) Genetic analysis of zinc-finger nuclease-induced gene targeting in Drosophila. Genetics 182:641–651

    Article  PubMed  CAS  Google Scholar 

  • Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH et al (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18:630–634

    Article  PubMed  CAS  Google Scholar 

  • Brent R (2000) Genomic biology. Cell 100:169–183

    Article  PubMed  CAS  Google Scholar 

  • Brown PJ, Upadyayula N, Mahone GS, Tian F, Bradbury PJ, et al (2011) Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genet 7:e1002383

    Google Scholar 

  • Buckler E (2007) TASSEL: Trait analysis by association, evolution, and linkage. User manual. http://www.maizegenetics.net/tassel

  • Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ et al (2009) The genetic architecture of maize flowering time. Science 325:714–718

    Article  PubMed  CAS  Google Scholar 

  • Burley SK, Almo SC, Bonanno JB, Capel M, Chance MR et al (1999) Structural genomics: beyond the Human Genome Project. Nat Genet 23:151–157

    Article  PubMed  CAS  Google Scholar 

  • Burton RA, Gibeaut DM, Bacic A, Findlay K, Roberts K et al (2000) Virus-induced silencing of a plant cellulose synthase gene. J Plant Cell 12:691–705

    CAS  Google Scholar 

  • Cai CQ, Doyon Y, Ainley WM, Miller JC, Dekelver RC et al (2009) Targeted transgene integration in plant cells using designed zing finger nucleases. Plant Mol Biol 69:699–709

    Article  PubMed  CAS  Google Scholar 

  • Casa AM, Mitchell SE, Hamblin MT, Sun H, Bowers JE et al (2005) Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats. Theor Appl Genet 111:23–30

    Article  PubMed  CAS  Google Scholar 

  • Cavanagh C, Morell M, Mackay I, Powell W (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr Opin Plant Biol 11:215–221

    Article  PubMed  CAS  Google Scholar 

  • Chain P, Kurtz S, Ohlebusch S, Slezak T (2003) An applications-focused review of comparative genomics tools: capabilities, limitations and future challenges. Brief Bioinform 4:106–123

    Article  Google Scholar 

  • Chang WW, Huang L, Shen M, Webster C, Burlingame AL, Roberts JK (2000) Patterns of protein synthesis and tolerance of anoxia in root tips of maize seedlings acclimated to a low-oxygen environment and identification of proteins by mass spectrometry. Plant Physiol 122:295–318

    Article  PubMed  CAS  Google Scholar 

  • Chapman MA, Pashley CH, Wenzler J, Hvala J, Tang S, Knapp SJ, Burke JM (2008) A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus). Plant Cell 20:2931–2945

    Article  PubMed  CAS  Google Scholar 

  • Christopher M, Mace E, Jordan D, Rodgers D, McGowan P et al (2007) Applications of pedigree-based genome mapping in wheat and barley breeding programs. Euphytica 154:307–316

    Article  Google Scholar 

  • Ciais P, Reichstein M, Viovy N, Granier A, Ogée J et al (2005) Europe-wide reduction in primary productivity caused by the heat and drought in 2003. Nature 437:529–533

    Article  PubMed  CAS  Google Scholar 

  • Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G et al (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317:338–342

    Article  PubMed  CAS  Google Scholar 

  • Clayton TA, Lindon JC, Cloarec O, Antti H, Charuel C et al (2006) Pharmaco-metabonomic phenotyping and personalized drug treatment. Nature 440:1073–1077

    Article  PubMed  CAS  Google Scholar 

  • Clegg MT, Allard RW, Kahler AL (1972) Is the gene the unit of selection? Evidence from two experimental plant populations. Proc Natl Acad Sci USA 69:2474–2478

    Article  PubMed  CAS  Google Scholar 

  • Corona G, Rizzolio F, Giordano A, Toffoli G (2012) Pharmaco-metabolomics: an emerging “Omics” tool for the personalization of anticancer treatments and identification of new valuable therapeutic targets. J Cell Phys 227:2827–2831. doi:10.1002/jcp. 24003

    Article  CAS  Google Scholar 

  • Crossa J, Burgueno J, Dreisigacker S, Vargas M et al (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177:1889–1913

    Article  PubMed  CAS  Google Scholar 

  • CSIRO (2011) A MAGIC approach to improve wheat quality. http://www.csiro.au/en/Organisation-Structure/Divisions/Plant-Industry/MAGIC_FFF_ResearchOverview.aspx

  • de Koning DJ, Haley CS (2005) Genetical genomics in humans and model organisms. Trends Genet 21:377–381

    Article  PubMed  CAS  Google Scholar 

  • Dixon J, Braun HJ, Kosina P, Couch J (eds) (2009) Wheat facts and futures. CIMMYT, Mexico DF

    Google Scholar 

  • Doyon Y, McCammon JM, Miller JC, Faraji F, Ngo C (2008) Heritable targeted gene disruption in zebra fish using designed zinc-finger nucleases. Nat Biotechnol 26:702–708

    Article  PubMed  CAS  Google Scholar 

  • Dressman D, Yan H, Traverso G, Kinzler KW, Vogelstein B (2003) Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci USA 100:8817–8822

    Article  PubMed  CAS  Google Scholar 

  • Earley EJ, Jones CD (2011) Next-generation mapping of complex traits with phenotype-based selection and introgression. Genetics 189:1203–1209

    Article  PubMed  CAS  Google Scholar 

  • Eathington SR, Crosbie TM, Edwards MD, Reiter RS, Bull JK (2007) Molecular markers in a commercial breeding program. Crop Sci 47(S3):S154–S163

    Google Scholar 

  • Edward M, Johnson L (1994) RFLPs for rapid recurrent selection. In: Analysis of molecular marker data. Joint plant breeding symposium series. Crop Science Society of America, Madison, WI, pp 33–40

    Google Scholar 

  • Ehrenreich IM, Torabi N, Jia Y, Kent J, Martis S et al (2010) Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature 464:1039–1042

    Article  PubMed  CAS  Google Scholar 

  • Eisen JA (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8:163–167

    PubMed  CAS  Google Scholar 

  • Ellis JG, Lawrence GJ, Luck JE, Dodds PN (1999) Identification of regions in alleles of the flax rust resistance gene L that determine differences in gene-for-gene specificity. Plant Cell 11:495–506

    PubMed  CAS  Google Scholar 

  • Eshed Y, 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

    PubMed  CAS  Google Scholar 

  • Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194

    PubMed  CAS  Google Scholar 

  • Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185

    PubMed  CAS  Google Scholar 

  • FAO (2011) Food and agriculture organization of the United Nations, State of food insecurity in the world 2010–2011. FAO, Rome

    Google Scholar 

  • FAOSTAT (2009) http://faostat.fao.org/default.aspx

  • Fedurco M, Romieu A, Williams S, Lawrence I, Turcatti G (2006) BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res 34:e22

    Article  PubMed  CAS  Google Scholar 

  • Fehr WR (1984) Genetic contributions to yield gains of five major crop plants (Spl Pub No 7). Crop Science Society of America, Madison, WI

    Google Scholar 

  • Fiehn O, Kloska K, Altmann T (2001) Integrated studies on plant biology using multiparallel techniques. Curr Opin Biotechnol 12:82–86

    Article  PubMed  CAS  Google Scholar 

  • Fisher RA, Edmeades GD (2010) Breeding and cereal yield progress. Crop Sci 50:585–598

    Google Scholar 

  • Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374

    Article  PubMed  CAS  Google Scholar 

  • Foley JE, Yeh JR, Maeder ML, Reyon D, Sander JD, Peterson RT, Joung JK (2009) Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by Oligomerized Pool ENgineering (OPEN). PLoS One 4:e4348

    Article  PubMed  CAS  Google Scholar 

  • Gale MD, Devos KM (1998) Plant comparative genetics after 10 years. Science 282:656–658

    Article  PubMed  CAS  Google Scholar 

  • Geurts AM, Cost GJ, Freyvert Y, Zeitler B, Miller JC et al (2009) Knock out rats via embryo microinjection of zinc-finger nucleases. Science 325:433–435

    Article  PubMed  CAS  Google Scholar 

  • Giles J (2007) Key biology databases go wiki. Nature 445:691

    Article  PubMed  CAS  Google Scholar 

  • Godfray HCJ, Beddington JR, Crute IR, Haddad L, Lawrence D et al (2010) Food security: the challenge of feeding 9 billion people. Science 327:812–818

    Article  PubMed  CAS  Google Scholar 

  • Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ et al (2010) Distinct factors controls histone variant H3.3 localization at specific genomic regions. Cell 140:678–691

    Article  PubMed  CAS  Google Scholar 

  • González-Martínez SC, Wheeler NC, Ersoz E, Nelson CD, Neale DB (2007) Association genetics in Pinus taeda L. I. wood property traits. Genetics 175:399–409

    Article  PubMed  Google Scholar 

  • Grandillo S, Tanksley SD (2003) Advanced backcross QTL analysis: results and perspectives. In: Tuberosa R, Phillips RL, Gale M (eds) Proceedings of the international congress on in the wake of the double helix: from the green revolution to the gene revolution, 27–31 May 2003, Bologna, Italy. Avenue Media, Italy, pp 115–132

    Google Scholar 

  • Grant MR, McDowell JM, Sharpe AG, de Torres Zabala M, Lydiate DJ, Dangl JL (1998) Independent deletions of a pathogen-resistance gene in Brassica and Arabidopsis. Proc Natl Acad Sci USA 95:15843–15848

    Article  PubMed  CAS  Google Scholar 

  • Grossman A, Takahashi H (2001) Macronutrient utilization by photosynthetic eukaryotes and the fabric of interactions. Annu Rev Plant Physiol Plant Mol Biol 52:163–210

    Article  PubMed  CAS  Google Scholar 

  • Gur A, Zamir D (2004) Unused natural variation can lift yield barriers in plant breeding. PLoS Biol 2:e245

    Article  PubMed  CAS  Google Scholar 

  • Hajjar R, Hodgkin T (2007) The use of wild relatives in crop improvement: a survey of development over the last 20 years. Euphytica 156:1–13

    Article  Google Scholar 

  • Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315–324

    Article  PubMed  CAS  Google Scholar 

  • Hamblin MT, Buckler ES, Jannink JL (2011) Population genetics of genomics-based crop improvement methods. Trends Genet 27:98–106

    Article  PubMed  CAS  Google Scholar 

  • Harlan HV, Martini ML (1929) A composite hybrid mixture. J Am Soc Agron 487–490

    Google Scholar 

  • Hedrick PW (1987) Gametic disequilibrium: proceed with caution. Genetics 117:331–341

    PubMed  CAS  Google Scholar 

  • Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231

    Article  Google Scholar 

  • Holte S, Quiaoit F, Hsu L, Davidov O, Zhao LP (1997) A population based family study of a common oligogenic disease. Part I: Association/aggregation analysis. Genet Epidemiol 14:803–807

    Article  PubMed  CAS  Google Scholar 

  • Horst I, Welham T, Kelly S, Kaneko T, Sato S, Tabata S, Parniske M, Wang TL (2007) TILLING mutants of Lotus japonicus reveal that nitrogen assimilation and fixation can occur in the absence of nodule-enhanced sucrose synthase. Plant Physiol 144:806–820

    Article  PubMed  CAS  Google Scholar 

  • Hospital F, Moreau L, Lacoudre F, Charcosset A, Gallais A (1997) More on the efficiency of marker-assisted selection. Theor Appl Genet 95:1181–1189

    Article  Google Scholar 

  • Howes NK, Woods SM, Towley Smith TF (1998) Simulations and practical problems of applying multiple marker assisted selection and doubled haploids to wheat breeding programs. Euphytica 100:225–230

    Article  Google Scholar 

  • Huang X, Feng Q, Qian Q, Zhao Q, Wang L et al (2009) High throughput genotyping by whole-genotyping resequencing. Genome Res 19:1068–1076

    Article  PubMed  CAS  Google Scholar 

  • Huang X, Sang T, Zhao Q, Wei X, Feng Q et al (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967

    Article  PubMed  CAS  Google Scholar 

  • Hunkapiller T, Kaiser RJ, Koop BF, Hood L (1991) Large-scale and automated DNA sequence determination. Science 254:59–67

    Article  PubMed  CAS  Google Scholar 

  • Issaq HJ, Conrads TP, Janini GM, Veenstra TD (2002) Methods for fractionation, separation and profiling of proteins and peptides. Electrophoresis 23:3048–3061

    Article  PubMed  CAS  Google Scholar 

  • Jackson SP, Bartek J (2009) The DNA-damage response in human biology and disease. Nature 461:1071–1078

    Article  PubMed  CAS  Google Scholar 

  • Jansen RC, Nap JP (2001) Genetical genomics: the added value from segregation. Trends Genet 17:388–391

    Article  PubMed  CAS  Google Scholar 

  • Johal GS, Briggs SP (1992) Reductase activity encoded by the HM1disease resistance gene in maize. Science 258:985–987

    Article  PubMed  CAS  Google Scholar 

  • Johal GS, Balint-Kurti P, Weil CF (2008) Mining and harnessing natural variation: a little MAGIC. Crop Sci 48:2066–2073

    Article  Google Scholar 

  • Johnson R (2004) Marker-assisted selection. Plant Breed Rev 24:293–309

    Google Scholar 

  • Karayiorgou M, Sobin C, Blundell ML, Galke BL, Malinova L, Goldberg P, Ott J, Gogos JA (1999) Family-based association studies support a sexually dimorphic effect of COMT and MAOA on genetic susceptibility to obsessive-compulsive disorder: extending the transmission disequilibrium test (TDT) to examine genetic heterogeneity. Biol Psychiatry 45:1178–1189

    Article  PubMed  CAS  Google Scholar 

  • Kazuki S (2006) Gene identification through metabolomics in plants. Cell Technol 25:1399–1403

    Google Scholar 

  • Kearsey MJ, Hyne V (1994) QTL analysis: a simple ‘marker regression’ approach. Theor Appl Genet 89:698–702

    Article  Google Scholar 

  • Keurentjes JJ, Angenent GC, Dicke M, Dos Santos VA, Molenaar J et al (2011) Redefining plant systems biology: from cell to ecosystem. Trends Plant Sci 6:183–190

    Article  CAS  Google Scholar 

  • Kim YG, Cha J, Chandrasegaran S (1996) Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci USA 93(1156):1160

    Google Scholar 

  • Kosina P, Reynolds MP, Dixon J, Joshi AK (2007) Stakeholder perception of wheat production constraints, capacity building needs, and research partnerships in developing countries. Euphytica 157:475–483

    Article  Google Scholar 

  • Koumproglou R, Wilkes TM, Towson P, Wang XY, Beyon J et al (2002) STAIS: a new genetic resource for functional genomics studies of Arabidopsis. Plant J 31:355–364

    Article  PubMed  CAS  Google Scholar 

  • Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, et al (2009) A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5:e1000551

    Google Scholar 

  • Kraakman ATW, Niks RE, Van den Berg PM, Stam P, Van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivar. Genetics 168:435

    Article  PubMed  CAS  Google Scholar 

  • Krysan PJ, Young JC, Tax F, Sussman MR (1996) Identification of transferred DNA insertions within Arabidopsis genes involved in signal transduction and ion transport. Proc Natl Acad Sci USA 93:8145–8150

    Article  PubMed  CAS  Google Scholar 

  • Kumagi MH, Donson J, Della-Cioppa G, Harvey D, Hanley K, Grill LK (1995) Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proc Natl Acad Sci USA 92:1679–1683

    Article  Google Scholar 

  • Kumar GR, Sakthivel K, Sundaram RM, Neeraja CN, Balachandran SM et al (2010) Allele mining in crops: prospects and potentials. Biotechnol Adv 28:451–461

    Article  PubMed  CAS  Google Scholar 

  • Kump KL, Bradbury PJ, Buckler ES, Belcher AR, Oropeza-Rosas M et al (2010) Genome-wide association study of quantitative resistance to Southern leaf blight in the maize nested association mapping population. Nat Genet 43:163–168

    Article  CAS  Google Scholar 

  • Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756

    PubMed  CAS  Google Scholar 

  • Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199

    PubMed  CAS  Google Scholar 

  • Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C et al (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci USA 94:13057–13062

    Article  PubMed  CAS  Google Scholar 

  • Latha R, Rubia L, Bennett J, Swaminathan MS (2004) Allele mining for stress tolerance genes in Oryza species and related germplasm. Mol Biotechnol 27:101–108

    Article  PubMed  CAS  Google Scholar 

  • Lewontin RC (1964) The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49:49–67

    PubMed  CAS  Google Scholar 

  • Lieber MR (2010) The mechanism of double-strand DNA break repair by the non-homologous DNA end-joining pathway. Annu Rev Biochem 79:181–211

    Article  PubMed  CAS  Google Scholar 

  • Liester D, Kurth J, Laurie DA, Yano M, Sasaki T, Graner A, Schulz-Lefert P (1998) Rapid reorganization of resistance gene homologues in cereal genomes. Proc Natl Acad Sci USA 95:370–375

    Article  Google Scholar 

  • Lincoln SE, Daly MJ, Lander ES (1993) Mapping genes controlling quantitative traits using MAPMAKET/QTL version 1.1: a tutorial and reference manual. Whitehead Institute, Cambridge, MA

    Google Scholar 

  • Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Harvey Millar A, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Louder O, Chaillou S, Camilleri C, Bouchez D, Daniel-Vedele F (2002) Bay-0x Shahdara recombinant inbred line population: a powerful tool for the genetic dissection of complex traits in Arabidopsis. Theor Appl Genet 104:1173–1184

    Article  CAS  Google Scholar 

  • Macdonald SJ, Long AD (2007) Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics 176:1261–1281

    Article  PubMed  CAS  Google Scholar 

  • Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM et al (2008) Rapid ‘open-source’ engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31:294–301

    Article  PubMed  CAS  Google Scholar 

  • Marteinssen RA (1998) Functional genomics: probing plant gene function and expression with transposons. Proc Natl Acad Sci USA 95:2021–2026

    Article  Google Scholar 

  • Maxted N, Scholten MA, Codd R, Ford-Lloyd BV (2007) Creation and use of a national inventory of crop wild relatives. Biol Conserv 140:142–159

    Article  Google Scholar 

  • Mayer JE, Pfeiffer WH, Beyer P (2008) Biofortified crops to alleviate micronutrient malnutrition. Curr Opin Plant Biol 11:166

    Article  PubMed  CAS  Google Scholar 

  • McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeted screening for induced mutations. Nat Biotechnol 18:455–457

    Article  PubMed  CAS  Google Scholar 

  • Meng X, Noyes MB, Zhu LJ, Lawson ND, Wolfe SA (2008) Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat Biotechnol 26:695–701

    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 

  • Meyer RC, Steinfath M, Lisec J, Becher M, Witucka-Wall H et al (2007) The metabolic signature related to high plant growth rate in Arabidopsis thaliana. Proc Natl Acad Sci USA 104:4759–4764

    Article  PubMed  CAS  Google Scholar 

  • Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW et al (1999) Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding super-family. Plant J 20:317–332

    Article  PubMed  CAS  Google Scholar 

  • Michelmore R (2000) Genomic approaches to plant disease resistance. Curr Opin Plant Biol 3:126–131

    Article  Google Scholar 

  • Mitra RD, Church GM (1999) In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res 27:e34

    Article  PubMed  CAS  Google Scholar 

  • Mitra RD, Shendure J, Olejnik J, Edyta Krzymanska O, Church GM (2003) Fluorescent in situ sequencing on polymerase colonies. Anal Biochem 320:55–65

    Article  PubMed  CAS  Google Scholar 

  • Mizoi J, Nakamura M, Nishida I (2006) Defects in CTP: phosphorylethanolamine cytidyl transferase affect embryonic and postembryonic development in Arabidopsis. Plant Cell 18:3370–3385

    Article  PubMed  CAS  Google Scholar 

  • Moehle EA, Rock JM, Lee YL, Jouvenot Y, DeKelver RC et al (2007) Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases. Proc Natl Acad Sci USA 104:3055–3060

    Article  PubMed  CAS  Google Scholar 

  • Moller IS, Gilliham M, Jha D, Mayo GM, Roy SJ et al (2009) Shoot Na+ exclusion and increased salinity tolerance engineered by cell type-specific alteration of NA+ transport in Arabidopsis. Plant Cell 21:2163–2178

    Article  PubMed  CAS  Google Scholar 

  • Morbitzer R, Romer P, Boch J, Lahaye T (2010) Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors. Proc Natl Acad Sci USA 107:21617–21622

    Article  PubMed  CAS  Google Scholar 

  • Morrell PL, Buckler ES, Ross-Ibarra J (2012) Crop genomics: advances and applications. Nat Rev Genet 12:85–96

    Google Scholar 

  • Moynahan ME, Jasin M (2010) Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis. Nat Rev Mol Cell Biol 11:196–207

    Article  PubMed  CAS  Google Scholar 

  • Myles S, Peiffera J, Browna PJ, Ersoza ES, Zhang ZW, Costicha DE, Buckler ES (2009) Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21:2194–2202

    Article  PubMed  CAS  Google Scholar 

  • Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–1349

    Article  PubMed  CAS  Google Scholar 

  • Nelson JC (1997) QGENE: Software for marker-based genomic analysis and breeding. Mol Breed 3:239–245

    Article  CAS  Google Scholar 

  • Nelson DE, Repetti PP, Adams TR, Creelman RA, Wu JR et al (2007) Plant nuclear factor Y (NF-Y) B sub-units confer drought tolerance and lead to improved corn yields on water-limited acres. Proc Natl Acad Sci USA 104:16450

    Article  PubMed  CAS  Google Scholar 

  • Nordborg M, Tavare S (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18:83–90

    Article  PubMed  CAS  Google Scholar 

  • Oliver SG, Winson MK, Kell DB, Baganz R (1998) Systematic functional analysis of the yeast genome. Trends Biotechnol 16:373–378

    Article  PubMed  CAS  Google Scholar 

  • Ortiz R, Sayre K, Govaerts B, Gupta R, Subbarao G et al (2008) Climate change: can wheat beat the heat? Agric Ecosyst Environ 126:46–58

    Article  Google Scholar 

  • Pan Q, Wendel J, Fluhr R (2000) Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. J Mol Evol 50:203–213

    PubMed  CAS  Google Scholar 

  • Pandey A, Chakraborty S, Datta A, Chakraborty N (2008) Proteomics approach to identify dehydration responsive nuclear proteins from chickpea (Cicer arietinum L.). Mol Cell Proteomics 7:88–107

    PubMed  CAS  Google Scholar 

  • Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:548–551

    Article  CAS  Google Scholar 

  • Paul Voosen (2009) Molecular breeding makes crops hardier and more nutritious. Scientific American. http://www.scientificamerican.com/article.cfm?id=molecular-breeding-crops-genetics-rice-soy-corn-wheat

  • Peltonen-Sainio P, Jauhiainen L, Trnka M, Olesen JE, Calanca P et al (2010) Coincidence of variation in yield and climate in Europe. Agric Ecosyst Environ 139:482–489

    Article  Google Scholar 

  • Prada D (2009) Molecular population genetics and agronomic alleles in seed banks: searching for a needle in a haystack? J Exp Bot 60:2541–2552

    Article  PubMed  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping structured populations. Am J Hum Genet 67:170–181

    Article  PubMed  CAS  Google Scholar 

  • Quarrie SA, Gulli M, Calestani C, Steed A, Marmiroli N (1994) Location of a gene regulating drought-induced abscisic acid production on the long arm of chromosome 5A of wheat. Theor Appl Genet 89:794–800

    Article  CAS  Google Scholar 

  • Rangan L, Constantino S, Khush GS, Swaminathan MS, Bennett J (1999) The feasibility of PCR-based allele mining for stress tolerance genes in rice and related germplasm. Rice Genet Newsl 16:43–47

    Google Scholar 

  • Ratcliff F, Martin-Hernandez AM, Baulcombe DC (2001) Technical Advance. Tobacco rattle virus as a vector for analysis of gene function by silencing. Plant J 25:237–245

    Article  PubMed  CAS  Google Scholar 

  • Ravi K, Vadez V, Isobe S, Mir RR, Guo Y et al (2011) Identification of several small-effect main QTL and large number of epistatic QTLs for drought tolerance in groundnut (Arachis hypogaea L.). Theor Appl Genet 122:1119–1132

    Article  PubMed  CAS  Google Scholar 

  • Reynolds M, Bonnett D, Chapman Scott C, Furbank Rober T, Manès Y et al (2011) Raising yield potential of wheat. I. Overview of a consortium approach and breeding strategies. J Exp Bot 62(2):439–452

    Article  PubMed  CAS  Google Scholar 

  • Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516–1517

    Article  PubMed  CAS  Google Scholar 

  • Rivkin MI, Vallejos CE, McClean PE (1999) Disease-resistance related sequences in common bean. Genome 42:41–47

    Article  PubMed  CAS  Google Scholar 

  • Rockman MV, Kruglyak L (2008) Breeding designs for recombinant inbred advanced intercross lines. Genetics 179:1069–1078

    Article  PubMed  Google Scholar 

  • Roessner U, Beckles DM (2009) Metabolite measurements. In:Junker B, Schwender J (eds) Plant metabolic networks. Springer, Heidelberg, pp 39–69

    Google Scholar 

  • Saghatelian A, Tauger SA, Want EJ, Hawkins EG, Siuzdak G, Cravatt BF (2004) Assignment of endogenous substrates to enzymes by global metabolite. Biochemistry 16:14332–14339

    Article  CAS  Google Scholar 

  • Sanchez AC, Subudhi PK, Rosenow DT, Nguyen HT (2002) Mapping QTLs associated with drought resistance in sorghum (Sorghum bicolor L. Moench). Plant Mol Biol 48:713–726

    Article  PubMed  CAS  Google Scholar 

  • Sanger F, Nicklen S, Coulson R (1977) DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467

    Article  PubMed  CAS  Google Scholar 

  • Santiago Y, Chan E, Liu PQ, Orlando S, Zhang L et al (2008) Targeted gene knockout in mammalian cells using engineered zinc finger nucleases. Proc Natl Acad Sci USA 105:5809–5814

    Article  PubMed  CAS  Google Scholar 

  • Saranga Y, Menz M, Jiang CX, Wright RJ, Yakir D, Paterson AH (2001) Genomic dissection of genotype × environment interactions conferring adaptation of cotton to arid conditions. Genome Res 11:1988–1995

    Article  PubMed  CAS  Google Scholar 

  • Sari-Gorla M, Krajewski P, Di Fonzo N, Villa M, Frova C (1999) Genetic analysis of drought tolerance in maize by molecular markers. II. Plant height and flowering. Theor Appl Genet 99:289–295

    Article  Google Scholar 

  • Sax K (1923) The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8:552–560

    PubMed  CAS  Google Scholar 

  • Scarcelli N, Cheverud JM, Schaal BA, Kover PX (2007) Antagonistic pleiotropic effects reduce the potential adaptive value of the FRIGIDA locus. Proc Natl Acad Sci USA 104:16986–16991

    Article  PubMed  CAS  Google Scholar 

  • Schauer N, Semel Y, Roessner U, Gur A, Balbo I et al (2006) Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol 24:447–454

    Article  PubMed  CAS  Google Scholar 

  • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Shendure J, Porreca GJ, Reppas NB, Lin XX, McCutcheon JP et al (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728–1732

    Article  PubMed  CAS  Google Scholar 

  • Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA et al (2009) Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459:437–441

    Article  PubMed  CAS  Google Scholar 

  • Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti D (2005) A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 23:75–81

    Article  PubMed  CAS  Google Scholar 

  • Stahl EA, Dwyer G, Mauricio R, Kreitman M, Bergelson J (1999) Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis. Nature 400:667–671

    Article  PubMed  CAS  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744

    Article  CAS  Google Scholar 

  • Suneson CA (1956) An evolutionary plant breeding method. Agron J 48:188–191

    Article  Google Scholar 

  • Talukdar A, Zhang GQ (2007) Construction and characterization of 3-S Lines, an alternative population for mapping studies in rice. Euphytica 156:237–246

    Article  CAS  Google Scholar 

  • Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:418–423

    Article  Google Scholar 

  • Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from un-adapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203

    Article  Google Scholar 

  • Taylor J, King RD, Altmann T, Fiehn O (2002) Application of metabolomics to plant genotype discrimination using statistics and machine learning. Bioinformatics 18:241–248

    Article  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 

  • Teulat B, Monneveux P, Wery J, Borriès C, Souyris I, Charrier A, This D (1997) Relationships between relative water content and growth parameters in barley: a QTL study. New Phytol 137:99–107

    Article  Google Scholar 

  • Tian F, Bradbury PJ, Brown PJ, Hung H et al (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 

  • Till BJ, Reynolds SH, Weil C, Springer N, Burtner C et al (2004) Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 4:12

    Article  PubMed  CAS  Google Scholar 

  • Townsend JA, Wright DA, Winfrey RJ, Fu FL, Maeder ML, Joung JK, Voytas DF (2009) High frequency modification of plant genes using engineered zinc-finger nucleases. Nature 459:442–445

    Article  PubMed  CAS  Google Scholar 

  • Tsiridis E, Giannoudis PV (2006) Transcriptomics and proteomics: advancing the understanding of genetic basis of fracture healing. Injury 37S:S13–S19

    Article  Google Scholar 

  • Tsugita A, Kamo M, Kawakami T, Ohki Y (1996) Two-dimensional electrophoresis of plant proteins and standardization of gel patterns. Electrophoresis 17:855–865

    Article  PubMed  CAS  Google Scholar 

  • Turcatti G, Romieu A, Fedurco M, Tairi AP (2008) A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res 36:e25

    Article  PubMed  CAS  Google Scholar 

  • Ungerer MC, Halldorsdottir SS, Modiszewski JL, Mackay TFC, Purugganan M (2002) Quantitative trait loci for inflorescence development in Arabidopsis thaliana. Genetics 160:1133–1151

    PubMed  CAS  Google Scholar 

  • Urnov FD, Miller JC, Lee YL, Beausejour CM, Rock JM et al (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435:646–651

    Article  PubMed  CAS  Google Scholar 

  • Utz HF, Melchinger AE (1996) PLABQTL: a program for composite interval mapping of QTL. J Quant Trait Loci 2:1–5

    Google Scholar 

  • Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L et al (2002) Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci USA 99:9650–9655

    Article  PubMed  CAS  Google Scholar 

  • Villas-Bôas SG, Roessner U, Hansen M, Smedsgaard J, Nielsen J (2007) Metabolome analysis: an introduction. Wiley, Hoboken, NJ

    Book  Google Scholar 

  • Wang H, Hanash S (2003) Multi-dimensional liquid phase based separations in proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 787:11–18

    Article  PubMed  CAS  Google Scholar 

  • Wang XY, Wan JM, Su CC, Wang CM, Shen WB et al (2004) QTL detection for eating quality of cooked rice in a population of chromosome segment substitution lines. Theor Appl Genet 110:71–79

    Article  PubMed  CAS  Google Scholar 

  • Wang J, Chapman SC, Bonnett DG, Rebetzke GJ, Crouch J (2007) Application of population genetic theory and simulation models to efficiently pyramid multiple genes via marker-assisted selection. Crop Sci 47:582–588

    Article  Google Scholar 

  • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63

    Article  PubMed  CAS  Google Scholar 

  • Wang J, Roe B, Macmil S, Yu Q, Murray JE et al (2010) Micro-collinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics 11:261

    Article  PubMed  CAS  Google Scholar 

  • Weinstein JN (1998) Fishing expeditions. Science 282:628–629

    Article  PubMed  CAS  Google Scholar 

  • Weinthal D, Tovkach A, Zeevi V, Tzfira T (2010) Genome editing in plant cells by zinc finger nucleases. Trands Plant Sci 15:308–321

    Article  CAS  Google Scholar 

  • Whitham S, Dinesh-Kumar SP, Choi D, Hehl R, Corr C, Baker B (1994) The product of the tobacco mosaic virus resistance gene N: similarity to toll and the interleukin-1 receptor. Cell 78:1101–1115

    Article  PubMed  CAS  Google Scholar 

  • Whittaker JC, Thompson R, Visscher PM (1996) On the mapping of QTL by regression of phenotypes on marker type. Heredity 77:23–32

    Article  Google Scholar 

  • Wilkins MR, Ou K, Appel RD, Sanchez JC et al (1996) Rapid protein identification using N-terminal “sequence tag” and amino acid analysis. Biochem Biophys Res Commun 221(3):609–613

    Article  PubMed  CAS  Google Scholar 

  • Wilson IW, Schiff CL, Hughes DE, Somerville SC (2001) Quantitative trait loci analysis of powdery mildew disease resistance in the Arabidopsis thaliana accession Kashmir-1. Genetics 158:1301–1309

    PubMed  CAS  Google Scholar 

  • Winkler RG, Frank MR, Galbraith DW, Feyereisen R, Feldmann KA (1998) Systematic reverse genetics of transfer-DNA-tagged lines of Arabidopsis. Isolation of mutations in the cytochrome P450 gene super family. Plant Physiol 118:743–750

    Article  PubMed  CAS  Google Scholar 

  • Wong CK, Bernardo R (2008) Genomewide selection in oil palm: increasing selection gain per unit time and cost with small populations. Theor Appl Genet 116:815

    Article  PubMed  CAS  Google Scholar 

  • Wood AJ, Te-Wen L, Bryan Z, Catherine SP, Edward JR et al (2011) Targeted genome editing across species using ZFNs and TALENs. Science 333:307

    Article  PubMed  CAS  Google Scholar 

  • Wright AJ, Mowers RP (1994) Multiple regression for molecular-marker, quantitative trait data from large F2 populations. Theor Appl Genet 89:305–312

    Google Scholar 

  • Xiao J, Li J, Yuan L, Tanksley SD (1996) Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a sub-specific rice cross. Theor Appl Genet 92:230–244

    Article  CAS  Google Scholar 

  • Yadav RS, Sehgal D, Vadez V (2011) Using genetic mapping and genomics approaches in understanding and improving drought tolerance in pearl millet. J Exp Bot 62:397–408

    Article  PubMed  CAS  Google Scholar 

  • Yamasaki M, Tenaillon MI, Vroh Bi I, Schroeder SG, Sanchez-Villeda H et al (2005) A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell 17:2859–2872

    Article  PubMed  CAS  Google Scholar 

  • Yan YP, Moult J (2005) Protein family clustering for structural genomics. J Mol Biol 353:744–759

    Article  PubMed  CAS  Google Scholar 

  • Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160

    Article  PubMed  CAS  Google Scholar 

  • Yu J, Pressoir G, Briggs WH, Vroh BI, Yamasaki M et al (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208

    Article  PubMed  CAS  Google Scholar 

  • Yu JM, Holland 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 

  • Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468

    PubMed  CAS  Google Scholar 

  • Zhu CS, Gore M, Buckler ES, Yu JM (2007) Status and prospects of association mapping in plants. Plant Genome 1:5–20

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India

    Akshay Talukdar

  2. Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, 785013, Assam, India

    Pranab Talukdar

Authors
  1. Akshay Talukdar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pranab Talukdar
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Akshay Talukdar .

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

Talukdar, A., Talukdar, P. (2013). Emerging Concepts and Strategies for Genomics and Breeding. In: Kole, C. (eds) Genomics and Breeding for Climate-Resilient Crops. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37045-8_6

Download citation

Publish with us

Policies and ethics

Search

Navigation