Abstract
The current progress in crop research has provided a useful benchmark to evaluate crop-breeding improvement using genomics and molecular breeding techniques. The generation of huge amounts of molecular-genetic data has provided several ways to utilize the available genetic resources and to find solutions to the demanding goals of plant breeding. Rice being a staple food is consumed as an essential part of the dietary requirement by most of the developing countries. With the increase in population growth, traditional breeding methods cannot find a viable solution for sustainable crop production and food security. Since genetics and breeding are closely associated, combining these two has resulted in remarkable progress in rice-breeding programs. The presence of genetic diversity within cultivated crops and their wild relatives provides a platform for gene discovery of the agronomical important traits yet to be sufficiently discovered and utilized. This progress of developing new rice varieties with specific agronomic characters was made by using marker-assisted selection that opened new avenues for basic plant research. Combining conventional methods with molecular genetics will help in understanding the inheritance pattern of targeted traits in plant breeding and thus will lead to crop improvement in the future. This in turn can open new ways of improving the efficiency of breeding programs. Next-generation sequencing is the largest advancement and a boon for gene identification and variations in the genome. Recent techniques like CRISPR/Cas9 system are creating a major revolution in genome editing by adding or removing the genetic material at particular locations in the genome. Hence, molecular techniques are influencing the breeding process from selection to introgression of known genes/traits and thus sustaining the world’s food productivity.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abe A, Kosugi S, Yoshida K et al (2012) Genome sequencing reveals agronomically important loci in rice using Mut Map. Nat Biotech 30:174–178
Aljumaili SJ, Rafii MY, Latif MA et al (2018) Genetic diversity of aromatic rice germplasm revealed by SSR markers. Bio Med Res Int 2018:7658032
Anupam A, Imam J, Quatadah SM et al (2017) Genetic diversity analysis of rice germplasm in Tripura state of Northeast India using drought and blast linked markers. Rice Sci 24:10–20
Anuradha K, Agarwal S, Rao YV et al (2012) Mapping QTLs and candidate genes for iron and zinc concentrations in unpolished rice of Madhukar×Swarna RILs. Gene 508:233–240
Arora L, Narula A (2017) Gene editing and crop improvement using CRISPR-Cas9 system. Front Plant Sci 8:1932
Arunakumari K, Durgarani CV, Satturu V et al (2016) Marker-assisted pyramiding of genes conferring resistance against bacterial blight and blast diseases into Indian rice variety MTU1010. Rice Sci 23:306–316
Ashkani S, Rafii MY, Shabanimofrad M et al (2015) Allele mining strategies: principles and utilisation for blast resistance genes in rice (Oryza sativa L.). Curr Issues Mol Biol 17:57–74
Bennetzen JL, Ramakrishna W (2002) Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol Biol 48:821–827
Boonchuay P, Cakmak I, Rerkasem B, Prom-U-Thai C (2013) Effect of different foliar zinc application at different growth stages on seed zinc concentration and its impact on seedling vigor in rice. Soil Sci Plant Nutr 59:180–188
Bouis HE, Saltzman A (2017) Improving nutrition through biofortification: a review of evidence from Harvest Plus, 2003 through 2016. Glob Food Sec 12:49–58
Brara B, Jaina RK, Jain S (2015) Correlation of molecular marker allele size with physio-morphological and micronutrient (Zn, Fe) traits among rice genotypes. Int J Curr Sci 15:42–50
Brozynska M, Furtado A, Henry RJ (2015) Genomics of crop wild relatives: expanding the gene pool for crop improvement. Pl Biotech J 14:1070–1085
Burkart-Waco D, Tsai H, Ngo K et al (2017) Next-generation sequencing for targeted discovery of rare mutations in rice. In: Jankowicz-Cieslak J, Tai T, Kumlehn J, Till B (eds) Biotechnologies for plant mutation breeding. Springer, Cham, pp 323–340
Butardo VM, Fitzgerald MA, Bird AR et al (2011) Impact of down-regulation of starch branching enzyme IIb in rice by artificial micro RNA-and hairpin RNA-mediated RNA silencing. J Exp Bot 62:4927–4941
Butt H, Eid A, Ali Z et al (2017) Efficient CRISPR/Cas9-mediated genome editing using a chimeric single-guide RNA molecule. Front Plant Sci 8:1441
Cakmak I, Kalayci M, Ekiz H et al (1999) Zn deficiency as an actual problem in plant and human nutrition in Turkey: a NATO- Science for Stability Project. Field Crops Res 60:175–188
Cao P, Jung KH, Choi D et al (2012) The rice oligonucleotide array database: an atlas of rice gene expression. Rice 5:17
Chandel G, Samuel P, Dubey M, Meena R (2011) In silico expression analysis of QTL specific candidate genes for grain micronutrient (Fe/Zn) content using ESTs and MPSS signature analysis in rice (Oryza sativa L). J Plant Genet Transgen 2:11–22
Chang Y, Long T, Wu C (2012) Effort and contribution of T-DNA insertion mutant library for rice functional genomics research in China: review and perspective. J Integr Plant Biol 54:953–966
Cheema KK, Grewal NK, Vikal Y et al (2008) A novel bacterial blight resistance gene from Oryza nivara mapped to 38 kb region on chromosome 4L and transferred to Oryza sativa L. Genet Res 90:397–407
Chen S, Jin W, Wang M et al (2003) Distribution and characterization of over 1000 T-DNA tags in rice genome. Plant J 36:105–113
Chen L, Gao W, Chen S et al (2016) High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice. Rice 9:48
Cheng S, Hu P (2008) Development strategy of rice science and technology in China. Chin J Rice Sci 22:223–226
Cho HY, Park SJ, Kim DS, Jang CS (2010) A TILLING rice population induced by gamma-ray irradiation and its genetic diversity. Korean J Breed Sci 42:365–373
Collard BCY, Cruz CMV, McNally KL et al (2008) Rice molecular breeding laboratories in the genomics era: current statusand future considerations. Int J Plant Genom 2008:524847
Cooper JL, Henikoff S, Comai L, Till BJ (2013) TILLING and ecotilling for rice. Methods Mol Biol 956:39–56
Dash S, Van Hemert J, Hong L et al (2012) PLEXdb: gene expression resources for plants and plant pathogens. Nucl Acids Res 40:D1194–D1201
De Abreu Neto JB, Frei M (2016) Microarray meta-analysis focused on the response of genes involved in redox homeostasis to diverseabiotic stresses in rice. Front Pl Sci 6:1260
De Steur H, Mogendi JB, Blancquaert D et al (2014) Genetically modified rice with health benefits as a means to reduce micronutrient malnutrition. Global status, consumer preferences, and potential health impacts of rice biofortification. In: Watson RR, Preedy W, Zibadi S (eds) Wheat and rice in disease prevention and health. Academic, Cambridge, pp 283–299
Devos KM, Beales J, Nagamura Y, Sasaki T (1999) Arabidopsis-rice: will colinearity allow gene prediction across the eudicot-monocot divide? Genome Res 9:825–829
Dillon SL, Lawrence PK, Henry RJ et al (2007) Sorghum resolved as a distinct genus based on combined ITS1, ndhF and Adh1 analyses. Plant Syst Evol 268:29–43
Ding D, Chen K, Chen Y et al (2018) Engineering introns to express RNA guides for Cas9- and Cpf1-mediated multiplex genome editing. Mol Plant 11:542–552
Dodeweerd AMV, Hall CR, Bent EG et al (1999) Identification and analysis of homologous segments of the genomes of rice and Arabidopsis thaliana. Genome 42:887–892
Duan M, Sun Z, Shu L et al (2013) Genetic analysis of an elite super-hybrid rice parent using high-density SNP markers. Rice 6:21
Fazaa M, EL Sabagh A, Anis G et al (2016) The agronomical performances of doubled haploid lines of rice (Oryza sativa L.) derived from anther culture. J Agric Sci 8:177–183
Fekih R, Takagi H, Tamiru M et al (2013) MutMap+: genetic mapping and mutant identification without crossing in rice. PLoS One 8:e68529
Fiyaz RA, Yadav AK, Krishnan SG et al (2016) Mapping quantitative trait loci responsible for resistance to bakanae disease in rice. Rice 9:45
Fuchs EJ, Meneses MartĂnez A, Calvo A et al (2016) Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa. Peer J 7:e1875
Fukuoka S, Saka N, Mizukami Y et al (2015) Gene pyramiding enhances durable blast disease resistance in rice. Sci Rep 5:7773
Gande NK, Kundur PJ, Soman R et al (2014) Identification of putative candidate gene markers for grain zinc content using recombinant inbred lines (RIL) population of IRRI38 × Jeerigesanna. Afr J Biotech 13:657–663
Gichuhi E, Himi E, Takahashi H et al (2016) Identification of QTLs for yield-related traits in RILs derived from the cross between pLIA-1 carrying Oryza longistaminata chromosome segments and Norin 18 in rice. Breed Sci 66:720–733
Grewal D, Manitoa C, Bartolome V (2011) Doubled haploids generated through anther culture from crosses of elite indica and japonica cultivars and/or lines of rice: large-scale production, agronomic performance, and molecular characterization. Crop Sci 51:2544–2553
Gueye T, Ndir KN (2010) In vitro production of double haploid plants from two rice species (Oryza sativa L. and Oryza glaberrima Steudt.) for the rapid development of new breeding material. Sci Res Essays 57:709–713
Hamada K, Hongo K, Suwabe K et al (2011) OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. Plant Cell Phys 52:220–229
Hansen TH, Laursen KH, Persson DP et al (2009) Micro-scaled high-throughput digestion of plant tissue samples for multi-elemental analysis. Plant Methods 5:12
Hill CB, Li C (2016) Genetic architecture of flowering phenology in cereals and opportunities for crop improvement. Front Plant Sci 7:1906
Hiwasa-Tanase K, Ezura H (2016) Molecular breeding to create optimized crops: from genetic manipulation to potential applications in plant factories. Front Plant Science 7:539
Hu KM, Qiu DY, Shen XL et al (2008) Isolation and manipulation of quantitative trait loci for disease resistance in rice using a candidate gene approach. Mol Plant 1:786–793
Huang N, Angeles ER, Domingo J et al (1997) Pyramiding of bacterial blight resistance genes in rice: marker-assisted selection using RFLP and PCR. Theor Appl Genet 95:313–320
Huang XZ, Zeng XF, Zhao DG et al (2017) Construction and analysis of tify1a and tify1b mutants in rice (Oryza sativa) based on CRISPR/Cas9 technology. J Agric Biotech 25:1003–1012
Ikehashi H, Araki H (1986) Rice genetics. Genetics of F1sterility in remote crosses of rice. International Rice Research Institute, Manila, pp 119–130
Ishikawa R, Iwata M, Taniko K et al (2017) Detection of quantitative trait loci controlling grain zinc concentration using Australian wild rice, Oryza meridionalis, a potential genetic resource for biofortification of rice. PLoS One 12:e0187224. https://doi.org/10.1371/journal.pone.0187224
Jain M, Moharana KC, Shankar R et al (2014) Genome wide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance. Plant Biotech J 12:53–264
Jeong DH, An S, Kang HG et al (2002) T-DNA Insertional mutagenesis for activation tagging in rice. Plant Phys 130:1636–1644
Ji Z, Yang S, Zeng Y et al (2016) Pyramiding blast, bacterial blight and brown planthopper resistance genes in rice restorer lines. J Integr Agric 15:1432–1440
Jiang N, Bao Z, Zhang X et al (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431:569–573
Jiang W, Zhou H, Bi H et al (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucl Acids Res 41:e188
Jin X, Chen Y, Liu P et al (2018) Introgression from cultivated rice alters genetic structures of wild relative populations: implications for in situ conservation. AoB Plants 10:plx055
Johnson-Beebout SE, Lauren JG, Duxbury JM (2009) Immobilization of zinc fertilizer in flooded soils monitored by adapted DTPA soil test. Comm Soil Sci Plant Anal 40:1842–1861
Joshi RK, Nayak S (2010) Gene pyramiding-abroad spectrum technique for developing durable stress resistance in crops. Biotech Mol Biol Rev 5:51–60
Jung KH, Kim SR, Giong HK et al (2015) Genome-wide identification and functional analysis of genes expressed ubiquitously in rice. Mol Plant 8:276–289
Khanin P, Sunayana R, Verma H et al (2016) Microsatellite based association studies for grain mineral content in local winter (Sali) rice of Assam. Indian J Genet Pl Breed 76:356–360
Kharabian-Masouleh A, Daniel LE, Waters DLE et al (2011) Discovery of polymorphisms in starch-related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing. Plant Biotech J 2011:1074–1085
Krishnan A, Guiderdoni E, An G et al (2009) Mutant resources in rice for functional genomics of the grasses. Plant Phys 149:165–170
Lee TH, Kim YK, Pham TTM et al (2009) Rice Array Net: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice. Plant Phys 151:16–33
Li T, Liu B, Spalding MH et al (2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30:390–392
Li J, Pan Y, Guo H et al (2018a) Fine mapping of QTL qCTB10-2 that confers cold tolerance at the booting stage in rice. Theor Appl Genet 131:157–166
Li Y, Xiao J, Chen L et al (2018b) Rice functional genomics research: past decade and future. Mol Plant 11:359–380
Li Q, Zhang D, Chen M et al (2016) Development of japonica photo-sensitive genic male sterile rice lines by editing carbon starved anther using CRISPR/Cas9. J Genet Genom 43:415–419
Li W, Gill BS (2002) The colinearity of the Sh2/A1 orthologous region in rice, sorghum and maize is interrupted and accompanied by genome expansion in the triticeae. Genet 160:1153–1162
Liu H, Sachidanandam R, Stein L (2001) Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order. Genome Res 11:2020–2026
Liu GF, Yang J, Zhu J (2006) Mapping QTL for biomass yield and its components in rice (Oryza sativa L.). Acta Genet Sin 33:607–616
Ma L, Chen C, Liu X et al (2005) A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res 15:1274–1283
Ma X, Zhang Q, Zhu Q et al (2015) A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant 8:1274–1284
Mayer KFX, Martis M, Hedley PE et al (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23:1249–1263
McCouch SR, Doerge RW (1995) QTL mapping in rice. Trends Genet 11:482–487
Minkenberg B, Wheatley M, Yang Y (2017) CRISPR/Cas9-enabled multiplex genome editing and its application. Prog Mol Biol Transl Sci 149:111–132
Mochida K, Shinozaki K (2013) Unlocking Triticeae genomics to sustainably feed the future. Plant Cell Phys l54:1931–1950
Mohapatra T, Robin S, Sarla N et al (2014) EMS induced mutants of upland rice variety Nagina 22: generation and characterization. Proc Indian Nat Sci Acad 80:163–172
Morell MK, Kosar-Hashemi B, Cmiel M et al (2003) Barley sex 6 mutants lack starch synthase IIa activity and contain a starch with novel properties. Plant J 34:173–185
Nakandalage N, Nicolas M, Norton RM et al (2016) Improving rice zinc biofortification success rates through genetic and crop management approaches in a changing environment. Front Plant Sci 7:764
Nelson DR, Schuler MA, Paquette SM et al (2004) Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P 450 genes and pseudogenes from a monocot and a dicot. Plant Phys 135:756–772
Nguyen H, Chen XY, Jiang M et al (2016) Development and molecular characterization of a doubled haploid population derived from a hybrid between japonica rice and wide compatible indica rice. Breed Sci 66:552–559
Ning J, Zhang B, Wang N et al (2011) Increased leaf angle1, a Raf-like MAPKKK that interacts with a nuclear protein family, regulates mechanical tissue formation in the lamina joint of rice. Plant Cell 23:4334–4347
Pauk J, Jancsó M, Simon-Kiss I (2009) Rice doubled haploids and breeding. In: Touraev A, Forster BP, Jain SM (eds) Advances in haploid production in higher plants. Springer, Dordrecht, pp 189–197
Phillips J, MagosBrehm J, van Oort B et al (2017) Climate change and national crop wild relative conservation planning. Ambio 46:630–643
Pradhan SK, Nayak DK, Mohanty S et al (2015) Pyramiding of three bacterial blight resistance genes for broad-spectrum resistance in deepwater rice variety, Jalmagna. Rice 8:19
Proost S, Van Bel M, Sterck L et al (2009) PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell 21:3718–3731
Qiu B, Zeng F, Xue D et al (2011) QTL mapping for chromium-induced growth and zinc, and chromium distribution in seedlings of a rice DH population. Euphytica 181:429–439
Rathinasabapathi P, Purushothaman N, Ramprasad VL, Parani M (2015) Whole genome sequencing and analysis of Swarna, a widely cultivated indica rice variety with low glycemic index. Sci Rep 5:11303
Reiffers I, Freire AB (1990) Production of doubled haploid rice plants (Oryza sativa L.) by anther culture. Plant Cell Tissue Organ Cult 21:165–170
Reig-Valiente JL, Viruel J, Sales E et al (2016) Genetic diversity and population structure of rice varieties cultivated in temperate regions. Rice 9:58
Ryohei T, Akira A, Hiroki T et al (2015) Whole genome sequencing to identify genes and QTL in rice. In: Advances in the understanding of biological sciences using next generation sequencing (NGS) approaches. Springer, Heidelberg, pp 33–42
Sasaki T, Sederoff RR (2003) Genome studies and molecular genetics. Rice genome Comp genomics High Plant Curr Opin Plant Biol 6:97–100
Sato Y, Antonio BA, Namiki N et al (2011) Rice XPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions. Nucl Acids Res 39:D1141–D1148
Shimamoto K, Kyozuka J (2002) Rice as model for comparative genomics of plants. Ann Rev Plant Biol 53:399–419
Sikora P, Chawade A, Larsson M et al (2011) Mutagenesis as a tool in plant genetics, functional genomics, and breeding. Int J Plant Genomics 2011:314829
Singh N, Choudhury DR, Tiwar G et al (2016) Genetic diversity trend in Indian rice varieties: an analysis using SSR markers. BMC Genet 17:127
Singh A, Carandang J, Gonzaga ZJC et al (2017) Identification of QTLs for yield and agronomic traits in rice under stagnant flooding conditions. Rice 10:15
Solis J, Gutierrez A, Mangu V et al (2018) Genetic mapping of quantitative trait loci for grain yield under drought in rice under controlled greenhouse conditions. Front Chem. https://doi.org/10.3389/fchem.2017.00129
Sorrells ME, La Rota M, Bermudez-Kandianis CE et al (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818–1827
Spindel JE, Begum H, Akdemir D et al (2016) Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement. Hered 116:395–408
Sun H, Peng T, Zhao Y et al (2015) Dynamic analysis of gene expression in rice superior and inferior grains by RNA-Seq. PLoS One 10:e0137168
Sun Q, Zhou DX (2008) Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development. Proc Natl Acad Sci U S A 105:13679–13684
Sun Y, Jiao G, Liu Z et al (2017) Generation of high-amylose rice through CRISPR/Cas9-mediated targeted mutagenesis of starch branching enzymes. Front Plant Sci 8. https://doi.org/10.3389/fpls.2017.00298
Sun J, Yang L, Wang J et al (2018) Identification of a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy. Rice 11:24
Sun Y, Zhang X, Wu C et al (2016) Engineering herbicide-resistant rice plants through CRISPR/Cas9-mediated homologous recombination of acetolactate synthase. Mol Plant 9:628–631
Susanto U (2008) Mapping of quantitative trait loci for high iron and zinc content in polished rice (Oryza sativa L) grain and some agronomic traits using simple sequence repeats markers. Ph.D thesis, Bogor Agricultural University, Bogor
Swamy BPM, Rahman MA, Inabangan-Asilo MA et al (2016) Advances in breeding for high grain zinc in rice. Rice 9:49
Takagi H, Abe A, Yoshida K et al (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183
Thomas E, Tovar E, Villafane C et al (2017) Distribution, genetic diversity and potential spatiotemporal scale of alien gene flow in crop wild relatives of rice (Oryza spp.) in Colombia. Rice (NY) 10:13
Till BJ, Cooper J, Tai TH et al (2007) Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol 7:19
Toufighi K, Brady SM, Austin R et al (2005) The Botany Array Resource: e-northerns, expression angling, and promoter analyses. Plant J 43:153–163
Trijatmiko KR, Duenas C, Tsakirpaloglou N et al (2016) Biofortified indica rice attains iron and zinc nutrition dietary targets in the field. Sci Rep 6:19792
Umemoto T, Aoki N (2005) Single-nucleotide polymorphisms in rice starch synthase IIa that alter starch gelatinisation and starch association of the enzyme. Funct Plant Biol 32:763–768
Wang F, Wang C, Liu P et al (2016) Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PLoSONE 11:e0154027
Wang N, Long T, Yao W et al (2013) Mutant resources for the functional analysis of the rice genome. Mol Plant 6:596–604
Wang X, Wang J, Jin D et al (2015) Genome alignment spanning major Poaceae lineages reveals heterogeneous evolutionary. Mol Plant 8:885–898
Wang Z, Liang Y, Li C et al (2005) Microarray analysis of gene expression involved in anther development in rice (Oryza sativa L.). Plant Mol Biol 58:721–737
Wei L, Liu Y, Dubchak I et al (2002) Comparative genomics approaches to study organism similarities and differences. J Biomed Informat 35:142–150
White PJ, Martin R (2009) Biofortification of crops with seven mineral elements often lacking in human diets – iron, zinc, copper, calcium, magnesium, selenium and iodine. New Phytol 182:49–84
Wu C, You C, Li C et al (2008) RID1, encoding a Cys2/His2-type zinc finger transcription factor, acts as a master switch from vegetative to floral development in rice. Proc Natl Acad Sci U S A 105:12915–12920
Wunna WKN, Ohsawa R et al (2016) Genetic variation of rice (Oryza sativa L.) germplasm in Myanmar based on genomic compositions of DNA markers. Breed Sci 66:762–767
Xue LJ, Zhang JJ, Xue HW (2009) Characterization and expression profiles of miRNAs in rice seeds. Nucl Acids Res 37:916–930
Xu R, Qin R, Li H et al (2017) Generation of targeted mutant rice using a CRISPR-Cpf1 system. Plant Biotech J 15:713–717
Yan L, Loukoianov A, Tranquilli G et al (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci U S A 100:6263–6368
Yano M, Katayose Y, Ashikari M et al (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2483
Yao N, Lee CR, Semagn K et al (2016) QTL mapping in threerice populations uncovers major genomic regions associated with African rice gall midge resistance. PLoSONE 11:e0160749
Zaman QU, Aslam Z, Yaseen M et al (2018) Zinc biofortification in rice: leveraging agriculture to moderate hidden hunger in developing countries. Arch Agron Soil Sci 64:147–116
Zeng YX, Xia LZ, Wen ZH et al (2015) Mapping resistant QTLs for rice sheath blight disease with a doubled haploid population. J Integr Agric 14:801–810
Zhang H, Mittal N, Leamy LJ et al (2016) Back into the wild-apply untapped genetic diversity of wild relatives for crop improvement. Evol Appl 10:5–24
Zhang M, Pinson SRM, Tarpley L et al (2014) Mapping and validation of quantitative trait loci associated with concentration of 16 elements in unmilled rice grain. Theor Appl Genet 127:137–165
Zhou H, He M, Li J et al (2016) Development of commercial thermo-sensitive genic male sterile rice accelerates hybrid rice breeding using the CRISPR/Cas9-mediated TMS5 editing system. Sci Rep 6:37395
Zhou T, Gao C, Du L et al (2014) Genetic analysis and QTL detection for resistance to white tip disease in rice. PLoSONE 9:e106099
Zhu M, Liu D, Liu W et al (2017) QTL mapping using an ultra-high-density SNP map reveals a major locus for grain yield in an elite rice restorer R998. Sci Rep 7:10914
Acknowledgement
The authors are thankful to the School of Biotechnology, University of Jammu, Jammu, India.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Appendices
Appendices
8.1.1 Appendix I: Research Institutes Relevant to Rice Genetic Improvement
Country | Institution | Specialization and research activities | Contact information and website |
---|---|---|---|
Africa | Africa Rice Centre | Conserving rice genetic resources, rice breeding, rice processing | 01 BP 4029, Abidjan 01, Côte d’Ivoire Tel: +225 22 48 09 10 Email: AfricaRice@cgiar.org |
America | University of California | Breeding and genetics | G. S. Khush 39399 Blackhawk Place, Davis, CA 95616, USA Tel: (+1-530) 750-2440 Email: gurdev@khush.org |
Arizona | The Arizona Genomics Institute | Facilitate the high throughput movement of genomic resources | 1657 E Helen St,Tucson, AZ 85705, USA Phone: +1 520-626-9596 |
Brazil | Agronomic Institute of Paraná (IAPAR) | Improvement of agronomic traits | Lutécia Beatriz Canalli InstitutoAgronômico do Paraná – IAPAR Rodovia Celso Garcia Cid, km 375. Londrina-PR 86047-902, Brazil. Tel: (+55) 42 3219 9712 Email: lutecia@iapar.br |
China | China National Rice Research Institute | Identification of genetic resources, investigation of new genes, functional genomic research | 359 Tiyuchang Road, Hangzhou City, Zhejiang Province310006, P.R. China Tel: +86-571-63370212 Email: icoffice_cnrri@126.com |
Huazhong Agricultural University | Plant protection | Chao-Xi Luo Huazhong Agricultural University, College of Plant Science and Technology, Shizishan, Hongshan District, Wuhan City, Hubei Province, China 430070 Tel: (27)-87281242 Email: cxluo@mail.hzau.edu.cn | |
Germany | University of Freiburg | Coordinator of Golden Rice – Project | Peter Beyer Institute of Biology II (Cell Biology), Fahnenbergplatz, 79085 Freiburg im Breisgau, Germany Tel: +49 761 203 2529 Email: peter.beyer@biologie.uni-freiburg.de |
India | Indian Institute of Rice Research | Genetic diversity, better rice varieties | V. Ravindra Babu Rajendranagar, Hyderabad, Telangana 500030 Email: director.iirr@icar.gov.in Tel: +91-40-24591218; Fax: +91-40-24591217 |
National Research Centre on Plant Biotechnology | Genome sequencing and annotation of crop plants | N. K. Singh Indian Council of Agricultural Research, Pusa Road, New Delhi Tel: 011-25860186 Email: nksingh@nrcpb.org | |
Nigeria | National Cereals Research Institute | Yield enhancement and grain quality | DanbabaNahemiahBadeggi, Nigeria Tel: +234 806 931 4862 |
Philippines | The International Rice Research Institute | Plant breeder, Project leader for Green Super Rice | Jauhar Ali International Rice Research Institute, Los Baños, Laguna, Philippines Tel: +63 2 580 5600 ext 2541 Email:j.ali@irri.org |
Taiwan | Institute of Molecular Biology | Rice transformation | Su-May Yu Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan Tel: 886-2-2788-2695 Email: sumay@imb.sinica.edu.tw |
8.1.2 Appendix II: Rice Genetic Resources
Cultivation location | Cultivar | Important traits |
---|---|---|
Thailand | Dinalaga | Drought resistant |
Africa | IRAT106 | Drought resistant |
Australia | Doongara | High amylase content |
Kyeema | Long grain and fragrant | |
Bangladesh | IR64-Sub1 | Submerged |
BRRI dhan69 | Saline, irrigated | |
BRRI Dhan72 | High Zn content | |
Brazil | Tre Smeses | Drought resistant |
China | Yunlu 99 | Drought resistant |
Huhan3 | Drought resistant | |
Ghana | CRI-Emopa | – |
CRI Aunty Jane | – | |
India | Pusa Sugandh 2 | Lodging tolerance, resistant to BB |
Ambemohar | Fragrant variety | |
Pusa Sugandh 2 | Lodging and shattering tolerance | |
DRR-Dhan 45 | Drought resistant | |
Sampada | Low glycemic index | |
CR Dhan10 | Protein rich | |
Kenya | Komboka | – |
Nepal | Sookha dhan4 | Rainfed, drought |
Sookha dhan1 | Drought | |
Sookha dhan2 | Drought | |
Nigeria | IAC47 | Drought resistant |
Ofada | Highlyaromatic | |
Nigeria | UPIA1 | Irrigated, rainfed, tolerance to toxicity |
Philippines | NSIC Rc25 | Upland |
NSIC Rc352 | Irrigated, inbred | |
NSIC Rc390 | Saline | |
Thailand | Dinalaga | Drought resistant |
Tanzania | Tai | Rainfed, irrigated |
Uganda | Okile | – |
Vietnam | 08Fan10 | Rainfed, lowland |
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Mahajan, R., Kapoor, N. (2019). Molecular Breeding Strategies for Genetic Improvement in Rice (Oryza sativa L.). In: Al-Khayri, J., Jain, S., Johnson, D. (eds) Advances in Plant Breeding Strategies: Cereals. Springer, Cham. https://doi.org/10.1007/978-3-030-23108-8_8
Download citation
DOI: https://doi.org/10.1007/978-3-030-23108-8_8
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-23107-1
Online ISBN: 978-3-030-23108-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)