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Genetic Enhancement of Nutritional Traits in Rice Grains Through Marker-Assisted Selection and Quantitative Trait Loci

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Rice Research for Quality Improvement: Genomics and Genetic Engineering

Abstract

Rice is a basic staple food of most countries including developed and less developed nations, and more importantly, 90% of population relies on rice across South Asian countries. Global climate change, increased urbanization, drought, and desertification have resulted in the significant drop in the rice production and also prompted researchers to develop novel varieties with increased productivity. Hence, novel varieties with enriched nutritional composition may offer wide benefits and could be a potential step in eradicating malnutrition among the less developed nations. According to the “International Rice Research Institute (IRRI),” 843 varieties have been developed until now, which have been generated by using both conventional and molecular breeding techniques. Genetic markers are forerunner in the present-day agriculture production system, which has anonymously contributed in the production of novel varieties with additional accuracy, reliability, and rapidity. Thus, it has significantly contributed in precision plant breeding, and dependency on molecular techniques such as marker-assisted selection and quantitative trait loci is inevitable for enhanced crop productivity in the near future. In the present chapter, an elaborate case study involving recent developments in enhancing the nutritional quality of rice crop using marker-assisted selection and quantitative trait loci has been represented.

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References

  • Adeyeye EI, Arogundade LA, Akintayo ET et al (2000) Calcium, zinc and phytate interrelationship in some foods of major consumption in Nigeria. Food Chem 71(4):435–441

    CAS  Google Scholar 

  • Anandan A, Rajiv G, Eswaran R et al (2011) Genotypic variation and relationships between quality traits and trace elements in traditional and improved rice (Oryza sativa L.) genotypes. J Food Sci 76:122–130

    Google Scholar 

  • 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(2):233–240

    CAS  PubMed  Google Scholar 

  • Bashir K, Takahashi R, Nakanishi H et al (2013) The road to micronutrient biofortification of rice: progress and prospects. Front Plant Sci 4:15

    CAS  PubMed  PubMed Central  Google Scholar 

  • Biradar H, Bhargavi MV, Sasalwad R et al (2007) Identification of QTL associated with silicon and zinc content in rice (Oryza sativa L.) and their role in blast disease resistance. Ind J Genet Plant Breed 67(2):105–109

    Google Scholar 

  • Choudhary K, Choudhary OP, Shekhawat NS (2008) Marker assisted selection: a novel approach for crop improvement. Am Eurasian J Agric 1:26–30

    Google Scholar 

  • Du J, Zeng D, Wang B et al (2013) Environmental effects on mineral accumulation in rice grains and identification of ecological specific QTLs. Environ Geochem Health 35(2):161–170

    CAS  PubMed  Google Scholar 

  • 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 X Jeerigesanna. Afr J Biotechnol 13(5):657–663

    CAS  Google Scholar 

  • Garcia-Oliveira AL, Tan L, Fu Y et al (2009) Genetic identification of quantitative trait loci for contents of mineral nutrients in rice grain. J Integr Plant Biol 51(1):84–92

    CAS  PubMed  Google Scholar 

  • Gearing ME (2015) Good as gold: Can golden rice and other biofortified crops prevent malnutrition? Science in the News. http://sitn.hms.harvard.edu/flash/2015/good-as-gold-can-golden-rice-and-other-biofortified-crops-prevent-malnutrition/

  • Genc Y, Verbyla AP, Torun AA et al (2009) Quantitative trait loci analysis of zinc efficiency and grain zinc concentration in wheat using whole genome average interval mapping. Plant Soil 314(1–2):49

    CAS  Google Scholar 

  • Ghasemi S, Kumleh HH, Kordrostami M (2019) Changes in the expression of some genes involved in the biosynthesis of secondary metabolites in Cuminum cyminum L. under UV stress. Protoplasma 256(1):279–290

    CAS  PubMed  Google Scholar 

  • Goto F, Yoshihara T, Shigemoto N et al (1999) Iron fortification of the rice seed by the soybean ferritin gene. Nat Biotechnol 17:282–286

    CAS  PubMed  Google Scholar 

  • Gregorio GB, Senadhira D, Htut H et al (2000) Breeding for trace mineral density in rice. Food Nutr Bull 21(4):382–386

    Google Scholar 

  • Jagadeesh BR, Krishnamurthy R, Surekha K et al (2013) Studies on high accumulation of iron and zinc contents in some selected rice genotypes. Glob J Biol Biotechnol 2(4):539–541

    Google Scholar 

  • James CR, Huynh BL, Welch RM et al (2007) Quantitative trait loci for phytate in rice grain and their relationship with grain micronutrient content. Euphytica 154(3):289–294

    Google Scholar 

  • Jin L, Xiao P, Lu Y et al (2009) Quantitative trait loci for brown rice color, phenolics, flavonoid contents, and antioxidant capacity in rice grain. Cereal Chem 86(6):609–615

    CAS  Google Scholar 

  • Johnson AA, Kyriacou B, Callahan DL et al (2011) Constitutive over expression of the OsNAS gene family reveals single gene strategies for effective iron- and zinc-biofortification of rice endosperm. PLoS One 6(9):e24476

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kaiyang L, Li L, Zheng X et al (2008) Quantitative trait loci controlling Cu, Ca, Zn, Mn and Fe content in rice grains. J Genet 87(3):305–310

    Google Scholar 

  • Kepiro JL, McClung AM, Chen MH et al (2008) Mapping QTLs for milling yield and grain characteristics in a tropical japonica long grain cross. J Cereal Sci 48:477–485

    CAS  Google Scholar 

  • Khalekuzzaman M, Datta K, Olival N et al (2006) Stable integration, expression and inheritance of the ferritin gene in transgenic elite indica rice cultivar BR29 with enhanced iron level in the endosperm. Indian J Biotechnol 5(1):26–31

    CAS  Google Scholar 

  • Kobayashi T, Nishizawa NK (2012) Iron uptake, translocation, and regulation in higher plants. Annu Rev Plant Biol 63:131–152

    CAS  PubMed  Google Scholar 

  • Lee S, Jeon US, Lee SJ et al (2009) Iron fortification of rice seeds through activation of the nicotianamine synthase gene. Proc Natl Acad Sci U S A 106:22014–22019

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lee S, Jeon JS, An G (2012) Iron homeostasis and fortification in rice. J Plant Biol 55:261–267

    CAS  Google Scholar 

  • Lee GH, Yun BW, Kim KM (2014) Analysis of QTLs associated with the rice quality related gene by double haploid populations. Int J Genom 2014:781832. https://doi.org/10.1155/2014/781832

    Article  CAS  Google Scholar 

  • Liu Q-L, Xu X-H, Ren X-L et al (2007) Generation and characterization of low phytic acid germplasm in rice (Oryza sativa L.). Theor Appl Genet 114(5):803–814

    CAS  PubMed  Google Scholar 

  • Liu W, Zeng J, Jiang G et al (2009) QTLs identification of crude fat content in brown rice and its genetic basis analysis using DH and two backcross populations. Euphytica 169(2):197–205

    CAS  Google Scholar 

  • Long JK, Bänziger M, Smith ME (2004) Diallel analysis of grain iron and zinc density in southern African-adapted maize inbreds. Crop Sci 44(6):2019–2026

    Google Scholar 

  • Lou J, Chen L, Yue G et al (2009) QTL mapping of grain quality traits in rice. J Cereal Sci 50:145–151

    CAS  Google Scholar 

  • Lu K, Li L, Zheng X et al (2008) Quantitative trait loci controlling Cu, Ca, Zn, Mn and Fe content in rice grains. J Genet 87:305–310

    PubMed  Google Scholar 

  • Lu K, Li L, Zheng X et al (2009) Genetic dissection of amino acid content in rice grain. J Sci Food Agric 89(14):2377–2382

    CAS  Google Scholar 

  • Lucca P, Hurrel R, Potrykus I (2001) Genetic engineering approaches to improve the bioavailability and the level of iron in the rice grains. Theor Appl Genet 102:392–397

    CAS  Google Scholar 

  • Mahender A, Anandan A, Pradhan SK et al (2016) Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches. Springerplus 5(1):1–18

    CAS  Google Scholar 

  • Martinez CP, Borrero J, Taboada R et al (2010) Rice cultivars with enhanced iron and zinc content to improve human nutrition. 28th International Rice Research Conference, 8–12 November 2010, Hanoi, Vietnam

    Google Scholar 

  • Masuda H, Usuda K, Kobayashi T et al (2009) Over expression of the barley nicotianamine synthase gene HvNAS1 increases iron and zinc concentrations in rice grains. Rice 2:155–166

    Google Scholar 

  • Masuda H, Kobayashi T, Ishimaru Y et al (2013) Iron-biofortification in rice by the introduction of three barley genes participated in mugineic acid biosynthesis with soybean ferritin gene. Front Plant Sci 4:132

    PubMed  PubMed Central  Google Scholar 

  • Ming F, Zheng X, Mi G et al (2001) Detection and verification of quantitative trait loci affecting tolerance to low phosphorus in rice. J Plant Nutr 24:1399–1408

    Google Scholar 

  • Ni JJ, Wu P, Senadhira D et al (1998) Mapping QTLs for phosphorus deficiency tolerance in rice (Oryza sativa L.). Theor Appl Genet 97:1361–1369

    CAS  Google Scholar 

  • Norton GJ, Deacon CM, Xiong L et al (2010) Genetic mapping of the rice ionome in leaves and grain: identification of QTLs for 17 elements including arsenic, cadmium, iron and selenium. Plant Soil 329(1–2):139–153

    CAS  Google Scholar 

  • Peng B, Wang L, Fan C et al (2014) Comparative mapping of chalkiness components in rice using five populations across two environments. BMC Genet 15:49

    PubMed  PubMed Central  Google Scholar 

  • Perez-de-Castro AM, Vilanova S, Canizares J et al (2012) Application of genomic tools in plant breeding. Curr Genomics 13(3):179–195

    CAS  PubMed  PubMed Central  Google Scholar 

  • Qin Y, Kim SM, Sohn JK (2009) QTL analysis of protein content in double-haploid lines of rice. Korean J Crop Sci 54(2):165–171

    Google Scholar 

  • Ravindra Babu V (2013) Importance and advantages of rice biofortification with iron and zinc. SAT eJournal 11:1–6

    Google Scholar 

  • Rohman A, Helmiyati S, Hapsari M et al (2014) Rice in health and nutrition. Int Food Res J 21(1):13

    Google Scholar 

  • Saunders RM (1990) The properties of rice bran as a foodstuff. Cereal Foods World 35(7):632–636

    Google Scholar 

  • Sellappan K, Datta K, Parkhi V et al (2009) Rice caryopsis structure in relation to distribution of micronutrients (iron, zinc, β-carotene) of rice cultivars including transgenic indica rice. Plant Sci 177:557–562

    CAS  Google Scholar 

  • Shao Y, Jin L, Zhang G et al (2011) Association mapping of grain color, phenolic content, flavonoid content and antioxidant capacity in dehulled rice. Theor Appl Genet 122(5):1005–1016

    CAS  PubMed  Google Scholar 

  • Shen Y, Zhang W, Liu X et al (2012) Identification of two stably expressed QTLs for fat content in rice (Oryza sativa). Genome 55(8):585–590

    CAS  PubMed  Google Scholar 

  • Slamet-Loedin IH, Johnson-Beebout SE, Impa S et al (2015) Enriching rice with Zn and Fe while minimizing Cd risk. Front Plant Sci 6:121

    PubMed  PubMed Central  Google Scholar 

  • Stangoulis JCR, Huynh B-L, Welch RM et al (2007) Quantitative trait loci for phytate in rice grain and their relationship with grain micronutrient content. Euphytica 154(3):289–294

    Google Scholar 

  • Tan YF, Sun M, Xing YZ et al (2001) Mapping quantitative trait loci for milling quality, protein content and color characteristics of rice using a recombinant inbred line population derived from an elite rice hybrid. Theor Appl Genet 103:1037–1045

    CAS  Google Scholar 

  • Tan Y-Y, Fu H-W, Zhao H-J et al (2013) Functional molecular markers and high-resolution melting curve analysis of low phytic acid mutations for marker-assisted selection in rice. Mol Breed 31(3):517–528

    CAS  Google Scholar 

  • Vasconcelos M, Datta K, Oliva N et al (2003) Enhanced iron and zinc accumulation in transgenic rice with the ferritin gene. Plant Sci 164:371–378

    CAS  Google Scholar 

  • Wang YX, Wu P, Wu YR et al (2002) Molecular marker analysis of manganese toxicity tolerance in rice under greenhouse conditions. Plant Soil 238:227–233

    CAS  Google Scholar 

  • Wang HL, Zhang WW, Liu LL et al (2008a) Dynamic QTL analysis on rice fat content and fat index using recombinant inbred lines. Cereal Chem 85(6):769–775

    CAS  Google Scholar 

  • Wang L, Zhong M, Li X et al (2008b) The QTL controlling amino acid content in grains of rice (Oryza sativa) are co-localized with the regions involved in the amino acid metabolism pathway. Mol Breed 21(1):127–137

    CAS  Google Scholar 

  • Welch R, Graham RD (1999) A new paradigm for world agriculture: meeting human needs productive, sustainable, nutritious. Field Crops Res 60:1–10

    Google Scholar 

  • Welch RM, Graham RD (2004) Breeding for micronutrients in staple food crops from a human nutrition perspective. J Exp Bot 55:353–364

    CAS  PubMed  Google Scholar 

  • Wissuwa M, Ae N (2001a) Genotypic variation for tolerance to phosphorus deficiency in rice and the potential for its exploitation in rice improvement. Plant Breed 120:43–48

    CAS  Google Scholar 

  • Wissuwa M, Ae N (2001b) Further characterization of two QTLs that increase phosphorus uptake of rice (Oryza sativa L.) under phosphorus deficiency. Plant Soil 237:275–286

    CAS  Google Scholar 

  • Wissuwa M, Yano M, Ae N (1998) Mapping of QTLs for phosphorus deficiency tolerance in rice (Oryza sativa L.). Theor Appl Genet 97:777–783

    CAS  Google Scholar 

  • Wu P, Ni JJ, Luo AC (1998) QTLs underlying rice tolerance to low potassium stress in rice seedlings. Crop Sci 38:1458–1462

    CAS  Google Scholar 

  • Ying J-Z, Shan J-X, Gao J-P et al (2012) Identification of quantitative trait loci for lipid metabolism in rice seeds. Mol Plant 5(4):865–875

    CAS  PubMed  Google Scholar 

  • Yongmei G, Ping M, Jiafu L et al (2007) QTL mapping and Q X E interactions of grain cooking and nutrient qualities in rice under upland and lowland environments. Acta Genet Sin 34:420–428

    Google Scholar 

  • Yu YH, Li G, Fan YY et al (2009) Genetic relationship between grain yield and the contents of protein and fat in a recombinant inbred population of rice. J Cereal Sci 50(1):121–125

    CAS  Google Scholar 

  • Yun BW, Kim MG, Handoyo T et al (2014) Analysis of rice grain quality-associated quantitative trait loci by using genetic mapping. Am J Plant Sci 5:1125–1132

    Google Scholar 

  • Zhang MW, Guo BJ, Peng ZM (2004) Genetic effects on Fe, Zn, Mn and P content in indica black pericarp rice and their genetic correlations with grain characteristics. Euphytica 135:315–323

    CAS  Google Scholar 

  • Zhang W, Bi J, Chen L et al (2008) QTL mapping for crude protein and protein fraction contents in rice (Oryza sativa L.). J Cereal Sci 48(2):539–547

    CAS  Google Scholar 

  • Zhang M, Pinson SRM, Tarpley L et al (2014) Mapping and validation of quantitative trait loci associated with concentrations of 16 elements in unmilled rice grain. Theor Appl Genet 127:137–165

    CAS  PubMed  Google Scholar 

  • Zhao H-J, Liu Q-L, Ren X-L et al (2008) Gene identification and allele-specific marker development for two allelic low phytic acid mutations in rice (Oryza sativa L.). Mol Breed 22(4):603–612

    CAS  Google Scholar 

  • Zheng L, Cheng Z, Ai C et al (2010) Nicotianamine, a novel enhancer of rice iron bioavailability to humans. PLoS One 5:e10190

    PubMed  PubMed Central  Google Scholar 

  • Zhong M, Wang L, Yuan J et al (2011) Identification of QTL affecting protein and amino acid contents in rice. Rice Sci 18(3):187–195

    Google Scholar 

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Thangadurai, D., Kordrostami, M., Islam, S., Sangeetha, J., Al-Tawaha, A.R.M.S., Jabeen, S. (2020). Genetic Enhancement of Nutritional Traits in Rice Grains Through Marker-Assisted Selection and Quantitative Trait Loci. In: Roychoudhury, A. (eds) Rice Research for Quality Improvement: Genomics and Genetic Engineering. Springer, Singapore. https://doi.org/10.1007/978-981-15-5337-0_21

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