African Journal of Agricultural Research
Subscribe to AJAR
Full Name*
Email Address*

Article Number - 05525EE59576


Vol.11(29), pp. 2599-2615 , July 2016
DOI: 10.5897/AJAR2016.11239
ISSN: 1991-637X



Full Length Research Paper

Screening of some rice varieties and landraces cultivated in Nigeria for drought tolerance based on phenotypic traits and their association with SSR polymorphism



Celestine Azubuike Afiukw
  • Celestine Azubuike Afiukw
  • Department of Biotechnology, Faculty of Sciences, Ebonyi State University, Abakaliki, Nigeria.
  • Google Scholar
Julius Olaoye Faluyi
  • Julius Olaoye Faluyi
  • Department of Botany, Faculty of Biological Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria.
  • Google Scholar
Christopher John Atkinson
  • Christopher John Atkinson
  • Department of Agriculture, Health and Environment, Natural Resources Institute, University of Greenwich, Kent, ME4 4TB, UK.
  • Google Scholar
Benjamin Ewa Ubi
  • Benjamin Ewa Ubi
  • Department of Biotechnology, Faculty of Sciences, Ebonyi State University, Abakaliki, Nigeria.
  • Google Scholar
David Okechukwu Igwe
  • David Okechukwu Igwe
  • Department of Biotechnology, Faculty of Sciences, Ebonyi State University, Abakaliki, Nigeria.
  • Google Scholar
Richard Olutayo Akinwale
  • Richard Olutayo Akinwale
  • Department of Crop Production and Protection, Faculty of Agriculture, Obafemi Awolowo University, Ile-Ife, Nigeria.
  • Google Scholar







 Received: 20 May 2016  Accepted: 08 June 2016  Published: 21 July 2016

Copyright © 2016 Author(s) retain the copyright of this article.
This article is published under the terms of the Creative Commons Attribution License 4.0


Breeding for drought tolerance based on direct selection for high grain yield under drought has been hindered by the complex nature of drought tolerance mechanisms and the approaches used. Molecular marker-based approaches are a promising alternative. In this study, 30 rice (Oryza sativa L.) accessions cultivated in Nigeria were screened in a greenhouse for drought tolerance based on morpho-physiological traits and assessed for DNA polymorphisms using SSR markers for possible marker-trait associations. Our results showed that five Nigerian rice landraces (IJS-02, IJS-09, IK-PS, IK-FS and Lad-f) and three improved varieties (FARO-44, IR-119 and IWA-8) were highly drought tolerant. Sixteen of 20 markers tested yielded amplified products and generated 221 alleles (4 to 5 alleles per marker) with PIC values ranging from 0.24 to 0.95 per marker. Although, none of the markers were present in all the accessions that were found to be highly drought tolerant with respect to any particular morph-physiological trait, some of the markers (RM252, RM331, RM432, RM36, RM525, RM260 and RM318) amplified alleles unique to nearly all the tolerant Nigerian landraces (IJS-02, IJS-09, IK-PS, IK-FS) and FARO-11, a drought tolerant control. These markers may be usefully exploited for molecular breeding of rice for drought tolerance.

Key words: Nigeria, climate change, rice, drought stress, drought tolerance, SSR markers, molecular breeding.

Akkaya MS, Bhagwat AA, Cregan PB (1992). Length polymorphisms of simple sequence repeat DNA in soybean. Genet. 132:1131-1139.

 

Ali ML, Sanchez PL, Yu S, Lorieux M, Eizenga GC (2010). Chromosome segment substitution lines: a powerful tool for the introgression of valuable genes from Oryza wild species into cultivated rice (O. sativa L.). Rice 3:218-234.
Crossref

 
 

Arai-Sanoh Y, Takai T, Yoshinaga S, Nakano H, Kojima M, Sakakibara H, Kondo M, Uga Y (2014). Deep rooting conferred by DEEPER ROOTING 1 enhances rice yield in paddy fields. Scientific Reports 4. Article Number: 5553.
Crossref

 
 

Araus JL, Slafer GA, Reynolds MP, Royo C (2002). Plant breeding and drought in C3 cereals: what should we breed for? Ann. Bot. 89:925-940.
Crossref

 
 

Atkinson NJ, Urwin PE (2012). The interaction of plant biotic and abiotic stresses: from genes to the field. J. Exp. Bot. 63:3523-3543.
Crossref

 
 

Atlin GN, Lafitte HR (2002). Marker-assisted breeding versus direct selection for drought tolerance in rice. In: Saxena N, P O'Toole JC (eds.). Field Screening for Drought Tolerance in Crop Plants with Emphasis on Rice. Proceedings of an International Workshop on Field Screening for Drought Tolerance in Rice, 11 – 14 December 2000, International Crop Research Institute for the Semi-Arid Tropics, 2002.

 
 

Bargaz A, Zaman-Allah M, Farissi M, Lazali M, Drevon J-J, Maougal RT, Georg C (2015). Physiological and molecular aspects of tolerance to environmental constraints in grain and forage legumes. Int. J. Mol. Sci. 16:18976-19008.
Crossref

 
 

Bimpong IK, Serraj R, Chin JH, Ramos J, Mendoza E, Hernandez J, Mendioro MS, Brar DS (2011). Identification of QTLs for drought-related traits in alien introgression lines derived from crosses of rice (Oryza sativa cv. IR64) × O. glaberrima under lowland moisture stress. J. Plant Biol. 54:237-250.
Crossref

 
 

Blum A, Shpiler L, Golan G, Mayer J (1989). Yield stability and canopy temperature of wheat genotypes under drought- stress. Field Crops Res. 22:289-296.
Crossref

 
 

Boonjung H, Fukai S (1996). Effects of soil water deficit at different growth stages on rice growth and yield under upland conditions. 1. Growth during drought. Field Crops Res. 48:37-45.
Crossref

 
 

Brondani C, Rangel N, Brondani V, Ferreira E (2002). QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theor. Appl. Genet. 104:1192-1203.
Crossref

 
 

Cal AJ, Liu D, Mauleon R, Hsing Y-lC, Serraj R (2013). Transcriptome profiling of leaf elongation zone under drought in contrasting rice cultivars. PLOS One: 8(1):54537.
Crossref

 
 

Cattivelli L, Rizza F, Badeck FW, Mazzucotelli E, Mastrangello AM, Francia E, Mare C, Tondelli A, Stanca M (2008). Drought tolerance improvement in crop plants: An integrated view from breeding to genomics. Field Crops Res. 105:1-14.
Crossref

 
 

Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000). Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100:713-722.
Crossref

 
 

Courtois B, Shen L, Petalcorin W, Carandang S, Mauleon R, Li Z (2003). Locating QTLs controlling constitutive root traits in the rice population IAC 165xCo39. Euphytica 134:335-345.
Crossref

 
 

Crouch JH, Ortiz R (2004). Applied genomics in the improvement of crops grown in Africa. Afr. J. Biotechnol. 3:489-496.
Crossref

 
 

Cutler JM, Shahan KW, Steponkus PL (1980). Influence of water deficits and osmotic adjustment on leaf elongation in rice. Crop Sci. 20:314-318.
Crossref

 
 

Dixit A, Jin M, Chung J, Yu J, Chung H, Ma K, Park Y, Cho E (2005). Development of polymorphic microsatellites markers in sesame (Sesamum indicum L.). Mol. Ecol. Notes 5:736-739.
Crossref

 
 

FAO (2011). Http://faostat.fao.org/.

 
 

Farooq M, Kobayashi N, Wahid A, Ito O, Basra SMA (2009). Strategies for producing more rice with less water. Adv. Agron. 101:351-388.
Crossref

 
 

Fischer RA, Maurer R (1978). Drought resistance in spring wheat cultivar: I- Grain yield response. Aust. J. Agric. Res. 29:897-912.
Crossref

 
 

Fleury D, Jefferies S, Kuchel H, Langridge P (2010). Genetic and genomic tools to improve drought tolerance in wheat. J. Exp. Bot. 61:3211-3222.
Crossref

 
 

Friis-Hansen E, Sthapit B (2000). Participatory approaches to the conservation of plant genetic resources. Int. Plant Genet. Resour. Institute, Italy, Rome, P 199.

 
 

Fukai S, Pantuwan G, Jongdee B, Cooper M (1999). Screening for drought resistance in rainfed lowland rice. Field Crops Res. 64:61-74.
Crossref

 
 

Garris A, Tai TH, Coburn J, Kresovich S, McCouch S (2005). Genetic structure and diversity in Oryza sativa L. Genet. 169:1631-1638.
Crossref

 
 

Gupta PK, Varshney RK, Sharm PC, Ramesh B (1999). Molecular markers and their applications in wheat breeding. Plant Breed. 118:369-390.
Crossref

 
 

Hong L, McCouch SR, Rutger JN, Coburn JR, Tai TH, Redus MA (2005). Population structure and breeding patterns of 145 US rice cultivars based on SSR marker analysis. Crop Sci. 45:66-76.
Crossref

 
 

Ingram KT, Bueno FD, Namuco OS, Yambao EB, Beyrouty CA (1994). Rice root traits for drought resistance and their genetic variation. In: Kirk GJD (ed) Rice Roots: Nutrient and Water Use. Selected papers from the International Rice Research Conference. International Rice Research Institute, Manila, Philippines, pp. 67-77.

 
 

IRRI (1996). Standard Evaluation System for Rice. 4th ed., International Network for Genetic Evaluation of Rice, Genetic Resource Center, Los Ba-os. The Philippines.

 
 

Jongdee B, Fukai S, Cooper M (2002). Leaf water potential and osmotic adjustment as physiological traits to improve drought tolerance in rice. Field Crops Res. 76:153-163.
Crossref

 
 

Kamoshita A, Babu RC, Boopathi NM, Fukai S (2008). Phenotypic and genotypic analysis of drought-resistance traits for development of rice cultivars adapted to rainfed environments. Field Crops Res. 109:1-23.
Crossref

 
 

Kato Y, Abe J, Kamoshita A, Yamagishi J (2006). Genotypic variation in root growth angle in rice (Oryza sativa L.) and its association with deep root development in upland fields with different water regimes. Plant Soil 287:117-129.
Crossref

 
 

Khush GS (2001). Green revolution: the way forward. Nat. Rev. Genet. 2:815-822.
Crossref

 
 

Khush GS (2005). What it will take to feed 5.0 billion rice consumers in 2030. Plant Mol. Biol. 59:1-6.
Crossref

 
 

Korzun V, Malyshev S, Voylokov AV, Borner A (2001). A genetic map of rye (Scale cereale L.) combining RFLP, isozyme, protein, microsatellite and gene loci. Theor. Appl. Genet. 102:709-717.

 
 

Kramer PJ (1969). Plant and Soil Water Relationships – A modern synthesis. McGraw-Hill Publication Company Ltd.

 
 

Li ZK, Xu JL (2007). Breeding for drought and salt tolerant rice (Oryza sativa L.): progress and perspectives. In: Jenks et al. (eds.). Advances in Molecular Breeding toward Drought and Salt Tolerant Crops, Springer pp. 531-564.
Crossref

 
 

McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002). Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9:199-207.
Crossref

 
 

Mitra J (2001). Genetics and genetic improvement of drought resistance in crop plants. Curr. Sci. Bangalore 80:758-763.

 
 

Ndjiondjop M, Cisse F, Futakuchi K, Lorieux M, Manneh B, Bocco R, Fatondji B (2010). Effect of drought on rice (Oryza spp.) genotypes according to their drought tolerance level. Second Africa Rice Congress, Bamako, Mali, 22–26 March 2010: Innovation and Partnerships to Realize Africa's Rice Potential, pp. 151-158.

 
 

Nguyen HT, Babu RC, Blum A (1997). Breeding for drought tolerance in rice: physiology and molecular genetics considerations. Crop Sci. 37:1426-1434.
Crossref

 
 

O'Toole JC (1982). Adaptation of rice to drought-prone environments. In: Drought Resistance in Crops with Emphasis on Rice. Int. Rice Res. Institute, Manila, Philippines, pp. 195-213.

 
 

Pandey S, Bhandari H (2009). Drought, Coping Mechanism and Poverty: Insights from rainfed rice farming in Asia. Occasional Paper, 7. Int. Fund Agric. Dev. (IFAD).

 
 

Parent B, Suard B, Serraj R, Tardieu F (2010). Rice leaf growth and water potential are resilient to evaporative demand and soil water deficit once the effects of root system are neutralized. Plant Cell Environ. 33:1256-1267.
Crossref

 
 

Powell W, Machray GC, Provan J (1996). Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1:215-222.
Crossref

 
 

Price AH, Cairns JE, Horton P, Jones HG, Griffiths H (2002). Linking drought-resistance mechanisms to drought avoidance in upland rice using a QTL approach: progress and new opportunities to integrate stomatal and mesophyll responses. J. Exp. Bot. 53:989-1004.
Crossref

 
 

Price AH, Steele KA, Moore BJ, Barraclough PB, Clark LJ (2000). A combined RFLP and AFLP map of upland rice (Oryza sativa L.) used to identify QTL for root-penetration ability. Theor. Appl. Genet. 100:49-56.
Crossref

 
 

Price AH, Tomos AD (1997). Genetic dissection of root growth in rice (Oryza sativa L.) II: mapping quantitative trait loci using molecular markers. Theor. Appl. Genet. 95:143-152.
Crossref

 
 

Reyniers FN, Truong B, Jacquinot L, Nicou R (1982). Breeding for drought resistance in dryland rice, In: Drought Resistance in Crops with Emphasis on Rice. IRRI, Los Ba-os, Philippines pp. 273-292.

 
 

Rosenzweig C, Iglesias A, Yang XB, Epstein PR, Chivian E (2000). Climate Change and U.S. Agriculture: The Impacts of Warming and Extreme Weather Events on Productivity, Plant Diseases, and Pests. Center for Health and The Global Environment Harvard Medical School.

 
 

Salunkhe AS, Poornima R, Prince KS, Kanagaraj P, Sheeba JA, Amudha K, Suji KK, Senthil A, Babu RC (2011). Fine mapping QTL for drought resistance traits in rice (Oryza sativa L.) using bulk segregant analysis. Mol. Biotechnol. 49:90-95.
Crossref

 
 

Samson B, Hasan M, Wade L (2002). Penetration of hardpans by rice lines in the rainfed lowlands. Field Crops Res. 76:175-188.
Crossref

 

Samuel O, Silva J, Oard JH (2010). Association mapping of grain quality and flowering time in elite japonica rice germplasm. J. Cereal Sci. 51:337-343.
Crossref

 

Sanchez PL, Wing RA, Brar DS (2014). The Wild Relative of Rice: Genomes and Genomics. In: Zhang Q., Wing A (eds.). Genetics and Genomics of Rice, Plant Genetics and Genomics. Springer New York, pp. 9-25.

 
 

Sellamuthu R, Liu GF, Ranganathan CB, Serraj R (2011). Genetic analysis and validation of quantitative trait loci associated with reproductive-growth traits and grain yield under drought stress in a doubled haploid line population of rice (Oryza sativa L.). Field Crops Res. 124:46-58.
Crossref

 
 

Senior ML, Murphy JP, Goodman MM, Stuber CW (1998). Utility of SSRs for determining genetic similarities and relationships in maize using an agarose gel system. Crop Sci. 38:1088-1098.
Crossref

 
 

Serraj R, Sinclair TR (2002). Osmolyte accumulation: can it really help increase crop yields under drought conditions? Plant Cell Environ. 25:333-341.
Crossref

 
 

Sibounheuang V, Basnayake J, Fukai S (2006). Genotypic consistency in the expression of leaf water potential in rice (Oryza sativa L.). Field Crops Res. 97:142-154.
Crossref

 
 

Singh N, Dang TT, Vergara GV, Pandey DM, Sanchez D, Neeraja CN, Septiningsih EM, Mendioro M, Tecson-Mendoza EM, Ismail AM, Mackill DJ, Heuer S (2010). Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A. Theor. Appl. Genet. 121:1441-1453.
Crossref

 
 

Singh S, Pradhan S, Singh A, Singh O (2012). Marker validation in recombinant inbred lines and random varieties of rice for drought tolerance. Aust. J. Crop Sci. 6:606-612.

 
 

Srividhya A, Vemireddy LR, Sridhar S, Jayaprada M, Ramanarao PV, Hariprasad AS, Reddy HK, Anuradha G, Siddiq E (2011). Molecular mapping of QTLs for yield and its components under two water supply conditions in rice (Oryza sativa L.). J. Crop Sci. Biotechnol. 14:45-56.
Crossref

 
 

Suji KK, Biji KR, Poornima R, Prince KS, Amudha K, Kavitha S, Mankar S, Babu RC (2011). Mapping QTLs for plant phenology and production traits using indica rice (Oryza sativa L.) lines adapted to rainfed environment. Mol. Biotechnol. 52:151-160.
Crossref

 
 

Swamy BP, Vikram P, Dixit S, Ahmed HU, Kumar A (2011). Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus. BMC Genom. 12:319.
Crossref

 
 

Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001). Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11:1441-1152.
Crossref

 
 

Turner NC (1979). Drought resistance and adaptation to water deficits in crop plants. In: Mussell H, Staples RC (eds.). Stress physiology in crop plants. John Wiley and Sons, New York, pp. 343-372.

 
 

Ubi BE, Efisue AA, Oselebe OH (2011). Diversity of drought stress tolerance response in rice cultivars and breeding lines at the vegetative stage. J. Agric. Biotechnol. Ecol. 4:70-89.

 
 

Uphoff N, Fasoula F, Iswandi A, Kassam A, Thakur AK (2015). Improving the phenotypic expression of rice genotypes: Rethinking "intensification for production systems and selection practices for rice breeding. Crop J. 3:174-189.
Crossref

 
 

Vasant DV (2012). Genome wide association mapping of drought resistance traits in rice (Oryza sativa L.). M Sc. Thesis, Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University Coimbatore, India.

 
 

Venuprasad R, Cruz MT, Amante M, Magbanua R, Kumar A, Atlin GN (2008). Response to two cycles of divergent selection for grain yield under drought stress in four rice breeding populations. Field Crops Res. 107:232-244.
Crossref

 
 

Vikram P, Swamy BM, Dixit S, Ahmed HU, Cruz MTS, Singh AK, Kumar A (2011). qDTY 1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC genet. 12(1)1.
Crossref

 
 

Villa TC, Maxted N, Scholten M, Ford-Lloyd B (2005). Defining and identifying crop landraces. Plant Genet. Resour. Characterization Utilization 3:373-384.
Crossref

 
 

Wang H, Inukai Y, Yamauchi A (2006). Root development and nutrient uptake. Crit. Rev. Plant Sci. 25:279-301.
Crossref

 
 

Xiong D, Yu T, Zhang T, Li Y, Peng S, Huang J (2015). Leaf hydraulic conductance is coordinated with leaf morpho-anatomical traits and nitrogen status in the genus Oryza. J. Exp. Bot. 66:741-748.
Crossref

 
 

Yang JC, Liu K, Zhang SF, Wang XM, Zh Q, Wang XM, Liu LJ (2008). Hormones in rice spikelets in responses to water stress during meiosis. Acta Agronomica Sinica 34:111-118.
Crossref

 
 

Yue B, Xiong L, Xue W, Xing Y, Luo L, Xu C (2005). Genetic analysis for drought resistance of rice at reproductive stage in field with different types of soil. Theor. Appl. Genet. 111(6)1127-1136.
Crossref

 
 

Zheng H, Babu RC, Pathan MS, Ali L, Huang N, Courtois B, Nguyen HT (2000). Quantitative trait loci for root-penetration ability and root thickness in rice: comparison of genetic backgrounds. Genome 43:53-61.
Crossref

 

 


APA Afiukwa, C. A., Faluyi, J. O., C. J.Atkinson, J. O., Ubi, B. E., Igwe, D.O., & Akinwale, R. O. (2016). Screening of some rice varieties and landraces cultivated in Nigeria for drought tolerance based on phenotypic traits and their association with SSR polymorphism. African Journal of Agricultural Research, 11(29), 2599-2615.
Chicago Celestine Azubuike Afiukwa, Julius Olaoye Faluyi, Christopher John Atkinson, Benjamin Ewa Ubi, David Okechukwu Igwe and Richard Olutayo Akinwale. "Screening of some rice varieties and landraces cultivated in Nigeria for drought tolerance based on phenotypic traits and their association with SSR polymorphism." African Journal of Agricultural Research 11, no. 29 (2016): 2599-2615.
MLA Celestine Azubuike Afiukwa, et al. "Screening of some rice varieties and landraces cultivated in Nigeria for drought tolerance based on phenotypic traits and their association with SSR polymorphism." African Journal of Agricultural Research 11.29 (2016): 2599-2615.
   
DOI 10.5897/AJAR2016.11239
URL http://academicjournals.org/journal/AJAR/article-abstract/05525EE59576

Subscription Form