Identifying and confirming quantitative trait loci associated with heat tolerance at flowering stage in different rice populations

BMC Genetics

Volumn 16, Issue 1, 2015, Pages

  Ye, Changrong ^a   Tenorio, Fatima A ^a   Argayoso, May A ^a   Laza, Marcelino A ^a   Koh, Hee Jong ^b   Redoña, Edilberto D ^a,c   Jagadish, Krishna ^a   Gregorio, Glenn B ^a  

^a INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

^b Seoul National University   (South Korea)

^c MISSISSIPPI STATE UNIVERSITY   (United States)

Author keywords

Global warming; Heat stress; Quantitative trait locus; Rice; Spikelet fertility

Indexed keywords

GENOMIC DNA; PLANT DNA;

ALLELE; ARTICLE; CHROMOSOME 1; CHROMOSOME 11; CHROMOSOME 2; CHROMOSOME 3; CHROMOSOME 4; CHROMOSOME 6; CROWDING (AREA); DNA EXTRACTION; FLOWERING; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; GENETIC LINKAGE; GENOTYPE; HEAT STRESS; HEAT TOLERANCE; HETEROZYGOTE; HIGH TEMPERATURE; MARKER ASSISTED BREEDING; MICROCLIMATE; NONHUMAN; PHENOTYPE; PLANT CHROMOSOME; PROGENY; QUANTITATIVE TRAIT LOCUS; QUANTITATIVE TRAIT LOCUS MAPPING; RECESSIVE GENE; RICE; SINGLE NUCLEOTIDE POLYMORPHISM; SPIKELET; ADAPTATION; CHROMOSOMAL MAPPING; FLOWER; GENETIC ASSOCIATION STUDY; GENETICS; HEAT; HYBRIDIZATION; METABOLISM; ORYZA; QUANTITATIVE TRAIT;

ADAPTATION, BIOLOGICAL; CHROMOSOME MAPPING; FLOWERS; GENETIC ASSOCIATION STUDIES; GENOTYPE; HOT TEMPERATURE; HYBRIDIZATION, GENETIC; ORYZA; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE;

EID: 84928537004     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/s12863-015-0199-7     Document Type: Article

References (46)

1. Jansen E, Overpeck J, Briffa KR, Duplessy J-C, Joos F, Masson-Delmotte V, et al. Palaeoclimate. In: Solomon S, Qin D, Manning M, Chen Z, Marquis M, Averyt KB, Tignor M, Miller HL, editors. Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge, United Kingdom and New York, NY, USA: Cambridge University Press; 2007.
2. IPCC. Summary for Policymakers. In: Stocker TF, Qin D, Plattner G-K, Tignor M, Allen SK, Boschung J, Nauels A, Xia Y, Bex V, Midgley PM, editors. Climate Change 2013: The Physical Science Basis Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge, United Kingdom and New York, NY, USA: Cambridge University Press; 2013. p. 1-30.
3. Collins M, Knutti R, Arblaster J, Dufresne J-L, Fichefet T, Friedlingstein P, et al. Long-term Climate Change: Projections, Commitments and Irreversibility. In: Stocker TF, Qin D, Plattner G-K, Tignor M, Allen SK, Boschung J, Nauels A, Xia Y, Bex V, Midgley PM, editors. Climate Change 2013: The Physical Science Basis Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge, United Kingdom and New York, NY, USA: Cambridge University Press; 2013. p. 1029-136.
4. Morice CP, Kennedy JJ, NA R, Jones PD. Quantifying uncertainties in global and regional temperature change using an ensemble of observational estimates: the HadCRUT4 dataset. Journal of Geophysical Research. 2012;117, D08101.
5. NOAA National Climatic Data Center: State of the Climate: Global Analysis for Annual 2011. published online December 2011, retrieved on April 5, 2015 from http://wwwncdcnoaagov/sotc/global/2011/13.
6. Osada A, Sasiprapa V, Rahong M, Dhammanuvong S, Chakrabandho H. Abnormal occurrence of empty grains of indica rice plants in the dry hot season in Thailand. Proceedings of Crop Science Society of Japan. 1973;42:103-9.
7. Matsushima S, Ikewada H, Maeda A, Honda S, Niki H. Studies on rice cultivation in the tropics. I Yielding and ripening responses of the rice plant to the extremely hot and dry climate in Sudan. Japan Journal of Tropical Agriculture. 1982;26:19-25.
8. Tian X, Luo H, Zhou H, Wu C. Research on heat stress of rice in China: progress and prospect. Chinese Agricultural Science Bulletin. 2009;25(22):166-8.
9. Hasegawa T, Kuwagata T, Nishimori M, Ishigooka Y, Murakami M, Yoshimoto M, et al. Recent warming trends and rice growth and yield in Japan. In: Proceeding of the MARCO Symposium. 2009. p. 44-51.
10. Lobell DBMB, Tebaldi C, Mastrandrea MD, Falcon WP, Naylor RL. Prioritizing Climate Change Adaptation Needs for Food Security in 2030. Science. 2008;319:607-10.
11. Cline W. Global warming and agriculture. Finnance and Development. 2008;45:23-7.
12. Battisti D, Naylor R. Historical Warnings of Future Food Insecurity with Unprecedented Seasonal Heat. Science. 2009;323(5911):240-4.
13. Basak J, Ali M, Islam MN, Rashid M. Assessment of the effect of climate change on boro rice production in Bangladesh using DSSAT model. Journal of Civil Engineering. 2010;38(2):95-108.
14. Karim MR, Ishikawa M, Ikeda M, Islam M. Climate change model predicts 33% rice yield decrease in 2100 in Bangladesh. Agronomy for Sustainable Development. 2012;32(4):821-30.
15. Satake T, Yoshida S. High temperature induced sterility in Indica rice at flowering. Japan Journal of Crop Science. 1978;47(1):6-17.
16. Sato K, Inaba K, Tosawa M. High temperature injury of ripening in rice plant. I The effects of high temperature treatment at different stages of panicle development on the ripening. Proceedings of Crop Science Society of Japan. 1973;42:207-13.
17. Matsui TON, Ziska LH, Horie T. Effect of high temperature and CO2 concentration on spikelet sterility in Indica rice. Field Crops Research. 1997;51:213-9.
18. Matsui T, Omasa K, Horie T. High temperature induced spikelet sterility of japonica rice at flowering in relation to air humidity and wind velocity conditions. Japan Journal of Crop Science. 1997;66:449-55.
19. Prasad P, Boote K, Allen L, Sheehy J, Thomas J. Species, ecotype and cultivar differences in spikelet fertility and harvest index of rice in response to high temperature stress. Field Crops Research. 2006;95:398-411.
20. Zhong L, Cheng F, Wen X, Sun X, Zhang G. The deterioration of eating and cooking quality caused by high temperature during grain filling in early-season indica rice cultivas. Journal of Agronomy and Crop Science. 2005;191(3):218-25.
21. Matsui T, Omasa K. Rice (Oryza sativa L.) cultivars tolerant to high temperature at flowering: anther characteristics. Ann Bot. 2002;89(6):683-7.
22. Matsui T, Omasa K, Horie T. The differences in sterility due to high temperature during the flowering period among japonica rice varieties. Plant Production Science. 2001;4(2):90-3.
23. Tenorio FA, Ye C, Redoña E, Sierra S, Laza M, Argayoso MA. Screening rice genetic resources for heat tolerance. SABRAO Journal of Breeding and Genetics. 2013;45(3):341-51.
24. Cao L, Zhao J, Zhan X, Li D, He L, Cheng S. Mapping QTLs for heat tolerance and correlation between heat tolerance and photosynthetic rate in rice. Chinese Journal of Rice Science. 2003;17(3):223-7.
25. Chen Q, Yu S, Li C, Mou T. Identification of QTLs for heat tolerance at flowering stage in rice. Scientia Agricultura Sinica. 2008;41(2):315-21.
26. Cheng L, Wang JM, Uzokwe V, Meng LJ, Wang Y, Sun Y, et al. GeneticAnalysis of ColdTolerance at SeedlingStage and HeatTolerance at Anthesis in Rice. Journal of Integrative Agriculture. 2012;11(3):359-67.
27. Zhang T, Yang L, Jiang K, Huang M, Sun Q, Chen W, et al. QTL mapping for heat tolerance of the tassel period of rice. Molecular Plant Breeding. 2008;6(5):867-73.
28. Jagadish S, Cairns J, Lafitte R, Wheeler T, Price A, Craufurd P. Genetic analysis of heat tolerance at anthesis in rice. Crop Science. 2010;50:1633-41.
29. Xiao Y, YP L, Luo G, Zhang H, Deng L, Dai X, et al. Wang: Quantitative trait loci associated with seed set under high temperature stress at the flowering stage in rice. Euphytica. 2011;178:331-8.
30. Ye C, Argayoso MA, Redoña ED, Sierra SN, Laza MA, Dilla CJ, et al. Mapping QTL for heat tolerance at flowering stage in rice using SNP markers. Plant Breeding. 2012;131(1):33-41.
31. Zhang G, Chen L, Xiao G, Xiao Y, Chen X, Zhang S. Bulked segregant analysis to detect QTL related to heat tolerance in rice using SSR markers. Agricultural Sciences in China. 2009;8(4):482-7.
32. Redona E, Manigbas N, Laza M, Sierra S, Bartolome V, Nora L, Barroga W, Noriel J. Identifying heat tolerant rice genotypes under different environments. SABRAO Journal of Breeding and Genetics 2009, 41 (special suppl.):Published in CD (ISSN 1029-7073).
33. Jagadish S, Muthurajan R, Oane R, Wheeler T, Heuer S, Bennett J, et al. Physiological and proteomic approaches to address heat tolerance during anthesis in rice. Journal of Experimental Botany. 2010;61(1):143-56.
34. Khush G, Virk P. IR varieties and their impact. Los Banos, Philippines: International Rice Research Institute (ISBN 971-22-0206-2); 2005.
35. Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, et al. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS ONE. 2010;5(5):e10780.
36. Thomson M, Zhao K, Wright M, McNally K, Rey J, Tung C, et al. High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Molecular Breeding. 2012;29:875-86.
37. McNally K, Childs K, Bohnert R, Davidson R, Zhao K, Ulat V, et al. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proceedings of the National Academy of Sciences USA. 2009;106(30):12273-8.
38. Wright M, Tung CW, Zhao KY, Reynolds A, McCouch SR, Bustamante C. ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics. 2010;26:2952-60.
39. Joehanes R, Nelson J. QGene 4.0, an extensible Java QTL-analysis platform. Bioinformatics. 2008;24:2788-9.
40. Churchill G, Doerg R. Empirical threshold values for quantitative trait mapping. Genetics. 1994;138:963-71.
41. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007;23(19):2633-5.
42. Bandillo N, Raghavan C, Muyco PA, Sevilla MA, Lobina IT, Dilla-Ermita CJ, et al. Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice. 2013;6(1):11-5.
43. McCouch SR, CGSNL. Gene nomenclature system for rice. Rice. 2008;1:72-84.
44. Morrell PL, Buckler ES, Ross-Ibarra J. Crop genomics: advances and applications. Nat Rev Genet. 2012;13(2):85-96.
45. Cavanagh C, Morell M, Mackay I, Powell W. From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Current opinion in plant biology. 2008;11(2):215-21.
46. Wang K, Zhang X, Goatley M, Ervin E. Heat Shock Proteins in Relation to Heat Stress Tolerance of Creeping Bentgrass at Different N Levels. PLoS ONE. 2014;9(7), e102914.