Euphytica

, Volume 197, Issue 2, pp 251–260 | Cite as

QTL mapping for tolerance of anaerobic germination from IR64 and the aus landrace Nanhi using SNP genotyping

  • Miriam D. Baltazar
  • John Carlos I. Ignacio
  • Michael J. Thomson
  • Abdelbagi M. Ismail
  • Merlyn S. Mendioro
  • Endang M. Septiningsih
Article

Abstract

Direct seeding is becoming more popular mainly due to its labor-saving nature. However, flooding during germination caused by unleveled fields and unpredicted heavy rain can prevent crop establishment. On the other hand, flooding just after sowing protects the seeds from rats and birds and is also a viable means of weed control. Thus, the development of varieties able to tolerate flooding during germination, referred to as anaerobic germination (AG), is essential. A study was conducted to identify QTLs associated with tolerance of flooding during germination from an F2:3 mapping population derived from the cross of IR64 and the tolerant aus landrace Nanhi. Phenotyping was performed by counting the rate of seedling survival of 300 lines under the stress. Selective genotyping was employed by genotyping the 48 most tolerant and 48 most susceptible lines using a 384-plex SNP Indica/Indica set on the Illumina BeadXpress Reader, resulting in 234 polymorphic markers for the study. A major QTL for AG derived from Nanhi, named qAG7, was detected on chromosome 7 with an LOD of 13.93 and 22.3 % of the phenotypic variance explained. A second QTL of smaller effect, qAG11, was also derived from Nanhi, while one QTL with an increased effect from IR64 was detected on chromosome 2 (qAG2.1). The QTLs detected in this study can be used to further elucidate the mechanisms underlying AG tolerance in rice, and can also be used in marker-assisted selection and QTL pyramiding to provide higher AG tolerance to enable improved crop establishment in direct-seeded systems.

Keywords

Rice (Oryza sativaQuantitative trait loci (QTLs) Anaerobic germination (AG) Direct-seeded rice 

Supplementary material

10681_2014_1064_MOESM1_ESM.pdf (291 kb)
Supplementary material 1 (PDF 291 kb)

References

  1. Angaji SA, Septiningsih EM, Mackill DJ, Ismail AM (2010) QTLs associated with tolerance of flooding during germination in rice (Oryza sativa L.). Euphytica 172:159–168CrossRefGoogle Scholar
  2. Biswas JK, Yamauchi M (1997) Mechanism of seedling establishment of direct-seeded rice (Oryza sativa L.) under lowland conditions. Bot Bull Acad Sin 38:29–32Google Scholar
  3. Darvasi A, Soller M (1992) Selective genotyping for determination of linkage between a marker locus and a quantitative trait locus. Theor Appl Genet 85:353–359PubMedGoogle Scholar
  4. Ella ES, Setter TL (1999) Importance of seed carbohydrates in rice seedling establishment under anoxia. Acta Hortic 504:209–216Google Scholar
  5. Foolad MR, Subbiah P, Zhang L (2007) Common QTL affect the rate of tomato seed germination under different stress and nonstress conditions. Int J Plant Genomics. doi:10.1155/2007/97386 Google Scholar
  6. Garavito A, Guyot R, Lozano J, Gavory F, Samain S et al (2010) A genetic model for the female sterility barrier between Asian and African cultivated rice species. Genetics 185:1425–1440PubMedCentralPubMedCrossRefGoogle Scholar
  7. Guo L, Zhu L, Xu Y, Zeng D, Wu P, Qia Q (2004) QTL analysis of seed dormancy in rice (Oryza sativa L.). Euphytica 140:155–162CrossRefGoogle Scholar
  8. Han LZ, Zhang YY, Qiao YL, Cao GL, Zhang SY, Kim JH, Koh HJ (2006) Genetic and QTL analysis for low-temperature vigor of germination in rice. Acta Genet Sin 33:998–1006PubMedCrossRefGoogle Scholar
  9. Huang J, Takano T, Akita S (2000) Expression of α-expansin genes in young seedlings of rice. Planta 211:467–473PubMedCrossRefGoogle Scholar
  10. Hwang YS, Thomas BR, Rodriguez RL (1999) Differential expression of rice α-amylase genes during seedling development under anoxia. Plant Mol Biol 40:911–920PubMedCrossRefGoogle Scholar
  11. International Rice Genome Sequencing Project (IRGSP) (2005) The map-based sequence of the rice genome. Nature 436:793–800CrossRefGoogle Scholar
  12. Ismail AM, Ella ES, Vergara GV, Mackill DJ (2009) Mechanisms associated with tolerance to flooding during germination and early seedling growth in rice (Oryza sativa L.). Ann Bot 103:197–209PubMedCentralPubMedCrossRefGoogle Scholar
  13. Ismail AM, Johnson DE, Ella ES, Vergara GV, Baltazar AM (2012) Adaptation to flooding during emergence and seedling growth in rice and weeds, and implications for crop establishment. AoB Plants. doi:10.1093/aobpla/pls019 PubMedCentralPubMedGoogle Scholar
  14. Iwata N, Nagamatsu J, Omura T (1964) Abnormal segregation of waxy and apiculus coloration by a gametophyte gene belonging to the first linkage group in rice. Jap J Breed 14:33–39CrossRefGoogle Scholar
  15. Iwata N, Shinada H, Kiuchi H, Sato T, Fujino K (2010) Mapping of QTLs controlling seedling establishment using a direct seeding method in rice. Breed Sci 60:353–360CrossRefGoogle Scholar
  16. Jiang L, Hou M, Wang C, Wan J (2004) Quantitative trait loci and epistatic analysis of seed anoxia germinability in rice (Oryza sativa L.). Rice Sci 11:238–244Google Scholar
  17. Jiang L, Liu S, Hou M, Tang J, Chen L, Zhai H, Wan J (2006) Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.). Field Crops Res 98:68–75CrossRefGoogle Scholar
  18. Lasanthi-Kudahettige R, Magneschi L, Loret E, Gonzali S, Licausi F, Novi G, Beretta O, Vituli F, Alpi A, Perata P (2007) Transcript profiling of the anoxic rice coleoptile. Plant Physiol 144:218–231PubMedCentralPubMedCrossRefGoogle Scholar
  19. Liedl B, Anderson NO (1993) Reproductive barriers: identification, uses and circumvention. Plant Breed Rev 11:11–154Google Scholar
  20. Lou Q, Chen L, Sun Z, Xing Y, Li J, Xu X et al (2007) A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L.). Euphytica 158:87–94CrossRefGoogle Scholar
  21. Manly KF, Cudmore RH Jr, Meer JM (2001) Map Manager QTX, cross-platform software for genetic mapping. Mamm Genome 12:930–932PubMedCrossRefGoogle Scholar
  22. McCouch SR, Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative (CGSNL) (2008) Gene nomenclature system for rice. Rice 1:72–84CrossRefGoogle Scholar
  23. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8:4321–4325PubMedCentralPubMedCrossRefGoogle Scholar
  24. Nagato Y, Yoshimura A, Conveners (1998) Report of the committee on gene symbolization, nomenclature and linkage groups. Rice Genetics Newsletter 15:34–74Google Scholar
  25. Pandey S, Velasco L (2002) Economics of direct seeding in Asia: patterns of adoption and research priorities. In: Pandey S, Mortimer M, Wade L, Tuong TP, Lopez K, Hardy B (eds) Direct seeding: research issues and opportunities. Proceedings of the International Workshop on Direct Seeding in Asian Rice Systems: Strategic Research Issues and Opportunities, 25–28 Jan 2000, Bangkok, Los Baños. International Rice Research Institute, pp 3–14Google Scholar
  26. Redoña ED, Mackill DJ (1996) Genetic variation for seedling-vigor traits in rice. Crop Sci 36:285–290CrossRefGoogle Scholar
  27. Satler SO, Kende H (1985) Ethylene and the growth of rice seedlings. Plant Physiol 79:194–198PubMedCentralPubMedCrossRefGoogle Scholar
  28. Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1419–1432PubMedCrossRefGoogle Scholar
  29. Septiningsih EM, Pamplona AM, Sanchez DL, Neeraja CN, Vergara GV, Heuer S, Ismail AM, Mackill DJ (2009) Development of submergence tolerant rice cultivars: the Sub1 locus and beyond. Ann Bot 103:151–160PubMedCentralPubMedCrossRefGoogle Scholar
  30. Septiningsih EM, Sanchez DL, Singh N, Sendon PMD, Pamplona AM, Heuer S, Mackill DJ (2012) Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru. Theor Appl Genet 124:867–874PubMedCrossRefGoogle Scholar
  31. Septiningsih EM, Collard BCY, Heuer S, Bailey-Serres J, Ismail AM, Mackill DJ (2013a) Applying genomics tools for breeding submergence tolerance in rice. In: Varshney RK, Tuberosa R (eds) Translational genomics for crop breeding, vol 2., Improvement for abiotic stress, quality and yield improvementWiley-Blackwell, Hoboken, pp 9–30CrossRefGoogle Scholar
  32. Septiningsih EM, Ignacio JCI, Sendon PMD, Sanchez DL, Ismail AM, Mackill DJ (2013b) QTL mapping and confirmation for tolerance of anaerobic conditions during germination derived from the rice landrace Ma-Zhan Red. Theor Appl Genet 126:1357–1366PubMedCrossRefGoogle Scholar
  33. Seshu DV, Krishnasamy V, Siddique SB (1988) Seed vigor in rice. Rice seed health. International Rice Research Institute, Manila, pp 315–329Google Scholar
  34. Thomson MJ, Tai TH, McClung AM, Hinga ME, Lobos KB, Xu Y, Martinez C, McCouch SR (2003) Mapping quantitative trait loci for yield, yield components, and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479–493PubMedCrossRefGoogle Scholar
  35. Thomson MJ, Zhao K, Wright M, McNally KL, Rey, Tung CW, Reynolds A, Scheffler B, Eizenga G, McClung A, Kim H, Ismail AM, de Ocampo M, Mojica C, Reveche MY, Dilla-Ermita CJ, Mauleon R, Leung H, Bustamante C, McCouch SR (2012) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Mol Breed 29:875–886CrossRefGoogle Scholar
  36. Wang C, Zhu C, Zhai H, Wan J (2005) Mapping segregation distortion loci and quantitative trait loci for spikelet sterility in rice (Oryza sativa L.). Genet Res 86:97–106Google Scholar
  37. Wang S, Basten CJ, Zeng Z-B (2010) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm. Accessed 20 Oct 2013
  38. Wright MH, Tung CW, Zhao K, Reynolds A, McCouch SR, Bustamante CD (2010) ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics 26:2952–2960PubMedCentralPubMedCrossRefGoogle Scholar
  39. Xian-Liang S, Xue-Zhen S, Tian-Zhen Z (2007) Segregation distortion and its effect on genetic mapping in plants. Chin J Agric Biotechnol 3:163–169. doi:10.1079/CJB2006110 CrossRefGoogle Scholar
  40. Xie XB, Jin FX, Song MH, Suh JP, Hwang HG, Kim YG, McCouch SR, Ahn SN (2008) Fine mapping of a yield-enhancing QTL cluster associated with transgressive variation in an Oryza sativa × O. rufipogon cross. Theor Appl Genet 116:613–622PubMedCrossRefGoogle Scholar
  41. Xu S (2008) Quantitative trait locus mapping can benefit from segregation distortion. Genetics 180:2201–2208PubMedCentralPubMedCrossRefGoogle Scholar
  42. Xu Y, Zhu L, Xiao J, Huang N, McCouch SR (1997) Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.). Mol Gen Genet 253:535–545PubMedCrossRefGoogle Scholar
  43. Yamauchi M, Winn T (1996) Rice seed vigor and seedling establishment in anaerobic soil. Crop Sci 36:680–686CrossRefGoogle Scholar
  44. Yang J, Zhu J (2005) Methods for predicting superior genotypes under multiple environments based on QTL effects. Theor Appl Genet 110:1268–1274PubMedCrossRefGoogle Scholar
  45. Yang J, Zhu J, Williams RW (2007) Mapping the genetic architecture of complex traits in experimental populations. Bioinformatics 23:1527–1536PubMedCrossRefGoogle Scholar
  46. Yang J, Hu CC, Hu H, Yu RD, Xia Z, Ye XZ, Zhu J (2008) QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics 24:721–723PubMedCrossRefGoogle Scholar
  47. Yu J, Hu S, Wang J, Wong G, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C (2002) A draft sequence of the rice genome. Science 296:79–92PubMedCrossRefGoogle Scholar
  48. Zhao B, Deng Q-M, Zhang Q-J, Li JQ, Ye SP, Liang YS, Peng Y, Li P (2006) Analysis of segregation distortion of molecular markers in F2 population of rice. Acta Genet Sinica 33:449–457Google Scholar
  49. Zhou L, Wang J-K, Yi Q, Wang YZ, Zhu YG, Zhang ZH (2007) Quantitative trait loci for seedling vigor in rice under field conditions. Field Crops Res 100:294–301CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Miriam D. Baltazar
    • 1
    • 2
  • John Carlos I. Ignacio
    • 1
  • Michael J. Thomson
    • 1
  • Abdelbagi M. Ismail
    • 1
  • Merlyn S. Mendioro
    • 2
  • Endang M. Septiningsih
    • 1
  1. 1.International Rice Research InstituteMetro ManilaPhilippines
  2. 2.University of the PhilippinesLos BanosPhilippines

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