, 215:140 | Cite as

Identification of favorable alleles for rice seedling anoxic tolerance using natural and bi-parental populations

  • Xiaojing Dang
  • Yanhui Li
  • Yuanqing Zhang
  • Jie Ji
  • Dalu Li
  • Xiaoxiao Hu
  • Shangshang Zhu
  • Zhiyao Dong
  • Erbao Liu
  • Hui Wang
  • Bingjie Fang
  • Delin HongEmail author


The acreage of submerged direct-sown cultivation of Oryza sativa is gradually increasing in China because of the constantly decreasing number of laborers in rural areas. Identifying favorable alleles for seedling anoxic tolerance (SAT) is necessary for improving cultivars suitable for submerged direct-sown rice cultivation. In this study, we used two populations to detect quantitative trait loci (QTLs) for SAT. In the natural population consisting of 542 accessions, seven simple sequence repeat marker loci associated with SAT were detected in both 2016 and 2017, with 22 favorable alleles. RM5340 on chromosome 2 and RM6811 on chromosome 6 were newly identified. Allele RM6811-160 bp had the largest phenotypic effect (1.09 cm/cm). Seventy-one accessions carried this allele. In the backcross inbred line population (115 lines) derived from Wuyunjing 7 hao/Ludao//Wuyunjing 7 hao, 8 QTLs for SAT were detected, with the phenotypic variance explained (PVE) ranging from 2.51 to 12.11%. The qCELpc2, qCELpc3, qCELpc5 and qCELpc11 loci were newly detected. The favorable alleles of loci qCELpc3, qCELpc5 and qCELpc11 were from Ludao. The locus qCELpc11 had the largest PVE of 10.39%, with a substitutive effect of 0.82 cm averaged over 2 years. By sequencing the gene locus OsBIERF, which was within a 15.50–16.08 Mb chromosome region harboring SAT-associated RM3600 on chromosome 9 and was detected in both populations, a single nucleotide polymorphism locus at the first exon was found between Wuyunjing 7 hao (T) and Ludao (C). The favorable alleles detected in this study could be used to improve SAT of rice cultivars.


Association mapping Direct-sown rice Favorable allele Linkage analysis Seedling anoxic tolerance 



This work was supported by a grant from the National Natural Science Foundation of China (31571743 and 31671658).

Author contributions

DH planned and designed the research; XD, YL and YZ performed the field experiment and germination experiment; XD, JJ, DL, XH, SZ, ZD, EL, HW and BF conducted the molecular experiment; XD, YL and YZ analysed the data and XD wrote the manuscript; and DH revised the manuscript. All authors read and approved the manuscript.

Compliance with ethical standards

Conflict of interest

None declared.

Supplementary material

10681_2019_2463_MOESM1_ESM.tif (131 kb)
Figure S1 Changes in the mean LnP (K) (A) and (ΔK) (B) for the number of subpopulations and the structure analysis of 542 rice accessions using STRUCTURE software; a) A graph with the mean LnP (K) on the Y axis and the number of subpopulations on the X axis; (B) A graph showing ΔK and the number of subpopulations to determine the optimal number of subpopulations; (C) The structure analysis of 542 rice accessions (TIFF 131 kb)
10681_2019_2463_MOESM2_ESM.tif (484 kb)
Figure S2 Relationship between Dʹ and the genetic distance of syntenic marker pairs in subpopulations (TIFF 483 kb)
10681_2019_2463_MOESM3_ESM.tif (578 kb)
Figure S3 Frequency distribution of CLn, CLa and CELpc in the natural population in 2016 and 2017 (TIFF 578 kb)
10681_2019_2463_MOESM4_ESM.tif (1.6 mb)
Figure S4 Graphical genotypes showing the 262 markers in chromosome positions (cM) and the significant marker-traits associations detected for CLn, CLa and CELpc in the natural population (TIFF 1608 kb)
10681_2019_2463_MOESM5_ESM.tif (670 kb)
Figure S5 Frequency distribution of CLn, CLa and CELpc in the WL-BIL population in 2016 and 2017 (TIFF 670 kb)
10681_2019_2463_MOESM6_ESM.docx (89 kb)
Supplementary material 6 (DOCX 88 kb)
10681_2019_2463_MOESM7_ESM.xlsx (1.7 mb)
Supplementary material 7 (XLSX 1742 kb)


  1. Angaji S, Septiningsih E, Mackill D, Ismail A (2010) QTLs associated with tolerance of flooding during germination in rice Oryza sativa L. Euphytica 172:159–168. CrossRefGoogle Scholar
  2. Baltazar M, Ignacio J, Thomson M et al (2014) QTL mapping for tolerance of anaerobic germination from IR64 and the aus landrace Nanhi using SNP genotyping. Euphytica 197:251–260. CrossRefGoogle Scholar
  3. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300. CrossRefGoogle Scholar
  4. Bradbury P, Zhang Z, Kroon D et al (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 2:2633–2635. CrossRefGoogle Scholar
  5. Cao Y, Song F, Goodman M, Zheng Z (2006) Molecular characterization of four rice genes encoding ethylene-responsive transcriptional factors and their expressions in response to biotic and abiotic stress. J Plant Physiol 163:1167–1178. CrossRefPubMedGoogle Scholar
  6. Cho J, Ryoo N, Ko S et al (2006) Structure, expression, and functional analysis of the hexokinase gene family in rice Oryza sativa L. Planta 224:598–611. CrossRefPubMedGoogle Scholar
  7. Dang XJ, Tran TTG, Dong GS et al (2014) Genetic diversity and association mapping of seed vigor in rice Oryza sativa L. Planta 239:1309–1319. CrossRefPubMedGoogle Scholar
  8. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620. CrossRefPubMedPubMedCentralGoogle Scholar
  9. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7:574–578. CrossRefPubMedPubMedCentralGoogle Scholar
  10. Farnir F, Coppieters W, Arranz JJ et al (2000) Extensive genome-wide linkage disequilibrium in Cattle. Genome Res 10:220–227. CrossRefPubMedGoogle Scholar
  11. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374. CrossRefPubMedPubMedCentralGoogle Scholar
  12. Gibbs J, Morrell S, Valdez A, Setter TL et al (2000) Regulation of alcoholic fermentation in coleoptiles of two rice cultivars differing in tolerance to anoxia. J Exp Bot 51:785–796. CrossRefPubMedGoogle Scholar
  13. Guglielminetti L, Yamaguchi J, Perata P, Alpi A (1995) Amylolytic activities in cereal seeds under aerobic and anaerobic conditions. Plant Physiol 109:1069–1076. CrossRefPubMedPubMedCentralGoogle Scholar
  14. Hsu SK, Tung CW (2015) Genetic mapping of anaerobic germination-associated QTLs controlling coleoptile elongation in rice. Rice 8:38. CrossRefPubMedPubMedCentralGoogle Scholar
  15. Huang SB, Greenway H, Colmer TD, Millar AH (2005) Protein synthesis by rice coleoptiles during prolonged anoxia: implications for glycolysis, growth and energy utilization. Ann Bot 96:703–715. CrossRefPubMedPubMedCentralGoogle Scholar
  16. 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 103:197–209. CrossRefPubMedGoogle Scholar
  17. Ismail AM, Johnson DE, Ella ES, Vergara GV et al (2012) Adaptation to flooding during emergence and seedling growth in rice and weeds, and implications for crop establishment. AoB Plants. CrossRefPubMedPubMedCentralGoogle Scholar
  18. Jiang H, Wu JL, Wang GL (1985) Studies on Ludao of Lianyungang. Crop Genet Resource 2:4–7Google Scholar
  19. Jiang L, Hou MY, Wang CM, Wan JM (2004) Quantitative trait loci and epistatic analysis of seed anoxia germinability in rice Oryza sativa L. Rice Sci 11:238–244Google Scholar
  20. Jiang L, Liu SJ, Hou MY et al (2006) Analysis of QTLs for seed low temperayure germinability and anoxia germinability in rice Oryza sativa L. Field Crop Res 98:68–75. CrossRefGoogle Scholar
  21. Kim SM, Reinke RF (2018) Identification of QTLs for tolerance to hypoxia during germination in rice. Euphytica 214:160. CrossRefGoogle Scholar
  22. Lander ES, Green P, Abrahamson J et al (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181. CrossRefPubMedGoogle Scholar
  23. Lasanthi-Kudahettige R, Magneschi L, Loreti E et al (2007) Transcript profiling of the anoxic rice coleoptile. Plant Physiol 144:218–231. CrossRefPubMedPubMedCentralGoogle Scholar
  24. Licausi F, Kosmacz M, Weits DA et al (2011) Oxygen sensing in plants is mediated by an N-end rule pathway for protein destabilization. Nature 479:419–423. CrossRefPubMedGoogle Scholar
  25. Liu RH, Meng JL (2003) MapDraw: a Microsoft Excel macro for drawing genetic linkage maps based on given genetic linkage data. Heraditas 3:317–321. CrossRefGoogle Scholar
  26. McCouch SR (2008) CGSNL Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative 2008 Gene nomenclature system for rice. Rice 1:72–84. CrossRefGoogle Scholar
  27. McCouch SR, Teytelman L, Xu YB et al (2002) Development and mapping of 2240 new SSR markers for rice Oryza sativa L. DNA Res 9:199–207. CrossRefPubMedGoogle Scholar
  28. Mithran M, Paparelli E, Novi G et al (2014) Analysis of the role of the pyruvate decarboxylase gene family in Arabidopsis thaliana under low-oxygen conditions. Plant Biol 16:28–34. CrossRefPubMedGoogle Scholar
  29. Moons A, Valcke R, Van Montagu M (1998) Low-oxygen stress and water deficit induce cytosolic pyruvate orthophosphate dikinase PPDK expression in roots of rice, a C-3 plant. Plant J 15:89–98. CrossRefPubMedGoogle Scholar
  30. Murray MG, Thompson WF (1980) Rapid isolation of high-molecular-weight-plant DNA. Nucleic Acids Res 8:4321–4325. CrossRefPubMedPubMedCentralGoogle Scholar
  31. Nakazono M, Tsuji H, Li YH et al (2000) Expression of a gene encoding mitochondrial aldehyde dehydrogenase in rice increases under submerged conditions. Plant Physiol 124:587–598. CrossRefPubMedPubMedCentralGoogle Scholar
  32. Perata P, Pozueta-Romero J, Akazawa T, Yamaguchi J (1992) Effect of anoxia on starch breakdown in rice and wheat seeds. Planta 188:611–618. CrossRefPubMedGoogle Scholar
  33. Perata P, Geshi N, Yamaguchi J, Akazawa T (1993) Effect of anoxia on the induction of alpha-amylase in cereal seeds. Planta 191:402–408. CrossRefGoogle Scholar
  34. Septiningsih EM, Ignacio JCI, Sendon PMD et al (2013) QTL mapping and confirmation for tolerance of anaerobic conditions during germination derived from the rice landrace Ma-Zhan Red. Theor Appl Genet 126:1357–1366. CrossRefPubMedGoogle Scholar
  35. Singh N, Dang TTM, Vergara GV et al (2010) Molecular marker survey and expression analyses of the rice submergence-tolerance genes SUB1A and SUB1C. Theor Appl Genet 121:1441–1453. CrossRefPubMedGoogle Scholar
  36. Takahashi H, Greenway H, Matsumura H et al (2014) Rice alcohol dehydrogenase 1 promotes survival and has a major impact on carbohydrate metabolism in the embryo and endosperm when seeds are germinated in partially oxygenated water. Ann Bot 113:851–859. CrossRefPubMedPubMedCentralGoogle Scholar
  37. Temnykh S, Park WD, Ayres N et al (2000) Mapping and genome organization of microsatellite sequence in rice Oryza sativa L. Theor Appl Genet 100:697–712. CrossRefGoogle Scholar
  38. Wang Y, Guo Y, Hong DL (2010) QTL analysis of the anoxic tolerance at the seedling stage in rice. Chin J Rice Sci 24:18–24. (in Chinese with English abstract) CrossRefGoogle Scholar
  39. Wang SC, Basten CJ, Zeng ZB (2012) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. Accessed 16 Dec 2017
  40. Wei XH, Yang ZR, Dong L et al (2004) SSR evidence for taxonomic position of weedy rice ‘Ludao’. Sci Agric Sin 7:937–942 (in Chinese with English abstract) Google Scholar
  41. Xu KN, Mackill DJ (1996) A major locus for submergence tolerance mapped on rice chromosome 9. Mol Breeding 2:219–224. CrossRefGoogle Scholar
  42. Xu KN, Xu X, Fukao T et al (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708. CrossRefPubMedGoogle Scholar
  43. Zhang M, Lu Q, Wu W et al (2017) Association mapping reveals novel genetic loci contributing to flooding tolerance during germination in indica rice. Front Plant Sci 8:678. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina

Personalised recommendations