Plant Molecular Biology Reporter

, Volume 34, Issue 1, pp 160–171 | Cite as

Identification of QTLs with Additive, Epistatic, and QTL × Seed Maturity Interaction Effects for Seed Vigor in Rice

Original Paper


Seed maturity is a critical process of seed vigor establishment. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of seed vigor, including the germination potential (GP), germination rate (GR), germination index (GI), and time for 50 % of germination (T50), at 4, 5, and 6 weeks after heading in 2 years. Significant differences of seed vigor were observed among two parents and RIL population; the heritability of four traits was more than 90 % at three maturity stages. A total of 19 additive and 2 epistatic quantitative trait loci (QTL) for seed vigor were identified using QTL Cartographer and QTLNetwork program, respectively, in 2012, while 16 simple sequence repeat (SSR) markers associated with seed vigor were detected using bulked segregant analysis (BSA) in 2013. The phenotypic variation explained by each additive, epistatic QTL, and QTL × seed maturity interaction ranged from 9.19 to 22.94 %, 7.23 to 7.75 %, and 0.05 to 0.63 %, respectively. Ten additive QTLs were stably expressed in 2 years which might play important roles in establishment of seed vigor in different environments. By comparing chromosomal positions of ten stably expressed additive QTLs with those previously identified, they might be true QTLs for seed vigor; the regions of QTLs for seed vigor are likely to coincide with QTLs for seed dormancy, seed reserve mobilization, low-temperature germinability, and seedling growth. Using four selected RILs, three cross-combinations were predicted to improve seed vigor; 9 to 10 elite alleles could be pyramided by each combination. The selected RILs and the identified QTLs might be applicable for the improvement of seed vigor by marker-assisted selection (MAS) in rice.


Rice Seed vigor Seed maturity Quantitative trait loci Elite allele 



This work was supported by the National Natural Science Foundation of China (Grant Nos. 31271806 and 31000748), the Fundamental Research Funds for the Central Universities (Grant No. KYZ201402 and KYZ201505), and the Special Fund for Agro-scientific Research in the Public Interest (Grant No. 201203052).


  1. Bethke PC, Libourel IG, Aoyama N, Chung YY, Still DW, Jones RL (2007) The Arabidopsis aleurone layer responds to nitric oxide, gibberellin, and abscisic acid and is sufficient and necessary for seed dormancy. Plant Physiol 143:1173–1188PubMedCentralCrossRefPubMedGoogle Scholar
  2. Bewley DJ, Bradford K, Hillorst H, Nonogaki H (2013) Seeds: physiology of development, germination and dormancy, 3rd Edn. SpringerGoogle Scholar
  3. Catusse J, Job C, Job D (2008) Transcriptome- and proteome-wide analyses of seed germination. C R Biol 31:815–822CrossRefGoogle Scholar
  4. Cheng X, Cheng J, Huang X, Lai Y, Wang L, Du W, Wang Z, Zhang H (2013) Dynamic quantitative trait loci analysis of seed reserve utilization during three germination stages in rice. PLoS One 8, e80002PubMedCentralCrossRefPubMedGoogle Scholar
  5. Cheng J, Wang L, Du W, Lai Y, Huang X, Wang Z, Zhang H (2014) Dynamic quantitative trait locus analysis of seed dormancy at three development stages in rice. Mol Breed 34:501–510CrossRefGoogle Scholar
  6. Fait A, Angelovici R, Less H, Ohad I, Urbanczyk-Wochniak E, Fernie AR, Galili G (2006) Arabidopsis seed development and germination is associated with temporally distinct metabolic switches. Plant Physiol 142:839–854PubMedCentralCrossRefPubMedGoogle Scholar
  7. Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin SY, Yano M (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 108:794–799CrossRefPubMedGoogle Scholar
  8. Fujino K, Sekiguchi H, Matsuda Y, Sugimoto K, Ono K, Yano M (2008) Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low temperature germinability in rice. Proc Natl Acad Sci U S A 105:12623–12628PubMedCentralCrossRefPubMedGoogle Scholar
  9. Guan YJ, Hu J, Wang ZF, Zhu SJ, Wang JC, Knapp A (2013) Time series regression analysis between changes in kernel size and seed vigor during developmental stage of sh2 sweet corn (Zea mays L.) seeds. Sci Hortic 154:25–30CrossRefGoogle Scholar
  10. 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 33:998–1006CrossRefPubMedGoogle Scholar
  11. Hayashi E, Aoyama N, Still DW (2008) Quantitative trait loci associated with lettuce seed germination under different temperature and light environments. Genome 51:928–947CrossRefPubMedGoogle Scholar
  12. Huang D, Koh C, Feurtado JA, Tsang EW, Cutler AJ (2013) MicroRNAs and their putative targets in Brassica napus seed maturation. BMC Genomics 14:140PubMedCentralCrossRefPubMedGoogle Scholar
  13. Ji SL, Jiang L, Wang YH, Zhang WW, Liu XL, Liu SJ, Chen LM, Zhai HQ, Wan JM (2009) Quantitative trait loci mapping and stability for low temperature germination ability of rice. Plant Breed 128:387–392CrossRefGoogle Scholar
  14. Jiang L, Liu SJ, Hou MY, Tang JY, Chen LM, Zhai HQ, Wan JM (2006) Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.). Field Crop Res 98:68–75CrossRefGoogle Scholar
  15. Joosen RV, Kodde J, Willems LA, Ligterink W, van der Plas LH, Hilhorst HW (2010) GERMINATOR: a software package for high-throughput scoring and curve fitting of Arabidopsis seed germination. Plant J 62:148–159CrossRefPubMedGoogle Scholar
  16. Marzougui S, Sugimoto K, Yamanouchi U, Shimono M, Hoshino T, Hori K, Kobayashi M, Ishiyama K, Yano M (2012) Mapping and characterization of seed dormancy QTLs using chromosome segment substitution lines in rice. Theor Appl Genet 124:893–902CrossRefPubMedGoogle Scholar
  17. McCouch SR, CGSNL (Committee on Gene Symbolization, Nomenclature, Linkage, Rice Genetics Cooperative) (2008) Gene nomenclature system for rice. Rice 1:72–84CrossRefGoogle Scholar
  18. Miura K, Lin Y, Yano M, Nagamine T (2002) Mapping quantitative trait loci controlling seed longevity in rice (Oryza sativa L.). Theor Appl Genet 104:981–986CrossRefPubMedGoogle Scholar
  19. Niu Y, Xu Y, Liu XF, Yang SX, Wei SP, Xie FT, Zhang YM (2013) Association mapping for seed size and shape traits in soybean cultivars. Mol Breed 31:785–794CrossRefGoogle Scholar
  20. Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H, Hara N, Ishiyama K, Kobayashi M, Ban Y, Hattori T, Yano M (2010) Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proc Natl Acad Sci U S A 107:5792–5797PubMedCentralCrossRefPubMedGoogle Scholar
  21. Sun Q, Wang JH, Sun BQ (2007) Advances on seed vigor physiological and genetic mechanisms. Agric Sci China 6:1060–1066CrossRefGoogle Scholar
  22. Sun Y, Wang J, Crouch JH, Xu Y (2010) Efficiency of selective genotyping for genetic analysis of complex traits and potential applications in crop improvement. Mol Breed 26:493–511CrossRefGoogle Scholar
  23. Takai T, Fukuta Y, Shiraiwa T, Horie T (2005) Time-related mapping of quantitative trait loci controlling grain-filling in rice (Oryza sativa L.). J Exp Bot 56:2107–2118CrossRefPubMedGoogle Scholar
  24. Venuprasad R, Dalid CO, Del Valle M, Zhao D, Espiritu M, Sta Cruz MT, Amante M, Kumar A, Atlin GN (2009) Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis. Theor Appl Genet 120:177–190CrossRefPubMedGoogle Scholar
  25. Wang ZF, Wang JF, Bao YM, Wang FH, Zhang HS (2010) Quantitative trait loci analysis for rice seed vigor during the germination stage. J Zhejiang Univ Sci B 11:958–964PubMedCentralCrossRefPubMedGoogle Scholar
  26. Wang Z, Wang J, Bao Y, Wu Y, Zhang H (2011) Quantitative trait loci controlling rice seed germination under salt stress. Euphytica 178:297–307CrossRefGoogle Scholar
  27. Wang Z, Cheng J, Chen Z, Huang J, Bao Y, Wang J, Zhang H (2012) Identification of QTLs with main, epistatic and QTL × environment interaction effects for salt tolerance in rice seedlings under different salinity conditions. Theor Appl Genet 125:807–815CrossRefPubMedGoogle Scholar
  28. Wang L, Cheng J, Lai Y, Du W, Huang X, Wang Z, Zhang H (2014) Identification of QTLs with additive, epistatic and QTL × development interaction effects for seed dormancy in rice. Planta 239:411–420CrossRefPubMedGoogle Scholar
  29. Wu R, Lin M (2006) Functional mapping-how to map and study the genetic architecture of dynamic complex traits. Nat Rev Genet 7:229–237CrossRefPubMedGoogle Scholar
  30. Xiao N, Huang WN, Li AH, Gao Y, Li YH, Pan CH, Ji H, Zhang XX, Dai Y, Dai ZY, Chen JM (2015) Fine mapping of the qLOP2 and qPSR2-1 loci associated with chilling stress tolerance of wild rice seedlings. Theor Appl Genet 128:173–185CrossRefPubMedGoogle Scholar
  31. Xie L, Tan Z, Zhou Y, Xu R, Feng L, Xing Y, Qi X (2014) Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice. J Integr Plant Biol 56:749–759CrossRefPubMedGoogle Scholar
  32. Yang J, Hu CC, Ye XZ, Zhu J (2005) QTLNetwork 2.0.
  33. You J, Li Q, Yue B, Xue WY, Luo LJ, Xiong LZ (2006) Identification of quantitative trait loci for ABA sensitivity at seed germination and seedling stages in rice. Yi Chuan Xue Bao 33:532–541PubMedGoogle Scholar
  34. Zhang ZH, Qu XS, Wan S, Chen LH, Zhu YG (2005) Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa). Ann Bot 95:423–429PubMedCentralCrossRefPubMedGoogle Scholar
  35. Zhu J (1995) Analysis of conditional genetic effects and variance components in developmental genetics. Genetics 141:1633–1639PubMedCentralPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.The Laboratory of Seed Science and Technology, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingPeople’s Republic of China

Personalised recommendations