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Euphytica

, Volume 206, Issue 1, pp 103–115 | Cite as

Association mapping of seed germination and seedling growth at three conditions in indica rice (Oryza sativa L.)

  • Jinping Cheng
  • Yongqi He
  • Bin Yang
  • Yanyan Lai
  • Zhoufei WangEmail author
  • Hongsheng ZhangEmail author
Article

Abstract

Seed germination and seedling establishment are critical phases in rice. In this study, 276 indica accessions were used to investigate the genetic control of seed germination and seedling growth under normal, drought and salt conditions by using the trait of germination percentage, germination index and seedling survival percentage. The significant natural variation of seed germination and seedling growth was observed among accessions at three conditions. Correlation analysis showed that the significant and positive relationship between drought and salt stress conditions was observed in seed germination while not in seedling growth. A total of 12, 14 and 9 simple sequence repeat (SSR) markers associated with three traits were identified under normal, drought and salt conditions respectively. Seven and two SSR loci were simultaneously identified at two and three conditions, respectively, five SSR loci each were specific for drought and salt stress condition. By comparing chromosomal positions of the markers here with previously studies, six SSR loci might represent novel. Several accessions with elite performance of seed germination and seedling growth under stress conditions were firstly identified, such as Gulfrose, Kaijiangliushizao, Yangxidao and Xincunheigu. Six cross combinations each for improving seed germination and seedling growth under stress conditions were predicted. The identified elite accessions and alleles might be applicable to improve rice seed germination and seedling growth by the marker-assisted selection approach.

Keywords

Rice Association mapping Seed germination Seedling growth Elite allele 

Abbreviations

ANOVA

Analysis of variance

GD

Gene diversity

GI

Germination index

GP

Germination percentage

HB2

Heritability in the broad sense

MAS

Marker-assisted selection

MLM

Mixed linear model

PIC

Polymorphism information content

QTL

Quantitative trait loci

RILs

Recombinant inbred lines

SSP

Seedling survival percentage

SSR

Simple sequence repeat

Notes

Acknowledgments

This work was supported by the National Natural Science Foundation of China (Grant No. 31271806), the Fundamental Research Funds for the Central Universities (Grant No. KYZ201402; KYZ201505), the Special Fund for Agro-scientific Research in the Public Interest (Grant No. 201203052) and the Jiangsu Agriculture Science and Technology Innovation Fund (CX(12)1003-3).

Conflict of interest

The authors have declared that no competing interests exist.

Supplementary material

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References

  1. Ahmadi N, Negrao S, Katsantonis D, Frouin J, Ploux J, Letourmy P, Droc G, Babo P, Trindade H, Bruschi G, Greco R, Oliveira MM, Piffanelli P, Courtois B (2011) Targeted association analysis identified japonica rice varieties achieving Na+/K+ homeostasis without the allelic make-up of the salt tolerant indica variety Nona Bokra. Theor Appl Genet 123:881–895CrossRefPubMedGoogle Scholar
  2. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635CrossRefPubMedGoogle Scholar
  3. Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177PubMedCentralCrossRefPubMedGoogle Scholar
  4. Bryant R, Proctor A, Hawkridge M, Jackson A, Yeater K, Counce P, Yan W, McClung A, Fjellstrom R (2011) Genetic variation and association mapping of silica concentration in rice hulls using a germplasm collection. Genetica 139:1383–1398CrossRefPubMedGoogle Scholar
  5. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553–567CrossRefGoogle Scholar
  6. Cheng L, Wang Y, Meng L, Hu X, Cui Y, Sun Y, Zhu L, Ali J, Xu J, Li Z (2012) Identification of salt-tolerant QTLs with strong genetic background effect using two sets of reciprocal introgression lines in rice. Genome 55:45–55CrossRefPubMedGoogle Scholar
  7. 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
  8. Cheng J, Wang L, Du W, Lai Y, Huang X, Wang Z, Zhang Zhang H (2014) Dynamic quantitative trait locus analysis of seed dormancy at three development stages in rice. Mol Breed 34:501–510CrossRefGoogle Scholar
  9. Courtois B, Audebert A, Dardou A, Roques S, Ghneim-Herrera T, Droc G, Frouin J, Rouan L, Goze E, Kilian A, Ahmadi N, Dingkuhn M (2013) Genome-wide association mapping of root traits in a japonica rice panel. PLoS ONE 8:e78037PubMedCentralCrossRefPubMedGoogle Scholar
  10. Cui K, Peng S, Xing Y, Xu C, Yu S, Zhang Q (2002) Molecular dissection of seedling-vigor and associated physiological traits in rice. Theor Appl Genet 105:745–753CrossRefPubMedGoogle Scholar
  11. Dang X, Thi TG, Dong G, Wang H, Edzesi WM, Hong D (2014) Genetic diversity and association mapping of seed vigor in rice (Oryza sativa L.). Planta 239:1309–1319CrossRefPubMedGoogle Scholar
  12. Ding X, Li X, Xiong L (2011) Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice. Theor Appl Genet 123:815–826CrossRefPubMedGoogle Scholar
  13. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol Notes 14:2611–2620CrossRefGoogle Scholar
  14. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7:574–578PubMedCentralCrossRefPubMedGoogle Scholar
  15. Famoso AN, Zhao K, Clark RT, Tung CW, Wright MH, Bustamante C, Kochian LV, McCouch SR (2011) Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genet 7:e1002221PubMedCentralCrossRefPubMedGoogle Scholar
  16. Fu XQ, He HH, Wen P, Luo XD, Xie JK (2012) Drought resistance evaluation system for backcross lines of Dongxiang common wild rice (Oryza rufipogon Griff.). Ying Yong Sheng Tai Xue Bao 23:1277–1285PubMedGoogle Scholar
  17. 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
  18. Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch SR (2005) Genetic structure and diversity in Oryza sativa L. Genetics 169:1631–1638PubMedCentralCrossRefPubMedGoogle Scholar
  19. 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. Yi Chuan Xue Bao 33:998–1006PubMedGoogle Scholar
  20. Hu BL, Fu XQ, Zhang T, Wan Y, Li X, Huang YH (2011) Genetic analysis on characteristics to measure drought resistance using Dongxiang wild rice (Oryza rufupogon Griff.) and its derived backcross inbred lines population at seedling stage. Agric Sci China 10:1653–1664CrossRefGoogle Scholar
  21. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang QF, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967CrossRefPubMedGoogle Scholar
  22. Huang J, Sun S, Xu D, Lan H, Sun H, Wang Z, Bao Y, Wang J, Tang H, Zhang H (2012) A TFIIIA-type zinc finger protein confers multiple abiotic stress tolerances in transgenic rice (Oryza sativa L.). Plant Mol Biol 80:337–350CrossRefPubMedGoogle Scholar
  23. Jia L, Yan W, Zhu C, Agrama HA, Jackson A, Yeater K, Li X, Huang B, Hu B, McClung A, Wu D (2012) Allelic analysis of sheath blight resistance with association mapping in rice. PLoS ONE 7:e32703PubMedCentralCrossRefPubMedGoogle Scholar
  24. 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
  25. Jin L, Lu Y, Xiao P, Sun M, Corke H, Bao J (2010) Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theor Appl Genet 121:475–487CrossRefPubMedGoogle Scholar
  26. Kamoshita A, Chandra Babu R, 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 109:1–23CrossRefGoogle Scholar
  27. Li M, Sun P, Zhou H, Chen S, Yu S (2011) Identification of quantitative trait loci associated with germination using chromosome segment substitution lines of rice (Oryza sativa L.). Theor Appl Genet 123:411–420CrossRefPubMedGoogle Scholar
  28. Li X, Yan W, Agrama H, Jia L, Jackson A, Moldenhauer K, Yeater K, McClung A, Wu D (2012) Unraveling the complex trait of harvest index with association mapping in rice (Oryza sativa L.). PLoS ONE 7:e29350PubMedCentralCrossRefPubMedGoogle Scholar
  29. Liu KJ, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129CrossRefPubMedGoogle Scholar
  30. Luo LJ (2010) Breeding for water-saving and drought-resistance rice (WDR) in China. J Exp Bot 61:3509–3517CrossRefPubMedGoogle Scholar
  31. McCouch SR, Teytelman L, Xu YB, Lobos KB, Clare K, Walton M, Fu BY, Maghirang R, Li ZK, Xing YZ, Zhang QF, Kono I, Yano M, Jellstorm RF, 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 9:199–207CrossRefPubMedGoogle Scholar
  32. Miura K, Lin S, Yano M, Nagamine T (2002) Mapping quantitative trait loci controlling seed longevity in rice (Oryza sativa L.). Theor Appl Genet 104:981–986CrossRefPubMedGoogle Scholar
  33. Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. II: gene frequency data. J Mol Evol 19:153–170CrossRefPubMedGoogle Scholar
  34. Nguyen HT, Babu RC, Blum A (1997) Breeding for drought resistance in rice: physiology and molecular genetics consideration. Crop Sci 37:1426–1434CrossRefGoogle Scholar
  35. 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
  36. Pandit A, Rai V, Bal S, Sinha S, Kumar V, Chauhan M, Gautam RK, Singh R, Sharma PC, Singh AK, Gaikwad K, Sharma TR, Mohapatra T, Singh NK (2010) Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.). Mol Genet Genomics 284:121–136CrossRefPubMedGoogle Scholar
  37. Sabouri H, Rezai AM, Moumeni A, Kavousi A, Katouzi M, Sabouri A (2009) QTLs mapping of physiological traits related to salt tolerance in young rice seedlings. Biol Plant 53:657–662CrossRefGoogle Scholar
  38. Sanguinetti CJ, Neto ED, Simpson AJG (1994) Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. Biotechniques 17:914–921PubMedGoogle Scholar
  39. Shao Y, Jin L, Zhang G, Lu Y, Shen Y, Bao J (2011) Association mapping of grain color, phenolic content, flavonoid content and antioxidant capacity in dehulled rice. Theor Appl Genet 122:1005–1016CrossRefPubMedGoogle Scholar
  40. Song S, Dai X, Zhang WH (2012) A rice F-box gene, OsFbx352, is involved in glucose-delayed seed germination in rice. J Exp Bot 63:5559–5568PubMedCentralCrossRefPubMedGoogle Scholar
  41. Swamy BP, Ahmed HU, Henry A, Mauleon R, Dixit S, Vikram P, Tilatto R, Verulkar SB, Perraju P, Mandal NP, Variar M, Robin S, Chandrababu R, Singh ON, Dwivedi JL, Das SP, Mishra KK, Yadaw RB, Aditya TL, Karmakar B, Satoh K, Moumeni A, Kikuchi S, Leung H, Kumar A (2013) Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought. PLoS ONE 8:e62795CrossRefPubMedGoogle Scholar
  42. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599CrossRefPubMedGoogle Scholar
  43. Teng S, Qian Q, Zeng DL, Kunihiro Y, Fujimoto K, Huang DN, Zhu LH (2002) Analysis of gene loci and epistasis for drought tolerance in seedling stage of rice (Oryza sativa L.). Yi Chuan Xue Bao 29:235–240CrossRefPubMedGoogle Scholar
  44. Thomson MJ, Polato NR, Prasetiyono J, Trijatmiko KR, Silitonga TS, McCouch SR (2009) Genetic diversity of isolated populations of Indonesian landraces of rice (Oryza sativa L.) collected in east Kalimantan on the island of Borneo. Rice 2:80–92CrossRefGoogle Scholar
  45. Tian L, Tan L, Liu F, Cai H, Sun C (2011) Identification of quantitative trait loci associated with salt tolerance at seedling stage from Oryza rufipogon. Yi Chuan Xue Bao 38:593–601CrossRefPubMedGoogle Scholar
  46. 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
  47. Wang ZF, Wang FH, Zhou R, Wang JF, Zhang HS (2011a) Identification of quantitative trait loci for cold tolerance during the germination and seedling stages in rice (Oryza sativa L.). Euphytica 181:405–413CrossRefGoogle Scholar
  48. Wang ZF, Wang JF, Bao YM, Wu YY, Zhang HS (2011b) Quantitative trait loci controlling rice seed germination under salt stress. Euphytica 178:297–307CrossRefGoogle Scholar
  49. Wang Z, Chen Z, Cheng J, Lai Y, Wang J, Bao Y, Huang J, Zhang H (2012a) QTL analysis of Na+ and K+ concentrations in roots and shoots under different levels of NaCl stress in rice (Oryza sativa L.). PLoS ONE 7:e51202PubMedCentralCrossRefPubMedGoogle Scholar
  50. Wang Z, Cheng J, Chen Z, Huang J, Bao Y, Wang J, Zhang H (2012b) 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
  51. 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
  52. Xu CG, Li XQ, Xue Y, Huang YW, Gao J, Xing YZ (2004) Comparison of quantitative trait loci controlling seedling characteristics at two seedling stages using rice recombinant inbred lines. Theor Appl Genet 109:640–647PubMedGoogle Scholar
  53. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208CrossRefPubMedGoogle Scholar
  54. Zhang ZH, Yu SB, Yu T (2005) Mapping quantitative trait loci (QTLs) for seedling-vigor using recombinant inbred lines of rice (Oryza sativa L.). Field Crops Res 91:161–170CrossRefGoogle Scholar
  55. Zhang DL, Zhang HL, Qi YW, Wang MX, Sun JL, Ding L, Li ZC (2013) Genetic structure and eco-geographical differentiation of cultivated Hsien rice (Oryza sativa L. subsp. indica) in China revealed by microsatellites. Chin Sci Bull 58:344–352CrossRefGoogle Scholar
  56. Zhou SX, Tian F, Zhu ZF, Fu YC, Wang XK, Sun CQ (2006) Identification of quantitative trait loci controlling drought tolerance at seedling stage in Chinese Dongxiang common wild rice (Oryza rufipogon Griff.). Yi Chuan Xue Bao 33:551–558PubMedGoogle Scholar
  57. Zhu CS, Gore M, Buckler ES, Yu JM (2008) Status and prospects of association mapping in plants. Plant Genome 1:5–20CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 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

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