, 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


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.


Rice Association mapping Seed germination Seedling growth Elite allele 



Analysis of variance


Gene diversity


Germination index


Germination percentage


Heritability in the broad sense


Marker-assisted selection


Mixed linear model


Polymorphism information content


Quantitative trait loci


Recombinant inbred lines


Seedling survival percentage


Simple sequence repeat



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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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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