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

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.