Scientia Agricultura Sinica ›› 2017, Vol. 50 ›› Issue (14): 2635-2646.doi: 10.3864/j.issn.0578-1752.2017.14.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS •     Next Articles

Genome-Wide Association Analysis on Flag Leaf Width Under Different Nitrogen Levels in Rice

GAO YiHong, YAN JinXiang, TU ZhengJun, LENG YuJia, CHEN Long, HUANG LiChao, DAI LiPing, ZHANG GuangHeng, ZHU Li, HU Jiang, REN DeYong, GUO LongBiao, QIAN Qian, WANG DanYing, ZENG DaLi   

  1. China National Rice Research Institute/State Key Laboratory of Rice Biology, HangZhou 310006
  • Received:2017-01-12 Online:2017-07-16 Published:2017-07-16

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Abstract: 【Objective】 The objective of this experiment is to study the genetic mechanism of flag leaf width and its response to different nitrogen fertilizer rates, and provide advantageous germplasm resources and genetic markers for the improvement of nitrogen use efficiency in rice breeding. 【Method】 Based on re-sequencing of 134 rice landraces, a total of 3 356 591 SNPs distributed on the whole genome were identified. Three different nitrogen levels were assigned as the main plot in the split-plot design, and rice landraces are assigned at random to the subplots within each whole plot. Three nitrogen levels including low nitrogen (no nitrogen fertilizer), normal nitrogen (96 kg·hm-2) and high nitrogen (192 kg·hm-2) were applied under normal field cultivation, respectively. The EMMAX method was used to analyze the genetic relationship and EIGENSOFT was employed to detect the population structure. The mixed linear model was used to detect the potential genome-wide association between single nucleotide polymorphisms (SNPs) and the flag leaf width performance or response under low, medium and high nitrogen treatments. 【Result】The results showed that the flag leaf width displayed normal distribution in N0, N1 and N2 treatments, respectively. The variation of flag leaf width caused by the varietal differences and the different nitrogen levels, and the significant positive correlation between nitrogen fertilizer and flag leaf width were detected at all nitrogen levels. A total of 14 SNPs on five chromosomes presented significant association with the flag leaf width under three different nitrogen levels. The estimated minimum allele frequency was 0.46 at low nitrogen level, which indicate those loci are widely distributed in the association population. While the estimated minimum allele frequencies were lower at normal nitrogen and high nitrogen levels. One SNP located on chromosome 12 was found both at normal nitrogen and high nitrogen levels. Besides, another SNP on chromosome 12 was also detected at high nitrogen. Its flank contained a candidate gene LOC_Os12g25660, which belongs to the super-family of cytochrome P450. It is a homologous gene of OsBR6ox which was confirmed in regulating the flag leaf width in rice. Based on the variation of leaf width at different nitrogen levels, twenty SNPs and eight SNPs were identified to low nitrogen and high nitrogen response, respectively. Among them, the nitrogen utilization related gene, OsATG7, was associated with high nitrogen response on chromosome 1. 【Conclusion】 In this study, a total of 42 SNPs associated with flag leaf width and response to different nitrogen were identified based on the genome-wide association analysis.

Key words: Oryza sativa, genome-wide association study, leaf width, nitrogen fertilizer

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