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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (8): 1189-1199.doi: 10.3724/SP.J.1006.2019.82058

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

Potassium uptake and genome-wide association analysis of rice under different nitrogen levels

ZOU Wei-Wei1,LU Xue-Li2,WANG Li1,XUE Da-Wei3,ZENG Da-Li2,*(),LI Zhi-Xin1,*()   

  1. 1 Agronomy Department, Yangtze University, Jingzhou 434025, Hubei, China
    2 China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
    3 School of Life Sciences, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China
  • Received:2018-11-22 Accepted:2019-01-19 Online:2019-08-12 Published:2019-03-11
  • Contact: Da-Li ZENG,Zhi-Xin LI E-mail:dalizeng@126.com;lizhixin09@163.com
  • Supported by:
    The study was supported by the Hubei Collaborative Innovation Center for Industrialization of Major Grain Crops(MS2015004)

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Abstract:

A total of 134 resequenced rice landraces were used for assessing the potassium content, plant dry weight and potassium accumulation at three different nitrogen levels including no nitrogen fertilizer (N0), 96 kg ha -1 (N1), and 192 kg ha -1 (N2) under normal field cultivation, respectively. All the three traits displayed normal distribution with abundant variations under N0, N1, and N2 nitrogen levels, respectively. K accumulation and plant dry weight showed positive correlation with nitrogen levels. Meanwhile, the negative correlation was detected between K content and dry weight, and there was positive correlation between dry weight and K accumulation. In addition, the K content showed significantly lower in indica than in japonica, while the dry weight and K accumulation in indica were significantly higher than those in japonica. A total of 12 SNPs presented significant association with the potassium content, plant dry weight and potassium accumulation under three diferent nitrogen levels, including two SNPs for K accumulation, five SNPs for K content and five SNPs for dry weight. A SNP (Chr6_1,524,776) associated with potassium content on chromosome 6 was detected at N1 level. Its flank contained a receptor-like kinase, RUPO, which interacts with potassium transporters in rice. According to the difference of potassium content, one SNP and three SNPs were identified with high nitrogen and low nitrogen response, respectively. While four candidate genes closed to the SNP (Chr10_2,822,026) were associated to K content relatively changed under both high nitrogen and low nitrogen levels, showing different expression levels under different nitrogen levels.

Key words: genome-wide association study, potassium content, dry weight, potassium accumulation, Oryza sativa

Table 1

RT-PCR primers"

候选基因
Candidate gene		 上游引物序列
Forward primer sequences (5°-3°)		 下游引物序列
Reverse primer sequences (5'-3')
LOC_Os10g05730 GGCATCAAAACAGGCTCACA GGCCAACTTTACAGGTACACA
LOC_Os10g05600 GCTGTTCTTGGTCCACGC GGCCTTACTGAGTCTCTCCC
LOC_Os10g05540 CTCGGCTTCTTCCACAACTC CCTGGATCTGGCTGGAGAC
LOC_Og05620 CACGAGCACCCACAATGTAG AACGGTCACCCCTTCATCTT

Table 2

K content, dry weight, and K accumulation under three nitrogen concentrations"

性状
Trait		 参数
Parameter		 氮水平 N level
N0 N1 N2
K含量K content (mg g-1) 均值Mean 28.87±2.85 28.05±3.35 28.05±3.20
变幅Range 22.21-35.12 20.02-37.03 19.23-38.92
干重Dry weight (g plant-1) 均值Mean 4.68±1.29 6.30±1.69 7.70±2.02
变幅Range 1.94-8.12 2.66-10.30 3.68-14.40
钾积累K accumulation (mg plant-1) 均值Mean 26.47±7.07 34.91±8.76 42.51±10.89
变幅Range 11.41-48.26 15.58-53.72 21.71-72.93

Fig. 1

Distribution of K content, dry weight, and K accumulation under three nitrogen levels a, c, and e are the distribution of K content, dry weight, and K accumulation under three nitrogen levels, respectively; b, d, and f are the distribution of K content, dry weight, and K accumulation in bubble chart under three nitrogen levels, respectively; the width of bubble represents the number of lines, and the red dotted line is the average value of every character."

Fig. 2

Distributions of relative changes of K content and K accumulation under different nitrogen levels a and b are the distributions of relative changes of K content and K accumulation under N0N1-N0 and N2N2-N1; KC: K content; KA: K accumulation."

Fig. 3

Comparisons of K content, dry weight and K accumulation between indica and japonica under three nitrogen levels a, b, and c are comparisons of K content, dry weight and K accumulation between indica and japonica under three nitrogen levels. C0i, C1i, and C2i are the K content of indica under N0, N1, and N2 nitrogen levels respectively; C0j, C1j, and C2j are the K content of japonica under N0, N1, and N2 nitrogen levels respectively; W0i, W1i, and W2i are the dry weight of indica under N0, N1, and N2 nitrogen levels respectively; W0j, W1j, and W2j are the dry weight of japonica under N0, N1, and N2 nitrogen levels respectively; A0i, A1i, and A2i are the K accumulation of indica under N0, N1, and N2 nitrogen levels respectively; A0j, A1j, and A2j are the K accumulation of japonica under N0, N1, and N2 nitrogen levels, respectively."

Table 3

Correlation coefficients of K content, dry weight, and K accumulation with nitrogen levels"

氮水平
N level		 钾含量
K content		 干重
Dry weight		 钾积累
K accumulation
N0 N1 N0 N1 N0 N1
N1 -0.11 0.48** 0.46**
N2 -0.14 -0.02 0.67** 0.35** 0.66** 0.37**

Table 4

Correlation coefficients among three traits under three nitrogen levels"

性状
Trait		 N0 N1 N2
K含量
K content		 干重
Dry weight		 K含量
K content		 干重
Dry weight		 K含量
K content		 干重
Dry weight
干重Dry weight -0.33** -0.38** -0.30**
K积累 K accumulation 0.06 0.92** 0.09 0.88** 0.16 0.89**

Table 5

Summary of SNP significantly associated with the K content, dry weight, and K accumulation at three nitrogen plots"

性状
Trait		 氮水平
Nitrogen level		 染色体
Chr.		 物理距离
Position (bp)		 主要等位基因
Major allele		 次要等位基因
Minor allele		 最小等位基因频率
Minor allele frequency		 P-value
(-lg P)
钾积累 N0 6 21,362,789 G A 0.087 6.803
K accumulation N1 6 21,336,732 A G 0.387 6.130
钾含量 N1 1 2,908,421 A G 0.302 6.313
K content N1 2 7,907,735 A C 0.477 6.900
N1 3 5,568,543 A G 0.317 6.791
N1 6 1,524,776 G A 0.228 7.643
N1 6 26,011,593 C T 0.077 6.400
植株干重 N0 6 21,337,192 T C 0.380 6.265
Plant weight N1 6 21,337,192 T C 0.378 7.303
N1 6 23,166,060 C T 0.049 6.267
N1 10 19,108,030 C A 0.105 6.248
N2 10 19,108,030 C A 0.105 6.282

Fig. 4

Genome-wide association studies of K content, dry weight, and K accumulation under three nitrogen levels a, b, and c are genome-wide association studies of K content, dry weight, and K accumulation under three nitrogen levels, respectively."

Table 6

Association sites of K content relative changes under N0 and N2 stress"

性状
Trait		 染色体
Chr.		 物理距离
Position (bp)		 主要等位基因
Major allele		 次要等位基因
Minor allele		 最小等位基因频率
Minor allele frequency		 P-value
(-lg P)
KCN1-N0 9 6,934,774 T A 0.149 6.672
KCN1-N0 10 2,822,026 C T 0.066 6.296
KCN1-N0 10 4,669,497 G A 0.030 6.201
KCN2-N1 10 2,822,026 C T 0.066 6.938

Fig. 5

Genome-wide association analysis of K content and K accumulation relative changes under N0 and N2 levels a and b are Genome-wide association analysis of K content and K accumulation relative changes under N0 and N2 levels. KC: K content; KA: K accumulation."

Fig. 6

Four candidate genes relative expression levels under three nitrogen levels Radar chart is based on expression level of 1 under N1 level among three nitrogen levels."

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