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Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer.

Yang W, Guo Z, Huang C, Wang K, Jiang N, Feng H, Chen G, Liu Q, Xiong L - J. Exp. Bot. (2015)

Bottom Line: Nine associated loci contained known leaf-related genes, such as Nal1 for controlling the leaf width.In addition, a total of 73, 123, and 177 new loci were detected for traits associated with leaf size, colour, and shape, respectively.In summary, after evaluating the performance with a large number of rice accessions, the combination of GWAS and high-throughput leaf phenotyping (HLS) has proven a valuable strategy to identify the genetic loci controlling rice leaf traits.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, PR China College of Engineering, Huazhong Agricultural University, Wuhan 430070, PR China Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, PR China.

No MeSH data available.


Related in: MedlinePlus

Genome-wide association studies of six leaf traits. Manhattan plots (left) and quantile-quantile plots (right) for (a) GLA2 and (b) GLAR3 at late tillering stage; (c) GLA and (d) ALWR at late booting stage; (e) LWSD and (f) APAR at milk grain stage. For Manhattan plots, -log10 P-values from a genome-wide scan are plotted against the position of the SNPs on each of 12 chromosomes and the horizontal grey dashed line indicates the genome-wide suggestive threshold (P = 1.21×10–6). The red dashed line indicates the genome-wide significant threshold (P = 6.03×10–8). For quantile-quantile plots, the horizontal axis shows the -log10-transformed expected P-values, and the vertical axis indicates -log10-transformed observed P-values. The names of known related genes near the association signals are shown.
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Figure 6: Genome-wide association studies of six leaf traits. Manhattan plots (left) and quantile-quantile plots (right) for (a) GLA2 and (b) GLAR3 at late tillering stage; (c) GLA and (d) ALWR at late booting stage; (e) LWSD and (f) APAR at milk grain stage. For Manhattan plots, -log10 P-values from a genome-wide scan are plotted against the position of the SNPs on each of 12 chromosomes and the horizontal grey dashed line indicates the genome-wide suggestive threshold (P = 1.21×10–6). The red dashed line indicates the genome-wide significant threshold (P = 6.03×10–8). For quantile-quantile plots, the horizontal axis shows the -log10-transformed expected P-values, and the vertical axis indicates -log10-transformed observed P-values. The names of known related genes near the association signals are shown.

Mentions: Using the HLS system, a total of 29 leaf traits were extracted from 533 rice accessions that have been re-sequenced for GWAS (Chen et al., 2014). These leaf traits can be classified into three groups as follows: 6 leaf size–related traits, 7 leaf colour–related traits, and 16 leaf shape–related traits (Supplementary Table S1). GWAS was performed on these traits at three growth stages (late tillering stage, late booting stage, and milk grain stage). Using a Bonferroni correction based on the effective numbers of independent markers (Li et al., 2012), the P-value thresholds were set at 1.21 × 10−6 (suggestive) and 6.03 × 10−8 (significant) (Supplementary Table S2). In this study, a total of 542 associations (462 lead SNPs) exceeding the suggestive threshold were identified (suggestive SNPs), of which 104 associations (96 significant SNPs) exceeded the significant threshold. For the convenience of presenting of the GWAS results, a chromosomal region in which the distance of adjacent pairs of associated SNPs was less than 300kb was defined as a locus (Chen et al., 2014). As a result, 291 loci containing 462 suggestive SNPs (suggestive loci), and 78 loci containing 96 significant SNPs (significant loci) were detected (Fig. 6 and Supplementary Tables S3 and S4). There were some loci with multiple associated SNPs, and loci were repeatedly detected for different traits or repeatedly detected by the same trait at different growth stages. For example, locus 158 was detected with green-4 leaf area ratio (GLAR4) at late booting stage and milk grain stage, green-2 leaf area (GLA2) at late booting stage, and maximum leaf area at milk grain stage, simultaneously. Furthermore, two independently associated SNPs (LD statistics r2 = 0.09) with GLAR4 at late booting stage, sf0620856382 and sf0620860929, were located at this locus at only a 4-kb distance. Among the 78 significant loci, 16 loci were repeatedly detected through different leaf traits; one locus was detected through the same trait at different growth stages; and two loci with multiple associated SNPs were detected (Supplementary Table S4). Manhattan plots for all the traits mentioned above are shown in Supplementary Fig. S5–S7. In total, 131, 62, and 173 suggestive loci and 37, 7, and 38 significant loci were detected at late tillering stage, late booting stage, and milk grain stage, respectively. Only five suggestive loci but no significant loci were detected at the three growth stages simultaneously. These results suggest that the genetic basis of these leaf traits at different growth stages may not be the same in rice (Fig. 7).


Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer.

Yang W, Guo Z, Huang C, Wang K, Jiang N, Feng H, Chen G, Liu Q, Xiong L - J. Exp. Bot. (2015)

Genome-wide association studies of six leaf traits. Manhattan plots (left) and quantile-quantile plots (right) for (a) GLA2 and (b) GLAR3 at late tillering stage; (c) GLA and (d) ALWR at late booting stage; (e) LWSD and (f) APAR at milk grain stage. For Manhattan plots, -log10 P-values from a genome-wide scan are plotted against the position of the SNPs on each of 12 chromosomes and the horizontal grey dashed line indicates the genome-wide suggestive threshold (P = 1.21×10–6). The red dashed line indicates the genome-wide significant threshold (P = 6.03×10–8). For quantile-quantile plots, the horizontal axis shows the -log10-transformed expected P-values, and the vertical axis indicates -log10-transformed observed P-values. The names of known related genes near the association signals are shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4585412&req=5

Figure 6: Genome-wide association studies of six leaf traits. Manhattan plots (left) and quantile-quantile plots (right) for (a) GLA2 and (b) GLAR3 at late tillering stage; (c) GLA and (d) ALWR at late booting stage; (e) LWSD and (f) APAR at milk grain stage. For Manhattan plots, -log10 P-values from a genome-wide scan are plotted against the position of the SNPs on each of 12 chromosomes and the horizontal grey dashed line indicates the genome-wide suggestive threshold (P = 1.21×10–6). The red dashed line indicates the genome-wide significant threshold (P = 6.03×10–8). For quantile-quantile plots, the horizontal axis shows the -log10-transformed expected P-values, and the vertical axis indicates -log10-transformed observed P-values. The names of known related genes near the association signals are shown.
Mentions: Using the HLS system, a total of 29 leaf traits were extracted from 533 rice accessions that have been re-sequenced for GWAS (Chen et al., 2014). These leaf traits can be classified into three groups as follows: 6 leaf size–related traits, 7 leaf colour–related traits, and 16 leaf shape–related traits (Supplementary Table S1). GWAS was performed on these traits at three growth stages (late tillering stage, late booting stage, and milk grain stage). Using a Bonferroni correction based on the effective numbers of independent markers (Li et al., 2012), the P-value thresholds were set at 1.21 × 10−6 (suggestive) and 6.03 × 10−8 (significant) (Supplementary Table S2). In this study, a total of 542 associations (462 lead SNPs) exceeding the suggestive threshold were identified (suggestive SNPs), of which 104 associations (96 significant SNPs) exceeded the significant threshold. For the convenience of presenting of the GWAS results, a chromosomal region in which the distance of adjacent pairs of associated SNPs was less than 300kb was defined as a locus (Chen et al., 2014). As a result, 291 loci containing 462 suggestive SNPs (suggestive loci), and 78 loci containing 96 significant SNPs (significant loci) were detected (Fig. 6 and Supplementary Tables S3 and S4). There were some loci with multiple associated SNPs, and loci were repeatedly detected for different traits or repeatedly detected by the same trait at different growth stages. For example, locus 158 was detected with green-4 leaf area ratio (GLAR4) at late booting stage and milk grain stage, green-2 leaf area (GLA2) at late booting stage, and maximum leaf area at milk grain stage, simultaneously. Furthermore, two independently associated SNPs (LD statistics r2 = 0.09) with GLAR4 at late booting stage, sf0620856382 and sf0620860929, were located at this locus at only a 4-kb distance. Among the 78 significant loci, 16 loci were repeatedly detected through different leaf traits; one locus was detected through the same trait at different growth stages; and two loci with multiple associated SNPs were detected (Supplementary Table S4). Manhattan plots for all the traits mentioned above are shown in Supplementary Fig. S5–S7. In total, 131, 62, and 173 suggestive loci and 37, 7, and 38 significant loci were detected at late tillering stage, late booting stage, and milk grain stage, respectively. Only five suggestive loci but no significant loci were detected at the three growth stages simultaneously. These results suggest that the genetic basis of these leaf traits at different growth stages may not be the same in rice (Fig. 7).

Bottom Line: Nine associated loci contained known leaf-related genes, such as Nal1 for controlling the leaf width.In addition, a total of 73, 123, and 177 new loci were detected for traits associated with leaf size, colour, and shape, respectively.In summary, after evaluating the performance with a large number of rice accessions, the combination of GWAS and high-throughput leaf phenotyping (HLS) has proven a valuable strategy to identify the genetic loci controlling rice leaf traits.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, PR China College of Engineering, Huazhong Agricultural University, Wuhan 430070, PR China Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, PR China.

No MeSH data available.


Related in: MedlinePlus