1. Volume 8, Issue 6, Pages 946-957 (June 2015)
Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study 
Quanxiu Wang, Weibo Xie, Hongkun Xing, Ju Yan, Xiangzhou Meng, Xinglei Li, Xiangkui Fu, Jiuyue Xu, Xingming Lian, Sibin Yu, Yongzhong Xing, Gongwei Wang 
Molecular Plant 
Volume 8, Issue 6, Pages (June 2015)
DOI: /j.molp
Copyright © 2015 The Author Terms and Conditions

2. Figure 1 GWAS of SPAD_FL in 2013 for the Whole Association Panel.
(A and B) The heatmap (A) and histogram (B) distribution of SPAD_FL in 2013 in 529 accessions.
(C and D) Q-Q plot of the expected null distribution and the observed P value using the linear mixed model (LMM) (C) and the simple linear regression (LR) model (D).
(E–G) Genome-wide P values for the LMM (E), simple LR model (F), and the MLMM (G). The horizontal dashed line indicates the significance thresholds set as P = 5.0 × 10−6 by LMM. The SNP positions of representative peak signals are denoted.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

3. Figure 2 GWAS of SPAD_FL in 2013 for indica.
(A and B) The heatmap (A) and histogram (B) distribution of SPAD_FL in 2013 in indica.
(C and D) Q-Q plot of the expected null distribution and the observed P value using the linear mixed model (LMM) (C) and the simple linear regression (LR) model (D).
(E–G) Genome-wide P values for the LMM (E), simple LR model (F), and multi-locus mixed model (MLMM) (G). The horizontal dashed line indicates the significance thresholds set as P = 5.0 × 10−6 by LMM. The SNP positions of representative peak signals are denoted.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

4. Figure 3 Expression Levels of Eight Genes in NIL(zs7) and NIL(mh7).
(A) LOC_Os01g52240 (chlorophyll a/b binding protein, Lhcb1.1).
(B) LOC_Os04g58200 (protochlorophyllide reductase A).
(C) LOC_Os08g33820 (chlorophyll a/b binding protein, Lhca4).
(D) LOC_Os07g37550 (chlorophyll a/b binding protein, Lhcb3).
(E) LOC_Os02g10390 (chlorophyll a/b binding protein, Lhca3).
(F) LOC_Os07g37240 (chlorophyll a/b binding protein, Lhcb4.1).
(G) LOC_Os03g36540 (magnesium-chelatase subunit chlI, OsChlI).
(H) LOC_Os08g12780 (chloroplast envelope membrane protein).
The leaves were sampled at 35 days after germination under natural long-day conditions in Wuhan and used for RNA preparation. Bars and error bars indicate average values and SE, respectively, based on 10 biological repeats. **The differences in expression levels between NIL(zs7) and NIL(mh7) are significant at P < 0.01.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

5. Figure 4
Haplotypes of NAL1 (LOC_Os04g52479) in the indica and japonica Groups.
Four haplotypes were detected and the number of accessions in each haplotype is shown. The positions of SNPs and InDels are shown in the first row. Ref, sequence identical to Nipponbare; −6, CCCGTA deleted; +13, GCATTTGCAGGTT inserted. Graphical representations of the gene structure are indicated.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions

6. Figure 5
Haplotypes and Expression Levels of the Gene (LOC_Os09g25150) in TeJ Group.
(A) Two haplotypes were detected and the number of accessions in each haplotype is shown. The positions of SNPs are shown in the first row. Trait value (13SPAD_FL) is indicated in the right column.
(B) Graphical representations of the gene structure and expression levels of the gene in different haplotypes are shown. **The differences in expression levels between hap1 and hap2 are significant at P < 0.01.
Molecular Plant 2015 8, DOI: ( /j.molp )
Copyright © 2015 The Author Terms and Conditions