Open Access Highly Accessed Research article

Grain protein content variation and its association analysis in barley

Shengguan Cai1, Gang Yu2, Xianhong Chen1, Yechang Huang1, Xiaogang Jiang3, Guoping Zhang1 and Xiaoli Jin1*

Author Affiliations

1 Agronomy Department, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China

2 Department of Nuclear Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China

3 Department of Life Science, Wenzhou Medical College, Wenzhou 325025, China

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BMC Plant Biology 2013, 13:35  doi:10.1186/1471-2229-13-35

Published: 3 March 2013

Additional files

Additional file 1: Figure S1:

Decay of linkage disequilibrium of the population of 158 accessions based on 1319 DArT markers. The equation of LD decay was y = −0.01ln(x) + 0.091, the decay of genetic distance is 0.40 cM (r2 = 0.1). The X-axis showed that the genetic distance, The Y-axis showed the r2, the squared allele frequency correlations, which is a measurement of the correlation between a pair of variables.

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Additional file 2: Table S1:

Summary of the logarithm of probability of data likelihoods (LnP(D)) for population structure of genome-wide association study (GWAS) in assessed barley genotypes. Note: Ln p(D), Natural logarithm of the probability of data. Likelihoods were calculated over ten independent runs of a burn-in of 100,000 iterations, followed by 100,000 iterations of using a model allowing for no admixture and correlated allele frequencies. K value was set up from 1 to 10 and 1319 DArT markers were used in this analysis.

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Additional file 3: Figure S2:

Population structure of 59 cultivated and 99 Tibetan wild barley accessions based on the genetic diversity detected by 1319 DArT markers. P1 to P7 represent the seven subpopulations.

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Additional file 4: Table S2:

Population sub-structuring in the 158 barley accessions. Note: C and W represent the cultivated barley and Tibetan wild barley, respectively.

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Additional file 5: Figure S3.:

The Manhattan plot of DArT markers used in association analysis. The DArT markers with unknown genetic location were excluded from the Manhattan plot. The P values were adjusted with permutation test using a step-down MinP procedure. 1H to 7H on the X-axis denoted the barley chromosomes from 1H to 7H, respectively. The Y-axis showed that the –Log10(P), The two dashed lines indicate the P value = 0.05 and 0.01.

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Additional file 6: Figure S4:

Multiple sequence alignment of HvNAM-1 gene for different haplotypes. The symbols under the sequence alignment indicate identical residues (*), and strongly conserved (:) and weakly conserved (.) substitutions by CLUSTALW (http://align.genome.jp/). Nucleotides belong to exon are shaded in gray. The SNPs are marked in red.

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Additional file 7: Figure S5:

Multiple sequence alignment of HvNAM-2 gene for different haplotypes. The symbols under the sequence alignment indicate identical residues (*), and strongly conserved (:) and weakly conserved (.) substitutions by CLUSTALW (http://align.genome.jp/). Nucleotides belong to exon are shaded in gray. The SNPs are marked in red.

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