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. 2024 Jun 3;14(1):12729.
doi: 10.1038/s41598-024-63308-0.

Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains

Niranjan Ravindra Thakur  1   2 , Sunita Gorthy  1 , AnilKumar Vemula  1 , Damaris A Odeny  1 , Pradeep Ruperao  1 , Pramod Ramchandra Sargar  1   2 , Shivaji Pandurang Mehtre  2 , Hirakant V Kalpande  2 , Ephrem Habyarimana  3
Affiliations

Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains

Niranjan Ravindra Thakur et al. Sci Rep. .

Abstract

Sorghum germplasm showed grain Fe and Zn genetic variability, but a few varieties were biofortified with these minerals. This work contributes to narrowing this gap. Fe and Zn concentrations along with 55,068 high-quality GBS SNP data from 140 sorghum accessions were used in this study. Both micronutrients exhibited good variability with respective ranges of 22.09-52.55 ppm and 17.92-43.16 ppm. Significant marker-trait associations were identified on chromosomes 1, 3, and 5. Two major effect SNPs (S01_72265728 and S05_58213541) explained 35% and 32% of Fe and Zn phenotypic variance, respectively. The SNP S01_72265728 was identified in the cytochrome P450 gene and showed a positive effect on Fe accumulation in the kernel, while S05_58213541 was intergenic near Sobic.005G134800 (zinc-binding ribosomal protein) and showed negative effect on Zn. Tissue-specific in silico expression analysis resulted in higher levels of Sobic.003G350800 gene product in several tissues such as leaf, root, flower, panicle, and stem. Sobic.005G188300 and Sobic.001G463800 were expressed moderately at grain maturity and anthesis in leaf, root, panicle, and seed tissues. The candidate genes expressed in leaves, stems, and grains will be targeted to improve grain and stover quality. The haplotypes identified will be useful in forward genetics breeding.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Relationship (Pearson correlation coefficient, r) between grain iron and zinc across four different combinations of environments with a confidence interval (CI) of 95%. Comb_1, _2, _3, _4, respectively, environments combination 1, 2, 3, and 4.
Figure 2
Figure 2
Graphical representation of grain iron and zinc frequency distributions for all four combinations. Comb_1, _2, _3, _4, respectively, environments combination 1, 2, 3, and 4. Red color bars indicate the distribution of grain iron and blue color bars indicate the grain zinc distribution. The distribution of population is normal in all four combinations as described in Shapiro–Wilk test for normality in frequentist statistics. The Ryan-Joiner (RJ) statistic also confirms that phenotypic data follow a normal distribution.
Figure 3
Figure 3
Distribution of SNP markers on ten chromosomes of the sorghum. Telomeric regions of the chromosomes are highly dense relative to the centromeric regions.
Figure 4
Figure 4
Informativeness of the markers and characterization of the structure of the genotypes used for GWAS. a. LD decay distance estimated at 51.77 Kb. b. A dendrogram showing the clustering of the genotypes used. Four clear clusters are observed with the rest appearing as admixtures. Cluster I—Caudatum and associated hybrids; Cluster 2—Kafir and associated hybrids; Cluster III—Caudatum-bicolor hybrids; Cluster IV—Durra genotypes. c. PCA showing informativeness of the markers and further confirming the clustering observed in the dendrogram. d. Optimum population size estimation confirms K = 4 as the point with the lowest CV error.
Figure 5
Figure 5
Manhattan plots along with their respective QQ-plots showing the association of sorghum accessions for grain Fe and Zn content. Manhattan (left) and respective QQ-plots (right) (from top to bottom) depicted for grain Fe using BLINK, FarmCPU and MLMM in combination 2; and combination 4 using BLINK; and for grain Zn combination 1 using MLMM; and combination 2 using MLMM and SUPER. Associations were detected using 55,068 high-quality SNPs. The green horizontal line in the Manhattan plot shows the Bonferroni threshold at a 5% level: -log10p.value < 6.04, above which solid dots indicated significant MTAs.
Figure 6
Figure 6
Haplotype blocks for the significant MTAs for traits studied. Five adjacent markers on both sides of the significant SNP were used to find the significant haplotype block. The ‘BlockPattern’ at the end of the haplotype blocks describes the pattern of the respective hapblock.
Figure 7
Figure 7
Tissue-specific expression of candidate genes identified for Fe and Zn contents. The expression of five candidate genes in 36 tissues from three different growth stages (juvenile, vegetative, and reproductive) are plotted in the heatmap. Juvenile, vegetative, and reproductive stages are depicted in green, brown, and black font color, respectively.
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