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

Thakur, N R and Gorthy, S and Vemula, A K and Odeny, D A and Ruperao, P and Sargar, P R and Mehtre, S P and Kalpande, H V and Habyarimana, E (2024) Genome‑wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains. Scientific Reports (TSI), 14. pp. 1-17. ISSN 2045-2322

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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.

Item Type:	Article
Divisions:	Global Research Program - Accelerated Crop Improvement
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Gene expression profiling, Genome-wide association studies, sorghum
Subjects:	Mandate crops > Sorghum Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	07 Jun 2024 09:56
Last Modified:	07 Jun 2024 09:56
URI:	http://oar.icrisat.org/id/eprint/12702
Official URL:	https://www.nature.com/articles/s41598-024-63308-0
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	Niranjan Ravindra Thakur acknowledges the funding support for this research from the International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India (ICRISAT). The authors thank Dr. Kamalakar Kamble and Mr. Jayakumar Jaganathan for their help in executing and managing the trials, and phenotypic data curation.
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