Identification and characterization of candidate genes involved in drought tolerance in finger millet using genome wide association mapping
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Date
2022-09
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G. B. Pant University of Agriculture and Technology, Pantnagar
G. B. Pant University of Agriculture and Technology, Pantnagar
G. B. Pant University of Agriculture and Technology, Pantnagar
Abstract
In the last two decades, drought stress has become one of the largest risks to agriculture. Drought stress negatively affects growth, development and productivity of crops. Therefore, development of climate- resilient crops is need of the hour. The identification and characterization of important candidate genes for drought tolerance and their markers will be an important step in this direction. Finger millet is a climate-resilient crop, making it the perfect crop for discovering the genes involved in drought tolerance. Morpho-physiological and biochemical parameters for 80 genotypes of finger millet from different parts of the world were phenotyped in both irrigated and drought conditions. Highly significant differences between accessions were found in the analysis of variance for both conditions for the majority of the characteristics, demonstrating that these traits are involve in drought stress. Additionally, the extensive variance in the accessions' agronomic performance suggested that these qualities would make strong candidates for marker-trait associations. Further, a analysis of genetic diversity and population structure was done and on the basis of their geographic location and drought resistance, the population was divided into two clusters, A and B, using neighbour joining cluster analysis. The major cluster A consisted broadly of all the Indian and drought tolerant genotypes whereas cluster B comprised of exotic and drought sensitive genotypes. Thus, there was good congruence between the phylogenetic tree and the population structure. Principal component analysis showed the same results as of phylogenetic and population structure which further validated that the SSR markers are related to drought tolerance. SSRs marker data along with morpho-physiological traits under both irrigated and a drought condition was used for association mapping to identify reliable marker(s) linked to drought tolerance in finger millet. A total of eleven SSR markers,SSR2, SSR3, SSR4, SSR5, SSR6, SSR9, SSR11, SSR12, SSR13, SSR14 and SSR16 with high r2 values for different morpho-physiological and biochemical traits are used for the identification of candidate genes. A total of eleven genes (ECERF1, ECERF2, ECERF3, ECCBF4, ECWRKY19, ECMYB44, ECBZIP1, ECZEP1, ECNFYB2, ECDREB1and ECNAC2) orthologous to CGs of Oryza sativa and Setaria italica putatively involved in drought tolerance homeostasis in finger millet were identified through Genome- Transcriptome transition approaches. The drought-tolerant finger millet variety PRM 6107 was utilized to study the expression of identified genes under various abiotic stress conditions, including heat, salt, and drought. In comparison to control, the genes expression increased from 10 to 14 fold under various abiotic stresses. Which further validate the role of these genes in drought stress. In silico structural and functional annotation of identified genes highlighted their significance in drought tolerance in finger millet. In light of the lack of information on the genetic and molecular basis of drought tolerance in the crop , the findings of the current investigations have opened up new opportunities for the successful use of finger millet in future crop improvement programs.
In the last two decades, drought stress has become one of the largest risks to agriculture. Drought stress negatively affects growth, development and productivity of crops. Therefore, development of climate- resilient crops is need of the hour. The identification and characterization of important candidate genes for drought tolerance and their markers will be an important step in this direction. Finger millet is a climate-resilient crop, making it the perfect crop for discovering the genes involved in drought tolerance. Morpho-physiological and biochemical parameters for 80 genotypes of finger millet from different parts of the world were phenotyped in both irrigated and drought conditions. Highly significant differences between accessions were found in the analysis of variance for both conditions for the majority of the characteristics, demonstrating that these traits are involve in drought stress. Additionally, the extensive variance in the accessions' agronomic performance suggested that these qualities would make strong candidates for marker-trait associations. Further, a analysis of genetic diversity and population structure was done and on the basis of their geographic location and drought resistance, the population was divided into two clusters, A and B, using neighbour joining cluster analysis. The major cluster A consisted broadly of all the Indian and drought tolerant genotypes whereas cluster B comprised of exotic and drought sensitive genotypes. Thus, there was good congruence between the phylogenetic tree and the population structure. Principal component analysis showed the same results as of phylogenetic and population structure which further validated that the SSR markers are related to drought tolerance. SSRs marker data along with morpho-physiological traits under both irrigated and a drought condition was used for association mapping to identify reliable marker(s) linked to drought tolerance in finger millet. A total of eleven SSR markers,SSR2, SSR3, SSR4, SSR5, SSR6, SSR9, SSR11, SSR12, SSR13, SSR14 and SSR16 with high r2 values for different morpho-physiological and biochemical traits are used for the identification of candidate genes. A total of eleven genes (ECERF1, ECERF2, ECERF3, ECCBF4, ECWRKY19, ECMYB44, ECBZIP1, ECZEP1, ECNFYB2, ECDREB1and ECNAC2) orthologous to CGs of Oryza sativa and Setaria italica putatively involved in drought tolerance homeostasis in finger millet were identified through Genome- Transcriptome transition approaches. The drought-tolerant finger millet variety PRM 6107 was utilized to study the expression of identified genes under various abiotic stress conditions, including heat, salt, and drought. In comparison to control, the genes expression increased from 10 to 14 fold under various abiotic stresses. Which further validate the role of these genes in drought stress. In silico structural and functional annotation of identified genes highlighted their significance in drought tolerance in finger millet. In light of the lack of information on the genetic and molecular basis of drought tolerance in the crop , the findings of the current investigations have opened up new opportunities for the successful use of finger millet in future crop improvement programs.
In the last two decades, drought stress has become one of the largest risks to agriculture. Drought stress negatively affects growth, development and productivity of crops. Therefore, development of climate- resilient crops is need of the hour. The identification and characterization of important candidate genes for drought tolerance and their markers will be an important step in this direction. Finger millet is a climate-resilient crop, making it the perfect crop for discovering the genes involved in drought tolerance. Morpho-physiological and biochemical parameters for 80 genotypes of finger millet from different parts of the world were phenotyped in both irrigated and drought conditions. Highly significant differences between accessions were found in the analysis of variance for both conditions for the majority of the characteristics, demonstrating that these traits are involve in drought stress. Additionally, the extensive variance in the accessions' agronomic performance suggested that these qualities would make strong candidates for marker-trait associations. Further, a analysis of genetic diversity and population structure was done and on the basis of their geographic location and drought resistance, the population was divided into two clusters, A and B, using neighbour joining cluster analysis. The major cluster A consisted broadly of all the Indian and drought tolerant genotypes whereas cluster B comprised of exotic and drought sensitive genotypes. Thus, there was good congruence between the phylogenetic tree and the population structure. Principal component analysis showed the same results as of phylogenetic and population structure which further validated that the SSR markers are related to drought tolerance. SSRs marker data along with morpho-physiological traits under both irrigated and a drought condition was used for association mapping to identify reliable marker(s) linked to drought tolerance in finger millet. A total of eleven SSR markers,SSR2, SSR3, SSR4, SSR5, SSR6, SSR9, SSR11, SSR12, SSR13, SSR14 and SSR16 with high r2 values for different morpho-physiological and biochemical traits are used for the identification of candidate genes. A total of eleven genes (ECERF1, ECERF2, ECERF3, ECCBF4, ECWRKY19, ECMYB44, ECBZIP1, ECZEP1, ECNFYB2, ECDREB1and ECNAC2) orthologous to CGs of Oryza sativa and Setaria italica putatively involved in drought tolerance homeostasis in finger millet were identified through Genome- Transcriptome transition approaches. The drought-tolerant finger millet variety PRM 6107 was utilized to study the expression of identified genes under various abiotic stress conditions, including heat, salt, and drought. In comparison to control, the genes expression increased from 10 to 14 fold under various abiotic stresses. Which further validate the role of these genes in drought stress. In silico structural and functional annotation of identified genes highlighted their significance in drought tolerance in finger millet. In light of the lack of information on the genetic and molecular basis of drought tolerance in the crop , the findings of the current investigations have opened up new opportunities for the successful use of finger millet in future crop improvement programs.