Genetic insights in pearl millet breeding in the genomic era: challenges and prospects

Singh, Mandeep; Nara, Usha

doi:10.1007/s11816-022-00767-9

Cited by 10 publications

(5 citation statements)

References 147 publications

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“…Pearl millet is a staple crop of arid and semi-arid tropics and is known for its unique ability to tolerate abiotic stress. Various studies used a genomic approach to identify genes and pathways related to abiotic stress in pearl millet [ 21 , 22 , 23 , 24 , 25 , 26 ]. However, none of the studies performed coexpression analysis to discover genes that regulate abiotic-stress-related traits.…”

Section: Discussionmentioning

confidence: 99%

Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet

Shinde

Dudhate

Sathe

et al. 2023

Plants

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Pearl millet is a significant crop that is tolerant to abiotic stresses and is a staple food of arid regions. However, its underlying mechanisms of stress tolerance are not fully understood. Plant survival is regulated by the ability to perceive a stress signal and induce appropriate physiological changes. Here, we screened for genes regulating physiological changes such as chlorophyll content (CC) and relative water content (RWC) in response to abiotic stress by using “weighted gene coexpression network analysis” (WGCNA) and clustering changes in physiological traits, i.e., CC and RWC associated with gene expression. Genes’ correlations with traits were defined in the form of modules, and different color names were used to denote a particular module. Modules are groups of genes with similar patterns of expression, which also tend to be functionally related and co-regulated. In WGCNA, the dark green module (7082 genes) showed a significant positive correlation with CC, and the black (1393 genes) module was negatively correlated with CC and RWC. Analysis of the module positively correlated with CC highlighted ribosome synthesis and plant hormone signaling as the most significant pathways. Potassium transporter 8 and monothiol glutaredoxin were reported as the topmost hub genes in the dark green module. In Clust analysis, 2987 genes were found to display a correlation with increasing CC and RWC. Furthermore, the pathway analysis of these clusters identified the ribosome and thermogenesis as positive regulators of RWC and CC, respectively. Our study provides novel insights into the molecular mechanisms regulating CC and RWC in pearl millet.

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Section: Discussionmentioning

confidence: 99%

Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet

Shinde

Dudhate

Sathe

et al. 2023

Plants

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“…Comparative and functional genomics have untangled several loci and genes that regulate adaptive and agronomic traits in pearl millet. The use of high‐throughput sequencing technology has boosted pearl millet genomic research, providing insights into its genetic and genomic characteristics (Singh and Nara, 2022). Combined studies of genomics and phenomics in pearl millet have demonstrated achievements in recent years.…”

Section: Integrating Phenomics and Genomicsmentioning

confidence: 99%

The role of phenomics and genomics in delineating the genetic basis of complex traits in millets

Jadhav,

Thakur,

Ingle

et al. 2024

Physiologia Plantarum

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Millets, comprising a diverse group of small‐seeded grains, have emerged as vital crops with immense nutritional, environmental, and economic significance. The comprehension of complex traits in millets, influenced by multifaceted genetic determinants, presents a compelling challenge and opportunity in agricultural research. This review delves into the transformative roles of phenomics and genomics in deciphering these intricate genetic architectures. On the phenomics front, high‐throughput platforms generate rich datasets on plant morphology, physiology, and performance in diverse environments. This data, coupled with field trials and controlled conditions, helps to interpret how the environment interacts with genetics. Genomics provides the underlying blueprint for these complex traits. Genome sequencing and genotyping technologies have illuminated the millet genome landscape, revealing diverse gene pools and evolutionary relationships. Additionally, different omics approaches unveil the intricate information of gene expression, protein function, and metabolite accumulation driving phenotypic expression. This multi‐omics approach is crucial for identifying candidate genes and unfolding the intricate pathways governing complex traits. The review highlights the synergy between phenomics and genomics. Genomically informed phenotyping targets specific traits, reducing the breeding size and cost. Conversely, phenomics identifies promising germplasm for genomic analysis, prioritizing variants with superior performance. This dynamic interplay accelerates breeding programs and facilitates the development of climate‐smart, nutrient‐rich millet varieties and hybrids. In conclusion, this review emphasizes the crucial roles of phenomics and genomics in unlocking the genetic enigma of millets.

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“…Pearl millet is a staple crop of arid and semi-arid tropics and is known for its unique ability to tolerate abiotic stress. Various studies used a genomic approach to identify genes and pathways related to abiotic stress in pearl millet (20)(21)(22)(23)(24)(25). But none of the studies performed a coexpression analysis to discover genes that regulate abiotic stress-related traits.…”

Section: Endocytosismentioning

confidence: 99%

Gene coexpression analysis identifies genes associated with chlorophyll content and relative water content in pearl millet

Shinde

Dudhate

Sathe

et al. 2023

Preprint

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Pearl millet is a significant crop tolerant to abiotic stresses and is a staple food of arid regions. However, its underlying mechanisms of stress tolerance is not fully understood. Plant survival is regulated by the ability to perceive a stress signal and induce appropriate physiological changes. Here, we screened for genes regulating physiological changes such as chlorophyll content (CC) and relative water content (RWC) in response to abiotic stress. Using weighted gene coexpression network analysis (WGCNA) and clustering associated changes in physiological traits, i.e., CC and RWC with gene expression. A group of genes showing correlation with traits was identified as modules, and different color names were used to denote a particular module. In WGCNA, the darkgreen module (7082 genes) showed a significant positive correlation with CC, and the black (1393 genes) module was negatively correlated with CC and RWC. Analysis of the module positively correlated with CC highlighted ribosome synthesis and plant hormone signaling as the most significant pathways. Potassium transporter 8 and monothiol glutaredoxin were reported as the topmost hub genes in the darkgreen module. In Clust analysis, 2987 genes were found to display a correlation with increasing CC and RWC. Further, the pathway analysis of these clusters identified ribosome and thermogenesis as positive regulators of RWC and CC, respectively. Our study provides novel insights into the molecular mechanisms regulating CC and RWC in pearl millet.

show abstract

Genetic insights in pearl millet breeding in the genomic era: challenges and prospects

Cited by 10 publications

References 147 publications

Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet

Gene Coexpression Analysis Identifies Genes Associated with Chlorophyll Content and Relative Water Content in Pearl Millet

The role of phenomics and genomics in delineating the genetic basis of complex traits in millets

Gene coexpression analysis identifies genes associated with chlorophyll content and relative water content in pearl millet

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