Integration of transcriptomic and proteomic analyses for finger millet [Eleusine coracana (L.) Gaertn.] in response to drought stress

Li, Ji‐Guang; Wang, Yanlan; Wang, Liqun; Zhu, Jianyu; Deng, Jing; Tang, Rui; Chen, Guanghui

doi:10.1371/journal.pone.0247181

Cited by 26 publications

(6 citation statements)

References 33 publications

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“…Further, Chandra et al (2020) used transcriptomics to study Fe and Zn homeostasis of finger millet and identified 15 putative iron and zinc homeostasis pathway candidate genes. Li et al (2021) deployed transcriptomics and proteomics to determine drought response mechanisms and identified 113 associated differentially expressed genes (DEGs) and differentially expressed proteins (DEPs). Brhane, Haileselassie, Tesfaye, Ortiz, Hammenhag, Abreha, Vetukuri, and Geleta (2022) exploited transcriptomics for both marker and trait discovery.…”

Section: Genetic and Genomic Resources Of Finger Milletmentioning

confidence: 99%

Finger millet (Eleusine coracana) improvement: Challenges and prospects—A review

Gebreyohannes,

Shimelis,

Mashilo

et al. 2024

Plant Breeding

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Finger millet is a climate‐resilient and highly nutritious small grain crop widely grown in the semi‐arid tropics. It has multiple uses, including for food, feed and beverage preparations. However, finger millet is an under‐utilized and under‐researched crop with a mean yield of <1.0 t/ha despite a potential productivity of up to 8 t/ha. The yield gap is attributed to several production constraints, such as biotic and abiotic stresses, a lack of access to improved seeds and production inputs and poor agronomic management practices. There are valuable genetic resources and genetic variability of finger millet in its centres of diversity and global gene banks for variety design, product development and commercialization. The genetic variability can be harnessed further to integrate essential traits into candidate varieties through conventional and modern breeding methods. Breeding and genetic innovations such as genomics‐assisted breeding, mutation breeding and genome editing would accelerate finger millet breeding and new variety design and deployment. The objective of this review was to document the opportunities, challenges and prospects of finger millet improvement as a guide for variety development and deployment with enhanced grain yield and nutritional contents. The first section describes global production status and yield gains, major production and productivity challenges in finger millet. This is followed by an in‐depth presentation on breeding and genetic progress on variety development with improved agronomic and nutritional quality traits, drought and salinity tolerance, and fungal diseases, weeds and insect pest resistance. Further, the review summarized finger millet's genetic and genomic resources, reference genomes, whole genome re‐sequencing and transcriptomics of finger millet technologies, genetic engineering and genome editing and their integration with conventional breeding methods for variety design with desired end‐use traits. The review provides foundational information to expedite the development of new‐generation finger millet cultivars with desirable product profiles, including high grain yield potential, early maturity, desirable seed colour, compact head type, food and feed nutrients quality and high marketability through modern breeding approaches.

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Section: Genetic and Genomic Resources Of Finger Milletmentioning

confidence: 99%

Finger millet (Eleusine coracana) improvement: Challenges and prospects—A review

Gebreyohannes,

Shimelis,

Mashilo

et al. 2024

Plant Breeding

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“…Transcriptome profiling has been successful in identifying calcium sensor genes and their potential role in calcium transport (Mirza et al 2014;Sood et al 2016;Kokane et al 2018). Functional validation of genes involved in drought tolerance, including EcDehydrin7, EcGBF3, CIPK31, and TAF6, has been conducted using qRT-PCR Ramegowda et al 2017;Hittalmani et al 2017;Parvathi and Nataraja 2017;Parvathi et al 2019;Li et al 2021). RNA-sequencing is used to study the expression patterns for drought tolerance, high calcium content, and other important features (Kumar et al 2016a,b).…”

Section: Genomics-assisted Breedingmentioning

confidence: 99%

Millets and pseudocereals: A treasure for climate resilient agriculture ensuring food and nutrition security

Nagaraja,

Parveen,

Aruna

et al. 2024

IJGPB

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Once, a staple food for civilizations and a popular feed for centuries, millets are a treasure trove of micronutrients and essential amino acids. Despite being side-lined during the Green Revolution, these small-seeded powerhouses are perfectly adapted to harsh dryland conditions such as low rainfall, drought, and high temperatures. The millets require minimal maintenance and thrive under stress, showcasing their rich genetic diversity and adaptability. However, boosting genetic gain and developing high-yielding varieties remains a challenge due to restricted research, limited genomic tools, poor market demand and accessibility to germplasm. As our climate and cropping systems are changing, millets offer a promising solution for diversification and adaptation. Beyond their impressive nutrition, they possess therapeutic benefits, making them valuable for medicinal purposes. However, the cultivation of millets, especially the minor millets, has declined due to their underutilization in daily diets. Genetic improvement and application of modern technologies are needed to increase production and integrate these millets as alternative food sources in Indian cuisine. Fortunately, growing awareness of their nutritional value, health benefits, and industrial uses is fuelling a revival. Recognizing their potential, national and international organizations are working to restore millet cultivation. The United Nations even declared 2023 as the “International Year of Millets" at Indian initiative. This review highlights the progress made in the genetic improvement of both major (sorghum, pearl millet, finger millet) and minor millets (foxtail, proso, kodo, barnyard, little and browntop millets). Additionally, pseudo-cereals like buckwheat and amaranth are included. The areas of future research have also been indicated for urgent attention and immediate action to make millets and pseudo-cereals a household food ensuring food and nutrition security and climate resilient agriculture in India.

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“…One of the significant drawbacks in this direction is the need for finger millet genomic resources. Transcriptome analysis of finger millet under salinity, drought stress, and developing spikes has been carried out in the past (Kumar et al 2015; Gururani et al 2020; Rahman et al 2014; Hittalmani et al 2017; Li et al 2021; Parvathi et al 2019).…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptome analysis in contrasting finger millet (Eleusine coracana(L.) Gaertn) genotypes for heat stress

Goyal

Singh

Mahajan

et al. 2023

Preprint

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Eleusine coracana (L.) Gaertn is a crucial C4 species renowned for its stress robustness and nutritional significance. Because of its adaptability traits, finger millet (ragi) is a storehouse of critical genomic resources for crop improvement. However, more knowledge about this crop's molecular responses to heat stress must be gained. Hence, in the present study, we generated RNA seq data from the leaf tissue of the finger millet to observe the physiological changes and gene expression study in heat-sensitive (KJNS-46) and heat-tolerant (PES-110) genotypes of Ragi in response to high temperatures. On average, each sample generated about 24 million reads. Nearly 684 transcripts were differentially expressed (DEGs) between the heat-stressed samples of both genotypes. Pathway analysis and functional annotation analysis revealed the activation of various genes involved in response to stress, precisely heat, oxidation-reduction process, water deprivation, heat shock protein and transcription factors, calcium, and kinase signaling. The basal regulatory genes, such as bZIP, were involved in response to heat stress, indicating that heat stress activates genes related to basal regulatory processes or housekeeping. A substantial percentage of the DEGs belonged to proteins of unknown functions (PUFs), i.e., uncharacterized. The expression pattern of a few selected DEGs genes was analyzed in both genotypes by quantitative RT-PCR. The present study found some candidate genes and pathways that may confer tolerance to heat stress in ragi. These results will provide valuable information to improve heat tolerance in heat-susceptible agronomically important varieties of ragi and other crop plants.

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Integration of transcriptomic and proteomic analyses for finger millet [Eleusine coracana (L.) Gaertn.] in response to drought stress

Cited by 26 publications

References 33 publications

Finger millet (Eleusine coracana) improvement: Challenges and prospects—A review

Finger millet (Eleusine coracana) improvement: Challenges and prospects—A review

Millets and pseudocereals: A treasure for climate resilient agriculture ensuring food and nutrition security

Comparative transcriptome analysis in contrasting finger millet (Eleusine coracana(L.) Gaertn) genotypes for heat stress

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