Genome-wide investigation on transcriptional responses to drought stress in wild and cultivated rice

Geng, Mu-Fan; Wang, Xiuhua; Wang, Meixia; Cai, Zhe; Meng, Qinglin; Zhou, Lian; Han, Jing-Dan; Li, Ji‐Long; Zhang, Fu‐Min; Guo, Ya‐Long; Ge, Song

doi:10.1016/j.envexpbot.2021.104555

Cited by 11 publications

(6 citation statements)

References 80 publications

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“…Indeed, accumulating studies in both plants (e.g., Nakazato et al ., 2013;Lowry et al ., 2015;Ferris et al ., 2017;Roda et al ., 2017) and animals (e.g., Linnen et al ., 2013;Jacobset al ., 2017;Archambeault et al ., 2020) revealed that many QTLs were not distributed randomly across the genome but rather in hotspots involving a variety of adaptive traits. Clustering of QTLs responsible for domestication-related traits is also common in crop species (e.g., Burke et al ., 2002;Cai & Morishima 2002;Wanget al ., 2011;Yang et al ., 2019;Geng et al ., 2021). These studies suggested that QTL clustering, due to either pleiotropy or tight linkage, might be a mechanism for preventing unfit combinations of genotypes and thus facilitates rapid adaptation and speciation (Peichel & Marques, 2017;Nosil et al ., 2021;Bomblies & Peichel, 2022).…”

Section: Introductionmentioning

confidence: 99%

Genetic architecture of ecological divergence between two wild rice species (Oryza rufipogon and O. nivara)

Meng,

Chenggen,

et al. 2023

Preprint

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Ecological divergence due to habitat difference plays a prominent role in the formation of new species but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild rice species (O. rufipogon and O. nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolved linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two wild rice species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and helps effective manipulation of specific genes or gene cluster in rice breeding.

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Section: Introductionmentioning

confidence: 99%

Genetic architecture of ecological divergence between two wild rice species (Oryza rufipogon and O. nivara)

Meng,

Chenggen,

et al. 2023

Preprint

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“…Among all the abiotic stresses, drought is one of the serious environmental stresses that affect plant growth, development, and productivity; thus, hsampering crop yield and productivity of several important food crops. This causes ecological imbalance and raises concerns about food/feed security the world over [ 1 , 2 ]. The rice cultivated in rain-fed conditions is severely affected by drought due to reduced precipitation and unpredictable rainfall [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

“…Several abiotic stress-associated genes have been reported over the last decade based on comparative expression profiling of stressed versus non-stressed plants/tissues [ 1 , 4 , 10 , 16 , 19 , 20 , 21 ]. Although global gene expression analysis in rice under drought stress has been performed in different tissues using the RNA-seq approach [ 2 , 4 , 11 , 22 , 23 ], most of the studies were conducted at early (seedling or vegetative) stages of plant growth/development using different tissues (leaf and root); consequently, only a little information is available about the tolerance mechanisms active/effective against reproductive-stage drought occurring at panicle (inflorescence, an agronomically/economically important tissue that bears spikelets which develop into rice grains) initiation stage (most sensitive/critical stage of drought stress in rice). Still, only little is known about the regulation of reproductive-stage drought stress in rice, particularly about the sensing/signal transduction pathways and their interactions with the genes/pathways that affect seed development and grain yield.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome and Physio-Biochemical Profiling Reveals Differential Responses of Rice Cultivars at Reproductive-Stage Drought Stress

Kaur

Seem

Duhan

et al. 2023

IJMS

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Drought stress severely affects the growth and development of rice, especially at the reproductive stage, which results in disturbed metabolic processes, reduced seed-set/grain filling, deteriorated grain quality, declined productivity, and lower yield. Despite the recent advances in understanding the responses of rice to drought stress, there is a need to comprehensively integrate the morpho-physio-biochemical studies with the molecular responses/differential expression of genes and decipher the underlying pathways that regulate the adaptability of rice at various drought-sensitive growth stages. Our comparative analysis of immature panicle from a drought-tolerant (Nagina 22) and a drought-sensitive (IR 64) rice cultivar grown under control (well-watered) and water-deficit/drought stress (treatment, imposed at the reproductive stage) conditions unraveled some novel stress-responsive genes/pathways responsible for reproductive-stage drought stress tolerance. The results revealed a more important role of upregulated (6706) genes in the panicle of N 22 at reproductive-stage drought stress compared to that (5590) in IR 64. Functional enrichment and MapMan analyses revealed that majority of the DEGs were associated with the phytohormone, redox signalling/homeostasis, secondary metabolite, and transcription factor-mediated mitigation of the adverse effects of drought stress in N 22. The upregulated expression of the genes associated with starch/sucrose metabolism, secondary metabolites synthesis, transcription factors, glutathione, linoleic acid, and phenylalanine metabolism in N 22 was significantly more than that in the panicle of IR 64. Compared to IR 64, 2743 genes were upregulated in N 22 under control conditions, which further increased (4666) under drought stress in panicle of the tolerant cultivar. Interestingly, we observed 6706 genes to be upregulated in the panicle of N 22 over IR 64 under drought and 5814 genes get downregulated in the panicle of N 22 over IR 64 under the stress. In addition, RT-qPCR analysis confirmed differential expression patterns of the DEGs. These genes/pathways associated with the reproductive-stage drought tolerance might provide an important source of molecular markers for genetic manipulation of rice for enhanced drought tolerance.

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“…Weighted gene co-expression network analysis has been used as a powerful tool in systematic biology for the identification of key genetic networks involved in many crops ( Xu et al, 2020 ; Geng et al, 2021 ; Xiao et al, 2021 ). In this study, WGCNA revealed three modules, i.e., sky blue, yellow, and purple module, to be significantly correlated with UFA content in soybean.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic Analysis Reveals the Regulatory Networks and Hub Genes Controlling the Unsaturated Fatty Acid Contents of Developing Seed in Soybean

et al. 2022

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Soybean [Glycine max (L.) Merr.] is one of the most important crops, which produces about 25% of the world’s edible oil. The nutritional value of soybean oil depends mostly on the relative contents of three unsaturated fatty acids (UFAs), i.e., oleic acid, linoleic acid (LA), and linolenic acid. However, the biosynthetic mechanism of UFAs remains largely unknown, and there are few studies on RNA-seq analysis of developing seeds. To identify the candidate genes and related pathways involved in the regulation of UFA contents during seed development in soybean, two soybean lines with different UFA profiles were selected from 314 cultivars and landraces originated from Southern China, and RNA-seq analysis was performed in soybean seeds at three developmental stages. Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, a series of genes and pathways related to fatty acid metabolism were identified, and 40 days after flowering (DAF) was found to be the crucial period in the formation of UFA profiles. Further, weighted gene co-expression network analysis identified three modules with six genes whose functions were highly associated with the contents of oleic and LA. The detailed functional investigation of the networks and hub genes could further improve the understanding of the underlying molecular mechanism of UFA contents and might provide some ideas for the improvement in fatty acids profiles in soybean.

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Genome-wide investigation on transcriptional responses to drought stress in wild and cultivated rice

Cited by 11 publications

References 80 publications

Genetic architecture of ecological divergence between two wild rice species (Oryza rufipogon and O. nivara)

Genetic architecture of ecological divergence between two wild rice species (Oryza rufipogon and O. nivara)

Transcriptome and Physio-Biochemical Profiling Reveals Differential Responses of Rice Cultivars at Reproductive-Stage Drought Stress

Transcriptomic Analysis Reveals the Regulatory Networks and Hub Genes Controlling the Unsaturated Fatty Acid Contents of Developing Seed in Soybean

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