Genetic loci mediating circadian clock output plasticity and crop productivity under barley domestication

Prusty, Manas Ranjan; Bdolach, Eyal; Yamamoto, Eiji; Tiwari, Lalit Dev; Silberman, Roi; Doron-Faigenbaum, Adi; Neyhart, Jeffrey L.; Bonfil, David J.; Kashkush, Khalil; Pillen, Klaus; Smith, Kevin P.; Fridman, Eyal

doi:10.1111/nph.17284

Cited by 15 publications

(17 citation statements)

References 63 publications

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“…Wild barley germplasm exhibited greater within-plant root plasticity to soil nutrient concentration and distribution when compared to domesticated cultivars ( Grossman and Rice, 2012 ). In barley, selection against thermal clock plasticity occurred during domestication ( Prusty et al , 2021 ). In a large study involving domesticated and wild chard, cabbage, sunflower, tomato, durum wheat, maize and pea, domesticated genotypes outperformed wild genotypes in favourable conditions but suffered greater reductions in performance in stressful conditions.…”

Section: Approaches Considerations and Promising Research Directions ...mentioning

confidence: 99%

Characterization, costs, cues and future perspectives of phenotypic plasticity

Schneider

2022

Annals of Botany

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Background Plastic responses of plants to the environment are ubiquitous. Phenotypic plasticity occurs in many forms and at many biological scales, and its adaptive value depends on the specific environment and interactions with other plant traits and organisms. Even though plasticity is the norm rather than the exception, its complex nature has been a challenge in characterizing the expression of plasticity, its adaptive value for fitness, and the environmental cues that regulate its expression. Scope This review discusses the characterization and costs of plasticity and approaches, considerations, and promising research directions in studying plasticity. Phenotypic plasticity is genetically controlled and heritable; however, little is known about how organisms perceive, interpret, and respond to environmental cues and the genes and pathways associated with plasticity. Not every genotype is plastic for every trait, and plasticity is not infinite, suggesting trade-offs, costs, and limits to express plasticity. The timing, specificity, and duration of plasticity are critical to their adaptive value for plant fitness. Conclusions There are many research opportunities to advance our understanding of plant phenotypic plasticity. New methodology and technological breakthroughs enable the study of phenotypic responses across biological scales and in multiple environments. Understanding mechanisms of plasticity and how the expression of specific phenotypes influences fitness in many environmental ranges would benefit many areas of plant science ranging from basic research to applied breeding for crop improvement.

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Section: Approaches Considerations and Promising Research Directions ...mentioning

confidence: 99%

Characterization, costs, cues and future perspectives of phenotypic plasticity

Schneider

2022

Annals of Botany

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“…Circadian clock together with light signals have gating effects on the expression of downstream genes at transcriptional and post-transcriptional levels, resulting in altered growth status under different photoperiods [9]. Many evidences in crop plants suggested that modulating the components of circadian clock pathway is an effective way to enhance the local adaption and abiotic resistance, thus enhancing agricultural productivity [10][11][12][13][14].…”

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confidence: 99%

Identification of the global diurnal rhythmic transcripts, transcription factors and time-of-day specific cis elements in Chenopodium quinoa

Bai

Luo

et al. 2023

BMC Plant Biol

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Background Photoperiod is an important environmental cue interacting with circadian clock pathway to optimize the local adaption and yield of crops. Quinoa (Chenopodium quinoa) in family Amaranthaceae has been known as superfood due to the nutritious elements. As quinoa was originated from the low-latitude Andes, most of the quinoa accessions are short-day type. Short-day type quinoa usually displays altered growth and yield status when introduced into higher latitude regions. Thus, deciphering the photoperiodic regulation on circadian clock pathway will help breed adaptable and high yielding quinoa cultivars. Results In this study, we conducted RNA-seq analysis of the diurnally collected leaves of quinoa plants treated by short-day (SD) and long-day conditions (LD), respectively. We identified 19,818 (44% of global genes) rhythmic genes in quinoa using HAYSTACK analysis. We identified the putative circadian clock architecture and investigated the photoperiodic regulatory effects on the expression phase and amplitude of global rhythmic genes, core clock components and transcription factors. The global rhythmic transcripts were involved in time-of-day specific biological processes. A higher percentage of rhythmic genes had advanced phases and strengthened amplitudes when switched from LD to SD. The transcription factors of CO-like, DBB, EIL, ERF, NAC, TALE and WRKY families were sensitive to the day length changes. We speculated that those transcription factors may function as key mediators for the circadian clock output in quinoa. Besides, we identified 15 novel time-of-day specific motifs that may be key cis elements for rhythm-keeping in quinoa. Conclusions Collectively, this study lays a foundation for understanding the circadian clock pathway and provides useful molecular resources for adaptable elites breeding in quinoa.

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“…We performed in silico analysis of the barley genome and identified seven homologs for the SIG gene, and based on phylogenetic analysis, realized the most probable ortholog of Arabidopsis SIG5 is HOR-VU1Hr1G093180 (SIG-B), which is present on chromosome 1 between chr1H: 552450872-552453097 (Figure S5B). Moreover, we realized that this position is within the previously defined DOC1.1 that was associated with the acceleration of the circadian clock output (Prusty et al, 2021). We therefore repeated the statistical analysis and, like for DOC3.…”

Section: Cni and Linkage Disequilibrium Between Chloroplastic Rpoc1 A...mentioning

confidence: 72%

Cytonuclear interactions modulate the plasticity of photosynthetic rhythmicity and growth in wild barley

Tiwari,

Bdolach,

Prusty

et al. 2024

Physiologia Plantarum

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In plants, the contribution of the plasmotype (mitochondria and chloroplast) in controlling the circadian clock plasticity and possible consequences on cytonuclear genetic makeup have yet to be fully elucidated. A genome‐wide association study in the wild barley (Hordeum vulgare ssp. spontaneum) B1K collection identified overlap with our previously mapped DRIVERS OF CLOCKS (DOCs) loci in wild‐cultivated interspecific population. Moreover, we identified non‐random segregation and epistatic interactions between nuclear DOCs loci and the chloroplastic RpoC1 gene, indicating an adaptive value for specific cytonuclear gene combinations. Furthermore, we show that DOC1.1, which harbours the candidate SIGMA FACTOR‐B (SIG‐B) gene, is linked with the differential expression of SIG‐B and CCA1 genes and contributes to the circadian gating response to heat. High‐resolution temporal growth and photosynthesis measurements of B1K also link the DOCs loci to differential growth, Chl content and quantum yield. To validate the involvement of the Plastid encoded polymerase (PEP) complex, we over‐expressed the two barley chloroplastic RpoC1 alleles in Arabidopsis and identified significant differential plasticity under elevated temperatures. Finally, enhanced clock plasticity of de novo ENU (N‐Ethyl‐N‐nitrosourea) ‐induced barley rpoB1 mutant further implicates the PEP complex as a key player in regulating the circadian clock output. Overall, this study highlights the contribution of specific cytonuclear interaction between rpoC1 (PEP gene) and SIG‐B with distinct circadian timing regulation under heat, and their pleiotropic effects on growth implicate an adaptive value.

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Genetic loci mediating circadian clock output plasticity and crop productivity under barley domestication

Cited by 15 publications

References 63 publications

Characterization, costs, cues and future perspectives of phenotypic plasticity

Characterization, costs, cues and future perspectives of phenotypic plasticity

Identification of the global diurnal rhythmic transcripts, transcription factors and time-of-day specific cis elements in Chenopodium quinoa

Cytonuclear interactions modulate the plasticity of photosynthetic rhythmicity and growth in wild barley

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