start-ver=1.4 cd-journal=joma no-vol=63 cd-vols= no-issue=12 article-no= start-page=1826 end-page=1839 dt-received= dt-revised= dt-accepted= dt-pub-year=2022 dt-pub=20220518 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Plant Hormonomics: A Key Tool for Deep Physiological Phenotyping to Improve Crop Productivity en-subtitle= kn-subtitle= en-abstract= kn-abstract=Agriculture is particularly vulnerable to climate change. To cope with the risks posed by climate-related stressors to agricultural production, global population growth, and changes in food preferences, it is imperative to develop new climate-smart crop varieties with increased yield and environmental resilience. Molecular genetics and genomic analyses have revealed that allelic variations in genes involved in phytohormone-mediated growth regulation have greatly improved productivity in major crops. Plant science has remarkably advanced our understanding of the molecular basis of various phytohormone-mediated events in plant life. These findings provide essential information for improving the productivity of crops growing in changing climates. In this review, we highlight the recent advances in plant hormonomics (multiple phytohormone profiling) and discuss its application to crop improvement. We present plant hormonomics as a key tool for deep physiological phenotyping, focusing on representative plant growth regulators associated with the improvement of crop productivity. Specifically, we review advanced methodologies in plant hormonomics, highlighting mass spectrometry- and nanosensor-based plant hormone profiling techniques. We also discuss the applications of plant hormonomics in crop improvement through breeding and agricultural management practices. en-copyright= kn-copyright= en-aut-name=HirayamaTakashi en-aut-sei=Hirayama en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=MochidaKeiichi en-aut-sei=Mochida en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= en-keyword=Biosensor kn-keyword=Biosensor en-keyword=Biostimulant kn-keyword=Biostimulant en-keyword=Breeding kn-keyword=Breeding en-keyword=Mass spectrometry kn-keyword=Mass spectrometry en-keyword=Phytohormone kn-keyword=Phytohormone END start-ver=1.4 cd-journal=joma no-vol=13 cd-vols= no-issue= article-no= start-page=1004184 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2022 dt-pub=20220915 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Time-series transcriptome of Brachypodium distachyon during bacterial flagellin-induced pattern-triggered immunity en-subtitle= kn-subtitle= en-abstract= kn-abstract=Plants protect themselves from microorganisms by inducing pattern-triggered immunity (PTI) via recognizing microbe-associated molecular patterns (MAMPs), conserved across many microbes. Although the MAMP perception mechanism and initial events during PTI have been well-characterized, knowledge of the transcriptomic changes in plants, especially monocots, is limited during the intermediate and terminal stages of PTI. Here, we report a time-series high-resolution RNA-sequencing (RNA-seq) analysis during PTI in the leaf disks of Brachypodium distachyon. We identified 6,039 differentially expressed genes (DEGs) in leaves sampled at 0, 0.5, 1, 3, 6, and 12 hours after treatment (hat) with the bacterial flagellin peptide flg22. The k-means clustering method classified these DEGs into 10 clusters (6 upregulated and 4 downregulated). Based on the results, we selected 10 PTI marker genes in B. distachyon. Gene ontology (GO) analysis suggested a tradeoff between defense responses and photosynthesis during PTI. The data indicated the recovery of photosynthesis started at least at 12 hat. Over-representation analysis of transcription factor genes and cis-regulatory elements in DEG promoters implied the contribution of 12 WRKY transcription factors in plant defense at the early stage of PTI induction. en-copyright= kn-copyright= en-aut-name=OgasaharaTsubasa en-aut-sei=Ogasahara en-aut-mei=Tsubasa kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=KouzaiYusuke en-aut-sei=Kouzai en-aut-mei=Yusuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=WatanabeMegumi en-aut-sei=Watanabe en-aut-mei=Megumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=TakahashiAkihiro en-aut-sei=Takahashi en-aut-mei=Akihiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TakahagiKotaro en-aut-sei=Takahagi en-aut-mei=Kotaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=KimJune-Sik en-aut-sei=Kim en-aut-mei=June-Sik kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=MatsuiHidenori en-aut-sei=Matsui en-aut-mei=Hidenori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=YamamotoMikihiro en-aut-sei=Yamamoto en-aut-mei=Mikihiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=ToyodaKazuhiro en-aut-sei=Toyoda en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=IchinoseYuki en-aut-sei=Ichinose en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=MochidaKeiichi en-aut-sei=Mochida en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=NoutoshiYoshiteru en-aut-sei=Noutoshi en-aut-mei=Yoshiteru kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=2 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=3 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=4 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=5 en-affil=Kihara Institute for Biological Research, Yokohama City University kn-affil= affil-num=6 en-affil=Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science kn-affil= affil-num=7 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=8 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=9 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=10 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=11 en-affil=Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science kn-affil= affil-num=12 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= en-keyword=Brachypodium distachyon kn-keyword=Brachypodium distachyon en-keyword=monocotyledonous plant kn-keyword=monocotyledonous plant en-keyword=microbe-associated molecular pattern kn-keyword=microbe-associated molecular pattern en-keyword=time-series transcriptome analysis kn-keyword=time-series transcriptome analysis en-keyword=reactive oxygen species kn-keyword=reactive oxygen species en-keyword=pattern-triggered immunity kn-keyword=pattern-triggered immunity END start-ver=1.4 cd-journal=joma no-vol=45 cd-vols= no-issue=11 article-no= start-page=3322 end-page=3337 dt-received= dt-revised= dt-accepted= dt-pub-year=2022 dt-pub=20220907 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=FE UPTAKE]INDUCING PEPTIDE1 maintains Fe translocation by controlling Fe deficiency response genes in the vascular tissue of Arabidopsis en-subtitle= kn-subtitle= en-abstract= kn-abstract=FE UPTAKE-INDUCING PEPTIDE1 (FEP1), also named IRON MAN3 (IMA3) is a short peptide involved in the iron deficiency response in Arabidopsis thaliana. Recent studies uncovered its molecular function, but its physiological function in the systemic Fe response is not fully understood. To explore the physiological function of FEP1 in iron homoeostasis, we performed a transcriptome analysis using the FEP1 loss-of-function mutant fep1-1 and a transgenic line with oestrogen-inducible expression of FEP1. We determined that FEP1 specifically regulates several iron deficiency-responsive genes, indicating that FEP1 participates in iron translocation rather than iron uptake in roots. The iron concentration in xylem sap under iron-deficient conditions was lower in the fep1-1 mutant and higher in FEP1-induced transgenic plants compared with the wild type (WT). Perls staining revealed a greater accumulation of iron in the cortex of fep1-1 roots than in the WT root cortex, although total iron levels in roots were comparable in the two genotypes. Moreover, the fep1-1 mutation partially suppressed the iron overaccumulation phenotype in the leaves of the oligopeptide transporter3-2 (opt3-2) mutant. These data suggest that FEP1 plays a pivotal role in iron movement and in maintaining the iron quota in vascular tissues in Arabidopsis. en-copyright= kn-copyright= en-aut-name=OkadaSatoshi en-aut-sei=Okada en-aut-mei=Satoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=LeiGui J. en-aut-sei=Lei en-aut-mei=Gui J. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=YamajiNaoki en-aut-sei=Yamaji en-aut-mei=Naoki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=HuangSheng en-aut-sei=Huang en-aut-mei=Sheng kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=MaJian F. en-aut-sei=Ma en-aut-mei=Jian F. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=MochidaKeiichi en-aut-sei=Mochida en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=HirayamaTakashi en-aut-sei=Hirayama en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= affil-num=1 en-affil=Group of Environmental Stress Response Systems, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Group of Plant Stress Physiology, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Group of Plant Stress Physiology, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=4 en-affil=Group of Plant Stress Physiology, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=5 en-affil=Group of Plant Stress Physiology, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=6 en-affil=Crop Design Research Team, Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=7 en-affil=Group of Environmental Stress Response Systems, Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=oestrogen induction system kn-keyword=oestrogen induction system en-keyword=fep1-1 kn-keyword=fep1-1 en-keyword=iron-deficiency response kn-keyword=iron-deficiency response en-keyword=transcriptome kn-keyword=transcriptome END start-ver=1.4 cd-journal=joma no-vol=22 cd-vols= no-issue=1 article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=20210511 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf en-subtitle= kn-subtitle= en-abstract= kn-abstract=Background The developmental gradient in monocot leaves has been exploited to uncover leaf developmental gene expression programs and chloroplast biogenesis processes. However, the relationship between the two is barely understood, which limits the value of transcriptome data to understand the process of chloroplast development. Results Taking advantage of the developmental gradient in the bread wheat leaf, we provide a simultaneous quantitative analysis for the development of mesophyll cells and of chloroplasts as a cellular compartment. This allows us to generate the first biologically-informed gene expression map of this leaf, with the entire developmental gradient from meristematic to fully differentiated cells captured. We show that the first phase of plastid development begins with organelle proliferation, which extends well beyond cell proliferation, and continues with the establishment and then the build-up of the plastid genetic machinery. The second phase is marked by the development of photosynthetic chloroplasts which occupy the available cellular space. Using a network reconstruction algorithm, we predict that known chloroplast gene expression regulators are differentially involved across those developmental stages. Conclusions Our analysis generates both the first wheat leaf transcriptional map and one of the most comprehensive descriptions to date of the developmental history of chloroplasts in higher plants. It reveals functionally distinct plastid and chloroplast development stages, identifies processes occurring in each of them, and highlights our very limited knowledge of the earliest drivers of plastid biogenesis, while providing a basis for their future identification. en-copyright= kn-copyright= en-aut-name=LoudyaNaresh en-aut-sei=Loudya en-aut-mei=Naresh kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=MishraPriyanka en-aut-sei=Mishra en-aut-mei=Priyanka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=TakahagiKotaro en-aut-sei=Takahagi en-aut-mei=Kotaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=Uehara-YamaguchiYukiko en-aut-sei=Uehara-Yamaguchi en-aut-mei=Yukiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=InoueKomaki en-aut-sei=Inoue en-aut-mei=Komaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=BogreLaszlo en-aut-sei=Bogre en-aut-mei=Laszlo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=MochidaKeiichi en-aut-sei=Mochida en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=Lopez-JuezEnrique en-aut-sei=Lopez-Juez en-aut-mei=Enrique kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= affil-num=1 en-affil=Department of Biological Sciences, Royal Holloway University of London kn-affil= affil-num=2 en-affil=Department of Biological Sciences, Royal Holloway University of London kn-affil= affil-num=3 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=4 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=5 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=6 en-affil=Department of Biological Sciences, Royal Holloway University of London kn-affil= affil-num=7 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=8 en-affil=Department of Biological Sciences, Royal Holloway University of London kn-affil= en-keyword=Wheat kn-keyword=Wheat en-keyword=Plastid kn-keyword=Plastid en-keyword=Chloroplast kn-keyword=Chloroplast en-keyword=Leaf development kn-keyword=Leaf development END start-ver=1.4 cd-journal=joma no-vol=2 cd-vols= no-issue=3 article-no= start-page=lqaa067 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=202009 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Parental legacy and regulatory novelty in Brachypodium diurnal transcriptomes accompanying their polyploidy en-subtitle= kn-subtitle= en-abstract= kn-abstract=Polyploidy is a widespread phenomenon in eukaryotes that can lead to phenotypic novelty and has important implications for evolution and diversification. The modification of phenotypes in polyploids relative to their diploid progenitors may be associated with altered gene expression. However, it is largely unknown how interactions between duplicated genes affect their diurnal expression in allopolyploid species. In this study, we explored parental legacy and hybrid novelty in the transcriptomes of an allopolyploid species and its diploid progenitors. We compared the diurnal transcriptomes of representative Brachypodium cytotypes, including the allotetraploid Brachypodium hybridum and its diploid progenitors Brachypodium distachyon and Brachypodium stacei. We also artificially induced an autotetraploid B. distachyon. We identified patterns of homoeolog expression bias (HEB) across Brachypodium cytotypes and time-dependent gain and loss of HEB in B. hybridum. Furthermore, we established that many genes with diurnal expression experienced HEB, while their expression patterns and peak times were correlated between homoeologs in B. hybridum relative to B. distachyon and B. stacei, suggesting diurnal synchronization of homoeolog expression in B. hybridum. Our findings provide insight into the parental legacy and hybrid novelty associated with polyploidy in Brachypodium, and highlight the evolutionary consequences of diurnal transcriptional regulation that accompanied allopolyploidy. en-copyright= kn-copyright= en-aut-name=InoueKomaki en-aut-sei=Inoue en-aut-mei=Komaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=TakahagiKotaro en-aut-sei=Takahagi en-aut-mei=Kotaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=KouzaiYusuke en-aut-sei=Kouzai en-aut-mei=Yusuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=KodaSatoru en-aut-sei=Koda en-aut-mei=Satoru kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=ShimizuMinami en-aut-sei=Shimizu en-aut-mei=Minami kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=Uehara-YamaguchiYukiko en-aut-sei=Uehara-Yamaguchi en-aut-mei=Yukiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=NakayamaRisa en-aut-sei=Nakayama en-aut-mei=Risa kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=KitaToshie en-aut-sei=Kita en-aut-mei=Toshie kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=OndaYoshihiko en-aut-sei=Onda en-aut-mei=Yoshihiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=NomuraToshihisa en-aut-sei=Nomura en-aut-mei=Toshihisa kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=MatsuiHidetoshi en-aut-sei=Matsui en-aut-mei=Hidetoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=NagakiKiyotaka en-aut-sei=Nagaki en-aut-mei=Kiyotaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= en-aut-name=NishiiRyuei en-aut-sei=Nishii en-aut-mei=Ryuei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=13 ORCID= en-aut-name=MochidaKeiichi en-aut-sei=Mochida en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=14 ORCID= affil-num=1 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=2 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=3 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=4 en-affil=Graduate School of Mathematics, Kyushu University kn-affil= affil-num=5 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=6 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=7 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=8 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=9 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=10 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=11 en-affil=Faculty of Data Science, Shiga University kn-affil= affil-num=12 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=13 en-affil=School of Information and Data Science, Nagasaki University kn-affil= affil-num=14 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= END start-ver=1.4 cd-journal=joma no-vol=22 cd-vols= no-issue=3 article-no= start-page=1024 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=20210120 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Genetic Elucidation for Response of Flowering Time to Ambient Temperatures in Asian Rice Cultivars en-subtitle= kn-subtitle= en-abstract= kn-abstract=Climate resilience of crops is critical for global food security. Understanding the genetic basis of plant responses to ambient environmental changes is key to developing resilient crops. To detect genetic factors that set flowering time according to seasonal temperature conditions, we evaluated differences of flowering time over years by using chromosome segment substitution lines (CSSLs) derived from japonica rice cultivars "Koshihikari" x "Khao Nam Jen", each with different robustness of flowering time to environmental fluctuations. The difference of flowering times in 9 years' field tests was large in "Khao Nam Jen" (36.7 days) but small in "Koshihikari" (9.9 days). Part of this difference was explained by two QTLs. A CSSL with a "Khao Nam Jen" segment on chromosome 11 showed 28.0 days' difference; this QTL would encode a novel flowering-time gene. Another CSSL with a segment from "Khao Nam Jen" in the region around Hd16 on chromosome 3 showed 23.4 days" difference. A near-isogenic line (NIL) for Hd16 showed 21.6 days' difference, suggesting Hd16 as a candidate for this QTL. RNA-seq analysis showed differential expression of several flowering-time genes between early and late flowering seasons. Low-temperature treatment at panicle initiation stage significantly delayed flowering in the CSSL and NIL compared with "Koshihikari". Our results unravel the molecular control of flowering time under ambient temperature fluctuations. en-copyright= kn-copyright= en-aut-name=HoriKiyosumi en-aut-sei=Hori en-aut-mei=Kiyosumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=SaishoDaisuke en-aut-sei=Saisho en-aut-mei=Daisuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=NagataKazufumi en-aut-sei=Nagata en-aut-mei=Kazufumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=NonoueYasunori en-aut-sei=Nonoue en-aut-mei=Yasunori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=Uehara-YamaguchiYukiko en-aut-sei=Uehara-Yamaguchi en-aut-mei=Yukiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=KanataniAsaka en-aut-sei=Kanatani en-aut-mei=Asaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=ShuKoka en-aut-sei=Shu en-aut-mei=Koka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=HirayamaTakashi en-aut-sei=Hirayama en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=YonemaruJun-Ichi en-aut-sei=Yonemaru en-aut-mei=Jun-Ichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=FukuokaShuichi en-aut-sei=Fukuoka en-aut-mei=Shuichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=MochidaKeiichi en-aut-sei=Mochida en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= affil-num=1 en-affil=National Agriculture and Food Research Organization, Institute of Crop Science kn-affil= affil-num=2 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=National Agriculture and Food Research Organization, Institute of Crop Science kn-affil= affil-num=4 en-affil=National Agriculture and Food Research Organization, Institute of Crop Science kn-affil= affil-num=5 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=6 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=7 en-affil=National Agriculture and Food Research Organization, Institute of Crop Science kn-affil= affil-num=8 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=9 en-affil=National Agriculture and Food Research Organization, Institute of Crop Science kn-affil= affil-num=10 en-affil=National Agriculture and Food Research Organization, Institute of Crop Science kn-affil= affil-num=11 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=rice kn-keyword=rice en-keyword=flowering time kn-keyword=flowering time en-keyword=ambient temperature fluctuation kn-keyword=ambient temperature fluctuation en-keyword=chromosome segment substitution line (CSSL) kn-keyword=chromosome segment substitution line (CSSL) en-keyword=quantitative trait locus (QTL) kn-keyword=quantitative trait locus (QTL) END start-ver=1.4 cd-journal=joma no-vol=61 cd-vols= no-issue=8 article-no= start-page=1408 end-page=1418 dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=20200511 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Decoding Plant?Environment Interactions That Influence Crop Agronomic Traits en-subtitle= kn-subtitle= en-abstract= kn-abstract=To ensure food security in the face of increasing global demand due to population growth and progressive urbanization, it will be crucial to integrate emerging technologies in multiple disciplines to accelerate overall throughput of gene discovery and crop breeding. Plant agronomic traits often appear during the plantsf later growth stages due to the cumulative effects of their lifetime interactions with the environment. Therefore, decoding plant?environment interactions by elucidating plantsf temporal physiological responses to environmental changes throughout their lifespans will facilitate the identification of genetic and environmental factors, timing and pathways that influence complex end-point agronomic traits, such as yield. Here, we discuss the expected role of the life-course approach to monitoring plant and crop health status in improving crop productivity by enhancing the understanding of plant?environment interactions. We review recent advances in analytical technologies for monitoring health status in plants based on multi-omics analyses and strategies for integrating heterogeneous datasets from multiple omics areas to identify informative factors associated with traits of interest. In addition, we showcase emerging phenomics techniques that enable the noninvasive and continuous monitoring of plant growth by various means, including three-dimensional phenotyping, plant root phenotyping, implantable/injectable sensors and affordable phenotyping devices. Finally, we present an integrated review of analytical technologies and applications for monitoring plant growth, developed across disciplines, such as plant science, data science and sensors and Internet-of-things technologies, to improve plant productivity. en-copyright= kn-copyright= en-aut-name=MochidaKeiichi en-aut-sei=Mochida en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=NishiiRyuei en-aut-sei=Nishii en-aut-mei=Ryuei kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=HirayamaTakashi en-aut-sei=Hirayama en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=School of Information and Data Sciences, Nagasaki University kn-affil= affil-num=3 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=Genome to phenome kn-keyword=Genome to phenome en-keyword=Life-course approach kn-keyword=Life-course approach en-keyword=Multi-omics kn-keyword=Multi-omics en-keyword=Plant phenomics kn-keyword=Plant phenomics en-keyword=Sensor. kn-keyword=Sensor. END start-ver=1.4 cd-journal=joma no-vol=104 cd-vols= no-issue=4 article-no= start-page=995 end-page=1008 dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=20201120 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=BdWRKY38 is required for the incompatible interaction of Brachypodium distachyon with the necrotrophic fungus Rhizoctonia solani en-subtitle= kn-subtitle= en-abstract= kn-abstract=Rhizoctonia solani is a soil]borne necrotrophic fungus that causes sheath blight in grasses. The basal resistance of compatible interactions between R. solani and rice is known to be modulated by some WRKY transcription factors (TFs). However, genes and defense responses involved in incompatible interaction with R. solani remain unexplored, because no such interactions are known in any host plants. Recently, we demonstrated that Bd3]1, an accession of the model grass Brachypodium distachyon, is resistant to R. solani and, upon inoculation with the fungus, undergoes rapid induction of genes responsive to the phytohormone salicylic acid (SA) that encode the WRKY TFs BdWRKY38 and BdWRKY44. Here, we show that endogenous SA and these WRKY TFs positively regulate this accession]specific R. solani resistance. In contrast to a susceptible accession (Bd21), the infection process in the resistant accessions Bd3]1 and Tek]3 was suppressed at early stages before the development of fungal biomass and infection machinery. A comparative transcriptome analysis during pathogen infection revealed that putative WRKY]dependent defense genes were induced faster in the resistant accessions than in Bd21. A gene regulatory network (GRN) analysis based on the transcriptome dataset demonstrated that BdWRKY38 was a GRN hub connected to many target genes specifically in resistant accessions, whereas BdWRKY44 was shared in the GRNs of all three accessions. Moreover, overexpression of BdWRKY38 increased R. solani resistance in Bd21. Our findings demonstrate that these resistant accessions can activate an incompatible host response to R. solani, and BdWRKY38 regulates this response by mediating SA signaling. en-copyright= kn-copyright= en-aut-name=KouzaiYusuke en-aut-sei=Kouzai en-aut-mei=Yusuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=ShimizuMinami en-aut-sei=Shimizu en-aut-mei=Minami kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=InoueKomaki en-aut-sei=Inoue en-aut-mei=Komaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=Uehara]YamaguchiYukiko en-aut-sei=Uehara]Yamaguchi en-aut-mei=Yukiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TakahagiKotaro en-aut-sei=Takahagi en-aut-mei=Kotaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=NakayamaRisa en-aut-sei=Nakayama en-aut-mei=Risa kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=MatsuuraTakakazu en-aut-sei=Matsuura en-aut-mei=Takakazu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=MoriIzumi C. en-aut-sei=Mori en-aut-mei=Izumi C. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=HirayamaTakashi en-aut-sei=Hirayama en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=AbdelsalamSobhy S. H. en-aut-sei=Abdelsalam en-aut-mei=Sobhy S. H. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=NoutoshiYoshiteru en-aut-sei=Noutoshi en-aut-mei=Yoshiteru kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=MochidaKeiichi en-aut-sei=Mochida en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= affil-num=1 en-affil=Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science kn-affil= affil-num=2 en-affil=Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science kn-affil= affil-num=3 en-affil=Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science kn-affil= affil-num=4 en-affil=Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science kn-affil= affil-num=5 en-affil=Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science kn-affil= affil-num=6 en-affil=Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science kn-affil= affil-num=7 en-affil=Institute of Plant Science and Resources (IPSR), Okayama University kn-affil= affil-num=8 en-affil=Institute of Plant Science and Resources (IPSR), Okayama University kn-affil= affil-num=9 en-affil=Institute of Plant Science and Resources (IPSR), Okayama University kn-affil= affil-num=10 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=11 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=12 en-affil=Institute of Plant Science and Resources (IPSR), Okayama University kn-affil= en-keyword=Brachypodium distachyon kn-keyword=Brachypodium distachyon en-keyword=disease resistance kn-keyword=disease resistance en-keyword=Rhizoctonia solani kn-keyword=Rhizoctonia solani en-keyword=salicylic acid kn-keyword=salicylic acid en-keyword=incompatible interaction kn-keyword=incompatible interaction en-keyword=sheath blight kn-keyword=sheath blight en-keyword=transcriptome kn-keyword=transcriptome en-keyword=WRKY kn-keyword=WRKY END start-ver=1.4 cd-journal=joma no-vol=61 cd-vols= no-issue=8 article-no= start-page=1438 end-page=1448 dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=20200415 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Life-Course Monitoring of Endogenous Phytohormone Levels under Field Conditions Reveals Diversity of Physiological States among Barley Accessions en-subtitle= kn-subtitle= en-abstract= kn-abstract=Agronomically important traits often develop during the later stages of crop growth as consequences of various plant?environment interactions. Therefore, the temporal physiological states that change and accumulate during the cropfs life course can significantly affect the eventual phenotypic differences in agronomic traits among crop varieties. Thus, to improve productivity, it is important to elucidate the associations between temporal physiological responses during the growth of different crop varieties and their agronomic traits. However, data representing the dynamics and diversity of physiological states in plants grown under field conditions are sparse. In this study, we quantified the endogenous levels of five phytohormones ? auxin, cytokinins (CKs), ABA, jasmonate and salicylic acid ? in the leaves of eight diverse barley (Hordeum vulgare) accessions grown under field conditions sampled weekly over their life course to assess the ongoing fluctuations in hormone levels in the different accessions under field growth conditions. Notably, we observed enormous changes over time in the development-related plant hormones, such as auxin and CKs. Using 3ΠRNA-seq-based transcriptome data from the same samples, we investigated the expression of barley genes orthologous to known hormone-related genes of Arabidopsis throughout the life course. These data illustrated the dynamics and diversity of the physiological states of these field-grown barley accessions. Together, our findings provide new insights into plant?environment interactions, highlighting that there is cultivar diversity in physiological responses during growth under field conditions. en-copyright= kn-copyright= en-aut-name=HirayamaTakashi en-aut-sei=Hirayama en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=SaishoDaisuke en-aut-sei=Saisho en-aut-mei=Daisuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=MatsuuraTakakazu en-aut-sei=Matsuura en-aut-mei=Takakazu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=OkadaSatoshi en-aut-sei=Okada en-aut-mei=Satoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TakahagiKotaro en-aut-sei=Takahagi en-aut-mei=Kotaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=KanataniAsaka en-aut-sei=Kanatani en-aut-mei=Asaka kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=ItoJun en-aut-sei=Ito en-aut-mei=Jun kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=TsujiHiroyuki en-aut-sei=Tsuji en-aut-mei=Hiroyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=IkedaYoko en-aut-sei=Ikeda en-aut-mei=Yoko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=MochidaKeiichi en-aut-sei=Mochida en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= affil-num=1 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=2 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=3 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=4 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=5 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=6 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=7 en-affil=Kihara Institute for Biological Research, Yokohama City University kn-affil= affil-num=8 en-affil=Kihara Institute for Biological Research, Yokohama City University kn-affil= affil-num=9 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= affil-num=10 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= en-keyword=transcriptome kn-keyword=transcriptome en-keyword=barley kn-keyword=barley en-keyword=filed conditions kn-keyword=filed conditions en-keyword=hormone profiling kn-keyword=hormone profiling en-keyword=life-course monitoring kn-keyword=life-course monitoring END start-ver=1.4 cd-journal=joma no-vol=10 cd-vols= no-issue=1 article-no= start-page=14889 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=20200910 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Identification of effector candidate genes of Rhizoctonia solani AG-1 IA expressed during infection in Brachypodium distachyon en-subtitle= kn-subtitle= en-abstract= kn-abstract=Rhizoctonia solani is a necrotrophic phytopathogen belonging to basidiomycetes. It causes rice sheath blight which inflicts serious damage in rice production. The infection strategy of this pathogen remains unclear. We previously demonstrated that salicylic acid-induced immunity could block R. solani AG-1 IA infection in both rice and Brachypodium distachyon. R. solani may undergo biotrophic process using effector proteins to suppress host immunity before necrotrophic stage. To identify pathogen genes expressed at the early infection process, here we developed an inoculation method using B. distachyon which enables to sample an increased amount of semi-synchronous infection hyphae. Sixty-one R. solani secretory effector-like protein genes (RsSEPGs) were identified using in silico approach with the publicly available gene annotation of R. solani AG-1 IA genome and our RNA-sequencing results obtained from hyphae grown on agar medium. Expression of RsSEPGs was analyzed at 6, 10, 16, 24, and 32 h after inoculation by a quantitative reverse transcription-polymerase chain reaction and 52 genes could be detected at least on a single time point tested. Their expressions showed phase-specific patterns which were classified into 6 clusters. The 23 RsSEPGs in the cluster 1-3 and 29 RsSEPGs in the cluster 4-6 are expected to be involved in biotrophic and necrotrophic interactions, respectively. en-copyright= kn-copyright= en-aut-name=AbdelsalamSobhy S. H. en-aut-sei=Abdelsalam en-aut-mei=Sobhy S. H. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=KouzaiYusuke en-aut-sei=Kouzai en-aut-mei=Yusuke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=WatanabeMegumi en-aut-sei=Watanabe en-aut-mei=Megumi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=InoueKomaki en-aut-sei=Inoue en-aut-mei=Komaki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=MatsuiHidenori en-aut-sei=Matsui en-aut-mei=Hidenori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=YamamotoMikihiro en-aut-sei=Yamamoto en-aut-mei=Mikihiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=IchinoseYuki en-aut-sei=Ichinose en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=ToyodaKazuhiro en-aut-sei=Toyoda en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=TsugeSeiji en-aut-sei=Tsuge en-aut-mei=Seiji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=MochidaKeiichi en-aut-sei=Mochida en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=NoutoshiYoshiteru en-aut-sei=Noutoshi en-aut-mei=Yoshiteru kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=2 en-affil=Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science kn-affil= affil-num=3 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=4 en-affil=Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science kn-affil= affil-num=5 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=6 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=7 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=8 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=9 en-affil=Graduate School of Agriculture, Kyoto Prefectural University kn-affil= affil-num=10 en-affil=Institute for Plant Science and Resources (IPSR), Okayama University kn-affil= affil-num=11 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= en-keyword=Fungi kn-keyword=Fungi en-keyword=Microbiology kn-keyword=Microbiology en-keyword=Pathogens kn-keyword=Pathogens en-keyword=Plant immunity kn-keyword=Plant immunity en-keyword=Plant sciences kn-keyword=Plant sciences en-keyword=Transcription kn-keyword=Transcription END start-ver=1.4 cd-journal=joma no-vol=1 cd-vols= no-issue=1 article-no= start-page=100023 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=20200619 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Highly Efficient CRISPR-Associated Protein 9 Ribonucleoprotein-Based Genome Editing in Euglena gracilis en-subtitle= kn-subtitle= en-abstract= kn-abstract=Euglena gracilis, a unicellular phytoflagellate microalga, is a promising biomaterial for foods, feeds, and biofuels. However, targeted mutagenesis in this species has been a long-standing challenge. We recently developed a transgene-free, highly efficient, genome editing method for E.?gracilis using CRISPR/Cas9 ribonucleoproteins (RNPs). Our method achieved mutagenesis rates of approximately 80% or more through an electroporation-based direct delivery of Cas9 RNPs. Therefore, this method is suitable for basic research and industrial applications, such as the breeding of Euglena. For complete details on the use and execution of this protocol, please refer to Nomura et?al. (2019). en-copyright= kn-copyright= en-aut-name=NomuraToshihisa en-aut-sei=Nomura en-aut-mei=Toshihisa kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=YoshikawaMizuki en-aut-sei=Yoshikawa en-aut-mei=Mizuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=SuzukiKengo en-aut-sei=Suzuki en-aut-mei=Kengo kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=MochidaKeiichi en-aut-sei=Mochida en-aut-mei=Keiichi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= affil-num=1 en-affil=RIKEN Center for Sustainable Resource Science kn-affil= affil-num=2 en-affil=RIKEN Baton Zone Program kn-affil= affil-num=3 en-affil=RIKEN Baton Zone Program kn-affil= affil-num=4 en-affil=Institute of Plant Science and Resources, Okayama University kn-affil= END