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Motoyuki Ashikari - One of the best experts on this subject based on the ideXlab platform.
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Correction to: Sucrose affects the developmental transition of rhizomes in Oryza longistaminata
Journal of Plant Research, 2019Co-Authors: Kanako Bessho‑uehara, Jovano Erris Nugroho, Hirono Kondo, Rosalyn B. Angeles-shim, Motoyuki AshikariAbstract:The article Sucrose affects the developmental transition of rhizomes in Oryza longistaminata , written by Kanako Bessho-Uehara, Jovano Erris Nugroho, Hirono Kondo, Rosalyn B. Angeles-Shim, Motoyuki Ashikari, was originally published electronically on the publisher’s internet portal (currently SpringerLink) on 8 May 2018 without open access.
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assembling the genome of the african wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species
Communications Biology, 2018Co-Authors: Stefan Reuscher, Tomoyuki Furuta, Kanako Besshouehara, Michele Cosi, Kshirod K Jena, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Motoyuki AshikariAbstract:The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo assembled a high-quality, haploid-phased genome. Here, we present our assembly, with a total length of 351 Mb, of which 92.2% was anchored onto 12 chromosomes. We detected 34,389 genes and 38.1% of the genome consisted of repetitive content. We validated our assembly by a comparative linkage analysis and by examining well-characterized gene families. This genome assembly will be a useful resource to exploit beneficial alleles found in O. longistaminata. Our results also show that it is possible to generate a high-quality, functionally complete rice genome assembly from moderate SMRT read coverage by exploiting synteny in a closely related Oryza species.
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Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species
Communications Biology, 2018Co-Authors: Stefan Reuscher, Kanako Bessho-uehara, Tomoyuki Furuta, Michele Cosi, Kshirod K Jena, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Motoyuki AshikariAbstract:The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo assembled a high-quality, haploid-phased genome. Here, we present our assembly, with a total length of 351 Mb, of which 92.2% was anchored onto 12 chromosomes. We detected 34,389 genes and 38.1% of the genome consisted of repetitive content. We validated our assembly by a comparative linkage analysis and by examining well-characterized gene families. This genome assembly will be a useful resource to exploit beneficial alleles found in O. longistaminata . Our results also show that it is possible to generate a high-quality, functionally complete rice genome assembly from moderate SMRT read coverage by exploiting synteny in a closely related Oryza species. Stefan Reuscher et al. assembled the genome of an African wild rice species to facilitate breeding efforts and functional genomic studies. They used SMRT sequencing, chromosomal synteny between rice species, and a linkage map to assemble the 351 Mb genome into 12 chromosomes.
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Sucrose affects the developmental transition of rhizomes in Oryza longistaminata.
Journal of Plant Research, 2018Co-Authors: Kanako Bessho-uehara, Jovano Erris Nugroho, Hirono Kondo, Rosalyn B. Angeles-shim, Motoyuki AshikariAbstract:Oryza longistaminata, the African wild rice, can propagate vegetatively through rhizomes. Rhizomes elongate horizontally underground as sink organs, however, they undergo a developmental transition that shifts their growth to the surface of the ground to become aerial stems. This particular stage is essential for the establishment of new ramets. While several determinants such as abiotic stimuli and plant hormones have been reported as key factors effecting developmental transition in aerial stem, the cause of this phenomenon in rhizome remains elusive. This study shows that depletion of nutrients, particularly sucrose, is the key stimulus that induces the developmental transition in rhizomes, as indicated by the gradient of sugars from the base to the tip of the rhizome. Sugar treatments revealed that sucrose specifically represses the developmental transition from rhizome to aerial stem by inhibiting the expression of sugar metabolism and hormone synthesis genes at the bending point. Sucrose depletion affected several factors contributing to the developmental transition of rhizome including signal transduction, transcriptional regulation and plant hormone balance.
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Analysis of Rhizome Development in Oryza longistaminata, a Wild Rice Species.
Plant and Cell Physiology, 2016Co-Authors: Akiko Yoshida, Yasuhiko Terada, Taiyo Toriba, Katsumi Kose, Motoyuki Ashikari, Junko KyozukaAbstract:: Vegetative reproduction is a form of asexual propagation in plants. A wide range of plants develop rhizomes, modified stems that grow underground horizontally, as a means of vegetative reproduction. In rhizomatous species, despite their distinct developmental patterns, both rhizomes and aerial shoots derive from axillary buds. Therefore, it is of interest to understand the basis of rhizome initiation and development. Oryza longistaminata, a wild rice species, develops rhizomes. We analyzed bud initiation and growth of O. longistaminata rhizomes using various methods of morphological observation. We show that, unlike aerial shoot buds that contain a few leaves only, rhizome buds initiate several leaves and bend to grow at right angles to the original rhizome. Rhizomes are maintained in the juvenile phase irrespective of the developmental phase of the aerial shoot. Stem elongation and reproductive transition are tightly linked in the aerial shoots, but are uncoupled in the rhizome. Our findings indicate that developmental programs operate independently in the rhizomes and aerial shoots. Temporal modification of the developmental pathways that are common to rhizomes and aerial shoots may be the source of developmental plasticity. Furthermore, the creation of new developmental systems appears to be necessary for rhizome development.
Pamela C. Ronald - One of the best experts on this subject based on the ideXlab platform.
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The Rice Xa3 Gene Confers Resistance to Xanthomonas Oryzae pv. Oryzae in the Model Rice Kitaake Genetic Background.
Frontiers in plant science, 2020Co-Authors: Furong Liu, Weiguo Zhang, Benjamin Schwessinger, Tong Wei, Deling Ruan, Pamela C. RonaldAbstract:The rice XA21 and XA3 pattern receptor kinases, derived from Oryza longistaminata and an Oryza. sativa japonica cultivar Wase Aikoku 3, respectively, confer resistance to strains of the Gram-negative bacterium Xanthomonas Oryzae pv. Oryzae (Xoo), the causal agent of rice bacterial blight disease. Previously, we showed that transfer of Xa21 to the model rice cultivar Kitaake enhances resistance to Xoo. In this manuscript we demonstrate that Kitaake expressing Xa3 confers resistance to Xoo strain PXO79 and that the stress-related marker genes PR10b and KO5 are upregulated in Xoo-infected Xa3 rice leaves. We also show that rice somatic embryogenesis receptor kinase 2 (OsSERK2) positively regulates XA3-mediated immunity in Kitaake. We found that overexpression of XA21 binding protein 15 (XB15) and XB24, two negative regulators of XA21-mediated immunity, do not affect XA3-mediated immunity in the Kitaake genetic background. Our results indicate that the rice immune receptors XA21 and XA3 employ both shared and distinct signaling components in their response to Xoo. The results are important to further understand pathogen-associated molecular pattern (PAMP)-triggered immunity in rice. Furthermore, the presence of Kitaake rice carrying Xa3 will facilitate genetic research to study the XA3-mediated immunity.
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Elucidation of XA21-mediated innate immunitycmi_1489 1..9
2014Co-Authors: Chang-jin Park, Sang-wook Han, Xuewei Chen, Pamela C. RonaldAbstract:In the early 1970s, the Xa21 gene from the wild rice species Oryza longistaminata drew attention of rice breeders because of its broad-spectrum resis-tance to diverse strains of a serious bacterial disease of rice in Asia and Africa, called ‘bacterial blight disease’, caused by the Gram-negative bac-terium, Xanthomonas Oryzae pv. Oryzae (Xoo). In 1995, we isolated the gene controlling this resis-tance and in 2009 demonstrated that XA21 recog-nizes a highly conserved peptide, called ‘Ax21’ (activator of XA21-mediated immunity). Tyrosine sulfation of Ax21 is required for recognition by rice XA21. A decade of genetic, molecular and bio-chemical studies have uncovered key components of the XA21-mediated signalling cascade. Ax21 recognition by XA21 at the cell surface induces phosphorylation-mediated events, which are pre-dicted to alter subcellular localization and/or DNA-binding activity of a WRKY family of transcription factors. Because XA21 is representative of the large number of predicted pattern recognition receptors (PRRs) in rice (n = 328), Arabidopsis (n = 35) and other plant species, further character-ization of XA21-mediated signalling pathways will contribute to elucidation of these important defence responses
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Elucidation of XA21-mediated innate immunity
Cellular microbiology, 2010Co-Authors: Chang-jin Park, Sang-wook Han, Xuewei Chen, Pamela C. RonaldAbstract:In the early 1970s, the Xa21 gene from the wild rice species Oryza longistaminata drew attention of rice breeders because of its broad-spectrum resistance to diverse strains of a serious bacterial disease of rice in Asia and Africa, called 'bacterial blight disease', caused by the Gram-negative bacterium, Xanthomonas Oryzae pv. Oryzae (Xoo). In 1995, we isolated the gene controlling this resistance and in 2009 demonstrated that XA21 recognizes a highly conserved peptide, called 'Ax21' (activator of XA21-mediated immunity). Tyrosine sulfation of Ax21 is required for recognition by rice XA21. A decade of genetic, molecular and biochemical studies have uncovered key components of the XA21-mediated signalling cascade. Ax21 recognition by XA21 at the cell surface induces phosphorylation-mediated events, which are predicted to alter subcellular localization and/or DNA-binding activity of a WRKY family of transcription factors. Because XA21 is representative of the large number of predicted pattern recognition receptors (PRRs) in rice (n = 328), Arabidopsis (n = 35) and other plant species, further characterization of XA21-mediated signalling pathways will contribute to elucidation of these important defence responses.
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Markers for selection of the rice Xa21 disease resistance gene.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 1996Co-Authors: C. E. Williams, B. Wang, T. E. Holsten, J. Scambray, F. De Assis Goes Da Silva, Pamela C. RonaldAbstract:Six molecular markers were mapped to a 7.4-cM region of rice chromosome 11 containing the Xa21 gene, which confers resistance to the pathogen Xanthomonas Oryzae pv Oryzae. Three markers, RG103, 248 and 818, co-segregated with Xa21 in a population of 1141 plants. Multiple copies of all marker loci were present within the region that was introgressed from Oryza longistaminata into O. sativa. The marker loci were cloned and primers were designed that defined sequence-tagged sites. Physical mapping of the three tightly linked central markers revealed that RG103, the marker that hybridizes to the Xa21 gene, resides on a separate DNA fragment from the other two markers.
Rosalyn B. Angeles-shim - One of the best experts on this subject based on the ideXlab platform.
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Correction to: Sucrose affects the developmental transition of rhizomes in Oryza longistaminata
Journal of Plant Research, 2019Co-Authors: Kanako Bessho‑uehara, Jovano Erris Nugroho, Hirono Kondo, Rosalyn B. Angeles-shim, Motoyuki AshikariAbstract:The article Sucrose affects the developmental transition of rhizomes in Oryza longistaminata , written by Kanako Bessho-Uehara, Jovano Erris Nugroho, Hirono Kondo, Rosalyn B. Angeles-Shim, Motoyuki Ashikari, was originally published electronically on the publisher’s internet portal (currently SpringerLink) on 8 May 2018 without open access.
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Sucrose affects the developmental transition of rhizomes in Oryza longistaminata.
Journal of Plant Research, 2018Co-Authors: Kanako Bessho-uehara, Jovano Erris Nugroho, Hirono Kondo, Rosalyn B. Angeles-shim, Motoyuki AshikariAbstract:Oryza longistaminata, the African wild rice, can propagate vegetatively through rhizomes. Rhizomes elongate horizontally underground as sink organs, however, they undergo a developmental transition that shifts their growth to the surface of the ground to become aerial stems. This particular stage is essential for the establishment of new ramets. While several determinants such as abiotic stimuli and plant hormones have been reported as key factors effecting developmental transition in aerial stem, the cause of this phenomenon in rhizome remains elusive. This study shows that depletion of nutrients, particularly sucrose, is the key stimulus that induces the developmental transition in rhizomes, as indicated by the gradient of sugars from the base to the tip of the rhizome. Sugar treatments revealed that sucrose specifically represses the developmental transition from rhizome to aerial stem by inhibiting the expression of sugar metabolism and hormone synthesis genes at the bending point. Sucrose depletion affected several factors contributing to the developmental transition of rhizome including signal transduction, transcriptional regulation and plant hormone balance.
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Development of chromosome segment substitution lines (CSSLs) of Oryza longistaminata A. Chev. & Röhr in the background of the elite japonica rice cultivar, Taichung 65 and their evaluation for yield traits
Euphytica, 2016Co-Authors: Joie M. Ramos, Rosalyn B. Angeles-shim, Motoyuki Ashikari, Darshan S. Brar, Tomoyuki Furuta, Kanako Uehara, Niwa Chihiro, Junghyun Shim, Kshirod K JenaAbstract:Oryza longistaminata (AA genome) is a wild rice species that is phenotypically inferior to cultivated rice but possesses useful alleles that can be used to improve agronomically important traits. Interspecific hybrids that are derived from cultivated rice and wild rice species with AA genome are important contributors of genetic diversity in rice. To illustrate the potential of wild rice relatives as a source of novel alleles for rice improvement, a total of 40 chromosome segment substitution lines (CSSLs) of O. longistaminata in the background of the elite japonica cultivar Taichung 65 were developed and evaluated for yield and various yield-related traits. A number of CSSLs carrying putative quantitative trait loci (QTLs) controlling different yield-related traits were identified during both dry and wet seasons. In particular, 10 major putative QTLs controlling early heading date, plant height, tiller number, panicle length, number of primary branches per panicle, grain number per panicle, grain width, and grain thickness were identified. Interestingly, one of the CSSL lines, LTSL26, with major putative QTLs on chromosomes 1 and 8 that increase grain number per panicle, showed pleiotropic effects on other traits such as plant height, days to flowering, tiller number, number of branches per panicle, and grain length. These results suggest that O. longistaminata is a good source of new alleles that can be used to improve yield-related traits in cultivated rice varieties.
Jing Zhang - One of the best experts on this subject based on the ideXlab platform.
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Genetic relatedness among Ethiopian Oryza longistaminata populations and other AA genome Oryza species
Plant Growth Regulation, 2020Co-Authors: Melaku Getachew, Shilai Zhang, Liyu Huang, Jing Zhang, Huang Guangfu, Tesfaye Kassahun, Haileselassie TeklehaimanotAbstract:Oryza longistaminata is the only AA-genome Oryza species that is perennial via rhizome production. This undomesticated rice species, which is native to Africa, is hypothesized to be a good candidate for expanding the cultivated rice gene pool. However, its phylogenetic relationships with other Oryza members are still unresolved, and it is underutilized as a genetic resource in the breeding of cultivated rice (Oryza sativa L.). This study therefore genotyped 361 O. longistaminata, 35 cultivated rice, 1 Japonica weedy-type, 25 AA genome and 8 CC genome wild rice accessions by using 67 SSR markers. Genotypic grouping confirmed the distinctness of O. longistaminata from other rice accessions and the sub-differentiation of this population influenced by eco-geographical conditions. The higher genetic diversity within the O. longistaminata population also implies its candidacy as a donor of diverse traits of interest.
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genotype by environment interactions for performance of perennial rice genotypes Oryza sativa l Oryza longistaminata relative to annual rice genotypes over regrowth cycles and locations in southern china
Field Crops Research, 2019Co-Authors: Shilai Zhang, Liyu Huang, Jing Zhang, Guangfu Huang, Mao Cheng, Zhili Wang, Yini Zhang, Chunli Wang, Pinfen Zhu, Ke TaoAbstract:Abstract Genotype by environment (GxE) interactions for performance of 5 perennial rice genotypes (Oryza sativa L./Oryza longistaminata) were examined relative to 1 mutant and 3 annual rice genotypes over 2–6 growth cycles at 7 locations in southern China between 2014 and 2017. Environment main effects accounted for 25.7% of the total sum of squares (SS), with genotype 33.8% and GxE 37.7%. Cluster analysis identified 6 genotype x 6 environment groups, which accounted for 77.9% of the GxE-SS. Principal component axes 1, 2 and 3 accounted for 54.7%, 25.1% and 9.4% of the GxE-SS, respectively, with PCA1 indicating yield potential, PCA2 performance over ratoon cycles, and PCA3 ratoon percentage. Environment groups differed in yield potential, which related to site favourability and whether it was low or high in the ratoon cycle. Genotype groups differed in yield potential and how well they performed in higher ratoon cycles. The medium-maturity (125 days) seasonally-replanted annual rice check BN21 was highest yielding (6.13 t ha−1). Perennial rice PR23 was high yielding and stable (5.25 t ha−1), with earlier maturity (119 days) and strong regrowth (82%). Ratooned annual rice RD23 was high yielding in original crops but poor yielding in ratoon crops, with a low ratoon percentage (16.5%). Similarly, perennial Bt71 and ratooned BN21 were high yielding in original crops and low-cycle ratoons under favourable conditions, but yielded poorly in high-cycle ratoons and less favourable conditions, with moderate regrowth (59.6%). Despite strong regrowth (77.5%), perennials 264 and Bt69 had low yield, as did perennial 139A and mutant TZ, and both these groups were late maturity. A combination of high yield potential, strong regrowth and earlier maturity resulted in higher performance of perennial rice over environments and regrowth cycles, with PR23 outstanding, and able to perform similarly to the seasonally-replanted annual check, BN21, over up to six growth cycles. Ratoon performance and trade-offs need to be examined further.
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Genotype by environment interactions for performance of perennial rice genotypes (Oryza sativa L./Oryza longistaminata) relative to annual rice genotypes over regrowth cycles and locations in southern China
Field Crops Research, 2019Co-Authors: Shilai Zhang, Liyu Huang, Jing Zhang, Huang Guangfu, Mao Cheng, Zhili Wang, Yini Zhang, Chunli Wang, Pinfen ZhuAbstract:Abstract Genotype by environment (GxE) interactions for performance of 5 perennial rice genotypes (Oryza sativa L./Oryza longistaminata) were examined relative to 1 mutant and 3 annual rice genotypes over 2–6 growth cycles at 7 locations in southern China between 2014 and 2017. Environment main effects accounted for 25.7% of the total sum of squares (SS), with genotype 33.8% and GxE 37.7%. Cluster analysis identified 6 genotype x 6 environment groups, which accounted for 77.9% of the GxE-SS. Principal component axes 1, 2 and 3 accounted for 54.7%, 25.1% and 9.4% of the GxE-SS, respectively, with PCA1 indicating yield potential, PCA2 performance over ratoon cycles, and PCA3 ratoon percentage. Environment groups differed in yield potential, which related to site favourability and whether it was low or high in the ratoon cycle. Genotype groups differed in yield potential and how well they performed in higher ratoon cycles. The medium-maturity (125 days) seasonally-replanted annual rice check BN21 was highest yielding (6.13 t ha−1). Perennial rice PR23 was high yielding and stable (5.25 t ha−1), with earlier maturity (119 days) and strong regrowth (82%). Ratooned annual rice RD23 was high yielding in original crops but poor yielding in ratoon crops, with a low ratoon percentage (16.5%). Similarly, perennial Bt71 and ratooned BN21 were high yielding in original crops and low-cycle ratoons under favourable conditions, but yielded poorly in high-cycle ratoons and less favourable conditions, with moderate regrowth (59.6%). Despite strong regrowth (77.5%), perennials 264 and Bt69 had low yield, as did perennial 139A and mutant TZ, and both these groups were late maturity. A combination of high yield potential, strong regrowth and earlier maturity resulted in higher performance of perennial rice over environments and regrowth cycles, with PR23 outstanding, and able to perform similarly to the seasonally-replanted annual check, BN21, over up to six growth cycles. Ratoon performance and trade-offs need to be examined further.
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Differential transcriptome profiling of chilling stress response between shoots and rhizomes of Oryza longistaminata using RNA sequencing.
PloS one, 2017Co-Authors: Ting Zhang, Shilai Zhang, Liyu Huang, Wensheng Wang, Xiuqin Zhao, Wang Yinxiao, Jing ZhangAbstract:Rice (Oryza sativa) is very sensitive to chilling stress at seedling and reproductive stages, whereas wild rice, O. longistaminata, tolerates non-freezing cold temperatures and has overwintering ability. Elucidating the molecular mechanisms of chilling tolerance (CT) in O. longistaminata should thus provide a basis for rice CT improvement through molecular breeding. In this study, high-throughput RNA sequencing was performed to profile global transcriptome alterations and crucial genes involved in response to long-term low temperature in O. longistaminata shoots and rhizomes subjected to 7 days of chilling stress. A total of 605 and 403 genes were respectively identified as up- and down-regulated in O. longistaminata under 7 days of chilling stress, with 354 and 371 differentially expressed genes (DEGs) found exclusively in shoots and rhizomes, respectively. GO enrichment and KEGG pathway analyses revealed that multiple transcriptional regulatory pathways were enriched in commonly induced genes in both tissues; in contrast, only the photosynthesis pathway was prevalent in genes uniquely induced in shoots, whereas several key metabolic pathways and the programmed cell death process were enriched in genes induced only in rhizomes. Further analysis of these tissue-specific DEGs showed that the CBF/DREB1 regulon and other transcription factors (TFs), including AP2/EREBPs, MYBs, and WRKYs, were synergistically involved in transcriptional regulation of chilling stress response in shoots. Different sets of TFs, such as OsERF922, OsNAC9, OsWRKY25, and WRKY74, and eight genes encoding antioxidant enzymes were exclusively activated in rhizomes under long-term low-temperature treatment. Furthermore, several cis-regulatory elements, including the ICE1-binding site, the GATA element for phytochrome regulation, and the W-box for WRKY binding, were highly abundant in both tissues, confirming the involvement of multiple regulatory genes and complex networks in the transcriptional regulation of CT in O. longistaminata. Finally, most chilling-induced genes with alternative splicing exclusive to shoots were associated with photosynthesis and regulation of gene expression, while those enriched in rhizomes were primarily related to stress signal transduction; this indicates that tissue-specific transcriptional and post-transcriptional regulation mechanisms synergistically contribute to O. longistaminata long-term CT. Our findings provide an overview of the complex regulatory networks of CT in O. longistaminata.
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genotype by environment interactions for grain yield of perennial rice derivatives Oryza sativa l Oryza longistaminata in southern china and laos
Field Crops Research, 2017Co-Authors: Shilai Zhang, Liyu Huang, Benjamin K. Samson, Chundao Yang, Haitao Liu, Feng Yang, Jihua Zhou, Chanthakhone Boualaphanh, Guangfu Huang, Jing ZhangAbstract:Perennial grains have been proposed to stabilise fragile lands while contributing grain and grazing in mixed farming systems. Genotype by environment (GxE) interactions for grain yield were investigated in 22 perennial rice (Oryza sativa L./Oryza longistaminata) derivatives over four successive growing seasons at three sites in Yunnan in southern China and one site in Lao PDR. The GxE interaction accounted for 25.7% of the total sum of squares, with environment and genotype responsible for 57.4% and 16.9%, respectively. Cluster analysis identified seven environment and six genotype groups, which accounted for 55.6% of the GxE sum of squares. Principal component axes 1, 2 and 3 accounted for 42.3%, 19.1% and 16.5% of the GxE-SS, respectively, with PCA1 indicating yield potential, PCA2 delay in phenology under environmental stress, and PCA3 ratoon percentage. Environment groups differed in mean temperature, whether dry season or wet season, and occurrence of environmental stresses, such as periods of low minimum temperature or periods of rainfall deficit. Genotype groups differed in adaptation to these diverse environments. For genotype groups, G5 (PR23) was highest-yielding and broadly adapted across environments, while G1 (line 188, both 137s, both 139s, both 147s) was low-yielding and poorly adapted. Other genotype groups showed preferential adaptation: G3 (lines 60, 251, 264, Bt69, Bt71) to Simao/Dry Season (E3 and E4), G4 (lines 75, 243, 246, 249, 255) to Menglian/Wet Season (E1 and E2), G2 (line TZ) to Jing Hong 2013 (E7), and G6 (lines 56, 59, 214) to Jing Hong 2102 and Na Pok (E6 and E5). The results imply that regrowth success and maintenance of spikelet fertility over regrowth cycles are important for adaptation of perennial rice, especially to low minimum temperature at higher altitude and rainfall deficit at lower altitude, and future breeding programmes in perennial rice should address these environmental stresses. The high yield and broad adaptation of PR23 (G5) over environments makes it a prime candidate for release to stabilise fragile lands in the humid and subhumid tropics, while contributing grain and forage in mixed-farming systems.
Shilai Zhang - One of the best experts on this subject based on the ideXlab platform.
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Genetic relatedness among Ethiopian Oryza longistaminata populations and other AA genome Oryza species
Plant Growth Regulation, 2020Co-Authors: Melaku Getachew, Shilai Zhang, Liyu Huang, Jing Zhang, Huang Guangfu, Tesfaye Kassahun, Haileselassie TeklehaimanotAbstract:Oryza longistaminata is the only AA-genome Oryza species that is perennial via rhizome production. This undomesticated rice species, which is native to Africa, is hypothesized to be a good candidate for expanding the cultivated rice gene pool. However, its phylogenetic relationships with other Oryza members are still unresolved, and it is underutilized as a genetic resource in the breeding of cultivated rice (Oryza sativa L.). This study therefore genotyped 361 O. longistaminata, 35 cultivated rice, 1 Japonica weedy-type, 25 AA genome and 8 CC genome wild rice accessions by using 67 SSR markers. Genotypic grouping confirmed the distinctness of O. longistaminata from other rice accessions and the sub-differentiation of this population influenced by eco-geographical conditions. The higher genetic diversity within the O. longistaminata population also implies its candidacy as a donor of diverse traits of interest.
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genotype by environment interactions for performance of perennial rice genotypes Oryza sativa l Oryza longistaminata relative to annual rice genotypes over regrowth cycles and locations in southern china
Field Crops Research, 2019Co-Authors: Shilai Zhang, Liyu Huang, Jing Zhang, Guangfu Huang, Mao Cheng, Zhili Wang, Yini Zhang, Chunli Wang, Pinfen Zhu, Ke TaoAbstract:Abstract Genotype by environment (GxE) interactions for performance of 5 perennial rice genotypes (Oryza sativa L./Oryza longistaminata) were examined relative to 1 mutant and 3 annual rice genotypes over 2–6 growth cycles at 7 locations in southern China between 2014 and 2017. Environment main effects accounted for 25.7% of the total sum of squares (SS), with genotype 33.8% and GxE 37.7%. Cluster analysis identified 6 genotype x 6 environment groups, which accounted for 77.9% of the GxE-SS. Principal component axes 1, 2 and 3 accounted for 54.7%, 25.1% and 9.4% of the GxE-SS, respectively, with PCA1 indicating yield potential, PCA2 performance over ratoon cycles, and PCA3 ratoon percentage. Environment groups differed in yield potential, which related to site favourability and whether it was low or high in the ratoon cycle. Genotype groups differed in yield potential and how well they performed in higher ratoon cycles. The medium-maturity (125 days) seasonally-replanted annual rice check BN21 was highest yielding (6.13 t ha−1). Perennial rice PR23 was high yielding and stable (5.25 t ha−1), with earlier maturity (119 days) and strong regrowth (82%). Ratooned annual rice RD23 was high yielding in original crops but poor yielding in ratoon crops, with a low ratoon percentage (16.5%). Similarly, perennial Bt71 and ratooned BN21 were high yielding in original crops and low-cycle ratoons under favourable conditions, but yielded poorly in high-cycle ratoons and less favourable conditions, with moderate regrowth (59.6%). Despite strong regrowth (77.5%), perennials 264 and Bt69 had low yield, as did perennial 139A and mutant TZ, and both these groups were late maturity. A combination of high yield potential, strong regrowth and earlier maturity resulted in higher performance of perennial rice over environments and regrowth cycles, with PR23 outstanding, and able to perform similarly to the seasonally-replanted annual check, BN21, over up to six growth cycles. Ratoon performance and trade-offs need to be examined further.
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Genotype by environment interactions for performance of perennial rice genotypes (Oryza sativa L./Oryza longistaminata) relative to annual rice genotypes over regrowth cycles and locations in southern China
Field Crops Research, 2019Co-Authors: Shilai Zhang, Liyu Huang, Jing Zhang, Huang Guangfu, Mao Cheng, Zhili Wang, Yini Zhang, Chunli Wang, Pinfen ZhuAbstract:Abstract Genotype by environment (GxE) interactions for performance of 5 perennial rice genotypes (Oryza sativa L./Oryza longistaminata) were examined relative to 1 mutant and 3 annual rice genotypes over 2–6 growth cycles at 7 locations in southern China between 2014 and 2017. Environment main effects accounted for 25.7% of the total sum of squares (SS), with genotype 33.8% and GxE 37.7%. Cluster analysis identified 6 genotype x 6 environment groups, which accounted for 77.9% of the GxE-SS. Principal component axes 1, 2 and 3 accounted for 54.7%, 25.1% and 9.4% of the GxE-SS, respectively, with PCA1 indicating yield potential, PCA2 performance over ratoon cycles, and PCA3 ratoon percentage. Environment groups differed in yield potential, which related to site favourability and whether it was low or high in the ratoon cycle. Genotype groups differed in yield potential and how well they performed in higher ratoon cycles. The medium-maturity (125 days) seasonally-replanted annual rice check BN21 was highest yielding (6.13 t ha−1). Perennial rice PR23 was high yielding and stable (5.25 t ha−1), with earlier maturity (119 days) and strong regrowth (82%). Ratooned annual rice RD23 was high yielding in original crops but poor yielding in ratoon crops, with a low ratoon percentage (16.5%). Similarly, perennial Bt71 and ratooned BN21 were high yielding in original crops and low-cycle ratoons under favourable conditions, but yielded poorly in high-cycle ratoons and less favourable conditions, with moderate regrowth (59.6%). Despite strong regrowth (77.5%), perennials 264 and Bt69 had low yield, as did perennial 139A and mutant TZ, and both these groups were late maturity. A combination of high yield potential, strong regrowth and earlier maturity resulted in higher performance of perennial rice over environments and regrowth cycles, with PR23 outstanding, and able to perform similarly to the seasonally-replanted annual check, BN21, over up to six growth cycles. Ratoon performance and trade-offs need to be examined further.
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Differential transcriptome profiling of chilling stress response between shoots and rhizomes of Oryza longistaminata using RNA sequencing.
PloS one, 2017Co-Authors: Ting Zhang, Shilai Zhang, Liyu Huang, Wensheng Wang, Xiuqin Zhao, Wang Yinxiao, Jing ZhangAbstract:Rice (Oryza sativa) is very sensitive to chilling stress at seedling and reproductive stages, whereas wild rice, O. longistaminata, tolerates non-freezing cold temperatures and has overwintering ability. Elucidating the molecular mechanisms of chilling tolerance (CT) in O. longistaminata should thus provide a basis for rice CT improvement through molecular breeding. In this study, high-throughput RNA sequencing was performed to profile global transcriptome alterations and crucial genes involved in response to long-term low temperature in O. longistaminata shoots and rhizomes subjected to 7 days of chilling stress. A total of 605 and 403 genes were respectively identified as up- and down-regulated in O. longistaminata under 7 days of chilling stress, with 354 and 371 differentially expressed genes (DEGs) found exclusively in shoots and rhizomes, respectively. GO enrichment and KEGG pathway analyses revealed that multiple transcriptional regulatory pathways were enriched in commonly induced genes in both tissues; in contrast, only the photosynthesis pathway was prevalent in genes uniquely induced in shoots, whereas several key metabolic pathways and the programmed cell death process were enriched in genes induced only in rhizomes. Further analysis of these tissue-specific DEGs showed that the CBF/DREB1 regulon and other transcription factors (TFs), including AP2/EREBPs, MYBs, and WRKYs, were synergistically involved in transcriptional regulation of chilling stress response in shoots. Different sets of TFs, such as OsERF922, OsNAC9, OsWRKY25, and WRKY74, and eight genes encoding antioxidant enzymes were exclusively activated in rhizomes under long-term low-temperature treatment. Furthermore, several cis-regulatory elements, including the ICE1-binding site, the GATA element for phytochrome regulation, and the W-box for WRKY binding, were highly abundant in both tissues, confirming the involvement of multiple regulatory genes and complex networks in the transcriptional regulation of CT in O. longistaminata. Finally, most chilling-induced genes with alternative splicing exclusive to shoots were associated with photosynthesis and regulation of gene expression, while those enriched in rhizomes were primarily related to stress signal transduction; this indicates that tissue-specific transcriptional and post-transcriptional regulation mechanisms synergistically contribute to O. longistaminata long-term CT. Our findings provide an overview of the complex regulatory networks of CT in O. longistaminata.
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Performance and survival of perennial rice derivatives (Oryza sativa L./Oryza longistaminata) in Lao PDR
Experimental Agriculture, 2017Co-Authors: Benjamin K. Samson, Shilai Zhang, Dayun Tao, Singtty Voradeth, Sisavanh Xayavong, Thiravong Khammone, Khamsouk Douangboupha, Vorachith Sihathep, Pheng Sengxua, Viengsavanh PhimphachanhvongsodAbstract:Genotype by environment (G x E) interactions for grain yield were investigated in 13 perennial rice (Oryza sativa L./Oryza longistaminata) derivatives over three sites and 2 years in Lao PDR. Genotype accounted for 29.0% of the total sum of squares, with environment and the G x E interaction responsible for 60.2 and 10.8%, respectively. Cluster analysis identified three environment and six genotype groups, which accounted for 49.7, 98.0 and 42.8% of the E, G and G x E sums of squares, respectively. Principal component axes 1, 2 and 3 accounted for 54.0, 30.6 and 11.7% of the G x E sum of squares, respectively, with PCA1 indicating yield potential, PCA2 timing of cessation of rainfall in the 2011 wet season, and PCA3 environmental stresses affecting regrowth in the 2012 wet season. Genotype groups differed in adaptation to these contrasting conditions. G6 (Line 213, 240 and RD23) was widely adapted to all environments, with G5 (Line 248) being especially adapted to the 2012 environments. G3 and G4 were neutral, though G3 (Line 53) showed some preference for the Na Pok environments. G1 and G2 were poorly adapted everywhere, with the tall and late G1 (Line 11) being especially poor at Na Pok 2011 in a dry finish. While yields were lower in 2012, all derivatives survived the dry season with access to life-saving irrigation. This is promising as the annual rice RD23 was unable to ratoon under these conditions, and had to be re-sown. Importantly, Line 213. 240 and 248 yielded comparably to RD23 from regrowth in 2012. Development of perennial rice should target rainfed and especially upland environments.