Juan B. Fontanet‐Manzaneque, Natalie Laibach, Iván Herrero‐García, Veredas Coleto‐Alcudia, David Blasco‐Escámez, Chen Zhang, Luis Orduña, Saleh Alseekh, Sara Miller, Nanna Bjarnholt, Alisdair R. Fernie, José Tomás Matus, Ana I. Caño‐Delgado
SummaryDrought is a critical issue in modern agriculture; therefore, there is a need to create crops with drought resilience. The complexity of plant responses to abiotic stresses, particularly in the field of brassinosteroid (BR) signalling, has been the subject of extensive research. In this study, we unveil compelling insights indicating that the BRASSINOSTEROID‐INSENSITIVE 1 (BRI1) receptor in Arabidopsis and Sorghum plays a critical role as a negative regulator of drought responses. Introducing untargeted mutation in the sorghum BRI1 receptor (SbBRI1) effectively enhances the plant's ability to withstand osmotic and drought stress. Through DNA Affinity Purification sequencing (DAP‐seq), we show that the sorghum BRI1‐EMS‐SUPPRESSOR 1 (SbBES1) transcription factor, a downstream player of the BR signalling, binds to a conserved G‐box binding motif, and it is responsible for regulating BR homeostasis, as its Arabidopsis ortholog AtBES1. We further characterized the drought tolerance of sorghum bri1 mutants and decipher SbBES1‐mediated regulation of phenylpropanoid pathway. Our findings suggest that SbBRI1 signalling serves a dual purpose: under normal conditions, it regulates lignin biosynthesis by SbBES1, but during drought conditions, BES1 becomes less active, allowing the activation of the flavonoid pathway. This adaptive shift improves the photosynthetic rate and photoprotection, reinforcing crop adaptation to drought.
{"title":"Untargeted mutagenesis of brassinosteroid receptor SbBRI1 confers drought tolerance by altering phenylpropanoid metabolism in Sorghum bicolor","authors":"Juan B. Fontanet‐Manzaneque, Natalie Laibach, Iván Herrero‐García, Veredas Coleto‐Alcudia, David Blasco‐Escámez, Chen Zhang, Luis Orduña, Saleh Alseekh, Sara Miller, Nanna Bjarnholt, Alisdair R. Fernie, José Tomás Matus, Ana I. Caño‐Delgado","doi":"10.1111/pbi.14461","DOIUrl":"https://doi.org/10.1111/pbi.14461","url":null,"abstract":"SummaryDrought is a critical issue in modern agriculture; therefore, there is a need to create crops with drought resilience. The complexity of plant responses to abiotic stresses, particularly in the field of brassinosteroid (BR) signalling, has been the subject of extensive research. In this study, we unveil compelling insights indicating that the BRASSINOSTEROID‐INSENSITIVE 1 (BRI1) receptor in Arabidopsis and Sorghum plays a critical role as a negative regulator of drought responses. Introducing untargeted mutation in the sorghum BRI1 receptor (SbBRI1) effectively enhances the plant's ability to withstand osmotic and drought stress. Through DNA Affinity Purification sequencing (DAP‐seq), we show that the sorghum BRI1‐EMS‐SUPPRESSOR 1 (SbBES1) transcription factor, a downstream player of the BR signalling, binds to a conserved G‐box binding motif, and it is responsible for regulating BR homeostasis, as its Arabidopsis ortholog AtBES1. We further characterized the drought tolerance of sorghum <jats:italic>bri1</jats:italic> mutants and decipher SbBES1‐mediated regulation of phenylpropanoid pathway. Our findings suggest that SbBRI1 signalling serves a dual purpose: under normal conditions, it regulates lignin biosynthesis by SbBES1, but during drought conditions, BES1 becomes less active, allowing the activation of the flavonoid pathway. This adaptive shift improves the photosynthetic rate and photoprotection, reinforcing crop adaptation to drought.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"24 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zhou Zhou, Rajvinder Kaur, Thomas Donoso, Jae‐Bom Ohm, Rajeev Gupta, Mark Lefsrud, Jaswinder Singh
SummaryThe endeavour to elevate the nutritional value of oat (Avena sativa) by altering the oil composition and content positions it as an optimal crop for fostering human health and animal feed. However, optimization of oil traits on oat through conventional breeding is challenging due to its quantitative nature and complexity of the oat genome. We introduced two constructs containing three key genes integral to lipid biosynthesis and/or regulatory pathways from Arabidopsis (AtWRI1 and AtDGAT1) and Sesame (SiOLEOSIN) into the oat cultivar ‘Park’ to modify the fatty acid composition. Four homozygous transgenic lines were generated with a transformation frequency of 7%. The expression of these introduced genes initiated a comprehensive transcriptional reprogramming in oat grains and leaves. Notably, endogenous DGAT, WRI1 and OLEOSIN genes experienced upregulation, while genes associated with fatty acid biosynthesis, such as KASII, SACPD and FAD2, displayed antagonistic expression patterns between oat grains and leaves. Transcriptomic analyses highlighted significant differential gene expression, particularly enriched in lipid metabolism. Comparing the transgenic oat plants with the wild type, we observed a remarkable increase of up to 34% in oleic acid content in oat grains. Furthermore, there were marked improvements in the total oil content in oat leaves, as well as primary metabolites changes in both oat grains and leaves, while maintaining homeostasis in the transgenic oat plants. These findings underscore the effectiveness of genetic engineering in manipulating oat oil composition and content, offering promising implications for human consumption and animal feeding through oat crop improvement programmes.
{"title":"Metabolic engineering‐induced transcriptome reprogramming of lipid biosynthesis enhances oil composition in oat","authors":"Zhou Zhou, Rajvinder Kaur, Thomas Donoso, Jae‐Bom Ohm, Rajeev Gupta, Mark Lefsrud, Jaswinder Singh","doi":"10.1111/pbi.14467","DOIUrl":"https://doi.org/10.1111/pbi.14467","url":null,"abstract":"SummaryThe endeavour to elevate the nutritional value of oat (<jats:italic>Avena sativa</jats:italic>) by altering the oil composition and content positions it as an optimal crop for fostering human health and animal feed. However, optimization of oil traits on oat through conventional breeding is challenging due to its quantitative nature and complexity of the oat genome. We introduced two constructs containing three key genes integral to lipid biosynthesis and/or regulatory pathways from Arabidopsis (<jats:italic>AtWRI1</jats:italic> and <jats:italic>AtDGAT1</jats:italic>) and Sesame (<jats:italic>SiOLEOSIN</jats:italic>) into the oat cultivar ‘Park’ to modify the fatty acid composition. Four homozygous transgenic lines were generated with a transformation frequency of 7%. The expression of these introduced genes initiated a comprehensive transcriptional reprogramming in oat grains and leaves. Notably, endogenous <jats:italic>DGAT</jats:italic>, <jats:italic>WRI1</jats:italic> and <jats:italic>OLEOSIN</jats:italic> genes experienced upregulation, while genes associated with fatty acid biosynthesis, such as <jats:italic>KASII</jats:italic>, <jats:italic>SACPD</jats:italic> and <jats:italic>FAD2</jats:italic>, displayed antagonistic expression patterns between oat grains and leaves. Transcriptomic analyses highlighted significant differential gene expression, particularly enriched in lipid metabolism. Comparing the transgenic oat plants with the wild type, we observed a remarkable increase of up to 34% in oleic acid content in oat grains. Furthermore, there were marked improvements in the total oil content in oat leaves, as well as primary metabolites changes in both oat grains and leaves, while maintaining homeostasis in the transgenic oat plants. These findings underscore the effectiveness of genetic engineering in manipulating oat oil composition and content, offering promising implications for human consumption and animal feeding through oat crop improvement programmes.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"24 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142321829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
It is well known that the overall quality of japonica/geng rice is superior to that of indica/xian rice varieties. However, the molecular mechanisms underlying the quality disparities between these two subspecies of rice are still largely unknown. In this study, we have pinpointed a gene homologous to SLR1, termed LCG1, exhibiting significant expression during early caryopsis development and playing a specific role in regulating rice chalkiness and taste by affecting the accumulation of grain storage components, starch granule structure and chain length distribution of amylopectin. LCG1 physically interacts with OsBP5 and indirectly influences the expression of the amylose synthesis gene Waxy (Wx) by hindering the transcriptional activity of the OsBP5/OsEBP89 complex. Notably, sequence variations in the promoter region of LCG1 result in enhanced transcription in japonica rice accessions. This leads to elevated LCG1 expression in CSSL-LCG1Nip, thereby enhancing rice quality. Our research elucidates the molecular mechanism underlying the impact of the LCG1-OsBP5/OsEBP89-Wx regulatory pathway on rice chalkiness and taste quality, offering new genetic resources for improving the indica rice quality.
{"title":"The LCG1-OsBP5/OsEBP89-Wx module regulates the grain chalkiness and taste quality in rice","authors":"Bin Tu, Tao Zhang, Pin Liu, Wen Yang, Ling Zheng, Ying Dai, Hao Wang, Song Lin, Zehua Zhang, Xiaohang Zheng, Mengting Yuan, Yong Chen, Xiaobo Zhu, Hua Yuan, Ting Li, Jiawei Xiong, Zhaohui Zhong, Weilan Chen, Bingtian Ma, Peng Qin, Yuping Wang, Shigui Li","doi":"10.1111/pbi.14475","DOIUrl":"https://doi.org/10.1111/pbi.14475","url":null,"abstract":"It is well known that the overall quality of <i>japonica/geng</i> rice is superior to that of <i>indica/xian</i> rice varieties. However, the molecular mechanisms underlying the quality disparities between these two subspecies of rice are still largely unknown. In this study, we have pinpointed a gene homologous to <i>SLR1</i>, termed <i>LCG1</i>, exhibiting significant expression during early caryopsis development and playing a specific role in regulating rice chalkiness and taste by affecting the accumulation of grain storage components, starch granule structure and chain length distribution of amylopectin. LCG1 physically interacts with OsBP5 and indirectly influences the expression of the amylose synthesis gene <i>Waxy</i> (<i>Wx</i>) by hindering the transcriptional activity of the OsBP5/OsEBP89 complex. Notably, sequence variations in the promoter region of <i>LCG1</i> result in enhanced transcription in <i>japonica</i> rice accessions. This leads to elevated <i>LCG1</i> expression in CSSL<i>-LCG1</i><sup>Nip</sup>, thereby enhancing rice quality. Our research elucidates the molecular mechanism underlying the impact of the LCG1-OsBP5/OsEBP89-<i>Wx</i> regulatory pathway on rice chalkiness and taste quality, offering new genetic resources for improving the <i>indica</i> rice quality.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"65 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Haipeng Zhang, Xiaodong Lian, Fan Gao, Conghao Song, Beibei Feng, Xianbo Zheng, Xiaobei Wang, Nan Hou, Jun Cheng, Wei Wang, Langlang Zhang, Jidong Li, Xia Ye, Jiancan Feng, Bin Tan
{"title":"A gap‐free genome of pillar peach (Prunus persica L.) provides new insights into branch angle and double flower traits","authors":"Haipeng Zhang, Xiaodong Lian, Fan Gao, Conghao Song, Beibei Feng, Xianbo Zheng, Xiaobei Wang, Nan Hou, Jun Cheng, Wei Wang, Langlang Zhang, Jidong Li, Xia Ye, Jiancan Feng, Bin Tan","doi":"10.1111/pbi.14480","DOIUrl":"https://doi.org/10.1111/pbi.14480","url":null,"abstract":"","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"21 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
<p>Weed species have increasingly emerged with resistance against previously effective herbicides, such as glyphosate and inhibitors of acetyl coenzyme A carboxylase (ACCase) and acetolactate synthase (ALS) (Heap, <span>2024</span>). Owing to its novel mode of action, 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibitors are effective in controlling herbicide-resistant weeds and recently attracted much attention. Resistance to HPPD-inhibitors has been slow to evolve in weeds, and only a few cases of resistant events have been reported and most of these are associated with enhanced herbicide metabolism (Heap, <span>2024</span>; Lu <i>et al</i>., <span>2023</span>). Since resistant sites in the entire target gene are largely unknown, we <i>in vivo</i> mutagenized the <i>HPPD</i> gene in Arabidopsis and rice using base editing libraries to uncover potential target-site resistant mutations.</p> <p>Arabidopsis are highly sensitive to mesotrione. After large-scale transformation of base editing pools (Figure S1), we found one T1 seedling growing normally in medium containing 100 nM mesotrione (Figure S2a). Genotyping showed that a heterozygous T-to-C substitution occurred, causing the Y342H mutation in the HPPD protein sequence (Figure S2b, c). Homozygous progenies of <i>HPPD</i><sup><i>Y342H</i></sup> (Figure S2d) were tolerant up to 200 nM mesotrione and 50 nM isoxaflutole in medium (Figures 1a and S3a) and had a much higher survival rate than wild type (WT) when sprayed with ≥1 μM mesotrione or isoxaflutole in pots (Figure 1b, c). <i>AtHPPD</i><sup><i>Y342H</i></sup> mutants exhibited similar phenotype and showed no significant differences in plant height and seed yield with the WT plants (Figure S4).</p> <figure><picture> <source media="(min-width: 1650px)" srcset="/cms/asset/0c020b3d-76a3-4853-894c-ba167297cbe4/pbi14478-fig-0001-m.jpg"/><img alt="Details are in the caption following the image" data-lg-src="/cms/asset/0c020b3d-76a3-4853-894c-ba167297cbe4/pbi14478-fig-0001-m.jpg" loading="lazy" src="/cms/asset/32583bc8-f9ce-44ae-816c-675d85c88574/pbi14478-fig-0001-m.png" title="Details are in the caption following the image"/></picture><figcaption> <div><strong>Figure 1<span style="font-weight:normal"></span></strong><div>Open in figure viewer<i aria-hidden="true"></i><span>PowerPoint</span></div> </div> <div>Target-site-mutations improve plant resistance to HPPD-inhibitors. The AtHPPD<sup>Y342H</sup> mutation significantly increases tolerance to mesotrione (MST) and isoxaflutole (IFT) during germination (a) and seedling (b). Bar equals 3 cm (a) or 7.5 cm (b). (c) Survival rate of the wild type (WT) Col-0 and <i>AtHPPD</i><sup><i>Y342H</i></sup> mutants after being sprayed with herbicides at the seedling stage. Phenotype of the soybean WT and <i>GmHPPD</i><sup><i>Y388H</i></sup> mutants after being sprayed with MST (d) or IFT (e). Bar equals 15 cm. (f) Seed amount and yield from soybean WT and <i>GmHPPD</i><sup><i>Y388H</i></sup> mutants grown in gr
{"title":"Identifying resistant mutations in the herbicide target site of the plant 4-hydroxyphenylpyruvate dioxygenase","authors":"Mugui Wang, Yingli Zhong, Yuxin He, Jiyong Xie, Hongtao Xie, Yingying Wang, Li Xue, Xin Wang, Gaurav Zinta, Vipasha Verma, Hongzhi Wang, Yanfei Mao, Jian-Kang Zhu","doi":"10.1111/pbi.14478","DOIUrl":"https://doi.org/10.1111/pbi.14478","url":null,"abstract":"<p>Weed species have increasingly emerged with resistance against previously effective herbicides, such as glyphosate and inhibitors of acetyl coenzyme A carboxylase (ACCase) and acetolactate synthase (ALS) (Heap, <span>2024</span>). Owing to its novel mode of action, 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibitors are effective in controlling herbicide-resistant weeds and recently attracted much attention. Resistance to HPPD-inhibitors has been slow to evolve in weeds, and only a few cases of resistant events have been reported and most of these are associated with enhanced herbicide metabolism (Heap, <span>2024</span>; Lu <i>et al</i>., <span>2023</span>). Since resistant sites in the entire target gene are largely unknown, we <i>in vivo</i> mutagenized the <i>HPPD</i> gene in Arabidopsis and rice using base editing libraries to uncover potential target-site resistant mutations.</p>\u0000<p>Arabidopsis are highly sensitive to mesotrione. After large-scale transformation of base editing pools (Figure S1), we found one T1 seedling growing normally in medium containing 100 nM mesotrione (Figure S2a). Genotyping showed that a heterozygous T-to-C substitution occurred, causing the Y342H mutation in the HPPD protein sequence (Figure S2b, c). Homozygous progenies of <i>HPPD</i><sup><i>Y342H</i></sup> (Figure S2d) were tolerant up to 200 nM mesotrione and 50 nM isoxaflutole in medium (Figures 1a and S3a) and had a much higher survival rate than wild type (WT) when sprayed with ≥1 μM mesotrione or isoxaflutole in pots (Figure 1b, c). <i>AtHPPD</i><sup><i>Y342H</i></sup> mutants exhibited similar phenotype and showed no significant differences in plant height and seed yield with the WT plants (Figure S4).</p>\u0000<figure><picture>\u0000<source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/0c020b3d-76a3-4853-894c-ba167297cbe4/pbi14478-fig-0001-m.jpg\"/><img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/0c020b3d-76a3-4853-894c-ba167297cbe4/pbi14478-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/32583bc8-f9ce-44ae-816c-675d85c88574/pbi14478-fig-0001-m.png\" title=\"Details are in the caption following the image\"/></picture><figcaption>\u0000<div><strong>Figure 1<span style=\"font-weight:normal\"></span></strong><div>Open in figure viewer<i aria-hidden=\"true\"></i><span>PowerPoint</span></div>\u0000</div>\u0000<div>Target-site-mutations improve plant resistance to HPPD-inhibitors. The AtHPPD<sup>Y342H</sup> mutation significantly increases tolerance to mesotrione (MST) and isoxaflutole (IFT) during germination (a) and seedling (b). Bar equals 3 cm (a) or 7.5 cm (b). (c) Survival rate of the wild type (WT) Col-0 and <i>AtHPPD</i><sup><i>Y342H</i></sup> mutants after being sprayed with herbicides at the seedling stage. Phenotype of the soybean WT and <i>GmHPPD</i><sup><i>Y388H</i></sup> mutants after being sprayed with MST (d) or IFT (e). Bar equals 15 cm. (f) Seed amount and yield from soybean WT and <i>GmHPPD</i><sup><i>Y388H</i></sup> mutants grown in gr","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"9 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Junxiang Zhang, Shuang Liu, Shuo Zhao, Yuxin Nie, Zhihong Zhang
<p>Cultivated strawberry (<i>Fragaria</i> × <i>ananassa</i>, 2<i>n</i> = 8<i>x</i> = 56) is an important horticultural crop with substantial economic and nutritional value. The improvement of cultivated strawberry is more challenging not only in its octoploid genome but also in the frequent homoeologous exchanges and polyploidization, which replaces substantial portions of some subgenomes with sequences derived from ancestrally related chromosomes (Edger <i>et al</i>., <span>2019</span>). Therefore, a high-quality genome for the cultivated strawberry will provide important information for identifying agriculturally important genes for breeding. Several cultivated strawberry genomes have been assembled. However, some published reference genomes of cultivated strawberries remained incomplete, and some published genomes of cultivated strawberries were not truly haplotype-resolved (Edger <i>et al</i>., <span>2019</span>; Lee <i>et al</i>., <span>2021</span>; Mao <i>et al</i>., <span>2023</span>; Song <i>et al</i>., <span>2024</span>).</p> <p>Here, we de novo assembled a telomere-to-telomere haplotype-resolved reference genome with 56 chromosomes (Figure 1a) of the white-fruited strawberry cultivar ‘Chulian’ (Figure S1) by incorporating PacBio HiFi, ONT ultra-long and Hi-C sequencing, and Illumina sequencing data. The centromere candidate sequences and regions of each chromosome were identified (Figure S2 and Table S1). We divided 56 chromosomes into two haplotypes, Hap1 (chr × − × −1) and Hap2 (chr × − × −2), and each haplotype includes 28 chromosomes. The final genome assembly sizes were 787.52 Mb with 33 contigs for Hap1 and 778.03 Mb with 34 contigs for Hap2, respectively. The contigs N50 of Hap1 and Hap2 were 27.92 Mb and 26.45 Mb, respectively. We identified 52 telomeres in Hap1 and 50 in Hap2 by investigating telomeric repeats (TTTAGGG)n (Figures S2; Table S2).</p> <figure><picture> <source media="(min-width: 1650px)" srcset="/cms/asset/d5382006-039b-40a0-bfe8-be1c111810fd/pbi14479-fig-0001-m.jpg"/><img alt="Details are in the caption following the image" data-lg-src="/cms/asset/d5382006-039b-40a0-bfe8-be1c111810fd/pbi14479-fig-0001-m.jpg" loading="lazy" src="/cms/asset/925952e6-fcf3-4bd2-9b4a-762e3c883dad/pbi14479-fig-0001-m.png" title="Details are in the caption following the image"/></picture><figcaption> <div><strong>Figure 1<span style="font-weight:normal"></span></strong><div>Open in figure viewer<i aria-hidden="true"></i><span>PowerPoint</span></div> </div> <div>Genomic features and the loss-of-anthocyanin phenotype of ‘Chulian’ strawberry. (a) The haplotype-resolved genome assembly of ‘Chulian’ strawberry. (b) Transient functional analysis of point mutation of ‘Chulian’ strawberry <i>FaMYB10</i> on chr1-2-2. Scale bar, 1 cm. (c) The phenotype of ‘Chulian’ strawberry under lighting and shading treatment. Scale bar, 1 cm.</div> </figcaption> </figure> <p>The integrity and accuracy of the genome assembly of ‘Chulian’ were evaluated by Benc
{"title":"A telomere-to-telomere haplotype-resolved genome of white-fruited strawberry reveals the complexity of fruit colour formation of cultivated strawberry","authors":"Junxiang Zhang, Shuang Liu, Shuo Zhao, Yuxin Nie, Zhihong Zhang","doi":"10.1111/pbi.14479","DOIUrl":"https://doi.org/10.1111/pbi.14479","url":null,"abstract":"<p>Cultivated strawberry (<i>Fragaria</i> × <i>ananassa</i>, 2<i>n</i> = 8<i>x</i> = 56) is an important horticultural crop with substantial economic and nutritional value. The improvement of cultivated strawberry is more challenging not only in its octoploid genome but also in the frequent homoeologous exchanges and polyploidization, which replaces substantial portions of some subgenomes with sequences derived from ancestrally related chromosomes (Edger <i>et al</i>., <span>2019</span>). Therefore, a high-quality genome for the cultivated strawberry will provide important information for identifying agriculturally important genes for breeding. Several cultivated strawberry genomes have been assembled. However, some published reference genomes of cultivated strawberries remained incomplete, and some published genomes of cultivated strawberries were not truly haplotype-resolved (Edger <i>et al</i>., <span>2019</span>; Lee <i>et al</i>., <span>2021</span>; Mao <i>et al</i>., <span>2023</span>; Song <i>et al</i>., <span>2024</span>).</p>\u0000<p>Here, we de novo assembled a telomere-to-telomere haplotype-resolved reference genome with 56 chromosomes (Figure 1a) of the white-fruited strawberry cultivar ‘Chulian’ (Figure S1) by incorporating PacBio HiFi, ONT ultra-long and Hi-C sequencing, and Illumina sequencing data. The centromere candidate sequences and regions of each chromosome were identified (Figure S2 and Table S1). We divided 56 chromosomes into two haplotypes, Hap1 (chr × − × −1) and Hap2 (chr × − × −2), and each haplotype includes 28 chromosomes. The final genome assembly sizes were 787.52 Mb with 33 contigs for Hap1 and 778.03 Mb with 34 contigs for Hap2, respectively. The contigs N50 of Hap1 and Hap2 were 27.92 Mb and 26.45 Mb, respectively. We identified 52 telomeres in Hap1 and 50 in Hap2 by investigating telomeric repeats (TTTAGGG)n (Figures S2; Table S2).</p>\u0000<figure><picture>\u0000<source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/d5382006-039b-40a0-bfe8-be1c111810fd/pbi14479-fig-0001-m.jpg\"/><img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/d5382006-039b-40a0-bfe8-be1c111810fd/pbi14479-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/925952e6-fcf3-4bd2-9b4a-762e3c883dad/pbi14479-fig-0001-m.png\" title=\"Details are in the caption following the image\"/></picture><figcaption>\u0000<div><strong>Figure 1<span style=\"font-weight:normal\"></span></strong><div>Open in figure viewer<i aria-hidden=\"true\"></i><span>PowerPoint</span></div>\u0000</div>\u0000<div>Genomic features and the loss-of-anthocyanin phenotype of ‘Chulian’ strawberry. (a) The haplotype-resolved genome assembly of ‘Chulian’ strawberry. (b) Transient functional analysis of point mutation of ‘Chulian’ strawberry <i>FaMYB10</i> on chr1-2-2. Scale bar, 1 cm. (c) The phenotype of ‘Chulian’ strawberry under lighting and shading treatment. Scale bar, 1 cm.</div>\u0000</figcaption>\u0000</figure>\u0000<p>The integrity and accuracy of the genome assembly of ‘Chulian’ were evaluated by Benc","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"186 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaomeng Shen, Lei Liu, Thu Tran, Qiang Ning, Manfei Li, Liangliang Huang, Ran Zhao, Yunfu Li, Xiangyu Qing, David Jackson, Yan Bai, Weibin Song, Jinsheng Lai, Zuxin Zhang, Haiming Zhao
Kernel row number (KRN) is a major yield related trait for maize (Zea mays L.) and is also a major goal of breeders, as it can increase the number of kernels per plant. Thus, identifying new genetic factors involving in KRN formation may accelerate improving yield-related traits genetically. We herein describe a new kernel number-related gene (KRN5b) identified from KRN QTL qKRN5b and encoding an inositol polyphosphate 5-phosphatase (5PTase). KRN5b has phosphatase activity towards PI(4,5)P2, PI(3,4,5)P3, and Ins(1,4,5)P3in vitro. Knocking out KRN5b caused accumulation of PI(4,5)P2 and Ins(1,4,5)P3, resulting in disordered kernel rows and a decrease in the number of kernels and tassel branches. The introgression of the allele with higher expression abundance into different inbred lines could increase the ear weight of the inbred lines and the corresponding hybrids by 10.1%–12.2% via increasing KRN, with no adverse effects on other agronomic traits. Further analyses showed that KRN5b regulates inflorescence development through affecting the synthesis and distribution of hormones. Together, KRN5b contributes to spikelet pair meristem development through inositol phosphate and phosphatidylinositols, making it a selecting target for yield improvement.
{"title":"KRN5b regulates maize kernel row number through mediating phosphoinositol signalling","authors":"Xiaomeng Shen, Lei Liu, Thu Tran, Qiang Ning, Manfei Li, Liangliang Huang, Ran Zhao, Yunfu Li, Xiangyu Qing, David Jackson, Yan Bai, Weibin Song, Jinsheng Lai, Zuxin Zhang, Haiming Zhao","doi":"10.1111/pbi.14463","DOIUrl":"https://doi.org/10.1111/pbi.14463","url":null,"abstract":"Kernel row number (KRN) is a major yield related trait for maize (<i>Zea mays</i> L.) and is also a major goal of breeders, as it can increase the number of kernels per plant. Thus, identifying new genetic factors involving in KRN formation may accelerate improving yield-related traits genetically. We herein describe a new kernel number-related gene (<i>KRN5b</i>) identified from KRN QTL <i>qKRN5b</i> and encoding an inositol polyphosphate 5-phosphatase (5PTase). KRN5b has phosphatase activity towards PI(4,5)P<sub>2</sub>, PI(3,4,5)P<sub>3</sub>, and Ins(1,4,5)P<sub>3</sub> <i>in vitro</i>. Knocking out <i>KRN5b</i> caused accumulation of PI(4,5)P<sub>2</sub> and Ins(1,4,5)P<sub>3</sub>, resulting in disordered kernel rows and a decrease in the number of kernels and tassel branches. The introgression of the allele with higher expression abundance into different inbred lines could increase the ear weight of the inbred lines and the corresponding hybrids by 10.1%–12.2% via increasing KRN, with no adverse effects on other agronomic traits. Further analyses showed that KRN5b regulates inflorescence development through affecting the synthesis and distribution of hormones. Together, <i>KRN5b</i> contributes to spikelet pair meristem development through inositol phosphate and phosphatidylinositols, making it a selecting target for yield improvement.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"2 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jatinder Singh, Santosh Gudi, Peter J. Maughan, Zhaohui Liu, James Kolmer, Meinan Wang, Xianming Chen, Matthew N. Rouse, Pauline Lasserre-Zuber, Héléne Rimbert, Sunish Sehgal, Jason D. Fiedler, Frédéric Choulet, Maricelis Acevedo, Rajeev Gupta, Upinder Gill
Aegilops umbellulata serve as an important reservoir for novel biotic and abiotic stress tolerance for wheat improvement. However, chromosomal rearrangements and evolutionary trajectory of this species remain to be elucidated. Here, we present a comprehensive investigation into Ae. umbellulata genome by generating a high-quality near telomere-to-telomere genome assembly of PI 554389 and resequencing 20 additional Ae. umbellulata genomes representing diverse geographical and phenotypic variations. Our analysis unveils complex chromosomal rearrangements, most prominently in 4U and 6U chromosomes, delineating a distinct evolutionary trajectory of Ae. umbellulata from wheat and its relatives. Furthermore, our data rectified the erroneous naming of chromosomes 4U and 6U in the past and highlighted multiple major evolutionary events that led to the present-day U-genome. Resequencing of diverse Ae. umbellulata accessions revealed high genetic diversity within the species, partitioning into three distinct evolutionary sub-populations and supported by extensive phenotypic variability in resistance against several races/pathotypes of five major wheat diseases. Disease evaluations indicated the presence of several novel resistance genes in the resequenced lines for future studies. Resequencing also resulted in the identification of six new haplotypes for Lr9, the first resistance gene cloned from Ae. umbellulata. The extensive genomic and phenotypic resources presented in this study will expedite the future genetic exploration of Ae. umbellulata, facilitating efforts aimed at enhancing resiliency and productivity in wheat.
{"title":"Genomes of Aegilops umbellulata provide new insights into unique structural variations and genetic diversity in the U-genome for wheat improvement","authors":"Jatinder Singh, Santosh Gudi, Peter J. Maughan, Zhaohui Liu, James Kolmer, Meinan Wang, Xianming Chen, Matthew N. Rouse, Pauline Lasserre-Zuber, Héléne Rimbert, Sunish Sehgal, Jason D. Fiedler, Frédéric Choulet, Maricelis Acevedo, Rajeev Gupta, Upinder Gill","doi":"10.1111/pbi.14470","DOIUrl":"https://doi.org/10.1111/pbi.14470","url":null,"abstract":"<i>Aegilops umbellulata</i> serve as an important reservoir for novel biotic and abiotic stress tolerance for wheat improvement. However, chromosomal rearrangements and evolutionary trajectory of this species remain to be elucidated. Here, we present a comprehensive investigation into <i>Ae. umbellulata</i> genome by generating a high-quality near telomere-to-telomere genome assembly of PI 554389 and resequencing 20 additional <i>Ae. umbellulata</i> genomes representing diverse geographical and phenotypic variations. Our analysis unveils complex chromosomal rearrangements, most prominently in 4U and 6U chromosomes, delineating a distinct evolutionary trajectory of <i>Ae. umbellulata</i> from wheat and its relatives. Furthermore, our data rectified the erroneous naming of chromosomes 4U and 6U in the past and highlighted multiple major evolutionary events that led to the present-day U-genome. Resequencing of diverse <i>Ae. umbellulata</i> accessions revealed high genetic diversity within the species, partitioning into three distinct evolutionary sub-populations and supported by extensive phenotypic variability in resistance against several races/pathotypes of five major wheat diseases. Disease evaluations indicated the presence of several novel resistance genes in the resequenced lines for future studies. Resequencing also resulted in the identification of six new haplotypes for <i>Lr9</i>, the first resistance gene cloned from <i>Ae. umbellulata.</i> The extensive genomic and phenotypic resources presented in this study will expedite the future genetic exploration of <i>Ae. umbellulata</i>, facilitating efforts aimed at enhancing resiliency and productivity in wheat.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"30 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142237027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Stevia rebaudiana Bertoni is popular source of plant-derived low/no-calorie natural sweeteners (LNCSs), collectively known as steviol glycosides (SGs). Nevertheless, genetic predisposition for targeted biosynthesis of SGs is complex due to multi-substrate functionality of key uridine diphosphate glycosyltransferases (UGTs). Here, we created a high-quality monoploid assembly of 1.34 Gb with N50 value of 110 Mb, 55 551 predicted protein-coding genes, and ~80% repetitive regions in Rebaudioside-A (Reb-A) enriched cultivar of S. rebaudiana. Additionally, a haplotype-based chromosome assembly consisting of haplotype A and haplotype B with an overall genome size of 2.33Gb was resolved, harbouring 639 634 variants including single nucleotide polymorphisms (SNPs), indels and structural variants (SVs). Furthermore, a lineage-specific whole genome duplication analysis revealed that gene families encoding UGTs and Cytochrome-P450 (CYPs) were tandemly duplicated. Additionally, expression analysis revealed five tandemly duplicated gene copies of UGT76G1 having significant correlations with Reb-A content, and identified key residue (leu200val) in the glycosylation of Reb-A. Furthermore, missense variations identified in the acceptor region of UGT76G1 in haplotype resolve genome, transcriptional and molecular docking analysis were confirmed with resequencing of 10 diverse stevia genotypes (~25X). Gene regulatory network analysis identified key transcription factors (MYB, bHLH, bZIP and AP2-ERF) as potential regulators of SG biosynthesis. Overall, this study provides haplotype-resolved chromosome-level genome assembly for genome editing and enhancing breeding efforts for targeted biosynthesis of SGs in S. rebaudiana.
{"title":"High-quality haplotype-resolved chromosome assembly provides evolutionary insights and targeted steviol glycosides (SGs) biosynthesis in Stevia rebaudiana Bertoni","authors":"Mamta Masand, Shikha Sharma, Sangeeta Kumari, Poonam Pal, Aasim Majeed, Gopal Singh, Ram Kumar Sharma","doi":"10.1111/pbi.14446","DOIUrl":"https://doi.org/10.1111/pbi.14446","url":null,"abstract":"<i>Stevia rebaudiana</i> Bertoni is popular source of plant-derived <i>low/no-calorie</i> natural sweeteners (LNCSs), collectively known as steviol glycosides (SGs). Nevertheless, genetic predisposition for targeted biosynthesis of SGs is complex due to multi-substrate functionality of key uridine diphosphate glycosyltransferases (UGTs). Here, we created a high-quality monoploid assembly of 1.34 Gb with N50 value of 110 Mb, 55 551 predicted protein-coding genes, and ~80% repetitive regions in Rebaudioside-A (Reb-A) enriched cultivar of <i>S. rebaudiana</i>. Additionally, a haplotype-based chromosome assembly consisting of haplotype A and haplotype B with an overall genome size of 2.33Gb was resolved, harbouring 639 634 variants including single nucleotide polymorphisms (SNPs), indels and structural variants (SVs). Furthermore, a lineage-specific whole genome duplication analysis revealed that gene families encoding UGTs and Cytochrome-P450 (CYPs) were tandemly duplicated. Additionally, expression analysis revealed five tandemly duplicated gene copies of UGT76G1 having significant correlations with Reb-A content, and identified key residue (leu200val) in the glycosylation of Reb-A. Furthermore, missense variations identified in the acceptor region of UGT76G1 in haplotype resolve genome, transcriptional and molecular docking analysis were confirmed with resequencing of 10 diverse stevia genotypes (~25X). Gene regulatory network analysis identified key transcription factors (MYB, bHLH, bZIP and AP2-ERF) as potential regulators of SG biosynthesis. Overall, this study provides haplotype-resolved chromosome-level genome assembly for genome editing and enhancing breeding efforts for targeted biosynthesis of SGs in <i>S. rebaudiana.</i>","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"103 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142234057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：