Plant Biotechnology Journal最新文献

{"title":"CRISPR/Cas9-mediated genomic editing of Brachytic2 creates semi-dwarf mutant alleles for tailored maize breeding","authors":"Binbin Zhao, Zhanchao Xia, Changhe Sun, Di Yang, Yuelei Zhao, Jiyuan Cao, Yaoyao Li, Haiyang Wang, Baobao Wang","doi":"10.1111/pbi.14571","DOIUrl":"https://doi.org/10.1111/pbi.14571","url":null,"abstract":"<p>Maize, now ranking #1 in world cereal production (accounting for ~42% of total cereal production worldwide), plays a pivotal role in securing food and feed supply globally (FAO, <span>2023</span>). Historically, increasing planting density has been adopted as a key measurement to increasing maize grain yield per unit land area (Mansfield and Mumm, <span>2014</span>). Plant height (PH) and ear height (EH) are key agronomic traits that determine lodging resistance and thus high-density planting tolerance of maize (Wang <i>et al</i>., <span>2020</span>). Recently, it has been proposed that “Short corn” may represent a future avenue for maize breeding, as it stands up better to windstorms, boost yields and benefit the environment (Stokstad, <span>2023</span>). Nevertheless, a major technical thwart in breeding “Short Corn” is the lack of deployable genes and elite germplasm.</p>\u0000<p><i>Brachytic2</i> (<i>Br2</i>) encodes a protein belonging to the multidrug resistant (MDR) class of P-glycoproteins harbouring two transmembrane domains (TMD1 and TMD2), and two nucleotide-binding domains (NBD1 and NBD2), and plays a role in regulating PH via mediating polar auxin transport (Multani <i>et al</i>., <span>2003</span>). Despite its loss-of-function mutants exhibit an extremely dwarf stature, several recent studies reported that mild mutations in the last (fifth) exon of <i>Br2</i> result in milder variation in PH without notable unfavourable effects on other agronomic traits (Wei <i>et al</i>., <span>2018</span>; Xing <i>et al</i>., <span>2015</span>).</p>\u0000<p>As PH and EH are complex traits regulated by a large number of quantitative loci and easily influenced by genetic backgrounds and environmental conditions, we wondered if it is possible to generate a series of <i>br2</i> mutant alleles, so as to expand the portfolios of semi-dwarf maize germplasm for tailored breeding of semi-dwarf maize cultivars in different genetic backgrounds.</p>\u0000<p>As a proof-of-concept study, we designed a CRISPR/Cas9 vector targeting the last exon of <i>Br2</i>. To increase the targeting efficiency and universality in different genetic backgrounds, we first examined the genetic variation of <i>Br2</i> in 45 representative inbred lines with reported high-quality genome assembly (https://www.maizegdb.org/), and designed 4 conserved targets, with three of them are completely conserved in all the 45 inbred lines, while Target3 is conserved in 38 of the 45 inbred lines (Figure 1a).</p>\u0000<figure><picture>\u0000<source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/23d4544b-6d99-49c0-8be3-fb6f4646dd11/pbi14571-fig-0001-m.jpg\"/><img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/23d4544b-6d99-49c0-8be3-fb6f4646dd11/pbi14571-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/774de94f-ada2-4ace-92a4-46a5a22514de/pbi14571-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","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"10 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142990589","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}

{"title":"Natural variation in the GmVPE1 promoter contributes to phosphorus re-translocation to seeds and improves soybean yield","authors":"Jiaxin Chen, Wenting Lian, Zhiang Li, Xin Guo, Yaning Li, Hongyu Zhao, Keke Yi, Xinxin Li, Hong Liao","doi":"10.1111/pbi.14592","DOIUrl":"https://doi.org/10.1111/pbi.14592","url":null,"abstract":"Phosphorus (P) is an essential yet frequently deficient plant nutrient. Optimizing P distribution and recycling between tissues is vital for improving P utilization efficiency (PUE). Yet, the mechanisms underlying the transport and re-translocation of P within plants remain unclear. Here, wide-ranging natural diversity in seed P allocation and positive correlations among yield traits were found using 190 soybean accessions in field trials. Among them, the P-efficient genotype BX10 outperformed BD2 in assessments of PUE that were largely explained through differences in P redistribution from pods to seeds under low P stress. Pods of BX10 were therefore subjected to transcriptome analysis, and GmVPE1 was identified as a vacuolar Pi transporter to investigate further. Importantly, significant DNA polymorphism in <i>GmVPE1</i> promoter regions was remarkably associated with seed weight among soybean accessions grown on P-deficient soils. Further analyses suggested that mRNA abundance of <i>GmVPE1</i> in haplotype 2 (Hap) is significantly higher than that <i>GmVPE1</i>^<i>Hap1</i>. <i>GmVPE1</i> was highly upregulated by P deficiency and preferentially expressed in pods, seeds, and seed coats, which was consistent with GUS staining using transgenic soybean plants carrying <i>pGmVPE1</i>^<i>Hap2</i>::GUS. Near-isogenic lines carrying the <i>GmVPE1</i>^<i>Hap2</i> allele, along with stable transgenic soybeans overexpressing <i>GmVPE1</i> in a <i>GmVPE1</i>^<i>Hap1</i> background, had increases in PUE, more seed setting, and greater yields in both greenhouse and field trials than control plants. In summary, natural variation among <i>GmVPE1</i> alleles determines genetic expression and subsequent P re-translocation phenotypes, which impacts PUE and yield, and thereby makes this an important genetic resource for soybean molecular breeding.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"30 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987141","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}

{"title":"Targeted deaminase-free T-to-G and C-to-K base editing in rice by fused human uracil DNA glycosylase variants","authors":"Yinghuang Wu, Xueying Wang, Haoyu Wang, Ying Han, Yaxuan Wang, Chunyu Zou, Jian-Kang Zhu, Ming Li","doi":"10.1111/pbi.14583","DOIUrl":"https://doi.org/10.1111/pbi.14583","url":null,"abstract":"&lt;p&gt;Base editors (BEs), a groundbreaking class of genome editing tools, enable precise single-nucleotide alterations at target genomic sites, leading to mutations that either disable or enhance gene functions, thus significantly advancing plant functional genomics research and crop enhancement (Li &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2023&lt;/span&gt;). In plants, significant advancements have been made in DNA base editors that can directly modify adenine (A), cytosine (C) and guanine (G) (Li &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2018&lt;/span&gt;; Zong &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2017&lt;/span&gt;). Nevertheless, a direct base editor for thymine (T) remains elusive. Recently, two innovative deaminase-free glycosylase-based base editors were developed: the gTBE for direct T editing (T-to-S conversion, S = G or C) and the gCBE for direct C editing (C-to-G), enabling orthogonal base modifications in mammalian cells (Figure 1a; Tong &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;). These base editors utilized the fusion of Cas9 nickase (nCas9) with engineered variants of human uracil DNA glycosylase (UNG), allowing for the direct excision of T or C to generate apurinic/apyrimidinic (AP) sites. However, such direct T base editor has not been developed in plants to date. In this study, we developed a deaminase-free direct T base editor (pTGBE) and direct C base editor (pCKBE, K = G or T) in rice, marking a substantial step forward in expanding genetic manipulation capabilities in plants.&lt;/p&gt;\u0000&lt;figure&gt;&lt;picture&gt;\u0000&lt;source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/0edf6cda-b5d9-4b60-9d14-b9b58df33379/pbi14583-fig-0001-m.jpg\"/&gt;&lt;img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/0edf6cda-b5d9-4b60-9d14-b9b58df33379/pbi14583-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/22aec75e-9993-4b32-bbad-22a05d09436c/pbi14583-fig-0001-m.png\" title=\"Details are in the caption following the image\"/&gt;&lt;/picture&gt;&lt;figcaption&gt;\u0000&lt;div&gt;&lt;strong&gt;Figure 1&lt;span style=\"font-weight:normal\"&gt;&lt;/span&gt;&lt;/strong&gt;&lt;div&gt;Open in figure viewer&lt;i aria-hidden=\"true\"&gt;&lt;/i&gt;&lt;span&gt;PowerPoint&lt;/span&gt;&lt;/div&gt;\u0000&lt;/div&gt;\u0000&lt;div&gt;Development of pTGBE and pCKBE base editors in rice. (a) Schematic diagram showing the editing mechanisms of deaminase-free glycosylase-based thymine base editor (gTBE) and deaminase-free glycosylase-based cytosine base editor (gCBE) in mammalian cells. mhUNG, engineered human uracil DNA glycosylase variants. PAM, Protospacer adjacent motif. AP, apurinic/apyrimidinic sites. Star (*) in magenta indicates the nick generated by nCas9. TLS, translesion synthesis. DSB, double-strand break. InDel, insertion and deletion. (b) Plasmid constructs of pTGBE and pCKBE in this study. Short vertical lines represent mutated amino acids. Δ1-88: 1–88 amino acid residue truncation of human UNG2. (c) Summary of the editing efficiencies of pTGBE and pCKBE at the endogenous genes in stable T&lt;sub&gt;0&lt;/sub&gt; transgenic lines. Ho, homozygous mutation; He, heterozyous mutation; Bi, biallelic mutation; Chi, chimeric mutation. The PAM sequence is highlighted in ","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"119 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987139","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}

{"title":"Enhancing quality and yield of recombinant secretory IgA antibodies in Nicotiana benthamiana by endoplasmic reticulum engineering","authors":"Kathrin Göritzer, Stanislav Melnik, Jennifer Schwestka, Elsa Arcalis, Margit Drapal, Paul Fraser, Julian K-C. Ma, Eva Stoger","doi":"10.1111/pbi.14576","DOIUrl":"https://doi.org/10.1111/pbi.14576","url":null,"abstract":"The production of complex multimeric secretory immunoglobulins (SIgA) in <i>Nicotiana benthamiana</i> leaves is challenging, with significant reductions in complete protein assembly and consequently yield, being the most important difficulties. Expanding the physical dimensions of the ER to mimic professional antibody-secreting cells can help to increase yields and promote protein folding and assembly. Here, we expanded the ER in <i>N. benthamiana</i> leaves by targeting the enzyme CTP:phosphocholine cytidylyltransferase (CCT), which catalyses the rate-limiting step in the synthesis of the key membrane component phosphatidylcholine (PC). We used CRISPR/Cas to perform site-directed mutagenesis of each of the three endogenous CCT genes in <i>N. benthamiana</i> by introducing frame-shifting indels to remove the auto-inhibitory C-terminal domains. We generated stable homozygous lines of <i>N. benthamiana</i> containing different combinations of the edited genes, including plants where all three isofunctional CCT homologues were modified. Changes in ER morphology in the mutant plants were confirmed by <i>in vivo</i> confocal imaging and substantially increased the yields of two fully assembled SIgAs by prolonging the ER residence time and boosting chaperone accumulation. Through a combination of ER engineering with chaperone overexpression, we increased the yields of fully assembled SIgA by an order of magnitude, reaching almost 1 g/kg fresh leaf weight. This strategy removes a major roadblock to producing SIgA and will likely facilitate the production of other complex multimeric biopharmaceutical proteins in plants.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"29 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987140","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}

{"title":"Two CYP72 enzymes function as Ent-labdane hydroxylases in the biosynthesis of andrographolide in Andrographis paniculata","authors":"Jian Wang, Ying Ma, Junhao Tang, Huixin Lin, Guanghong Cui, Jinfu Tang, Juan Liu, Ping Su, Yujun Zhao, Juan Guo, Luqi Huang","doi":"10.1111/pbi.14572","DOIUrl":"https://doi.org/10.1111/pbi.14572","url":null,"abstract":"&lt;p&gt;&lt;i&gt;Andrographis paniculata&lt;/i&gt; (Burm.f.) Wall. Ex Nees in Wallich (&lt;i&gt;A. paniculata&lt;/i&gt;), an annual medicinal herb of the &lt;i&gt;Acanthaceae&lt;/i&gt; family, is widely cultivated for its various medicinal utilities in Southeast and South Asia. Its total extract and monomeric components have a broad range of pharmacological effects including anti-inflammatory, anti-microbial, hepatoprotective and anticancer (Subramanian &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2012&lt;/span&gt;). Numerous bioactive secondary metabolites have been isolated from the leaves and roots of &lt;i&gt;A. paniculata&lt;/i&gt;, andrographolide, an &lt;i&gt;ent&lt;/i&gt;-labdane diterpenoid, is considered the main bioactive compound (Subramanian &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2012&lt;/span&gt;). For example, Xiyanping®, a traditional Chinese medicine injection made of andrographolide sulfonate, is widely used to treat upper respiratory tract infection, viral pneumonia and bronchitis in China. Due to their medicinal properties, andrographolide biosynthesis has been intensively investigated, genomic data and terpene synthase functions have been reported (Sun &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2019&lt;/span&gt;). However, the enzymes responsible for structural modification that form the key pharmacologically active groups in its biosynthetic pathway remain unknown.&lt;/p&gt;\u0000&lt;p&gt;The modification steps in andrographolide biosynthesis include hydroxylations at C3, C14, C18 and lactone ring formation at C15–C16. This series of oxidation processes were supposed to be mediated by cytochrome P450 enzymes (CYP450s). In order to accurately screen the CYP450s in andrographolide biosynthesis pathway, we constructed the differential bio-accumulation samples of andrographolide seedlings (Figure S1). After 100 μM MeJA treatment, the production of andrographolide demonstrated significant enhancement at 24 h post-inoculation (hpi) and reached 37.8 mg/g DW at 72 hpi in the leaves, which is approximately 10 times greater than that in the control (Figure 1a). We then constructed the expression atlas and investigated the time-series expression changes of &lt;i&gt;A. paniculata&lt;/i&gt;. The expression profiles of samples at 12 hpi, 24 hpi and 48 hpi exhibited significantly different patterns compared to the samples collected at 0 hpi (Figure S2). By applying a cutoff of a four-folds difference in FPKM and a false discovery rate of less than 0.05, we identified that the expression levels of 4463 genes were up-regulated at 12 hpi, 24 hpi or 48 hpi in comparison to the control samples (Figure 1b).&lt;/p&gt;\u0000&lt;figure&gt;&lt;picture&gt;\u0000&lt;source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/3b09830f-074d-4137-b9dc-665ca6ab4fee/pbi14572-fig-0001-m.jpg\"/&gt;&lt;img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/3b09830f-074d-4137-b9dc-665ca6ab4fee/pbi14572-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/8c424ac0-7049-492b-92fa-d222a99632a4/pbi14572-fig-0001-m.png\" title=\"Details are in the caption following the image\"/&gt;&lt;/picture&gt;&lt;figcaption&gt;\u0000&lt;div&gt;&lt;strong&gt;Figure 1&lt;span style=\"font-weight:normal\"&gt;&lt;/span&gt;&lt;/s","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"31 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981900","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}

{"title":"The natural variation in shoot Na+ content and salt tolerance in maize is attributed to various minor-effect variants, including an SNP located in the promoter of ZmHAK11","authors":"Xiaoyan Liang, Limin Wang, Yin Pan, Wenqi Jing, Heyang Wang, Fang Liu, Caifu Jiang","doi":"10.1111/pbi.14553","DOIUrl":"https://doi.org/10.1111/pbi.14553","url":null,"abstract":"&lt;p&gt;Exclusion of Na&lt;sup&gt;+&lt;/sup&gt; from the above-ground tissues serves as an important salt-tolerant mechanism in most glycophyte plants, such as maize (Munns and Tester, &lt;span&gt;2008&lt;/span&gt;). Existing studies have corroborated that different maize varieties exhibit significant diversity in shoot Na&lt;sup&gt;+&lt;/sup&gt; content and then salt tolerance (Liang &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;). However, the genetic basis underlying this diversity remains largely unknown, necessitating a comprehensive understanding to sustain breeding for salt-tolerant maize cultivars.&lt;/p&gt;\u0000&lt;p&gt;In recent decades, numerous genes have been identified to regulate Na&lt;sup&gt;+&lt;/sup&gt; transport. The well-known include genes from the &lt;i&gt;NHX&lt;/i&gt;, &lt;i&gt;HKT&lt;/i&gt;, &lt;i&gt;HAK&lt;/i&gt;, &lt;i&gt;CBL&lt;/i&gt;, and &lt;i&gt;CIPK&lt;/i&gt; gene families (Yang and Guo, &lt;span&gt;2018&lt;/span&gt;). Maize has 13 &lt;i&gt;NHX&lt;/i&gt;, 3 &lt;i&gt;HKT&lt;/i&gt;, 28 &lt;i&gt;HAK&lt;/i&gt;, 11 &lt;i&gt;CBL&lt;/i&gt;, and 45 &lt;i&gt;CIPK&lt;/i&gt; family members (Table S1), which exhibit a varied expression pattern and responses to salt treatment (Method S1; Figure 1a; Figure S1). Given that several genes within these families have been shown to underlie the diversity of shoot Na&lt;sup&gt;+&lt;/sup&gt; content and then salt tolerance in maize (Liang &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2024&lt;/span&gt;), we hypothesized that functional variation of additional members of these gene families may also do so. To substantiate this speculation, we obtained 14–623 SNP variants for each of these genes from the genotype data of a population comprised of 508 maize inbred lines (Zhang &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2019&lt;/span&gt;) (Table S1), then analyse the association between these SNP variants and Na&lt;sup&gt;+&lt;/sup&gt; content in the shoot tissue of salt-grown seedlings (Method S2). The result indicated that the peak SNP in 17 of these genes respectively explained &gt;1% diversity of the shoot Na&lt;sup&gt;+&lt;/sup&gt; content (Figure 1b). Notably, 12 out of these 17 cases explained &lt;2% diversity of the shoot Na&lt;sup&gt;+&lt;/sup&gt; content, supporting the notion that various minor-effect variants result in the diversity in the shoot Na&lt;sup&gt;+&lt;/sup&gt; content and salt tolerance in maize.&lt;/p&gt;\u0000&lt;figure&gt;&lt;picture&gt;\u0000&lt;source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/8e4bbbc2-3ff7-4170-9019-fbe04fae8566/pbi14553-fig-0001-m.jpg\"/&gt;&lt;img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/8e4bbbc2-3ff7-4170-9019-fbe04fae8566/pbi14553-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/c93d960c-5a9f-4f6f-90f3-868b9035436f/pbi14553-fig-0001-m.png\" title=\"Details are in the caption following the image\"/&gt;&lt;/picture&gt;&lt;figcaption&gt;\u0000&lt;div&gt;&lt;strong&gt;Figure 1&lt;span style=\"font-weight:normal\"&gt;&lt;/span&gt;&lt;/strong&gt;&lt;div&gt;Open in figure viewer&lt;i aria-hidden=\"true\"&gt;&lt;/i&gt;&lt;span&gt;PowerPoint&lt;/span&gt;&lt;/div&gt;\u0000&lt;/div&gt;\u0000&lt;div&gt;Various minor-effect variants including an SNP located in the promoter of &lt;i&gt;ZmHAK11&lt;/i&gt; underlie the variation in shoot Na&lt;sup&gt;+&lt;/sup&gt; content in maize. (a) The transcript levels of the indicated &lt;i&gt;ZmHAK&lt;/i&gt;, &lt;i&gt;ZmHKT&lt;/i&gt;, &lt;i&gt;ZmNHX&lt;/i&gt;, &lt;i&gt;ZmCBL&lt;/i&gt;, and &lt;i&gt;ZmCIPK&lt;/i&gt; genes under control and s","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"2 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981901","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}

{"title":"Manipulation of WUSCHEL orthologue expression improves the forage yield and quality in Medicago","authors":"Hongfeng Wang, Yiteng Xu, Yan Wang, Zhiqun Gu, Feng Yuan, Lu Han, Shupeng Liu, Shuwei Liu, Zhichao Lu, Ying'e Chen, Qiaolan Liang, Chunxiang Fu, Ruicai Long, Qingchuan Yang, Zeng-Yu Wang, Chuanen Zhou","doi":"10.1111/pbi.14569","DOIUrl":"https://doi.org/10.1111/pbi.14569","url":null,"abstract":"&lt;p&gt;Alfalfa (&lt;i&gt;Medicago sativa&lt;/i&gt; L.) is a perennial leguminous forage extensively planted around the world (Annicchiarico &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2015&lt;/span&gt;). As a result, improving alfalfa forage yield and quality is a crucial agricultural goal (Kumar, &lt;span&gt;2011&lt;/span&gt;). Branching traits has a significant impact on the yield of alfalfa (Gou &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2018&lt;/span&gt;). The previous report showed that &lt;i&gt;HEADLESS&lt;/i&gt; (&lt;i&gt;HDL&lt;/i&gt;), the orthologue of &lt;i&gt;WUSCHEL&lt;/i&gt; (&lt;i&gt;WUS&lt;/i&gt;) in &lt;i&gt;M. truncatula&lt;/i&gt;, is required for axillary meristem maintenance (Wang &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2019&lt;/span&gt;), implying &lt;i&gt;HDL&lt;/i&gt; has the potential to regulate the number of branches. To test this hypothesis, 35S promoter-driven &lt;i&gt;HDL&lt;/i&gt; transgene was introduced into alfalfa. Ten transgenic plants (OX-1, OX-3 and OX-5) with high expression were selected for phenotypic investigation (Figure S1a). Compared with the wild-type, the &lt;i&gt;HDL-OX&lt;/i&gt; plants display more branches (Figure 1a–c). Furthermore, overexpressing &lt;i&gt;HDL&lt;/i&gt; increases plant height and produces larger, dark green leaves (Figures 1d,e, S1b–f), suggesting that increased &lt;i&gt;HDL&lt;/i&gt; activity affects not only branching but also leaf development in alfalfa.&lt;/p&gt;\u0000&lt;figure&gt;&lt;picture&gt;\u0000&lt;source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/568e93da-4021-431b-a271-b21b7e0bffa2/pbi14569-fig-0001-m.jpg\"/&gt;&lt;img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/568e93da-4021-431b-a271-b21b7e0bffa2/pbi14569-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/b048812f-4047-4b7e-be75-5b9bf97a45fe/pbi14569-fig-0001-m.png\" title=\"Details are in the caption following the image\"/&gt;&lt;/picture&gt;&lt;figcaption&gt;\u0000&lt;div&gt;&lt;strong&gt;Figure 1&lt;span style=\"font-weight:normal\"&gt;&lt;/span&gt;&lt;/strong&gt;&lt;div&gt;Open in figure viewer&lt;i aria-hidden=\"true\"&gt;&lt;/i&gt;&lt;span&gt;PowerPoint&lt;/span&gt;&lt;/div&gt;\u0000&lt;/div&gt;\u0000&lt;div&gt;&lt;i&gt;HDL-OX&lt;/i&gt; improves forage biomass and quality of alfalfa. (a–c) Primary and secondary branch phenotype (a, b) and number (c) of the wild-type and &lt;i&gt;HDL-OX&lt;/i&gt; plants. Bars = 4 cm. (d, e) Plant height (d) and internode (IN) length (e). (f) &lt;i&gt;HDL&lt;/i&gt; binding to the CNNGCNA motif (upper panel); Interaction of &lt;i&gt;HDL&lt;/i&gt; with the CNNGCNA and its substituted sequences in LUC assays (lower panel). (g) Expression of branch regulation genes. (h) LUC assay showing repression of &lt;i&gt;MsMAX3&lt;/i&gt; by &lt;i&gt;HDL&lt;/i&gt; in &lt;i&gt;Arabidopsis&lt;/i&gt; protoplasts. (i) Location of the fragments (P1–P3) used for ChIP-qPCR assays in the &lt;i&gt;MsMAX3&lt;/i&gt; promoter. (j, k) ChIP-qPCR and EMSA assays showing that &lt;i&gt;HDL&lt;/i&gt; binds to the P2 fragment of the &lt;i&gt;MsMAX3&lt;/i&gt; promoter. (l) Flowering phenotype. Bars = 4 cm. (m) Days of the first flower flowering. (n) Expression of &lt;i&gt;MsFTa1&lt;/i&gt;. (o) LUC assay showing repression of &lt;i&gt;MsFTa1&lt;/i&gt; by &lt;i&gt;HDL&lt;/i&gt;. (p) Location of the fragments (P1–P5) used for ChIP-qPCR assays in the &lt;i&gt;MsFTa1&lt;/i&gt; promoter. (q, r) ChIP-qPCR and EMSA assays showing that &lt;i&gt;HDL&lt;/i&gt; binds to the P3 fragment of the &lt;i&gt;MsFTa1&lt;/i&gt; promoter in vivo. (s–u) The &lt;i&gt;HDL-OX&lt;","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"68 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981899","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}

{"title":"Engineering an optimized hypercompact CRISPR/Cas12j-8 system for efficient genome editing in plants","authors":"Shasha Bai, Xingyu Cao, Lizhe Hu, Danling Hu, Dongming Li, Yongwei Sun","doi":"10.1111/pbi.14574","DOIUrl":"https://doi.org/10.1111/pbi.14574","url":null,"abstract":"The Cas12j-8 nuclease, derived from the type V CRISPR system, is approximately half the size of Cas9 and recognizes a 5′-TTN-3′ protospacer adjacent motif sequence, thus potentially having broad application in genome editing for crop improvement. However, its editing efficiency remains low in plants. In this study, we rationally engineered both the crRNA and the Cas12j-8 nuclease. The engineered crRNA and Cas12j-8 markedly improved genome editing efficiency in plants. When combined, they exhibited robust editing activity in soybean and rice, enabling the editing of target sites that were previously uneditable. Notably, for certain target sequences, the editing activity was comparable to that of SpCas9 when targeting identical sequences, and it outperformed the Cas12j-2 variant, nCas12j-2, across all tested targets. Additionally, we developed cytosine base editors based on the engineered crRNA and Cas12j-8, demonstrating an average increase of 5.36- to 6.85-fold in base-editing efficiency (C to T) compared with the unengineered system in plants, with no insertions or deletions (indels) observed. Collectively, these findings indicate that the engineered hypercompact CRISPR/Cas12j-8 system serves as an efficient tool for genome editing mediated by both nuclease cleavage and base editing in plants.","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"4 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967869","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}

{"title":"Integrative molecular and physiological insights into the phytotoxic impact of liquid crystal monomer exposure and the protective strategy in plants","authors":"Dong Jiang,&nbsp;Guoqun Yang,&nbsp;Li-Jun Huang,&nbsp;Xia Peng,&nbsp;Chuantong Cui,&nbsp;Yakov Kuzyakov,&nbsp;Ning Li","doi":"10.1111/pbi.14526","DOIUrl":"10.1111/pbi.14526","url":null,"abstract":"<p>Liquid crystal monomers (LCMs), the integral components in the manufacture of digital displays, have engendered environmental concerns due to extensive utilization and intensive emission. Despite their prevalence and ecotoxicity, the LCM impacts on plant growth and agricultural yield remain inadequately understood. In this study, we investigated the specific response mechanisms of tobacco, a pivotal agricultural crop and model plant, to four representative LCMs (2OdF3B, 5CB, 4PiMeOP, 2BzoCP) through integrative molecular and physiological approaches. The findings reveal specific impacts, with 4PiMeOP exerting the most pronounced effects, followed by 2BzoCP, 5CB, and 2OdF3B. LCM exposure disrupts the photosynthetic apparatus, exacerbating reactive oxygen species (ROS) levels in leaves, which in turn triggers the upregulation of antioxidative enzymes and the synthesis of antioxidant substances. Additionally, LCMs strongly stimulate the expression of genes involved in abscisic acid (ABA) biosynthesis and signalling pathways. The AI-assisted meta-analysis implicates ABA as a critical regulator in the tobacco response to LCMs. Notably, exogenous application of ABA alleviates LCM-induced toxicities, highlighting the pivotal role of ABA in stress amelioration. Our study provides novel insights into the toxicity and tolerance mechanisms of LCMs in plants, shedding light on both their harmful effects on the ecosystems and potential adaptation responses. This is crucial to develop sustainable agricultural systems by reducing the negative environmental impacts caused by emerging organic pollutants.</p>","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"23 2","pages":"644-659"},"PeriodicalIF":10.1,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/pbi.14526","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142961843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MFMGP: an integrated machine learning fusion model for genomic prediction","authors":"Chaopu Zhang, Qiqi Liang, Yuye Yu, Shaojuan Jin, Jinmei Huang, Zhongping Xu, Erbao Liu, Wensheng Wang, Fan Zhang, Fangzhou Liu, Yingyao Shi, Fenge Li, Zhikang Li, Shuangxia Jin, Min Li","doi":"10.1111/pbi.14532","DOIUrl":"https://doi.org/10.1111/pbi.14532","url":null,"abstract":"&lt;p&gt;Genome-wide selection (GS) represents a contemporary methodology that harnesses a comprehensive array of molecular markers across the entire genome. However, challenges such as lack of informative molecular markers and selection of appropriate and efficient GS model(s) have confined most GS-based breeding efforts to the realm of laboratory simulations (Wang &lt;i&gt;et al&lt;/i&gt;., &lt;span&gt;2023&lt;/span&gt;). Compared to the conventional prediction models, the machine learning (ML) algorithm provides new insights for solving challenges such as big data analysis and high-performance parallel computing. GS using ML also has some limitations at the current stage such as limitations in model selection.&lt;/p&gt;\u0000&lt;p&gt;Here, the MFMGP software is a fusion model that is based on a variety of ML training methods. The normalization fusion method with exponential decay weights involves assigning weights to the prediction results of each model and applying the exponential decay to these weights, so that more recent and/or more relevant model predictions have higher weights. Then, a weighted average of the model's prediction results is calculated to obtain the final fusion prediction by normalizing these weights (Figure 1a). The software of MFMGP for interactive GS analyses was made available at website: http://www.biohuaxing.com/#/MFMGP. To verify the prediction accuracy of the MFMGP model, we compared MFMGP with seven commonly used GS models. These included the classical GS model (GBLUP), four ML-based models (LightGBM, SVR, XGBoost and HGBoost) and two DL-based (DNNGP and DeepCCR) models.&lt;/p&gt;\u0000&lt;figure&gt;&lt;picture&gt;\u0000&lt;source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/96b5e04f-412c-4447-a23e-77f24ecd952c/pbi14532-fig-0001-m.jpg\"/&gt;&lt;img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/96b5e04f-412c-4447-a23e-77f24ecd952c/pbi14532-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/cde0d7f6-73bd-41fa-819c-73433ebc1c88/pbi14532-fig-0001-m.png\" title=\"Details are in the caption following the image\"/&gt;&lt;/picture&gt;&lt;figcaption&gt;\u0000&lt;div&gt;&lt;strong&gt;Figure 1&lt;span style=\"font-weight:normal\"&gt;&lt;/span&gt;&lt;/strong&gt;&lt;div&gt;Open in figure viewer&lt;i aria-hidden=\"true\"&gt;&lt;/i&gt;&lt;span&gt;PowerPoint&lt;/span&gt;&lt;/div&gt;\u0000&lt;/div&gt;\u0000&lt;div&gt;Prediction accuracy of eight methods based on three crop datasets. (a) The design and algorithmic framework for Multiple Machine Learning Fusion Model for Genomics Prediction (MFMGP). (b) Phenotypic variation of the agronomic traits in rice. (c) Performance of eight methods in predicting 13 traits using rice 3KRP (&lt;i&gt;n&lt;/i&gt; = 2110). The red arrow and text box indicate the proportion by which the MFMGP model can improve accuracy compared to the other seven models. (d) Performance of eight methods in predicting six traits using wheat dataset (&lt;i&gt;n&lt;/i&gt; = 2000). (e) Performance of eight methods in predicting four traits using cotton dataset (&lt;i&gt;n&lt;/i&gt; = 1245). Prediction accuracy of eight methods based on maize (&lt;i&gt;n&lt;/i&gt; = 6210) (f) and pig datasets (&lt;i&gt;n&lt;/i&gt; = 1490) (g). (h) The relationshi","PeriodicalId":221,"journal":{"name":"Plant Biotechnology Journal","volume":"39 1","pages":""},"PeriodicalIF":13.8,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142962671","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}