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A gene cluster for polyamine transport and modification improves salt tolerance in tomato. 多胺转运和修饰基因簇提高了番茄的耐盐性。
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-14 DOI: 10.1111/tpj.17074
Jie Yang, Zhonghui Zhang, Xianggui Li, Langchen Guo, Chun Li, Jun Lai, Yige Han, Weizhen Ye, Yuanyuan Miao, Meng Deng, Peng Cao, Yueran Zhang, Xiangyu Ding, Jianing Zhang, Jun Yang, Shouchuang Wang

Polyamines act as protective compounds directly protecting plants from stress-related damage, while also acting as signaling molecules to participate in serious abiotic stresses. However, the molecular mechanisms underlying these effects are poorly understood. Here, we utilized metabolome genome-wide association study to investigate the polyamine content of wild and cultivated tomato accessions, and we discovered a new gene cluster that drove polyamine content during tomato domestication. The gene cluster contains two polyphenol oxidases (SlPPOE and SlPPOF), two BAHD acyltransferases (SlAT4 and SlAT5), a coumaroyl-CoA ligase (Sl4CL6), and a polyamine uptake transporter (SlPUT3). SlPUT3 mediates polyamine uptake and transport, while the five other genes are involved in polyamine modification. Further salt tolerance assays demonstrated that SlPPOE, SlPPOF, and SlAT5 overexpression lines showed greater phenolamide accumulation and salt tolerance as compared with wild-type (WT). Meanwhile, the exogenous application of Spm to SlPUT3-OE lines displayed salt tolerance compared with WT, while having the opposite effect in slput3 lines, confirms that the polyamine and phenolamide can play a protective role by alleviating cell damage. SlPUT3 interacted with SlPIP2;4, a H2O2 transport protein, to maintain H2O2 homeostasis. Polyamine-derived H2O2 linked Spm to stress responses, suggesting that Spm signaling activates stress response pathways. Collectively, our finding reveals that the H2O2-polyamine-phenolamide module coordinately enhanced tomato salt stress tolerance and provide a foundation for tomato stress-resistance breeding.

多胺是一种保护性化合物,可直接保护植物免受与胁迫相关的损害,同时还可作为信号分子参与严重的非生物胁迫。然而,人们对这些作用的分子机制知之甚少。在此,我们利用代谢组全基因组关联研究调查了野生番茄和栽培番茄的多胺含量,并发现了一个在番茄驯化过程中驱动多胺含量的新基因簇。该基因簇包含两个多酚氧化酶(SlPPOE和SlPPOF)、两个BAHD酰基转移酶(SlAT4和SlAT5)、一个香豆酰-CoA连接酶(Sl4CL6)和一个多胺吸收转运体(SLPUT3)。SlPUT3 介导多胺的吸收和转运,而其他五个基因则参与多胺的修饰。进一步的耐盐性实验表明,与野生型(WT)相比,SlPPOE、SlPPOF 和 SlAT5 过表达株表现出更高的苯甲酰胺积累和耐盐性。同时,与 WT 相比,SlPUT3-OE 株系外源施用 Spm 会表现出耐盐性,而 slput3 株系则相反,这证实了多胺和苯酚酰胺可以通过减轻细胞损伤发挥保护作用。SlPUT3 与 H2O2 转运蛋白 SlPIP2;4 相互作用,维持 H2O2 平衡。多胺衍生的 H2O2 将 Spm 与应激反应联系起来,表明 Spm 信号激活了应激反应途径。总之,我们的发现揭示了H2O2-多胺-苯酚酰胺模块协调地增强了番茄对盐胁迫的耐受性,为番茄抗逆育种提供了基础。
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引用次数: 0
The histone chaperones ASF1 and HIRA are required for telomere length and 45S rDNA copy number homeostasis 组蛋白伴侣 ASF1 和 HIRA 是端粒长度和 45S rDNA 拷贝数平衡所必需的。
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-14 DOI: 10.1111/tpj.17041
Adéla Machelová, Martina Nešpor Dadejová, Michal Franek, Guillaume Mougeot, Lauriane Simon, Samuel Le Goff, Céline Duc, Jasmin Bassler, Martin Demko, Jana Schwarzerová, Sophie Desset, Aline V. Probst, Martina Dvořáčková

Genome stability is significantly influenced by the precise coordination of chromatin complexes that facilitate the loading and eviction of histones from chromatin during replication, transcription, and DNA repair processes. In this study, we investigate the role of the Arabidopsis H3 histone chaperones ANTI-SILENCING FUNCTION 1 (ASF1) and HISTONE REGULATOR A (HIRA) in the maintenance of telomeres and 45S rDNA loci, genomic sites that are particularly susceptible to changes in the chromatin structure. We find that both ASF1 and HIRA are essential for telomere length regulation, as telomeres are significantly shorter in asf1a1b and hira mutants. However, these shorter telomeres remain localized around the nucleolus and exhibit a comparable relative H3 occupancy to the wild type. In addition to regulating telomere length, ASF1 and HIRA contribute to silencing 45S rRNA genes and affect their copy number. Besides, ASF1 supports global heterochromatin maintenance. Our findings also indicate that ASF1 transiently binds to the TELOMERE REPEAT BINDING 1 protein and the N terminus of telomerase in vivo, suggesting a physical link between the ASF1 histone chaperone and the telomere maintenance machinery.

染色质复合物在复制、转录和 DNA 修复过程中促进组蛋白从染色质中装载和排出,染色质复合物的精确协调对基因组稳定性有重大影响。在这项研究中,我们研究了拟南芥 H3 组蛋白伴侣素 ANTI-SILENCING FUNCTION 1(ASF1)和 HISTONE REGULATOR A(HIRA)在维护端粒和 45S rDNA 位点中的作用,这些基因组位点特别容易受到染色质结构变化的影响。我们发现 ASF1 和 HIRA 对端粒长度的调节都至关重要,因为 ASF1a1b 和 HIRA 突变体的端粒明显缩短。然而,这些较短的端粒仍然定位在核仁周围,并表现出与野生型相当的相对 H3 占有率。除了调节端粒长度,ASF1 和 HIRA 还有助于沉默 45S rRNA 基因并影响其拷贝数。此外,ASF1还支持全球异染色质的维持。我们的研究结果还表明,ASF1能瞬时结合体内的端粒重复结合1蛋白和端粒酶的N末端,这表明ASF1组蛋白伴侣与端粒维持机制之间存在物理联系。
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引用次数: 0
The all-day pollinator visits of sunflower inflorescences in Helianthus annuus plantations are independent of head orientation: Testing a widespread hypothesis. 向日葵种植园中向日葵花序的全天候授粉者访问与花头方向无关:检验一个普遍的假设
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-12 DOI: 10.1111/tpj.17070
Gábor Horváth, Bence Dárdai, Máté Bíró, Judit Slíz-Balogh, Dénes Száz, András Barta, Ádám Egri

Mature inflorescences of sunflowers (Helianthus annuus) orient constantly on average to the geographical east. According to one of the explanations of this phenomenon, the eastward orientation of sunflower inflorescences increases the number of attracted insect pollinators. We tested this hypothesis in three field experiments performed in flowering sunflower plantations. In experiments 1 and 2 we measured the number of insects trapped by the vertical walls of sticky sunflower models facing north, east, south, and west. In experiment 3 we counted the pollinators' landings on real sunflower inflorescences facing naturally east or turned artificially toward north, south, and west. We found that the all-day number of pollinators (predominantly bees) attracted to model and real sunflowers in H. annuus plantations is independent of the azimuth direction of sunflower heads, and after 10 h in the morning, the average number of pollinators counted every 20 min is practically constant in the rest of the day.

向日葵(Helianthus annuus)的成熟花序平均向东生长。对这一现象的解释之一是,向日葵花序向东会增加吸引昆虫授粉者的数量。我们在开花的向日葵种植园中进行了三次实地实验来验证这一假设。在实验 1 和 2 中,我们测量了朝北、朝东、朝南和朝西的向日葵模型的垂直壁所捕获的昆虫数量。在实验 3 中,我们统计了传粉昆虫落在自然向东或人为向北、向南和向西的向日葵花序上的数量。我们发现,在向日葵种植园中,全天吸引到模型向日葵和真向日葵上的传粉昆虫(主要是蜜蜂)的数量与向日葵花头的方位角方向无关。
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引用次数: 0
SlMYB72 interacts with SlTAGL1 to regulate the cuticle formation in tomato fruit. SlMYB72 与 SlTAGL1 相互作用,调控番茄果实角质层的形成。
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-12 DOI: 10.1111/tpj.17072
Mengbo Wu, Yuanyi Zhou, Haifeng Ma, Xin Xu, Mingchun Liu, Wei Deng

The cuticle is the first physical barrier covering the surface of tomatoes and plays an important role in multiple stress responses. But the molecular regulatory networks of cuticle formation are not fully understood. In this study, we found that SlMYB72 can interact with SlTAGL1 to regulate the formation of fruit cuticle in tomato. Downregulating the expression of SlMYB72 inhibits the formation of fruit cuticle, resulting in a reduced fruit cuticle thickness, accelerated postharvest water loss, and increased susceptibility to Botrytis cinerea. RNA sequencing analysis showed that downregulation of the SlMYB72 gene decreased the expression levels of genes related to fatty acid and cuticle metabolism. SlMYB72 regulates the cuticle formation by directly binding to the promoter of long-chain acyl-coA synthetases (SlLACS1) and medium-chain alkane hydroxylase (SlMAH1). Moreover, SlMYB72 interacts with SlTAGL1, which can enhance the transcriptional activation of SlMYB72 on the SlMAH1 promoter. Overall, our study expands our understanding of the regulation of cuticle formation by SlMYB72 and provides new insights into fruit shelf life extension via manipulation of cuticle content.

角质层是覆盖在番茄表面的第一道物理屏障,在多种应激反应中发挥着重要作用。但目前对角质层形成的分子调控网络还不完全清楚。本研究发现,SlMYB72能与SlTAGL1相互作用,调控番茄果实角质层的形成。下调 SlMYB72 的表达会抑制果实角质层的形成,导致果实角质层厚度降低、采后失水加速以及对灰霉病的易感性增加。RNA 测序分析表明,下调 SlMYB72 基因会降低脂肪酸和角质层代谢相关基因的表达水平。SlMYB72 通过直接与长链酰基-coA 合成酶(SlLACS1)和中链烷烃羟化酶(SlMAH1)的启动子结合来调控角质层的形成。此外,SlMYB72 与 SlTAGL1 相互作用,可增强 SlMYB72 在 SlMAH1 启动子上的转录激活。总之,我们的研究拓展了我们对 SlMYB72 调控角质层形成的认识,并为通过操纵角质层含量延长水果货架期提供了新的见解。
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引用次数: 0
Acyl-turnover of acylplastoquinol enhances recovery of photodamaged PSII in Synechocystis. 酰基葡糖苷醌的酰基翻转增强了 Synechocystis 中光损伤 PSII 的恢复能力。
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-10 DOI: 10.1111/tpj.17051
Haruhiko Jimbo, Mana Torii, Yuichiro Fujino, Yoshiki Tanase, Kazuki Kurima, Naoki Sato, Hajime Wada

Photosynthetic electron transport is carried out by the electron carrier, plastoquinone (PQ). Recently, another form of PQ, acylplastoquinol (APQ), was discovered in Synechocystis sp. PCC 6803 (Synechocystis), but its physiological function in photosynthesis is unclear. In the present study, we identified a lipase encoded in sll0482 gene in Synechocystis that deacylates APQ and releases a free fatty acid and a reduced PQ (plastoquinol, PQH2), which we named acylplastoquinol lipase (APL). Disruption of apl gene increased APQ content, and recovery of photodamaged PSII under low light (LL) after the exposure to very high light (vHL) at 2500 μmol photons m-2 sec-1 without aeration (vHL) for 60 min, was suppressed in the Δapl cells. Δapl cells also show the slow rate of de novo synthesis of D1, a reaction center of PSII under such condition. Under high light, the cellular growth of Δapl was inhibited; however, disruption of apl gene did not affect the photosynthetic activity or photoinhibition of PSII. In wild-type cells, APQ content increased under vHL condition. Also, APQ was converted to PQH2 after transfer to LL with aeration by ambient air. Such striking changes in APQ were not observed in Δapl cells. The deacylation of APQ by APL may help repair PSII when PSII cannot drive photosynthetic electron transport efficiently.

光合作用的电子传递是由电子载体质醌(PQ)完成的。最近,在 Synechocystis sp. PCC 6803(Synechocystis)中发现了另一种形式的 PQ,即酰基质醌(acylplastoquinol,APQ),但其在光合作用中的生理功能尚不清楚。在本研究中,我们发现了一种由 Synechocystis sll0482 基因编码的脂肪酶,它能使 APQ 脱乙酰基,并释放出游离脂肪酸和还原型 PQ(plastoquinol,PQH2),我们将其命名为酰基plastoquinol 脂肪酶(APL)。破坏 apl 基因会增加 APQ 的含量,在弱光(LL)下,PSII 在 2500 μmol 光子 m-2 sec-1 不通气的强光(vHL)下暴露 60 分钟后,光损伤 PSII 的恢复在 Δapl 细胞中受到抑制。在这种条件下,Δapl 细胞中 PSII 反应中心 D1 的从头合成速度也很慢。在强光下,Δapl 的细胞生长受到抑制;但 apl 基因的破坏并不影响光合作用活性或 PSII 的光抑制作用。在 vHL 条件下,野生型细胞中的 APQ 含量增加。此外,在转移到 LL 并通过环境空气通气后,APQ 被转化为 PQH2。在Δapl细胞中没有观察到 APQ 的这种显著变化。当PSII不能有效驱动光合电子传递时,APL对APQ的脱乙酰化可能有助于修复PSII。
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引用次数: 0
Exploring an economic and highly efficient genetic transformation and genome-editing system for radish through developmental regulators and visible reporter. 通过发育调节剂和可见报告基因,探索经济高效的萝卜遗传转化和基因组编辑系统。
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-10 DOI: 10.1111/tpj.17068
Xiaofang Yi, Congcong Wang, Xiaoqi Yuan, Mi Zhang, Changwei Zhang, Tiaojiao Qin, Haiyun Wang, Liang Xu, Liwang Liu, Yan Wang

Radish (Raphanus sativus L.) is one of the most important root vegetable crops worldwide. However, gene function exploration and germplasm innovation still face tremendous challenges due to its extremely low transformation efficiency. Here, an economic and highly efficient genetic transformation method for radish was explored by Agrobacterium rhizogenes-mediated transformation with the help of combining special developmental regulator (DR) genes and the visual identification reporter. Firstly, the RUBY gene, a betalain biosynthesis system, could result in a visual red-violet color used as a convenient and effective reporter for monitoring transgenic hairy roots screening of radish. However, the hairy roots-to-shoots conversion system of radish still stands as a barrier to the obtainment of whole transgenic plants, although different hormone combinations and various culture conditions were tried. Following, two DR genes including Wuschel2 (Wus2) and isopentenyl transferase (ipt), as well as their combination Wus2-ipt were introduced for the shoot regeneration capacity improvement. The results showed that the transgenic shoots could be directly generated without externally supplying any hormones in the presence of a Wus2-ipt combination. Then, Wus2-ipt along with the RUBY reporter was employed to establish an efficient genetic transformation system of radish. Moreover, this system was applied in generating gene-edited radish plants and the phytoene desaturase (RsPDS) gene was effectively knockout through albino phenotype observation and sequencing analysis. These findings have the potential to be widely applied in genetic transformation and genome-editing genetic improvement of other vegetable species.

萝卜(Raphanus sativus L.)是世界上最重要的根茎蔬菜作物之一。然而,由于其转化效率极低,基因功能探索和种质创新仍面临巨大挑战。本文通过根瘤农杆菌介导的转化,结合特殊的发育调节因子(DR)基因和视觉识别报告基因,探索了一种经济、高效的萝卜遗传转化方法。首先,RUBY 基因是一种甜菜碱生物合成系统,可产生视觉上的红紫色,是监测萝卜转基因毛细根筛选的一种方便有效的报告基因。然而,尽管尝试了不同的激素组合和各种培养条件,萝卜毛细根到根的转化系统仍然是获得完整转基因植株的障碍。为了提高萝卜芽的再生能力,研究人员引入了两个 DR 基因,包括 Wuschel2(Wus2)和异戊烯基转移酶(ipt),以及它们的组合 Wus2-ipt。结果表明,在 Wus2-ipt组合存在的情况下,无需外部提供任何激素就能直接产生转基因芽。随后,Wus2-ipt 与 RUBY 报告基因一起被用于建立一个高效的萝卜遗传转化系统。此外,该系统还被应用于生成基因编辑萝卜植株,通过白化表型观察和测序分析,植二烯去饱和酶(RsPDS)基因被有效敲除。这些发现有望广泛应用于其他蔬菜物种的遗传转化和基因组编辑遗传改良。
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引用次数: 0
Genomic signatures of inbreeding and mutation load in tree ferns. 树蕨类植物近亲繁殖和变异负荷的基因组特征。
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-10 DOI: 10.1111/tpj.17064
Huiqin Yi, Jing Wang, Shiyong Dong, Ming Kang

Ferns (Pteridophyta), as the second largest group of vascular plants, play important roles in ecosystem functioning. Homosporous ferns exhibit a remarkable range of mating systems, from extreme inbreeding to obligate outcrossing, which may have significant evolutionary and ecological implications. Despite their significance, the impact of genome-wide inbreeding on genetic diversity and mutation load within the fern lineage remain largely unexplored. In this study, we utilized whole-genome sequencing to investigate the genomic signatures of inbreeding and genetic load in three Alsophila tree fern species. Our analysis revealed extremely high inbreeding in A. spinulosa, in contrast to the predominantly outcrossing observed in A. costularis and A. latebrosa. This difference likely reflects divergent mating systems and demographic histories. Consistent with its extreme inbreeding propensity, A. spinulosa exhibits reduced genetic diversity and a pronounced decline in effective population size. Comparison of genetic load revealed an overall reduction in deleterious mutations in the highly inbred A. spinulosa, highlighting that long-term inbreeding may have contributed to the purging of strongly deleterious mutations, thereby prolonging the survival of A. spinulosa. Despite this, however, A. spinulosa carries a substantive realized genetic load that may potentially instigate future fitness decline. Our findings illuminate the complex evolutionary interplay between inbreeding and mutation load in homosporous ferns, yielding insights with important implications for the conservation and management of these species.

蕨类植物(翼手目)是第二大维管束植物类群,在生态系统功能中发挥着重要作用。同孢蕨类植物的交配系统种类繁多,从极端近交到强制外交,这可能会对进化和生态产生重大影响。尽管其意义重大,但全基因组近交对蕨类植物系遗传多样性和变异负荷的影响在很大程度上仍未得到探讨。在这项研究中,我们利用全基因组测序技术研究了三种蕨类植物近交和遗传负荷的基因组特征。我们的分析发现,A. spinulosa 的近交率极高,而在 A. costularis 和 A. latebrosa 中观察到的则主要是外交。这种差异可能反映了不同的交配系统和人口历史。与极度近交倾向相一致的是,A. spinulosa 的遗传多样性减少,有效种群数量明显下降。遗传负荷的比较显示,在高度近亲繁殖的桫椤中,有害突变总体上有所减少,这表明长期近亲繁殖可能有助于清除强有害突变,从而延长了桫椤的生存期。然而,尽管如此,桫椤仍携带着大量已实现的遗传负荷,有可能导致未来的适应性下降。我们的发现揭示了同孢蕨类植物近亲繁殖与突变负荷之间复杂的进化相互作用,对这些物种的保护和管理具有重要意义。
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引用次数: 0
LlbHLH87 interacts with LlSPT to modulate thermotolerance via activation of LlHSFA2 and LlEIN3 in lily. LlbHLH87 与 LlSPT 相互作用,通过激活百合中的 LlHSFA2 和 LlEIN3 来调节耐热性。
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-09 DOI: 10.1111/tpj.17060
Ze Wu, Xue Gong, Yinyi Zhang, Ting Li, Jun Xiang, Qianqian Fang, Junpeng Yu, Liping Ding, Jiahui Liang, Nianjun Teng

Basic helix-loop-helix (bHLH) proteins comprise one of the largest families of transcription factors in plants, which play roles in plant development, secondary metabolism, and the response to biotic/abiotic stresses. However, the roles of bHLH proteins in thermotolerance are largely unknown. Herein, we identified a heat-inducible member of the bHLH family in lily (Lilium longiflorum), named LlbHLH87, which plays a role in thermotolerance. LlbHLH87 was rapidly induced by transient heat stress, and its encoded protein was localized to the nucleus, exhibiting transactivation activity in both yeast and plant cells. Overexpression of LlbHLH87 in Arabidopsis enhanced basal thermotolerance, while silencing of LlbHLH87 in lily reduced basal thermotolerance. Further analysis showed that LlbHLH87 bound to the promoters of HEAT STRESS TRANSCRIPTION FACTOR A2 (LlHSFA2) and ETHYLENE-INSENSITIVE 3 (LlEIN3) to directly activate their expression. In addition, LlbHLH87 interacted with itself and with SPATULA (LlSPT) protein. LlSPT was activated by extended heat stress and its protein competed for the homologous interaction of LlbHLH87, which reduced the transactivation ability of LlbHLH87 for target genes. Compared with that observed under LlbHLH87 overexpression alone, co-overexpression of LlbHLH87 and LlSPT reduced the basal thermotolerance of lily to sudden heat shock, but improved its thermosensitivity to prolonged heat stress treatment. Overall, our data demonstrated that LlbHLH87 regulates thermotolerance via activation of LlEIN3 and LlHSFA2, along with an antagonistic interaction with LlSPT.

碱性螺旋-环-螺旋(bHLH)蛋白是植物中最大的转录因子家族之一,在植物发育、次生代谢和对生物/非生物胁迫的反应中发挥作用。然而,bHLH 蛋白在耐热性中的作用在很大程度上是未知的。在此,我们在百合(Lilium longiflorum)中发现了一种热诱导的 bHLH 家族成员,命名为 LlbHLH87,它在耐热性中发挥作用。LlbHLH87能被瞬时热胁迫快速诱导,其编码蛋白定位于细胞核,在酵母和植物细胞中均表现出转录激活活性。在拟南芥中过表达LlbHLH87可增强基础热耐受性,而在百合中沉默LlbHLH87可降低基础热耐受性。进一步的分析表明,LlbHLH87与热胁迫转录因子A2(LlHSFA2)和乙烯-INSENSITIVE 3(LlEIN3)的启动子结合,直接激活它们的表达。此外,LlbHLH87 与自身和 SPATULA(LlSPT)蛋白相互作用。LlSPT被延长的热胁迫激活,其蛋白竞争LlbHLH87的同源相互作用,从而降低了LlbHLH87对目的基因的转录激活能力。与单独过表达LlbHLH87的情况相比,LlbHLH87和LlSPT的共重表达降低了百合对骤热冲击的基础耐热性,但提高了其对延长热胁迫处理的热敏感性。总之,我们的数据表明,LlbHLH87通过激活LlEIN3和LlHSFA2以及与LlSPT的拮抗相互作用来调节耐热性。
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引用次数: 0
Deep learning to capture leaf shape in plant images: Validation by geometric morphometrics. 深度学习捕捉植物图像中的叶形:几何形态计量学验证。
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-09 DOI: 10.1111/tpj.17053
Ladislav Hodač, Kevin Karbstein, Lara Kösters, Michael Rzanny, Hans Christian Wittich, David Boho, David Šubrt, Patrick Mäder, Jana Wäldchen

Plant leaves play a pivotal role in automated species identification using deep learning (DL). However, achieving reproducible capture of leaf variation remains challenging due to the inherent "black box" problem of DL models. To evaluate the effectiveness of DL in capturing leaf shape, we used geometric morphometrics (GM), an emerging component of eXplainable Artificial Intelligence (XAI) toolkits. We photographed Ranunculus auricomus leaves directly in situ and after herbarization. From these corresponding leaf images, we automatically extracted DL features using a neural network and digitized leaf shapes using GM. The association between the extracted DL features and GM shapes was then evaluated using dimension reduction and covariation models. DL features facilitated the clustering of leaf images by source populations in both in situ and herbarized leaf image datasets, and certain DL features were significantly associated with biological leaf shape variation as inferred by GM. DL features also enabled leaf classification into morpho-phylogenomic groups within the intricate R. auricomus species complex. We demonstrated that simple in situ leaf imaging and DL reproducibly captured leaf shape variation at the population level, while combining this approach with GM provided key insights into the shape information extracted from images by computer vision, a necessary prerequisite for reliable automated plant phenotyping.

植物叶片在使用深度学习(DL)进行物种自动识别中发挥着关键作用。然而,由于深度学习模型固有的 "黑箱 "问题,实现对叶片变异的可重现捕捉仍具有挑战性。为了评估深度学习在捕捉叶片形状方面的有效性,我们使用了几何形态计量学(GM),它是可扩展人工智能(XAI)工具包的一个新兴组件。我们直接在原地和草本化后拍摄了 Ranunculus auricomus 的叶片。从这些相应的叶片图像中,我们使用神经网络自动提取了DL特征,并使用GM对叶片形状进行了数字化处理。然后,我们使用降维和协变模型评估了提取的 DL 特征与 GM 形状之间的关联。在原位和草本化叶片图像数据集中,DL特征有助于按来源种群对叶片图像进行聚类,而且某些DL特征与GM推断的生物叶片形状变化有显著关联。DL 特征还能在错综复杂的 R. auricomus 种群中将叶片分类为形态-系统发生组。我们证明,简单的原位叶片成像和 DL 可以在种群水平上重复捕捉叶片形状的变异,而将这种方法与基因改造相结合,则可以深入了解计算机视觉从图像中提取的形状信息,这是可靠的自动化植物表型的必要前提。
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引用次数: 0
Knockdown of β-conglycinin α' and α subunits alters seed protein composition and improves salt tolerance in soybean. 敲除β-共霉素α'和α亚基可改变种子蛋白质组成并提高大豆的耐盐性。
IF 6.2 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-10-09 DOI: 10.1111/tpj.17062
Rufei Yang, Yujie Ma, Zhongyi Yang, Yixiang Pu, Mengyu Liu, Jingyi Du, Zhiri Xu, Zefei Xu, Shanshan Zhang, Hengyou Zhang, Wei Zhang, Deyue Yu, Guizhen Kan

Soybean is an important plant source of protein worldwide. Increasing demands for soybean can be met by improving the quality of its seed protein. In this study, GmCG-1, which encodes the β-conglycinin α' subunit, was identified via combined genome-wide association study and transcriptome analysis. We subsequently knocked down GmCG-1 and its paralogues GmCG-2 and GmCG-3 with CRISPR-Cas9 technology and generated two stable multigene knockdown mutants. As a result, the β-conglycinin content decreased, whereas the 11S/7S ratio, total protein content and sulfur-containing amino acid content significantly increased. Surprisingly, the globulin mutant exhibited salt tolerance in both the germination and seedling stages. Little is known about the relationship between seed protein composition and the salt stress response in soybean. Metabonomics and RNA-seq analysis indicated that compared with the WT, the mutant was formed through a pathway that was more similar to that of active salicylic acid biosynthesis; however, the synthesis of cytokinin exhibited greater defects, which could lead to increased expression of plant dehydrin-related salt tolerance proteins and cell membrane ion transporters. Population evolution analysis suggested that GmCG-1, GmCG-2, and GmCG-3 were selected during soybean domestication. The soybean accessions harboring GmCG-1Hap1 presented relatively high 11S/7S ratios and relatively high salt tolerance. In conclusion, knockdown of the β-conglycinin α and α' subunits can improve the nutritional quality of soybean seeds and increase the salt tolerance of soybean plants, providing a strategy for designing soybean varieties with high nutritional value and high salt tolerance.

大豆是全球重要的植物蛋白来源。提高大豆种子蛋白质的质量可以满足人们对大豆日益增长的需求。本研究通过全基因组关联研究和转录组分析,确定了编码β-共霉素α'亚基的GmCG-1。随后,我们利用CRISPR-Cas9技术敲除了GmCG-1及其对映体GmCG-2和GmCG-3,并产生了两个稳定的多基因敲除突变体。结果发现,β-共霉素含量下降,而11S/7S比值、总蛋白含量和含硫氨基酸含量显著增加。令人惊讶的是,球蛋白突变体在萌芽和幼苗阶段都表现出耐盐性。人们对大豆种子蛋白质组成与盐胁迫反应之间的关系知之甚少。代谢组学和 RNA-seq 分析表明,与 WT 相比,突变体的形成途径更类似于活性水杨酸的生物合成途径;但细胞分裂素的合成表现出更大的缺陷,这可能导致植物脱水素相关耐盐蛋白和细胞膜离子转运体的表达增加。群体进化分析表明,GmCG-1、GmCG-2 和 GmCG-3 是在大豆驯化过程中被选择的。携带 GmCG-1Hap1 的大豆品种具有相对较高的 11S/7S 比率和相对较高的耐盐性。总之,敲除β-共霉素α和α'亚基可以改善大豆种子的营养品质,提高大豆植株的耐盐性,为设计高营养价值和高耐盐性的大豆品种提供了一种策略。
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