Saisai Cheng,Xin Gong,Wenfeng Xue,Paul Kardol,Manuel Delgado-Baquerizo,Ning Ling,Xiaoyun Chen,Manqiang Liu
Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.
{"title":"Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species.","authors":"Saisai Cheng,Xin Gong,Wenfeng Xue,Paul Kardol,Manuel Delgado-Baquerizo,Ning Ling,Xiaoyun Chen,Manqiang Liu","doi":"10.1111/nph.20118","DOIUrl":"https://doi.org/10.1111/nph.20118","url":null,"abstract":"Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142165959","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":"Establishing a highly efficient diploid seedless watermelon production system through manipulation of the SPOROCYTELESS gene.","authors":"Jiao Jiang,Qin Feng,Zijun Zhao,Qiyan Liu,Man Liu,Jiafa Wang,Feishi Luan,Xian Zhang,Shujuan Tian,Shi Liu,Li Yuan","doi":"10.1111/nph.20108","DOIUrl":"https://doi.org/10.1111/nph.20108","url":null,"abstract":"","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142170692","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}
Nannochloropsis oceanica is an industrially relevant marine microalga rich in eicosapentaenoic acid (EPA, a valuable ω-3 polyunsaturated fatty acid), yet the algal production potential remains to be unlocked. Here we engineered N. oceanica to synthesize the high-value carotenoid astaxanthin independent of high-light (HL) induction for achieving multifaceted benefits. By screening β-carotenoid ketolases and hydroxylases of various origins, and strategically manipulating compartmentalization, fusion patterns, and linkers of the enzyme pair, a remarkable 133-fold increase in astaxanthin content was achieved in N. oceanica. Iterative metabolic engineering efforts led to further increases in astaxanthin synthesis up to 7.3 mg g-1, the highest reported for microalgae under nonstress conditions. Astaxanthin was found in the photosystem components and allowed the alga HL resistance and augmented EPA production. Besides, we achieved co-production of astaxanthin and EPA by the engineered alga through a fed-batch cultivation approach. Our findings unveil the untapped potential of N. oceanica as a robust, light-driven chassis for constitutive astaxanthin synthesis and provide feasible strategies for the concurrent production of multiple high-value biochemicals from CO2, thereby paving the way for sustainable biotechnological applications of this alga.
Nannochloropsis oceanica 是一种富含二十碳五烯酸（EPA，一种有价值的ω-3 多不饱和脂肪酸）的工业用海洋微藻，但其生产潜力仍有待挖掘。在这里，我们改造了 N. oceanica，使其能够在不受强光（HL）诱导的情况下合成高价值的类胡萝卜素虾青素，从而获得多方面的益处。通过筛选不同来源的β-类胡萝卜素酮酶和羟化酶，并战略性地操纵酶对的区隔、融合模式和连接体，N. oceanica的虾青素含量显著增加了133倍。通过迭代代谢工程，虾青素的合成量进一步增加到 7.3 毫克/克，这是微藻在非应激条件下的最高合成量。在光系统成分中发现了虾青素，这使得藻类具有抗 HL 能力，并提高了 EPA 的产量。此外，我们还通过分批喂养的培养方法，实现了工程藻类对虾青素和 EPA 的联合生产。我们的研究结果揭示了 N. oceanica 作为强健的光驱动底盘进行组成型虾青素合成的尚未开发的潜力，并为同时利用 CO2 生产多种高价值生化物质提供了可行的策略，从而为这种藻类的可持续生物技术应用铺平了道路。
{"title":"Turning the industrially relevant marine alga Nannochloropsis red: one move for multifaceted benefits.","authors":"Meijing Liu,Lihua Yu,Jie Zheng,Shengxi Shao,Yufang Pan,Hanhua Hu,Lili Shen,Wenda Wang,Wenguang Zhou,Jin Liu","doi":"10.1111/nph.20114","DOIUrl":"https://doi.org/10.1111/nph.20114","url":null,"abstract":"Nannochloropsis oceanica is an industrially relevant marine microalga rich in eicosapentaenoic acid (EPA, a valuable ω-3 polyunsaturated fatty acid), yet the algal production potential remains to be unlocked. Here we engineered N. oceanica to synthesize the high-value carotenoid astaxanthin independent of high-light (HL) induction for achieving multifaceted benefits. By screening β-carotenoid ketolases and hydroxylases of various origins, and strategically manipulating compartmentalization, fusion patterns, and linkers of the enzyme pair, a remarkable 133-fold increase in astaxanthin content was achieved in N. oceanica. Iterative metabolic engineering efforts led to further increases in astaxanthin synthesis up to 7.3 mg g-1, the highest reported for microalgae under nonstress conditions. Astaxanthin was found in the photosystem components and allowed the alga HL resistance and augmented EPA production. Besides, we achieved co-production of astaxanthin and EPA by the engineered alga through a fed-batch cultivation approach. Our findings unveil the untapped potential of N. oceanica as a robust, light-driven chassis for constitutive astaxanthin synthesis and provide feasible strategies for the concurrent production of multiple high-value biochemicals from CO2, thereby paving the way for sustainable biotechnological applications of this alga.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142165960","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}
Wei Liu,Yushu Wang,Tuo Ji,Chengqiang Wang,Qinghua Shi,Chuanyou Li,Jin-Wei Wei,Biao Gong
Soil nitrogen (N) significantly influences the interaction between plants and pathogens, yet its impact on host defenses and pathogen strategies via alterations in plant metabolism remains unclear. Through metabolic and genetic studies, this research demonstrates that high-N-input exacerbates tomato bacterial wilt by altering γ-aminobutyric acid (GABA) metabolism of host plants. Under high-N conditions, the nitrate sensor NIN-like protein 7 (SlNLP7) promotes the glutamate decarboxylase 2/4 (SlGAD2/4) transcription and GABA synthesis by directly binding to the promoters of SlGAD2/4. The tomato plants with enhanced GABA levels showed stronger immune responses but remained susceptible to Ralstonia solanacearum. This led to the discovery that GABA produced by the host actually heightens the pathogen's virulence. We identified the R. solanacearum LysR-type transcriptional regulator OxyR protein, which senses host-derived GABA and, upon interaction, triggers a response involving protein dimerization that enhances the pathogen's oxidative stress tolerance by activating the expression of catalase (katE/katGa). These findings reveal GABA's dual role in activating host immunity and enhancing pathogen tolerance to oxidative stress, highlighting the complex relationship between tomato plants and R. solanacearum, influenced by soil N status.
{"title":"High-nitrogen-induced γ-aminobutyric acid triggers host immunity and pathogen oxidative stress tolerance in tomato and Ralstonia solanacearum interaction.","authors":"Wei Liu,Yushu Wang,Tuo Ji,Chengqiang Wang,Qinghua Shi,Chuanyou Li,Jin-Wei Wei,Biao Gong","doi":"10.1111/nph.20102","DOIUrl":"https://doi.org/10.1111/nph.20102","url":null,"abstract":"Soil nitrogen (N) significantly influences the interaction between plants and pathogens, yet its impact on host defenses and pathogen strategies via alterations in plant metabolism remains unclear. Through metabolic and genetic studies, this research demonstrates that high-N-input exacerbates tomato bacterial wilt by altering γ-aminobutyric acid (GABA) metabolism of host plants. Under high-N conditions, the nitrate sensor NIN-like protein 7 (SlNLP7) promotes the glutamate decarboxylase 2/4 (SlGAD2/4) transcription and GABA synthesis by directly binding to the promoters of SlGAD2/4. The tomato plants with enhanced GABA levels showed stronger immune responses but remained susceptible to Ralstonia solanacearum. This led to the discovery that GABA produced by the host actually heightens the pathogen's virulence. We identified the R. solanacearum LysR-type transcriptional regulator OxyR protein, which senses host-derived GABA and, upon interaction, triggers a response involving protein dimerization that enhances the pathogen's oxidative stress tolerance by activating the expression of catalase (katE/katGa). These findings reveal GABA's dual role in activating host immunity and enhancing pathogen tolerance to oxidative stress, highlighting the complex relationship between tomato plants and R. solanacearum, influenced by soil N status.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142165958","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}
Advances in bryophyte genomics and the phylogenetic recovery of hornworts, mosses, and liverworts as a clade have spurred considerable recent interest in character evolution among early embryophytes. Discussion of stomatal evolution, however, has been incomplete; the result of the neglect of certain potential stomate homologues, namely the two-celled epidermal gametophytic pores of hornworts (typically referred to as 'mucilage clefts'). Confusion over the potential homology of these structures is the consequence of a relatively recent consensus that hornwort gametophytic pores ('HGPs' - our term) are not homologous to stomates. We explore the occurrence and diverse functions of stomates throughout the evolutionary history and diversity of extinct and extant embryophytes. We then address arguments for and against homology between known sporophyte- and gametophyte-borne stomates and HGPs and conclude that there is little to no evidence that contradicts the hypothesis of homology. We propose that 'intergenerational heterotopy' might well account for the novel expression of stomates in gametophytes of hornworts, if stomates first evolved in the sporophyte generation of embryophytes. We then explore phylogenetically based hypotheses for the evolution of stomates in both the gametophyte and sporophyte generations of early lineages of embryophytes.
{"title":"A stomate by any other name? The open question of hornwort gametophytic pores, their homology, and implications for the evolution of stomates.","authors":"James Paul Fortin,William E Friedman","doi":"10.1111/nph.20094","DOIUrl":"https://doi.org/10.1111/nph.20094","url":null,"abstract":"Advances in bryophyte genomics and the phylogenetic recovery of hornworts, mosses, and liverworts as a clade have spurred considerable recent interest in character evolution among early embryophytes. Discussion of stomatal evolution, however, has been incomplete; the result of the neglect of certain potential stomate homologues, namely the two-celled epidermal gametophytic pores of hornworts (typically referred to as 'mucilage clefts'). Confusion over the potential homology of these structures is the consequence of a relatively recent consensus that hornwort gametophytic pores ('HGPs' - our term) are not homologous to stomates. We explore the occurrence and diverse functions of stomates throughout the evolutionary history and diversity of extinct and extant embryophytes. We then address arguments for and against homology between known sporophyte- and gametophyte-borne stomates and HGPs and conclude that there is little to no evidence that contradicts the hypothesis of homology. We propose that 'intergenerational heterotopy' might well account for the novel expression of stomates in gametophytes of hornworts, if stomates first evolved in the sporophyte generation of embryophytes. We then explore phylogenetically based hypotheses for the evolution of stomates in both the gametophyte and sporophyte generations of early lineages of embryophytes.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142170694","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}
Sandra Grünig, Theofania Patsiou, Christian Parisod
<h2> Introduction</h2> <p>The rise of barriers to gene flow eventually promoting reproductive isolation between previously interbreeding populations at the origin of new species typically requires thousands of generations (Rieseberg & Willis, <span>2007</span>; Sobel <i>et al</i>., <span>2010</span>). Although selection likely speeds up speciation, its interactions with recombination and the rise of reproductive isolation under environmental changes are insufficiently understood (Schluter & Rieseberg, <span>2022</span>). Accordingly, to what extent climate-induced range shifts due to cold and warm phases of the Quaternary ice ages have hindered speciation because allopatric differentiation was repeatedly counteracted by homogenising gene flow remains debated (Willis & Niklas, <span>2004</span>; Kadereit & Abbott, <span>2021</span>). In contrast to homoploid divergence, whole-genome duplication (WGD) immediately confers strong reproductive isolation from progenitor species (Levin, <span>1975</span>; Ramsey & Schemske, <span>1998</span>; Barker <i>et al</i>., <span>2016</span>) and supports polyploidy as a major driver of plant speciation (Wood <i>et al</i>., <span>2009</span>). However, to what extent polyploidy promotes the origin of new plant species during periods of climate changes remains elusive (Levin, <span>2019</span>; Van de Peer <i>et al</i>., <span>2021</span>).</p> <p>Polyploid speciation couples WGD with the combination of more or less divergent gene sets either within or between species at the origin of autopolyploid or allopolyploid species, respectively (Parisod <i>et al</i>., <span>2010</span>). At one end of the spectrum, autopolyploids derived from homologous chromosomes are characterised by tetrasomic inheritance, whereas the merging of divergent genomes results in allopolyploids displaying disomic inheritance and fixed heterozygosity. As natural polyploids can arise anywhere between these endpoints and be described as intervarietal autopolyploids or segmental allopolyploids derived from different taxa, whose homoploid hybrids are (semi-)sterile and increase their fertility through WGD (Stebbins, <span>1950</span>), it is crucial to infer the exact mechanisms at their origin to address the consequences of polyploidy (Tayalé & Parisod, <span>2013</span>). According to the secondary contact hypothesis (Stebbins, <span>1984</span>), climate-induced range shifts typical of the Quaternary likely promoted admixture between locally adapted diploid lineages favouring the emergence of new hybrid and polyploid species, as reported for several narrow neoendemic species of allopolyploid origin (e.g. Grünig <i>et al</i>., <span>2021</span>). This may partially explain the origin of polyploids around the last glacial maximum (LGM, <i>c</i>. 22 000 yr ago; Seguinot <i>et al</i>., <span>2018</span>), as documented in for example the <i>Arabidopsis</i> genus (Novikova <i>et al</i>., <span>2018</span>). Additionally, the
laevigata，再加上二倍体种群在中欧地区的零散分布，导致该物种群中出现了 20 个种、亚种或变种（Machatschki-Laurich, 1926; Olowokudejo & Heywood, 1984; Raffaelli & Baldoin, 1997）。由于之前的遗传研究只关注分布区的一部分（如阿尔卑斯山西部；Parisod & Besnard, 2007）或使用分辨率较低的遗传标记（如同工酶；Tremetsberger 等人, 2002），阿尔卑斯山二倍体的时空分化和四倍体的起源仍然难以捉摸。因此，在本研究中，我们结合了 ddRAD-seq（双位限制性位点相关 DNA 测序）来描述全基因组的遗传变异模式和生态位模型，以重新审视 B. laevigata 在欧洲阿尔卑斯山的进化历史。基于对阿尔卑斯山周围和阿尔卑斯山内的二倍体B. laevigata种群的全面取样以及对整个阿尔卑斯山的四倍体B. laevigata种群的密集取样，我们评估了它们在空间和时间上的遗传和生态分化，以具体解决以下问题：（1）杂交在阿尔卑斯山四倍体B. laevigata起源中的作用；（2）四倍体B. laevigata是通过单一起源还是多重起源进化而来；以及（3）倍性转变是否伴随着气候生态位的转变。
{"title":"Ice age-driven range shifts of diploids and expanding autotetraploids of Biscutella laevigata within a conserved niche","authors":"Sandra Grünig, Theofania Patsiou, Christian Parisod","doi":"10.1111/nph.20103","DOIUrl":"https://doi.org/10.1111/nph.20103","url":null,"abstract":"<h2> Introduction</h2>\u0000<p>The rise of barriers to gene flow eventually promoting reproductive isolation between previously interbreeding populations at the origin of new species typically requires thousands of generations (Rieseberg & Willis, <span>2007</span>; Sobel <i>et al</i>., <span>2010</span>). Although selection likely speeds up speciation, its interactions with recombination and the rise of reproductive isolation under environmental changes are insufficiently understood (Schluter & Rieseberg, <span>2022</span>). Accordingly, to what extent climate-induced range shifts due to cold and warm phases of the Quaternary ice ages have hindered speciation because allopatric differentiation was repeatedly counteracted by homogenising gene flow remains debated (Willis & Niklas, <span>2004</span>; Kadereit & Abbott, <span>2021</span>). In contrast to homoploid divergence, whole-genome duplication (WGD) immediately confers strong reproductive isolation from progenitor species (Levin, <span>1975</span>; Ramsey & Schemske, <span>1998</span>; Barker <i>et al</i>., <span>2016</span>) and supports polyploidy as a major driver of plant speciation (Wood <i>et al</i>., <span>2009</span>). However, to what extent polyploidy promotes the origin of new plant species during periods of climate changes remains elusive (Levin, <span>2019</span>; Van de Peer <i>et al</i>., <span>2021</span>).</p>\u0000<p>Polyploid speciation couples WGD with the combination of more or less divergent gene sets either within or between species at the origin of autopolyploid or allopolyploid species, respectively (Parisod <i>et al</i>., <span>2010</span>). At one end of the spectrum, autopolyploids derived from homologous chromosomes are characterised by tetrasomic inheritance, whereas the merging of divergent genomes results in allopolyploids displaying disomic inheritance and fixed heterozygosity. As natural polyploids can arise anywhere between these endpoints and be described as intervarietal autopolyploids or segmental allopolyploids derived from different taxa, whose homoploid hybrids are (semi-)sterile and increase their fertility through WGD (Stebbins, <span>1950</span>), it is crucial to infer the exact mechanisms at their origin to address the consequences of polyploidy (Tayalé & Parisod, <span>2013</span>). According to the secondary contact hypothesis (Stebbins, <span>1984</span>), climate-induced range shifts typical of the Quaternary likely promoted admixture between locally adapted diploid lineages favouring the emergence of new hybrid and polyploid species, as reported for several narrow neoendemic species of allopolyploid origin (e.g. Grünig <i>et al</i>., <span>2021</span>). This may partially explain the origin of polyploids around the last glacial maximum (LGM, <i>c</i>. 22 000 yr ago; Seguinot <i>et al</i>., <span>2018</span>), as documented in for example the <i>Arabidopsis</i> genus (Novikova <i>et al</i>., <span>2018</span>). Additionally, the","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142160993","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}
I grew up in the countryside of the Netherlands where I attended a very small primary school with only two classrooms. At this school, I had the same teacher for 3 years, who was fascinated by nature, and I think he sparked my interest in biology. Later in high school, we had some practical courses in biology, and I found it easy to understand the experimental approaches that were used and to interpret the outcomes of these experiments. This made me decide to study biology, for which I went to Groningen, the nearest city to my home village. In those days, most biology students were keen to specialize in human physiology or microbiology. I wondered why so few of them were interested in plants, since one would expect similar physiological systems to work in plants, as in humans and bacteria. Because of this consideration, I decided to write my master's thesis in molecular plant biology and I have remained in that area of science until now.
{"title":"Rob Roelfsema","authors":"","doi":"10.1111/nph.20086","DOIUrl":"https://doi.org/10.1111/nph.20086","url":null,"abstract":"<h2> What inspired your interest in plant science?</h2>\u0000<p>I grew up in the countryside of the Netherlands where I attended a very small primary school with only two classrooms. At this school, I had the same teacher for 3 years, who was fascinated by nature, and I think he sparked my interest in biology. Later in high school, we had some practical courses in biology, and I found it easy to understand the experimental approaches that were used and to interpret the outcomes of these experiments. This made me decide to study biology, for which I went to Groningen, the nearest city to my home village. In those days, most biology students were keen to specialize in human physiology or microbiology. I wondered why so few of them were interested in plants, since one would expect similar physiological systems to work in plants, as in humans and bacteria. Because of this consideration, I decided to write my master's thesis in molecular plant biology and I have remained in that area of science until now.</p>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142160997","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}
<div>With the expansion of technologies available to biological science has come an enormous rise in the amount and diverse nature of data. How we interrogate and combine ‘big data’ in different biological contexts has become the new challenge for crop biologists, be it at the genetic, phenotypic or environmental level (Pal <i>et al</i>., <span>2020</span>). An enormous amount of environmental data is now being collected globally using instruments such as remote satellites and automated weather stations, ranging from rainfall and temperature to light intensity and soil characteristics. The challenge plant breeders now face is how to use these data effectively when evaluating the typical differential responses of genotypes to environments (Resende <i>et al</i>., <span>2021</span>). Resende <i>et al</i>. (<span>2024b</span>; doi: 10.1111/nph.19951) begin to address the challenge of how to use ‘big data’ in an article recently published in <i>New Phytologist</i>. The study focuses on the application of machine learning to develop enviromic markers, providing a more precise and efficient method for predicting maize hybrid performance across diverse environments. The research aims to enhance maize crop yield and genetic selection gains, particularly in Brazil's four southernmost states. <blockquote><p>‘The ability to accurately predict crop performance in untested environments holds substantial promise for addressing the challenges of global food security…’</p> <div></div> </blockquote> </div> <p>Resende <i>et al</i>.'s research is particularly significant given the extensive geographical range and environmental variability within which maize is cultivated. Indeed, the range of environments and environmental measures is ambitious: 183 field trials conducted across four Brazilian states, involving 79 phenotyped maize hybrids and their 85 nonphenotyped parents. Data collection was carried out from 2017 to 2021, encompassing various environmental covariates sourced from weather, soil, sensors, and satellites, adding up to over 1300 envirotypic covariates. By focusing on precise environmental characterization, the study aimed to optimize the breeding of high-yielding, stable maize hybrids.</p> <p>The concepts of envirotypes and enviromics are relatively new, certainly as applied to plant breeding efforts (Costa-Neto & Fritsche-Neto, <span>2021</span>; Resende <i>et al</i>., <span>2021</span>). Enviromics is a field that integrates environmental data with genomics to better understand and predict the interactions between an organism's genetic makeup and its environment. This interdisciplinary approach leverages the variety of environmental data mentioned above to study how these factors collectively influence phenotypic traits. Resende <i>et al</i>.'s most recent study (<span>2024b</span>) extends their proposed methodology (Resende <i>et al</i>., <span>2024a</span>) to use a Geographic Information Systems (GIS) platform for the purpose of high-density
{"title":"A demonstration of the enviromics approach to integrating environmental ‘big data’ problems","authors":"Andrew F. Bowerman","doi":"10.1111/nph.20079","DOIUrl":"https://doi.org/10.1111/nph.20079","url":null,"abstract":"<div>With the expansion of technologies available to biological science has come an enormous rise in the amount and diverse nature of data. How we interrogate and combine ‘big data’ in different biological contexts has become the new challenge for crop biologists, be it at the genetic, phenotypic or environmental level (Pal <i>et al</i>., <span>2020</span>). An enormous amount of environmental data is now being collected globally using instruments such as remote satellites and automated weather stations, ranging from rainfall and temperature to light intensity and soil characteristics. The challenge plant breeders now face is how to use these data effectively when evaluating the typical differential responses of genotypes to environments (Resende <i>et al</i>., <span>2021</span>). Resende <i>et al</i>. (<span>2024b</span>; doi: 10.1111/nph.19951) begin to address the challenge of how to use ‘big data’ in an article recently published in <i>New Phytologist</i>. The study focuses on the application of machine learning to develop enviromic markers, providing a more precise and efficient method for predicting maize hybrid performance across diverse environments. The research aims to enhance maize crop yield and genetic selection gains, particularly in Brazil's four southernmost states. <blockquote><p>‘The ability to accurately predict crop performance in untested environments holds substantial promise for addressing the challenges of global food security…’</p>\u0000<div></div>\u0000</blockquote>\u0000</div>\u0000<p>Resende <i>et al</i>.'s research is particularly significant given the extensive geographical range and environmental variability within which maize is cultivated. Indeed, the range of environments and environmental measures is ambitious: 183 field trials conducted across four Brazilian states, involving 79 phenotyped maize hybrids and their 85 nonphenotyped parents. Data collection was carried out from 2017 to 2021, encompassing various environmental covariates sourced from weather, soil, sensors, and satellites, adding up to over 1300 envirotypic covariates. By focusing on precise environmental characterization, the study aimed to optimize the breeding of high-yielding, stable maize hybrids.</p>\u0000<p>The concepts of envirotypes and enviromics are relatively new, certainly as applied to plant breeding efforts (Costa-Neto & Fritsche-Neto, <span>2021</span>; Resende <i>et al</i>., <span>2021</span>). Enviromics is a field that integrates environmental data with genomics to better understand and predict the interactions between an organism's genetic makeup and its environment. This interdisciplinary approach leverages the variety of environmental data mentioned above to study how these factors collectively influence phenotypic traits. Resende <i>et al</i>.'s most recent study (<span>2024b</span>) extends their proposed methodology (Resende <i>et al</i>., <span>2024a</span>) to use a Geographic Information Systems (GIS) platform for the purpose of high-density","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142102020","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}
Christian Damian Lorenzo, David Blasco‐Escámez, Arthur Beauchet, Pieter Wytynck, Matilde Sanches, Jose Rodrigo Garcia del Campo, Dirk Inzé, Hilde Nelissen
SummaryMutations play a pivotal role in shaping the trajectory and outcomes of a species evolution and domestication. Maize (Zea mays) has been a major staple crop and model for genetic research for more than 100 yr. With the arrival of site‐directed mutagenesis and genome editing (GE) driven by the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), maize mutational research is once again in the spotlight. If we combine the powerful physiological and genetic characteristics of maize with the already available and ever increasing toolbox of CRISPR‐Cas, prospects for its future trait engineering are very promising. This review aimed to give an overview of the progression and learnings of maize screening studies analyzing forward genetics, natural variation and reverse genetics to focus on recent GE approaches. We will highlight how each strategy and resource has contributed to our understanding of maize natural and induced trait variability and how this information could be used to design the next generation of mutational screenings.
{"title":"Maize mutant screens: from classical methods to new CRISPR‐based approaches","authors":"Christian Damian Lorenzo, David Blasco‐Escámez, Arthur Beauchet, Pieter Wytynck, Matilde Sanches, Jose Rodrigo Garcia del Campo, Dirk Inzé, Hilde Nelissen","doi":"10.1111/nph.20084","DOIUrl":"https://doi.org/10.1111/nph.20084","url":null,"abstract":"SummaryMutations play a pivotal role in shaping the trajectory and outcomes of a species evolution and domestication. Maize (<jats:italic>Zea mays</jats:italic>) has been a major staple crop and model for genetic research for more than 100 yr. With the arrival of site‐directed mutagenesis and genome editing (GE) driven by the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), maize mutational research is once again in the spotlight. If we combine the powerful physiological and genetic characteristics of maize with the already available and ever increasing toolbox of CRISPR‐Cas, prospects for its future trait engineering are very promising. This review aimed to give an overview of the progression and learnings of maize screening studies analyzing forward genetics, natural variation and reverse genetics to focus on recent GE approaches. We will highlight how each strategy and resource has contributed to our understanding of maize natural and induced trait variability and how this information could be used to design the next generation of mutational screenings.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142102017","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}
<div>Plants constantly face the challenge of obtaining adequate nutrients from the soil, with phosphorus (P) being one of the most essential yet frequently limited nutrients. Plants absorb phosphorus in the form of inorganic orthophosphate (Chiou & Lin, <span>2011</span>). Under phosphate-limiting conditions, a phosphate starvation response (PSR) is activated in the plants, initiated by derepression of transcriptional regulators known as PHOSPHATE STARVATION RESPONSE (PHR). PHR proteins induce the gene expression of PSR-induced (PSI) genes by binding to the conserved P1BS <i>cis</i>-elements in the promoters of PSI genes, enhancing the plants ability to acquire phosphate from the soil through various morphological adaptations in root development (direct pathway) or via promotion of mutualistic association with beneficial fungi called arbuscular mycorrhizal (AM) symbiosis (indirect pathway). Most land plants engage in this symbiotic association to acquire phosphate in exchange for the photosynthates such as sugars and lipids, facilitated by tree-shaped hyphal structures called arbuscules (Luginbuehl & Oldroyd, <span>2017</span>). Recently, several independent studies have demonstrated the essential role of PHR in activating AM symbiosis under low-phosphate conditions in monocot rice (Shi <i>et al</i>., <span>2021</span>; Das <i>et al</i>., <span>2022</span>). Additionally, Shi <i>et al</i>. (<span>2021</span>) showed that rice <i>SPXs</i> suppress the OsPHR2-mediated enrichment of symbiosis-related genes and have a negative role in AM colonization. This complements another study in rice which had shown that PHR2 activity is repressed by SPX proteins (SPX1 and SPX2) (Wang <i>et al</i>., <span>2014</span>). However, in the dicotyledonous plant <i>Medicago truncatula</i>, it was demonstrated that the transcript levels of <i>MtSPX1</i> and <i>MtSPX3</i> were significantly higher in arbuscule-containing cells and play a positive role in the regulation of fungal colonization and arbuscule degeneration (Wang <i>et al</i>., <span>2021</span>). This suggests that the role of SPX can be different depending on the species (Das & Gutjahr, <span>2022</span>). More importantly, the role of PHR in arbuscule development and maintenance in <i>M. truncatula</i> also needed exploration given the species-specific differences observed for the role of SPX proteins in AM symbiosis. <blockquote><p>‘…spatial and temporal regulation of MtPHR2 expression is critical for its role in arbuscule maintenance thus making it a complex regulation process.’</p> <div></div> </blockquote> </div> <p>In an article recently published in <i>New Phytologist</i>, Wang <i>et al</i>. (<span>2024</span>; doi: 10.1111/nph.19869) explore the role of <i>Mt</i><i>PHR2</i> in arbuscule maintenance in <i>M. truncatula</i>, providing new insights into the complex relationship between nutrient acquisition and AM symbiosis (Fig. 1). Phylogenetic analysis identified three PHR genes, <i>Mt</i
{"title":"Dynamic regulation of PHR2 is essential for arbuscule maintenance","authors":"Sagar Bashyal, Chandan Kumar Gautam, Debatosh Das","doi":"10.1111/nph.20044","DOIUrl":"https://doi.org/10.1111/nph.20044","url":null,"abstract":"<div>Plants constantly face the challenge of obtaining adequate nutrients from the soil, with phosphorus (P) being one of the most essential yet frequently limited nutrients. Plants absorb phosphorus in the form of inorganic orthophosphate (Chiou & Lin, <span>2011</span>). Under phosphate-limiting conditions, a phosphate starvation response (PSR) is activated in the plants, initiated by derepression of transcriptional regulators known as PHOSPHATE STARVATION RESPONSE (PHR). PHR proteins induce the gene expression of PSR-induced (PSI) genes by binding to the conserved P1BS <i>cis</i>-elements in the promoters of PSI genes, enhancing the plants ability to acquire phosphate from the soil through various morphological adaptations in root development (direct pathway) or via promotion of mutualistic association with beneficial fungi called arbuscular mycorrhizal (AM) symbiosis (indirect pathway). Most land plants engage in this symbiotic association to acquire phosphate in exchange for the photosynthates such as sugars and lipids, facilitated by tree-shaped hyphal structures called arbuscules (Luginbuehl & Oldroyd, <span>2017</span>). Recently, several independent studies have demonstrated the essential role of PHR in activating AM symbiosis under low-phosphate conditions in monocot rice (Shi <i>et al</i>., <span>2021</span>; Das <i>et al</i>., <span>2022</span>). Additionally, Shi <i>et al</i>. (<span>2021</span>) showed that rice <i>SPXs</i> suppress the OsPHR2-mediated enrichment of symbiosis-related genes and have a negative role in AM colonization. This complements another study in rice which had shown that PHR2 activity is repressed by SPX proteins (SPX1 and SPX2) (Wang <i>et al</i>., <span>2014</span>). However, in the dicotyledonous plant <i>Medicago truncatula</i>, it was demonstrated that the transcript levels of <i>MtSPX1</i> and <i>MtSPX3</i> were significantly higher in arbuscule-containing cells and play a positive role in the regulation of fungal colonization and arbuscule degeneration (Wang <i>et al</i>., <span>2021</span>). This suggests that the role of SPX can be different depending on the species (Das & Gutjahr, <span>2022</span>). More importantly, the role of PHR in arbuscule development and maintenance in <i>M. truncatula</i> also needed exploration given the species-specific differences observed for the role of SPX proteins in AM symbiosis. <blockquote><p>‘…spatial and temporal regulation of MtPHR2 expression is critical for its role in arbuscule maintenance thus making it a complex regulation process.’</p>\u0000<div></div>\u0000</blockquote>\u0000</div>\u0000<p>In an article recently published in <i>New Phytologist</i>, Wang <i>et al</i>. (<span>2024</span>; doi: 10.1111/nph.19869) explore the role of <i>Mt</i><i>PHR2</i> in arbuscule maintenance in <i>M. truncatula</i>, providing new insights into the complex relationship between nutrient acquisition and AM symbiosis (Fig. 1). Phylogenetic analysis identified three PHR genes, <i>Mt</i","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":null,"pages":null},"PeriodicalIF":9.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142100955","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}
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