Plant Gene最新文献_第6页

Revealing drought tolerance mechanisms in Pongamia pinnata through integrated physiological, biochemical, and transcriptomic profiling 通过综合生理、生化和转录组学分析揭示凤梨的耐旱机制

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-06-21 DOI: 10.1016/j.plgene.2025.100527

K. Rajarajan , Sandhya Sharma , Harsha Srivastava , Kumari Arpita , A.K. Handa , A. Arunachalam , S.K. Dhyani

Pongamia pinnata is a promising industrial species for biofuel production. However, the detrimental effects of drought stress on the initial growth phases pose significant challenges to germination and seedling development. This problem impedes the establishment of commercial plantations in drought-prone areas, primarily because of the lack of cultivar stability. To address this issue, understanding their physiochemical and molecular responses is crucial. To elucidate the intricate molecular mechanisms underlying drought tolerance, two contrasting Pongamia genotypes, NRCP9 (tolerant) and NRCP10 (sensitive), were subjected to drought stress and watered conditions. Drought stress significantly reduced the chlorophyll content and relative water content in the NRCP10 (susceptible) genotype. In contrast, drought stress induced greater increases in peroxidase activity and proline accumulation in NRCP9 than in NRCP10. Furthermore, transcriptome analysis revealed a total of 26,195 and 18,742 differentially expressed genes (DEGs) in the tolerant and susceptible genotypes, respectively. Additionally, 128 common DEGs were commonly expressed under drought stress conditions, whereas 10,271 DEGs were commonly expressed under well-watered conditions. Among the DEGs in the TF families, the major were bHLH, NAC, ERF, WRKY, MYB, Trihelix, bZIP, FAR1, B3, C3H, STAT, and C2H2. Furthermore, transcriptome analyses revealed the significant genes involved in hormone biosynthesis, secondary metabolite accumulation, cofactor and carbon metabolism, and MAPK signaling. Additionally, the selected genes were validated by qRT-PCR, the transcriptome analysis and expression patterns were found to be corresponded. These findings reveal Pongamia's stress-adaptive mechanism and shed light on the physicochemical and differential gene responses to drought stress.

凤尾花是一种很有前途的生物燃料工业树种。然而，干旱胁迫对幼苗生长初期的不利影响对种子萌发和幼苗发育构成了重大挑战。这个问题阻碍了在干旱易发地区建立商业种植园，主要是因为缺乏品种稳定性。为了解决这个问题，了解它们的物理化学和分子反应是至关重要的。为了阐明干旱耐旱性的复杂分子机制，研究了两种不同基因型——NRCP9（耐旱性）和NRCP10（敏感性）——在干旱胁迫和水分条件下的差异。干旱胁迫显著降低了NRCP10（易感）基因型的叶绿素含量和相对含水量。相比之下，干旱胁迫诱导NRCP9过氧化物酶活性和脯氨酸积累的增加幅度大于NRCP10。此外，转录组分析显示，耐受性基因型和易感基因型分别有26,195和18,742个差异表达基因（deg）。此外，干旱胁迫条件下共有128个基因表达，而水分充足条件下共有10271个基因表达。TF家族的deg主要为bHLH、NAC、ERF、WRKY、MYB、Trihelix、bZIP、FAR1、B3、C3H、STAT和C2H2。此外，转录组分析还揭示了参与激素生物合成、次生代谢物积累、辅因子和碳代谢以及MAPK信号传导的重要基因。此外，对所选基因进行qRT-PCR验证，发现转录组分析和表达模式相对应。这些研究结果揭示了干旱胁迫对蓬棉的胁迫适应机制，揭示了干旱胁迫对蓬棉的理化和差异基因反应。

{"title":"Revealing drought tolerance mechanisms in Pongamia pinnata through integrated physiological, biochemical, and transcriptomic profiling","authors":"K. Rajarajan , Sandhya Sharma , Harsha Srivastava , Kumari Arpita , A.K. Handa , A. Arunachalam , S.K. Dhyani","doi":"10.1016/j.plgene.2025.100527","DOIUrl":"10.1016/j.plgene.2025.100527","url":null,"abstract":"<div><div><em>Pongamia pinnata</em> is a promising industrial species for biofuel production. However, the detrimental effects of drought stress on the initial growth phases pose significant challenges to germination and seedling development. This problem impedes the establishment of commercial plantations in drought-prone areas, primarily because of the lack of cultivar stability. To address this issue, understanding their physiochemical and molecular responses is crucial. To elucidate the intricate molecular mechanisms underlying drought tolerance, two contrasting Pongamia genotypes, NRCP9 (tolerant) and NRCP10 (sensitive), were subjected to drought stress and watered conditions. Drought stress significantly reduced the chlorophyll content and relative water content in the NRCP10 (susceptible) genotype. In contrast, drought stress induced greater increases in peroxidase activity and proline accumulation in NRCP9 than in NRCP10. Furthermore, transcriptome analysis revealed a total of 26,195 and 18,742 differentially expressed genes (DEGs) in the tolerant and susceptible genotypes, respectively. Additionally, 128 common DEGs were commonly expressed under drought stress conditions, whereas 10,271 DEGs were commonly expressed under well-watered conditions. Among the DEGs in the TF families, the major were bHLH, NAC, ERF, WRKY, MYB, Trihelix, bZIP, FAR1, B3, C3H, STAT, and C2H2. Furthermore, transcriptome analyses revealed the significant genes involved in hormone biosynthesis, secondary metabolite accumulation, cofactor and carbon metabolism, and MAPK signaling. Additionally, the selected genes were validated by qRT-PCR, the transcriptome analysis and expression patterns were found to be corresponded. These findings reveal Pongamia's stress-adaptive mechanism and shed light on the physicochemical and differential gene responses to drought stress.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100527"},"PeriodicalIF":2.2,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144481781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular network, structural and expression analyses of NHX genes in Phaseolus vulgaris in response to salt stress 盐胁迫下菜豆NHX基因的分子网络、结构及表达分析

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-06-18 DOI: 10.1016/j.plgene.2025.100526

Faten Mhadhbi, Hatem Boubakri

Salt stress is one of the most serious abiotic stresses limiting plant productivity worldwide. Here, we identified and characterized Sodium/Hydrogen antiporter (NHX) family in Phaseolus vulgaris genome and studied their expression in response to salt stress, for the first time, using RT q-PCR. In total, we identified 9 PvNHX genes from the common bean genome. Phylogeny, gene structure, motif patterns were performed and allowed the classification of these genes according to their subcellular localization into three subfamilies termed vacuolar (Vac-class), plasma membrane (PM-class) and endosomal (Endo-class). Conserved motifs and gene structures showed that most of which had an amiloride-binding site (FFI/LY/FLLPPI). RT q-PCR analysis revealed that salt stress induced the expression of specific PvNHX genes in both leaves (PvNHX1, PvNHX2, PvNHX3, and PvNHX7) and roots (PvNHX1, PvNHX2, PvNHX3, PvNHX4 and PvNHX7), suggesting their potential role in regulating salinity tolerance in P. vulgaris. Protein-protein interaction (PPI) network indicated that several PvNHX proteins interact with CIPK24 (CBL-interacting serine/threonine-protein kinase 24), CBL4 (Calcineurin B-like protein 4) and KEA4 (K⁺ efflux antiporter 4) proteins, implying their involvement in CBL-CIPK pathway during salinity adaptation. These findings provide valuable targets within the PvNHX family for genetic engineering aimed at improving salinity tolerance in Phaseolus vulgaris.

盐胁迫是世界范围内限制植物生产力的最严重的非生物胁迫之一。本研究首次利用RT - q-PCR技术，鉴定了菜豆（Phaseolus vulgaris）基因组中钠/氢反转运蛋白（Sodium/Hydrogen antiporter， NHX）家族，并对其在盐胁迫下的表达进行了研究。我们一共从普通豆基因组中鉴定出9个PvNHX基因。系统发育、基因结构、基序模式进行了分析，并根据亚细胞定位将这些基因分为三个亚家族，即空泡亚家族（vac类）、质膜亚家族（pm类）和内体亚家族（endo类）。保守的基序和基因结构表明，其中大部分具有一个酰胺结合位点（FFI/LY/FLLPPI）。RT - q-PCR分析结果显示，盐胁迫诱导PvNHX基因在植物叶片（PvNHX1、PvNHX2、PvNHX3和PvNHX7）和根系（PvNHX1、PvNHX2、PvNHX3、PvNHX4和PvNHX7）中表达，提示PvNHX基因可能在盐胁迫下调控植物耐盐性。蛋白质-蛋白质相互作用（PPI）网络表明，PvNHX蛋白与CIPK24 （cbl -相互作用丝氨酸/苏氨酸-蛋白激酶24）、CBL4（钙调磷酸酶b样蛋白4）和KEA4 （K+外排反转运蛋白4）蛋白相互作用，暗示它们在盐度适应过程中参与了CBL-CIPK途径。这些发现为提高菜豆耐盐性的基因工程提供了PvNHX家族有价值的靶点。

{"title":"Molecular network, structural and expression analyses of NHX genes in Phaseolus vulgaris in response to salt stress","authors":"Faten Mhadhbi, Hatem Boubakri","doi":"10.1016/j.plgene.2025.100526","DOIUrl":"10.1016/j.plgene.2025.100526","url":null,"abstract":"<div><div>Salt stress is one of the most serious abiotic stresses limiting plant productivity worldwide. Here, we identified and characterized Sodium/Hydrogen antiporter (NHX) family in <em>Phaseolus vulgaris</em> genome and studied their expression in response to salt stress, for the first time, using RT q-PCR. In total, we identified 9 <em>PvNHX</em> genes from the common bean genome. Phylogeny, gene structure, motif patterns were performed and allowed the classification of these genes according to their subcellular localization into three subfamilies termed vacuolar (Vac-class), plasma membrane (PM-class) and endosomal (Endo-class). Conserved motifs and gene structures showed that most of which had an amiloride-binding site (FFI/LY/FLLPPI). RT q-PCR analysis revealed that salt stress induced the expression of specific <em>PvNHX</em> genes in both leaves (<em>PvNHX1</em>, <em>PvNHX2</em>, Pv<em>NHX3</em>, and <em>PvNHX7</em>) and roots (<em>PvNHX1</em>, <em>PvNHX2</em>, <em>PvNHX3</em>, <em>PvNHX4</em> and <em>PvNHX7</em>), suggesting their potential role in regulating salinity tolerance in <em>P. vulgaris.</em> Protein-protein interaction (PPI) network indicated that several PvNHX proteins interact with CIPK24 (CBL-interacting serine/threonine-protein kinase 24), CBL4 (Calcineurin B-like protein 4) and KEA4 (K<sup>+</sup> efflux antiporter 4) proteins, implying their involvement in CBL-CIPK pathway during salinity adaptation. These findings provide valuable targets within the <em>PvNHX</em> family for genetic engineering aimed at improving salinity tolerance in <em>Phaseolus vulgaris</em>.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100526"},"PeriodicalIF":2.2,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144321044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The 14-3-3 gene family in Nicotiana tabacum: Genome-wide identification, expression profiling, subcellular localization, and protein interaction analysis in response to cadmium stress 烟草14-3-3基因家族：全基因组鉴定、表达谱、亚细胞定位和镉胁迫下蛋白相互作用分析

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-06-11 DOI: 10.1016/j.plgene.2025.100525

Tengfei Ma , Kunjian Yang , Fang Yang , Li Chen , Ji Chen , Shunqin Zhu , Wanhong Liu

Plant 14-3-3 proteins play a crucial role in the fine-tuning of growth and development, stress resistance, and nutrient metabolism. Tobacco is recognized as a hyperaccumulator of cadmium (Cd), yet the understanding of the Nt14-3-3 gene family remains limited in tobacco (Nicotiana tabacum L.). This study systematically identified 28 members (designated as NtGRF1 through NtGRF28) of the Nt14-3-3 family in the cultivated variety TN90 and categorized them into ε and non-ε groups. Genes within the same evolutionary branch exhibited similar conserved motif patterns and intron-exon structures. Promoter cis-acting element analysis indicated that the expression of NtGRF genes is regulated by plant hormones, particularly abscisic acid (ABA) and jasmonic acid (JA), as well as various stress factors. RNA-seq-based analysis revealed three expression patterns for the Nt14-3-3 family genes: constitutively high-expressing, low-expressing, and tissue-specific expression groups, corroborating these findings with qPCR results. Cd stress significantly enhanced the expression levels of six out of eight randomly screened NtGRF genes (NtGRF8, NtGRF15, NtGRF16, NtGRF21, NtGRF22, and NtGRF28). Subcellular localization analysis showed that NtGRF8, NtGRF16, and NtGRF22 were expressed in the cytoplasm and nucleus, while NtGRF26 was restricted to the cytoplasm. Yeast two-hybrid assays demonstrated that NtGRF16 and NtGRF22 formed homodimers, with heterodimer formation also prevalent. These results offer important insights into the potential biological functions of the Nt14-3-3 gene family, emphasizing their role in various biological processes, particularly in the response of tobacco to cadmium stress.

植物14-3-3蛋白在植物生长发育、抗逆性和养分代谢的调控中起着至关重要的作用。烟草被认为是镉（Cd）的高蓄积者，但对烟草（Nicotiana tabacum L.） Nt14-3-3基因家族的了解仍然有限。本研究系统鉴定了栽培品种TN90中Nt14-3-3家族的28个成员（指定为NtGRF1 ~ NtGRF28），并将其分为ε族和非ε族。同一进化分支内的基因表现出相似的保守基序模式和内含子-外显子结构。启动子顺式作用元件分析表明，NtGRF基因的表达受植物激素，特别是脱落酸（ABA）和茉莉酸（JA）以及各种胁迫因子的调控。基于rna序列的分析揭示了Nt14-3-3家族基因的三种表达模式：组成性高表达、低表达和组织特异性表达组，与qPCR结果证实了这些发现。Cd胁迫显著提高了随机筛选的8个NtGRF基因中的6个（NtGRF8、NtGRF15、NtGRF16、NtGRF21、NtGRF22和NtGRF28）的表达水平。亚细胞定位分析显示，NtGRF8、NtGRF16和NtGRF22在细胞质和细胞核中表达，而NtGRF26仅限于细胞质中表达。酵母双杂交实验表明，NtGRF16和NtGRF22形成同型二聚体，异源二聚体也普遍存在。这些结果为Nt14-3-3基因家族的潜在生物学功能提供了重要的见解，强调了它们在各种生物过程中的作用，特别是在烟草对镉胁迫的反应中。

{"title":"The 14-3-3 gene family in Nicotiana tabacum: Genome-wide identification, expression profiling, subcellular localization, and protein interaction analysis in response to cadmium stress","authors":"Tengfei Ma , Kunjian Yang , Fang Yang , Li Chen , Ji Chen , Shunqin Zhu , Wanhong Liu","doi":"10.1016/j.plgene.2025.100525","DOIUrl":"10.1016/j.plgene.2025.100525","url":null,"abstract":"<div><div>Plant 14-3-3 proteins play a crucial role in the fine-tuning of growth and development, stress resistance, and nutrient metabolism. Tobacco is recognized as a hyperaccumulator of cadmium (Cd), yet the understanding of the <em>Nt14-3-3</em> gene family remains limited in tobacco (<em>Nicotiana tabacum</em> L.). This study systematically identified 28 members (designated as NtGRF1 through NtGRF28) of the <em>Nt14-3-3</em> family in the cultivated variety TN90 and categorized them into ε and non-ε groups. Genes within the same evolutionary branch exhibited similar conserved motif patterns and intron-exon structures. Promoter <em>cis</em>-acting element analysis indicated that the expression of <em>NtGRF</em> genes is regulated by plant hormones, particularly abscisic acid (ABA) and jasmonic acid (JA), as well as various stress factors. RNA-seq-based analysis revealed three expression patterns for the <em>Nt14-3-3</em> family genes: constitutively high-expressing, low-expressing, and tissue-specific expression groups, corroborating these findings with qPCR results. Cd stress significantly enhanced the expression levels of six out of eight randomly screened <em>NtGRF</em> genes (<em>NtGRF8, NtGRF15, NtGRF16, NtGRF21, NtGRF22,</em> and <em>NtGRF28</em>). Subcellular localization analysis showed that <em>NtGRF8, NtGRF16,</em> and <em>NtGRF22</em> were expressed in the cytoplasm and nucleus, while <em>NtGRF26</em> was restricted to the cytoplasm. Yeast two-hybrid assays demonstrated that <em>NtGRF16</em> and <em>NtGRF22</em> formed homodimers, with heterodimer formation also prevalent. These results offer important insights into the potential biological functions of the <em>Nt14-3-3</em> gene family, emphasizing their role in various biological processes, particularly in the response of tobacco to cadmium stress.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100525"},"PeriodicalIF":2.2,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144279366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Azomite, a volcanic ash-based fertilizer modulates gene expression during photomorphogenesis through phyB-dependent and independent pathways Azomite是一种火山灰肥料，通过phyb依赖和独立的途径调节光形态发生过程中的基因表达

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-06-06 DOI: 10.1016/j.plgene.2025.100523

Elijah Mehlferber , Kent F. McCue , Yang Bi , Robert Reed , Jon Ferrel , Rajnish Khanna

Azomite is a lightly weathered dacitic (rhyolitic) tuff breccia (DTB), it is silicon-based with over 70 minerals and trace elements (micronutrients). In previous studies, application of Azomite increased greenhouse tomato production. In the tomato root endosome, Azomite caused functional shifts from higher abundance of microbes involved in metabolism of 2- to 4- carbon compounds to higher levels of microbes involved in carbohydrate metabolism. This suggested a possible increase in carbohydrate production and shift in exudates involved in microbial recruitment. Parallel studies with 4-day old Arabidopsis seedlings revealed that photosynthetically active radiation was required for Azomite-induced increase in both hypocotyl length and cotyledon area. These data suggested that Azomite may influence growth through changes in photosynthesis, leading to carbohydrate-enriched root exudates and increased growth. Here, we present RNAseq analysis in response to Azomite of 4-day old Arabidopsis seedlings grown either in continuous darkness (Dc) or under continuous red-light (Rc). Significant changes in genes involved in carbon assimilation and nutrient uptake, amongst other functional pathway categories are reported. Comparison with phyB (phytochrome B, red-light photoreceptor) mutant seedlings is shown to determine the overlap between phyB-regulated genes and Azomite-responsive genes. Two concentrations, 0.5 g and 1.0 g of Azomite were included because our previous results with tomato and Arabidopsis exhibited a dose-dependent response. Several genes are identified as responding differentially, including SUBERMAN, a myb-family transcription factor that regulates suberization of the root endodermis. This study advances our understanding of how complex mixtures of micronutrients such as Azomite influence gene expression during plant growth and development.

偶氮石是一种浅风化的英灰质（流纹岩）凝灰岩角砾岩（DTB），它以硅为基，含有70多种矿物质和微量元素（微量元素）。在以往的研究中，偶氮石的施用提高了温室番茄的产量。在番茄根内体中，Azomite引起了从参与2- 4碳化合物代谢的高丰度微生物到参与碳水化合物代谢的高水平微生物的功能转变。这表明碳水化合物的产生可能增加，参与微生物募集的渗出物可能发生变化。对4日龄拟南芥幼苗的平行研究表明，azomia诱导的下胚轴长度和子叶面积的增加都需要光合有效辐射。这些数据表明，Azomite可能通过改变光合作用影响生长，导致富含碳水化合物的根分泌物和生长增加。在这里，我们分析了在连续黑暗（Dc）和连续红光（Rc）下生长4天的拟南芥幼苗对Azomite的响应。据报道，在其他功能途径类别中，参与碳同化和营养吸收的基因发生了重大变化。与phyB（光敏色素B，红色光感受器）突变苗进行比较，可以确定phyB调控基因和azomite响应基因之间的重叠。由于我们之前对番茄和拟南芥的研究结果显示出剂量依赖性，因此我们纳入了0.5 g和1.0 g两种浓度的Azomite。几个基因被确定为有差异的反应，包括SUBERMAN，一个myb家族转录因子，调节根内胚层的suberization。这项研究促进了我们对复杂的微量元素混合物（如Azomite）如何影响植物生长发育过程中的基因表达的理解。

{"title":"Azomite, a volcanic ash-based fertilizer modulates gene expression during photomorphogenesis through phyB-dependent and independent pathways","authors":"Elijah Mehlferber , Kent F. McCue , Yang Bi , Robert Reed , Jon Ferrel , Rajnish Khanna","doi":"10.1016/j.plgene.2025.100523","DOIUrl":"10.1016/j.plgene.2025.100523","url":null,"abstract":"<div><div>Azomite is a lightly weathered dacitic (rhyolitic) tuff breccia (DTB), it is silicon-based with over 70 minerals and trace elements (micronutrients). In previous studies, application of Azomite increased greenhouse tomato production. In the tomato root endosome, Azomite caused functional shifts from higher abundance of microbes involved in metabolism of 2- to 4- carbon compounds to higher levels of microbes involved in carbohydrate metabolism. This suggested a possible increase in carbohydrate production and shift in exudates involved in microbial recruitment. Parallel studies with 4-day old Arabidopsis seedlings revealed that photosynthetically active radiation was required for Azomite-induced increase in both hypocotyl length and cotyledon area. These data suggested that Azomite may influence growth through changes in photosynthesis, leading to carbohydrate-enriched root exudates and increased growth. Here, we present RNAseq analysis in response to Azomite of 4-day old Arabidopsis seedlings grown either in continuous darkness (Dc) or under continuous red-light (Rc). Significant changes in genes involved in carbon assimilation and nutrient uptake, amongst other functional pathway categories are reported. Comparison with <em>phyB</em> (phytochrome B, red-light photoreceptor) mutant seedlings is shown to determine the overlap between phyB-regulated genes and Azomite-responsive genes. Two concentrations, 0.5 g and 1.0 g of Azomite were included because our previous results with tomato and Arabidopsis exhibited a dose-dependent response. Several genes are identified as responding differentially, including <em>SUBERMAN</em>, a myb-family transcription factor that regulates suberization of the root endodermis. This study advances our understanding of how complex mixtures of micronutrients such as Azomite influence gene expression during plant growth and development.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100523"},"PeriodicalIF":2.2,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144314498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reference gene selection and expression analyses of anthocyanin biosynthetic genes in flower and vegetative tissues of Clivia miniata L. 丁香花及营养组织花青素合成基因的内参基因选择及表达分析。

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-05-30 DOI: 10.1016/j.plgene.2025.100521

Mathabatha F. Maleka , Johan J. Spies

Pigmentation is one of the most variable traits in plants, with flowers typically being the main tissue that displays such diversity. Unlike other horticulturally valuable plants, the genetic basis of flower pigmentation in Clivia species remains poorly understood. Therefore, this study aimed to analyze the expression of numerous anthocyanin biosynthetic genes in flower and vegetative tissues of the most popular Clivia species, Clivia miniata. Such information can facilitate the breeding and biotechnological use of Clivia in the global horticulture value-chain. Initially, we mined a previously assembled C. miniata flower transcriptome for WDR transcripts that are homologous to key pigmentation genes from maize (PAC1) and Arabidopsis thaliana (TTG1). Subsequently, we identified and tested eight candidate reference genes (18S, ACT, EF1α, G6PDH, PP2A, RNPII, TUBα and UBQ) for expression stability in Clivia tissues using geNorm, NormFinder, BestKeeper, and the comparative Delta-Ct method. Homology analysis revealed a transcript encoding a partial protein with specific motifs that are common in pigmentation-related WDR proteins. Further, three reference genes (CmiPP2A, CmiEF1α and Cmi18S) were most stable in tested Clivia tissues. Quantitative real-time PCR (qPCR) analyses of ten anthocyanin biosynthetic genes (CmiDFR, CmiF3H, CmiF3’H, CmiUF3GT, CmibHLH001, CmibHLH002, CmiMYB001, CmiMYB002, CmiMYB003 and CmiWDR001) normalized against the three reference genes revealed that most had relatively higher expression levels in flower than vegetative tissues. Also, expression was generally higher during anthesis than in buds, but some genes remarkably showed marked expression in roots too. Overall, this is the first study to systematically select and validate reference genes for expression analysis of anthocyanin biosynthetic genes in Clivia.

色素沉着是植物中最多变的特征之一，花通常是表现这种多样性的主要组织。与其他有园艺价值的植物不同，Clivia花色素沉着的遗传基础仍然知之甚少。因此，本研究旨在分析众多花青素生物合成基因在最常见的Clivia Clivia miniata的花和营养组织中的表达。这些信息可以促进Clivia在全球园艺价值链中的育种和生物技术应用。首先，我们挖掘了先前组装的小红花转录组，以寻找与玉米（PAC1）和拟南芥（TTG1）的关键色素沉着基因同源的WDR转录本。随后，我们利用geNorm、NormFinder、BestKeeper和比较Delta-Ct方法，鉴定并检测了8个候选内参基因（18S、ACT、EF1α、G6PDH、PP2A、RNPII、TUBα和UBQ）在Clivia组织中的表达稳定性。同源性分析显示，该转录本编码的部分蛋白具有在色素相关WDR蛋白中常见的特定基序。此外，三个内参基因（CmiPP2A、cmif1 α和Cmi18S）在Clivia组织中最稳定。对10个花青素生物合成基因（CmiDFR、CmiF3H、CmiF3'H、cmuf3gt、CmibHLH001、CmibHLH002、CmiMYB001、CmiMYB002、CmiMYB003和CmiWDR001）与3个内参基因进行归一化的实时荧光定量PCR （qPCR）分析显示，大多数花青素生物合成基因在花中的表达水平相对高于营养组织。花期表达量普遍高于花蕾，但部分基因在根中也有显著表达。总的来说，这是第一次系统地选择和验证Clivia花青素生物合成基因表达分析的内参基因。

{"title":"Reference gene selection and expression analyses of anthocyanin biosynthetic genes in flower and vegetative tissues of Clivia miniata L.","authors":"Mathabatha F. Maleka , Johan J. Spies","doi":"10.1016/j.plgene.2025.100521","DOIUrl":"10.1016/j.plgene.2025.100521","url":null,"abstract":"<div><div>Pigmentation is one of the most variable traits in plants, with flowers typically being the main tissue that displays such diversity. Unlike other horticulturally valuable plants, the genetic basis of flower pigmentation in <em>Clivia</em> species remains poorly understood. Therefore, this study aimed to analyze the expression of numerous anthocyanin biosynthetic genes in flower and vegetative tissues of the most popular <em>Clivia</em> species, <em>Clivia miniata</em>. Such information can facilitate the breeding and biotechnological use of <em>Clivia</em> in the global horticulture value-chain. Initially, we mined a previously assembled <em>C. miniata</em> flower transcriptome for <em>WDR</em> transcripts that are homologous to key pigmentation genes from maize (<em>PAC1</em>) and <em>Arabidopsis thaliana</em> (<em>TTG1</em>). Subsequently, we identified and tested eight candidate reference genes (<em>18S</em>, <em>ACT</em>, <em>EF1</em>α, <em>G6PDH</em>, <em>PP2A</em>, <em>RNPII</em>, <em>TUB</em>α and <em>UBQ</em>) for expression stability in <em>Clivia</em> tissues using geNorm, NormFinder, BestKeeper, and the comparative Delta-Ct method. Homology analysis revealed a transcript encoding a partial protein with specific motifs that are common in pigmentation-related WDR proteins. Further, three reference genes (<em>CmiPP2A</em>, <em>CmiEF1</em>α and <em>Cmi18S</em>) were most stable in tested <em>Clivia</em> tissues. Quantitative real-time PCR (qPCR) analyses of ten anthocyanin biosynthetic genes (<em>CmiDFR</em>, <em>CmiF3H</em>, <em>CmiF3’H</em>, <em>CmiUF3GT</em>, <em>CmibHLH001</em>, <em>CmibHLH002</em>, <em>CmiMYB001</em>, <em>CmiMYB002</em>, <em>CmiMYB003</em> and <em>CmiWDR001</em>) normalized against the three reference genes revealed that most had relatively higher expression levels in flower than vegetative tissues. Also, expression was generally higher during anthesis than in buds, but some genes remarkably showed marked expression in roots too. Overall, this is the first study to systematically select and validate reference genes for expression analysis of anthocyanin biosynthetic genes in <em>Clivia</em>.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100521"},"PeriodicalIF":2.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144263937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide identification of aldehyde dhydrogenase (ALDH) family genes in pepper (Capsicum annuum) reveals involvement of CaALDH7B1 in heat and drought stress tolerance 辣椒（Capsicum annuum）醛氢酶（ALDH）家族基因的全基因组鉴定揭示了CaALDH7B1参与辣椒耐热和干旱胁迫耐受

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-05-30 DOI: 10.1016/j.plgene.2025.100524

Bo Yang , Yifen Shang , Lang Wen , Yijia Cui , Zixing Li , Yuan Cheng , Chaochao Liu

Abiotic stresses such as heat and drought lead to oxidative damage in plants by inducing excessive accumulation of reactive oxygen species (ROS). Aldehyde dehydrogenases (ALDHs), which detoxify reactive aldehydes, play critical roles in stress responses, but their functions in pepper (Capsicum annuum) remain largely unexplored. In this study, 28 CaALDH genes were identified and categorized into nine families. Phylogenetic and synteny analyses revealed strong evolutionary conservation, highlighting CaALDH2B4 and CaALDH7B1 as key members. Expression profiling showed distinct tissue-specific patterns and robust induction under heat and drought stress. Functional analysis via virus-induced gene silencing (VIGS) confirmed that CaALDH7B1 enhances stress tolerance by limiting ROS accumulation, promoting antioxidant enzyme activity (SOD, CAT, APX, POD), and maintaining NADPH/NADP⁺ homeostasis. Comparative genomics and structural modeling further revealed that CaALDH7B1 is evolutionarily conserved, with critical NADP⁺-binding residues retained across plant species. These findings underscore the pivotal role of CaALDH7B1 in oxidative stress regulation and provide new insights into the functional evolution of the ALDH gene family in pepper.

高温和干旱等非生物胁迫通过诱导活性氧（ROS）的过度积累而导致植物的氧化损伤。醛脱氢酶（ALDHs）是一种脱毒活性醛的酶，在胁迫反应中起着重要作用，但其在辣椒中的功能尚未得到充分研究。本研究共鉴定出28个CaALDH基因，并将其分为9个家族。系统发育和合成分析显示，CaALDH2B4和CaALDH7B1是关键成员，具有较强的进化保守性。在高温和干旱胁迫下，表达谱显示出明显的组织特异性模式和强大的诱导。通过病毒诱导基因沉默（VIGS）的功能分析证实，CaALDH7B1通过限制ROS积累、促进抗氧化酶（SOD、CAT、APX、POD）活性和维持NADPH/NADP+稳态来增强胁迫耐性。比较基因组学和结构建模进一步表明，CaALDH7B1具有进化保守性，在植物物种中保留了关键的NADP+结合残基。这些发现强调了CaALDH7B1在氧化应激调控中的关键作用，并为辣椒ALDH基因家族的功能进化提供了新的见解。

{"title":"Genome-wide identification of aldehyde dhydrogenase (ALDH) family genes in pepper (Capsicum annuum) reveals involvement of CaALDH7B1 in heat and drought stress tolerance","authors":"Bo Yang , Yifen Shang , Lang Wen , Yijia Cui , Zixing Li , Yuan Cheng , Chaochao Liu","doi":"10.1016/j.plgene.2025.100524","DOIUrl":"10.1016/j.plgene.2025.100524","url":null,"abstract":"<div><div>Abiotic stresses such as heat and drought lead to oxidative damage in plants by inducing excessive accumulation of reactive oxygen species (ROS). Aldehyde dehydrogenases (ALDHs), which detoxify reactive aldehydes, play critical roles in stress responses, but their functions in pepper (<em>Capsicum annuum</em>) remain largely unexplored. In this study, 28 CaALDH genes were identified and categorized into nine families. Phylogenetic and synteny analyses revealed strong evolutionary conservation, highlighting CaALDH2B4 and CaALDH7B1 as key members. Expression profiling showed distinct tissue-specific patterns and robust induction under heat and drought stress. Functional analysis via virus-induced gene silencing (VIGS) confirmed that CaALDH7B1 enhances stress tolerance by limiting ROS accumulation, promoting antioxidant enzyme activity (SOD, CAT, APX, POD), and maintaining NADPH/NADP<sup>+</sup> homeostasis. Comparative genomics and structural modeling further revealed that CaALDH7B1 is evolutionarily conserved, with critical NADP<sup>+</sup>-binding residues retained across plant species. These findings underscore the pivotal role of CaALDH7B1 in oxidative stress regulation and provide new insights into the functional evolution of the ALDH gene family in pepper.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100524"},"PeriodicalIF":2.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144194646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The calmodulin-binding transcriptional activator transcription factor family in foxtail millet (Setaria italica L.): Molecular characterization, codon bias, and evolutionary trajectory 谷子（Setaria italica L.）钙调素结合转录激活因子家族：分子特征、密码子偏好和进化轨迹

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-05-29 DOI: 10.1016/j.plgene.2025.100522

Huilong Chen , Kexin Ji , Yun Bai , Yuxian Li , Ying Liu , Fang Liu , Yutong Cui , Weina Ge , Zhenyi Wang

Calmodulin-binding transcriptional activator (CAMTA) is a calmodulin-binding transcription factor, which plays an important role in calcium/calmodulin transduction signaling pathway. Foxtail millet (Setaria italica L.) is an economically important C4 model crop, but the genome-wide identification and molecular evolution of the CAMTA family is not yet available. In this study, seven CAMTA genes were identified from the foxtail millet genome via bioinformatics methods. They were overall similar in structure but differed, and all showed tissue expression specificity. Regarding molecular evolution, codon bias contributed to the evolution of the CAMTA family, and interestingly, base mutation was not the main factor affecting their codon bias, and may also be affected by factors such as natural selection and other factors. Multiple traces indicated that polyploidization events primarily led to the expansion of the plant CAMTA family, with overall similar but differentiated expansion histories in different species, and that Selaginella moellendorfii possesses the most paralogous genes being the most distinctive. More intriguingly, we found the opposite quantitative evolutionary history of terrestrial plants to that of the algal CAMTA family. Therefore, we firstly analyzed the molecular properties of the CAMTA transcription factor family in foxtail millet and explored its molecular evolutionary trajectory, and constructed a flow of evolutionary trajectories from monospecies transition to the plant kingdom for reference.

calmodulin-binding transcriptional activator （CAMTA）是一种钙调素结合转录因子，在钙/钙调素转导信号通路中起重要作用。谷子（Setaria italica L.）是一种重要的C4模式作物，但CAMTA家族的全基因组鉴定和分子进化尚不清楚。本研究利用生物信息学方法从谷子基因组中鉴定出7个CAMTA基因。它们在结构上大体相似，但存在差异，且均具有组织表达特异性。在分子进化方面，密码子偏倚促进了CAMTA家族的进化，有趣的是，碱基突变并不是影响其密码子偏倚的主要因素，还可能受到自然选择等因素的影响。多重线索表明，植物CAMTA家族的扩展主要是由多倍体事件引起的，不同种间的扩展历史总体相似但又有差异，其中卷柏（Selaginella moellendorfii）具有最多的同源基因，最具差异性。更有趣的是，我们发现陆生植物的数量进化史与藻类CAMTA家族相反。因此，我们首先分析了谷子CAMTA转录因子家族的分子特性，探索其分子进化轨迹，构建了谷子从单物种向植物界过渡的进化轨迹流，以供参考。

{"title":"The calmodulin-binding transcriptional activator transcription factor family in foxtail millet (Setaria italica L.): Molecular characterization, codon bias, and evolutionary trajectory","authors":"Huilong Chen , Kexin Ji , Yun Bai , Yuxian Li , Ying Liu , Fang Liu , Yutong Cui , Weina Ge , Zhenyi Wang","doi":"10.1016/j.plgene.2025.100522","DOIUrl":"10.1016/j.plgene.2025.100522","url":null,"abstract":"<div><div>Calmodulin-binding transcriptional activator (CAMTA) is a calmodulin-binding transcription factor, which plays an important role in calcium/calmodulin transduction signaling pathway. Foxtail millet (<em>Setaria italica</em> L.) is an economically important C4 model crop, but the genome-wide identification and molecular evolution of the CAMTA family is not yet available. In this study, seven CAMTA genes were identified from the foxtail millet genome via bioinformatics methods. They were overall similar in structure but differed, and all showed tissue expression specificity. Regarding molecular evolution, codon bias contributed to the evolution of the CAMTA family, and interestingly, base mutation was not the main factor affecting their codon bias, and may also be affected by factors such as natural selection and other factors. Multiple traces indicated that polyploidization events primarily led to the expansion of the plant CAMTA family, with overall similar but differentiated expansion histories in different species, and that <em>Selaginella moellendorfii</em> possesses the most paralogous genes being the most distinctive. More intriguingly, we found the opposite quantitative evolutionary history of terrestrial plants to that of the algal CAMTA family. Therefore, we firstly analyzed the molecular properties of the CAMTA transcription factor family in foxtail millet and explored its molecular evolutionary trajectory, and constructed a flow of evolutionary trajectories from monospecies transition to the plant kingdom for reference.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100522"},"PeriodicalIF":2.2,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144194647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of medicinal plant Solanum procumbens Lour. using DNA barcodes and morphology 药用植物天竺葵的鉴定。利用DNA条形码和形态学

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-05-26 DOI: 10.1016/j.plgene.2025.100517

Lieu Thi Thuy Nguyen , Quyen Thi Thao Tran , Dan Thai Vo , Tri Minh Bui , Biet Van Huynh , Dung Minh Ha-Tran

Background

This study employed DNA barcoding to identify and differentiate Solanum procumbens, a potential medicinal plant used from other species in Solanaceae family. Eleven plant samples of Solanum spp. with morphological characteristics similar with those of S. procumbens and S. trilobatum were collected from various locations across Vietnam. Five DNA barcode markers were analyzed for identifying Solanum procumbens and its morphologically cryptic species Solanum trilobatum.

Results

Ten putative S. procumbens samples displayed a high identity (99.6–99.7 %) with the reference sequence within the transfer RNA leucine-transfer RNA phenylalanine (trnL–trnF) region. DNA sequences of the Internal Transcribed Spacer (ITS) region exhibited lower identity with the reference sequence, ranging from 94 % to 97.25 %. Despite this difference, DNA barcoding effectively differentiated these individuals, with both chloroplast trnL–trnF and nuclear ITS barcodes achieving high identification accuracy. The precision of trnL–trnF and ITS in species identification was validated using dried leaf samples of the putative S. procumbens and S. trilobatum. The consistency between fresh and dried samples confirms that our results are reliable and applicable in the pharmaceutical industry.

Conclusions

Phylogenetic analysis based on barcoding data aligned with morphology-based phenogram. These findings demonstrate the effectiveness of DNA barcoding for accurate identification of S. procumbens, particularly when morphological traits are ambiguous.

摘要本研究利用DNA条形码技术对茄科植物中具有潜在药用价值的原蛮茄（Solanum procumbens）进行鉴定和区分。在越南不同地点采集了11种形态特征与原藜和三叶草相似的茄属植物标本。对5种DNA条形码标记进行了分析，用于鉴别原甘菊及其形态隐种三叶甘菊。结果10份推定样品与参考序列在转移RNA亮氨酸-转移RNA苯丙氨酸（trnL-trnF）区具有较高的一致性（99.6 ~ 99.7%）。ITS区域的DNA序列与参考序列的一致性较低，在94% ~ 97.25%之间。尽管存在这种差异，但DNA条形码可以有效地区分这些个体，叶绿体trnL-trnF和核ITS条形码都具有很高的识别精度。利用推定的原藜和三叶草的干叶样品，验证了trnL-trnF和ITS在物种鉴定中的精度。新鲜和干燥样品之间的一致性证实了我们的结果是可靠的，适用于制药行业。结论基于条形码数据的系统发育分析与基于形态学的表型图一致。这些发现证明了DNA条形码在准确鉴定原藜的有效性，特别是在形态特征不明确的情况下。

{"title":"Identification of medicinal plant Solanum procumbens Lour. using DNA barcodes and morphology","authors":"Lieu Thi Thuy Nguyen , Quyen Thi Thao Tran , Dan Thai Vo , Tri Minh Bui , Biet Van Huynh , Dung Minh Ha-Tran","doi":"10.1016/j.plgene.2025.100517","DOIUrl":"10.1016/j.plgene.2025.100517","url":null,"abstract":"<div><h3>Background</h3><div>This study employed DNA barcoding to identify and differentiate <em>Solanum procumbens</em>, a potential medicinal plant used from other species in Solanaceae family. Eleven plant samples of <em>Solanum</em> spp. with morphological characteristics similar with those of <em>S. procumbens</em> and <em>S. trilobatum</em> were collected from various locations across Vietnam. Five DNA barcode markers were analyzed for identifying <em>Solanum procumbens</em> and its morphologically cryptic species <em>Solanum trilobatum</em>.</div></div><div><h3>Results</h3><div>Ten putative <em>S. procumbens</em> samples displayed a high identity (99.6–99.7 %) with the reference sequence within the transfer RNA leucine-transfer RNA phenylalanine <em>(trnL</em>–<em>trnF)</em> region. DNA sequences of the Internal Transcribed Spacer (ITS) region exhibited lower identity with the reference sequence, ranging from 94 % to 97.25 %. Despite this difference, DNA barcoding effectively differentiated these individuals, with both chloroplast <em>trnL</em>–<em>trnF</em> and nuclear ITS barcodes achieving high identification accuracy. The precision of <em>trnL</em>–<em>trnF</em> and ITS in species identification was validated using dried leaf samples of the putative <em>S. procumbens</em> and <em>S. trilobatum</em>. The consistency between fresh and dried samples confirms that our results are reliable and applicable in the pharmaceutical industry.</div></div><div><h3>Conclusions</h3><div>Phylogenetic analysis based on barcoding data aligned with morphology-based phenogram. These findings demonstrate the effectiveness of DNA barcoding for accurate identification of <em>S. procumbens</em>, particularly when morphological traits are ambiguous.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100517"},"PeriodicalIF":2.2,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144166991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide analysis of receptor-like 2 kinase 1-like genes reveals involvement of a RLK1L member in tolerance to salt stress in Medicago sativa 受体样2激酶1样基因的全基因组分析揭示了RLK1L成员参与苜蓿对盐胁迫的耐受性

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-05-23 DOI: 10.1016/j.plgene.2025.100520

Yiping Wei , Tian Zhang , Qinyan Bao, Zhaozhu Wen, Shuzhi Ma, Yanbo Zhang, Wenxuan Du

The Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) family constitutes a specialized group within plant receptor-like protein kinases that has been detected in numerous plant varieties. However, RLK1L members have not been characterized in alfalfa. Through systematic analysis, this study examined the features and identification of RLK1L genes within alfalfa based on known gene sequences from the model plants within the Arabidopsis genus, specifically Arabidopsis thaliana, and those in the Medicago genus, such as Medicago truncatula. Phylogenetic analysis of AtCrRLK1Ls, MtCrRLK1Ls, and MsCrRLK1Ls led to the classification of 19 MsCrRLK1L genes in alfalfa into eight distinct clusters. Bioinformatic analyses revealed that the molecular masses of MsCrRLK1L proteins spanned from 29.17 to 167.36 kDa. Subcellular targeting predictions indicated predominant cell membrane localization for these polypeptides Conserved domain profiling demonstrated the ubiquitous presence of a malectin-like domain across all MsCrRLK1L members. Chromosome localization and collinearity analysis showed that the 19 MsCrRLK1L genes were unevenly distributed across five alfalfa chromosomes, with four gene pairs exhibiting intra-species collinearity. Cis-Acting element analysis identified stress- and hormone-responsive motifs, suggesting that MsCrRLK1Ls are involved in abiotic stress signaling. Gene expression profiling under salt stress (200 mM NaCl) demonstrated tissue-specific induction patterns, with six MsCrRLK1L genes significantly upregulated in aerial and root tissues. Furthermore, MsCrRLK1L2 overexpression in Arabidopsis improved the germination rate and growth status under salt stress. This study comprehensively profiles the MsCrRLK1L family in alfalfa, confirming its role in salt tolerance and suggesting genetic targets to boost crop resilience.

Catharanthus roseus receptor-like kinase 1-like （CrRLK1L）家族是植物受体样蛋白激酶中的一个特殊类群，已在许多植物品种中检测到。然而，RLK1L成员尚未在苜蓿中被表征。本研究通过系统分析，利用拟南芥属模式植物（特别是拟南芥）和紫花苜蓿属模式植物（如truncatula紫花苜蓿）的已知基因序列，对紫花苜蓿RLK1L基因的特征和鉴定进行了研究。通过对AtCrRLK1Ls、MtCrRLK1Ls和MsCrRLK1Ls的系统发育分析，将苜蓿中19个MsCrRLK1L基因分为8个不同的基因簇。生物信息学分析显示，MsCrRLK1L蛋白的分子质量在29.17 ~ 167.36 kDa之间。亚细胞靶向预测表明这些多肽的主要细胞膜定位保守结构域分析表明，在所有MsCrRLK1L成员中普遍存在雄性凝集素样结构域。染色体定位和共线性分析表明，19个MsCrRLK1L基因不均匀分布在5条苜蓿染色体上，其中4对基因在种内共线性。顺式作用元件分析确定了应激和激素反应基序，表明mscrrlk1l参与非生物应激信号传导。盐胁迫（200 mM NaCl）下的基因表达谱显示出组织特异性诱导模式，6个MsCrRLK1L基因在地上和根组织中显著上调。此外，MsCrRLK1L2在拟南芥中的过表达改善了盐胁迫下的发芽率和生长状况。本研究全面分析了苜蓿中MsCrRLK1L家族，证实了其在耐盐性中的作用，并提出了提高作物抗逆性的遗传靶点。

{"title":"Genome-wide analysis of receptor-like 2 kinase 1-like genes reveals involvement of a RLK1L member in tolerance to salt stress in Medicago sativa","authors":"Yiping Wei , Tian Zhang , Qinyan Bao, Zhaozhu Wen, Shuzhi Ma, Yanbo Zhang, Wenxuan Du","doi":"10.1016/j.plgene.2025.100520","DOIUrl":"10.1016/j.plgene.2025.100520","url":null,"abstract":"<div><div>The <em>Catharanthus roseus</em> receptor-like kinase 1-like (CrRLK1L) family constitutes a specialized group within plant receptor-like protein kinases that has been detected in numerous plant varieties. However, <em>RLK1L</em> members have not been characterized in alfalfa. Through systematic analysis, this study examined the features and identification of <em>RLK1L</em> genes within alfalfa based on known gene sequences from the model plants within the Arabidopsis genus, specifically <em>Arabidopsis thaliana</em>, and those in the Medicago genus, such as <em>Medicago truncatula</em>. Phylogenetic analysis of <em>AtCrRLK1Ls</em>, <em>MtCrRLK1Ls</em>, and <em>MsCrRLK1Ls</em> led to the classification of 19 <em>MsCrRLK1L</em> genes in alfalfa into eight distinct clusters<em>.</em> Bioinformatic analyses revealed that the molecular masses of MsCrRLK1L proteins spanned from 29.17 to 167.36 kDa. Subcellular targeting predictions indicated predominant cell membrane localization for these polypeptides Conserved domain profiling demonstrated the ubiquitous presence of a malectin-like domain across all MsCrRLK1L members. Chromosome localization and collinearity analysis showed that the 19 <em>MsCrRLK1L</em> genes were unevenly distributed across five alfalfa chromosomes, with four gene pairs exhibiting intra-species collinearity. <em>Cis</em>-Acting element analysis identified stress- and hormone-responsive motifs, suggesting that <em>MsCrRLK1Ls</em> are involved in abiotic stress signaling. Gene expression profiling under salt stress (200 mM NaCl) demonstrated tissue-specific induction patterns, with six <em>MsCrRLK1L</em> genes significantly upregulated in aerial and root tissues. Furthermore, <em>MsCrRLK1L2</em> overexpression in <em>Arabidopsis</em> improved the germination rate and growth status under salt stress. This study comprehensively profiles the <em>MsCrRLK1L</em> family in alfalfa, confirming its role in salt tolerance and suggesting genetic targets to boost crop resilience.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100520"},"PeriodicalIF":2.2,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144139563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic diversity analysis in cytoplasmic male sterile ‘A’ lines and restorer ‘R’ lines of Indian mustard using SSR markers 利用SSR标记分析印度芥菜细胞质雄性不育系A和恢复系R的遗传多样性

IF 2.2 Q3 GENETICS & HEREDITY

Plant Gene

Pub Date : 2025-05-11 DOI: 10.1016/j.plgene.2025.100518

K.H. Singh, Lal Singh, Nehanjali Parmar, Deepika Sharma, J. Nanjundan, Ajay Kumar Thakur

Indian mustard (Brassica juncea L. Czern & Coss.) is a highly economically important oilseed crop of India. An accurate estimation of genetic diversity inherent in breeding material is a pre-requisite for the success of any hybrid breeding programme, as it leads to identification of genetically divergent parents for exploiting high heterotic levels. In the present study, 200 genome-wide spanned simple sequence repeat (SSR) markers were used for estimation of genetic diversity and identification of genetically divergent parental combinations in a panel of 28 parental lines of Indian mustard comprising of 21 cytoplasmic male sterile (CMS) ‘A' lines and 7 restrorer ‘R' lines. A total of 179 SSR markers resulted in positive amplification with 155 (81.57 %) SSRs producing polymorphic amplicons and 24 (13.41 %) SSRs resulted into monomorphic products. Allele number varied from 2 to 6 with a mean value of 3.27 alleles per SSR marker. PIC values ranged from 0.23 to 0.7 with a mean value of 0.38 per SSR marker. Gene diversity values were in the range of 0.27–0.75 with average value of 0.47, inferring the presence of a moderate level of genetic diversity in the plant material. Neighbor-Joining dendrogram could not exactly differentiate ‘A' and ‘R' lines into different groups. This study led to identification of few genetically diverse A and R lines, suitable for making crosses for heterotic hybrid development in Indian mustard. On the basis of Euclidean distances, various cross-combinations viz. MJA10 & MJR3/EC597313, MJA 14 & MJR3/EC597313, and MH 12–12/EC597313S & MJR9 were designated as genetically diverse genotypes. These cross-combinations may be used in hybrid breeding program to exploit heterosis in Indian mustard improvement.

印度芥菜(Brassica juncea L. Czern；是印度一种经济上非常重要的油籽作物。准确估计育种材料中固有的遗传多样性是任何杂交育种计划成功的先决条件，因为它导致鉴定遗传上不同的亲本，以利用高杂种优势水平。本研究利用200个全基因组跨简单序列重复（SSR）标记，对21个细胞质雄性不育（CMS）“a”系和7个恢复系“R”系28个亲本组合进行了遗传多样性估计和遗传分化鉴定。共有179个SSR标记产生阳性扩增，其中155个（81.57%）SSR标记产生多态性扩增，24个（13.41%）SSR标记产生单态扩增。等位基因数为2 ~ 6个，平均每个SSR标记有3.27个等位基因。PIC值为0.23 ~ 0.7，平均为0.38。基因多样性值在0.27 ~ 0.75之间，平均值为0.47，表明该植物材料具有中等水平的遗传多样性。Neighbor-Joining tree - plan不能准确区分A和R线。本研究鉴定出了少数遗传多样性较好的A、R系，适合用于印度芥菜杂种开发。在欧氏距离的基础上，各种交叉组合即MJA10 &；MJR3/EC597313, MJA 14 &；MJR3/EC597313和MH 12-12 /EC597313S &；MJR9基因型具有遗传多样性。这些杂交组合可用于杂交育种计划，利用杂种优势改良印度芥菜。

{"title":"Genetic diversity analysis in cytoplasmic male sterile ‘A’ lines and restorer ‘R’ lines of Indian mustard using SSR markers","authors":"K.H. Singh, Lal Singh, Nehanjali Parmar, Deepika Sharma, J. Nanjundan, Ajay Kumar Thakur","doi":"10.1016/j.plgene.2025.100518","DOIUrl":"10.1016/j.plgene.2025.100518","url":null,"abstract":"<div><div>Indian mustard (<em>Brassica juncea</em> L. Czern & Coss.) is a highly economically important oilseed crop of India. An accurate estimation of genetic diversity inherent in breeding material is a pre-requisite for the success of any hybrid breeding programme, as it leads to identification of genetically divergent parents for exploiting high heterotic levels. In the present study, 200 genome-wide spanned simple sequence repeat (SSR) markers were used for estimation of genetic diversity and identification of genetically divergent parental combinations in a panel of 28 parental lines of Indian mustard comprising of 21 cytoplasmic male sterile (CMS) ‘A' lines and 7 restrorer ‘R' lines. A total of 179 SSR markers resulted in positive amplification with 155 (81.57 %) SSRs producing polymorphic amplicons and 24 (13.41 %) SSRs resulted into monomorphic products. Allele number varied from 2 to 6 with a mean value of 3.27 alleles per SSR marker. PIC values ranged from 0.23 to 0.7 with a mean value of 0.38 per SSR marker. Gene diversity values were in the range of 0.27–0.75 with average value of 0.47, inferring the presence of a moderate level of genetic diversity in the plant material. Neighbor-Joining dendrogram could not exactly differentiate ‘A' and ‘R' lines into different groups. This study led to identification of few genetically diverse A and R lines, suitable for making crosses for heterotic hybrid development in Indian mustard. On the basis of Euclidean distances, various cross-combinations viz. MJA10 & MJR3/EC597313, MJA 14 & MJR3/EC597313, and MH 12–12/EC597313S & MJR9 were designated as genetically diverse genotypes. These cross-combinations may be used in hybrid breeding program to exploit heterosis in Indian mustard improvement.</div></div>","PeriodicalId":38041,"journal":{"name":"Plant Gene","volume":"43 ","pages":"Article 100518"},"PeriodicalIF":2.2,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144068341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0