Divergence in basic chromosome numbers among closely related species is widespread in plants, yet a fundamental question regarding the evolutionary direction of karyotype—whether descending (from higher to lower numbers) or ascending (from lower to higher)—remains contentious. Alfalfa (Medicago sativa L.), a key forage crop, displays two basic chromosome numbers (x = 8 and x = 7) within the genus, and whether this divergence arose through descending evolution from 8 to 7 or the reverse remains unclear. Here, we developed a set of chromosome-specific painting markers capable of tracing chromosomal evolutionary trajectories among Medicago species. Comparative cytological analysis of seven accessions (x = 8) from the Medicago sativa L. complex revealed conserved chromosomal synteny in both diploid and autotetraploid species, with no detectable inter-chromosomal rearrangements. In Medicago polymorpha (x = 7), we discovered that the divergence in basic chromosome numbers (x = 7 vs. x = 8) resulted from large-scale fission-fusion events involving chromosomes 3, 5, and 6, rather than the simple fusion of chromosomes 3 and 7 as previously published genomic hypotheses. Further supporting evidence from rDNA remodeling and phylogenetic analysis indicates a descending evolutionary pathway, with the ancestral x = 8 transitioning to x = 7 approximately Mid-Miocene (~12 million years ago). Our results offer new insights into Medicago speciation and evolutionary origins, and instantiate a strategy for studying karyotypic evolutionary direction in other plant taxa with similar chromosomal dynamics.
{"title":"Chromosome-specific painting provides insights into the karyotype evolutionary direction and trajectory in the genus Medicago","authors":"Wei Wang, Yuanbin Zhu, Xia Wu, Zixiang Guo, Qian Zheng, Guangzhen Shi, Yuanhao Li, Wenjun Luo, Fei Wang, Haitao Shen, Sheng Zuo, Quanliang Xie, Hongbin Li, Zhuang Meng","doi":"10.1093/hr/uhaf313","DOIUrl":"https://doi.org/10.1093/hr/uhaf313","url":null,"abstract":"Divergence in basic chromosome numbers among closely related species is widespread in plants, yet a fundamental question regarding the evolutionary direction of karyotype—whether descending (from higher to lower numbers) or ascending (from lower to higher)—remains contentious. Alfalfa (Medicago sativa L.), a key forage crop, displays two basic chromosome numbers (x = 8 and x = 7) within the genus, and whether this divergence arose through descending evolution from 8 to 7 or the reverse remains unclear. Here, we developed a set of chromosome-specific painting markers capable of tracing chromosomal evolutionary trajectories among Medicago species. Comparative cytological analysis of seven accessions (x = 8) from the Medicago sativa L. complex revealed conserved chromosomal synteny in both diploid and autotetraploid species, with no detectable inter-chromosomal rearrangements. In Medicago polymorpha (x = 7), we discovered that the divergence in basic chromosome numbers (x = 7 vs. x = 8) resulted from large-scale fission-fusion events involving chromosomes 3, 5, and 6, rather than the simple fusion of chromosomes 3 and 7 as previously published genomic hypotheses. Further supporting evidence from rDNA remodeling and phylogenetic analysis indicates a descending evolutionary pathway, with the ancestral x = 8 transitioning to x = 7 approximately Mid-Miocene (~12 million years ago). Our results offer new insights into Medicago speciation and evolutionary origins, and instantiate a strategy for studying karyotypic evolutionary direction in other plant taxa with similar chromosomal dynamics.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"58 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145509489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qiang Lai, Zeng Wang, Changfu Jia, Xiner Qumu, Rui Wang, Zhipeng Zhao, Yao Liu, Yukang Hou, Jianquan Liu, Pär K Ingvarsson, Jing Wang
Polyploidization has occurred throughout the tree of life and is particularly common in plants. Despite its ubiquity, our understanding of the short- and long-term effects and consequences of genome doubling in natural populations remains incomplete. In this study, we identified a novel ploidy-variable species system within the ornamental and industrial oilseed genus Orychophragmus (Brassicaceae), which comprises six species, including diploid and tetraploid cytotypes of O. taibaiensis. By integrating population-scale genomic and transcriptomic datasets across the species in this genus, we constructed a robust phylogenetic framework and investigated the divergence and demographic history of O. taibaiensis in comparison to its relatives. Specifically, we characterized the geographical distribution patterns of diploids and tetraploids in natural populations of O. taibaiensis, confirmed the autopolyploid origin of tetraploids, and inferred their origin time relative to diploid counterparts. Our findings further revealed that, following genome doubling, tetraploids accumulated a higher genetic load of deleterious mutations, likely due to relaxed purifying selection facilitated by allelic redundancy. Additionally, genome doubling was associated with pronounced changes in gene expression patterns, with differentially expressed genes evolving under relaxed selective constraints. These results highlight that the initial masking of deleterious mutations, changes in expression regulation, and divergent efficacy of selection likely all contribute to shaping the establishment and evolutionary potential of polyploids.
多倍体化发生在整个生命之树上，在植物中尤为常见。尽管它无处不在，但我们对自然种群中基因组加倍的短期和长期影响和后果的理解仍然不完整。摘要本研究在观赏和工业油籽属（芸苔科）中鉴定了一个新的倍性变异物种系统，该系统包括6个种，包括O. taibaiensis的二倍体和四倍体细胞型。通过整合该属物种的种群尺度基因组和转录组学数据，我们构建了一个强大的系统发育框架，并与其近缘种进行了比较，研究了太白猿猴的分化和人口统计学历史。具体来说，我们分析了太白O. O. taibaiensis自然居群中二倍体和四倍体的地理分布格局，证实了四倍体的自多倍体起源，并推断了它们相对于二倍体的起源时间。我们的研究结果进一步表明，在基因组加倍之后，四倍体积累了更高的有害突变遗传负荷，这可能是由于等位基因冗余促进了宽松的纯化选择。此外，基因组加倍与基因表达模式的显著变化有关，差异表达基因在宽松的选择约束下进化。这些结果强调，有害突变的初始掩蔽、表达调控的变化和选择的不同效力可能都有助于形成多倍体的建立和进化潜力。
{"title":"Evolutionary History and Genomic Consequences of Polyploidization in Natural Populations of Orychophragmus taibaiensis","authors":"Qiang Lai, Zeng Wang, Changfu Jia, Xiner Qumu, Rui Wang, Zhipeng Zhao, Yao Liu, Yukang Hou, Jianquan Liu, Pär K Ingvarsson, Jing Wang","doi":"10.1093/hr/uhaf314","DOIUrl":"https://doi.org/10.1093/hr/uhaf314","url":null,"abstract":"Polyploidization has occurred throughout the tree of life and is particularly common in plants. Despite its ubiquity, our understanding of the short- and long-term effects and consequences of genome doubling in natural populations remains incomplete. In this study, we identified a novel ploidy-variable species system within the ornamental and industrial oilseed genus Orychophragmus (Brassicaceae), which comprises six species, including diploid and tetraploid cytotypes of O. taibaiensis. By integrating population-scale genomic and transcriptomic datasets across the species in this genus, we constructed a robust phylogenetic framework and investigated the divergence and demographic history of O. taibaiensis in comparison to its relatives. Specifically, we characterized the geographical distribution patterns of diploids and tetraploids in natural populations of O. taibaiensis, confirmed the autopolyploid origin of tetraploids, and inferred their origin time relative to diploid counterparts. Our findings further revealed that, following genome doubling, tetraploids accumulated a higher genetic load of deleterious mutations, likely due to relaxed purifying selection facilitated by allelic redundancy. Additionally, genome doubling was associated with pronounced changes in gene expression patterns, with differentially expressed genes evolving under relaxed selective constraints. These results highlight that the initial masking of deleterious mutations, changes in expression regulation, and divergent efficacy of selection likely all contribute to shaping the establishment and evolutionary potential of polyploids.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"5 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145535811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Woo-Taek Jeon, Jeong-A Kim, Ahyeon Cheon, Shawn S Y Lee, Joohyun Kang, Jung-Min Lee, Yuree Lee
Organ abscission is essential for optimal reproduction, yet its regulation in perennial woody plant species is poorly understood. To investigate how abscission is spatially and temporally regulated during reproduction, we analyzed five sequential abscission events in the cherry species Prunus × yedoensis (Cerasus × yedoensis, Somei-Yoshino) and Prunus sargentii var. verecunda (Bunhong-Beot): abscission of the petals, calyces, flower pedicels, fruit pedicels, and peduncles. The abscission zone of the calyx formed de novo upon activation, whereas other abscission zones were pre-formed but developmentally arrested. Localized ethylene responsiveness reactivated these zones, promoting cell division, differentiation of residuum and secession cells on either side of the abscission zone, and lignin deposition in some cases. This progression was accompanied by reactive oxygen species accumulation and pH shifts. We observed species-specific differences during early floral abscission: P. yedoensis shed petals rapidly in a pollination-independent manner, whereas P. sargentii retained petals on unpollinated flowers, which later abscised with the pedicel, potentially extending the fertilization window. Both species employed a post-fertilization developmental gate via fruit pedicel abscission to selectively eliminate small, slow-growing fruits. These findings reveal that Prunus species coordinate a hierarchical abscission program functioning as a multilayered reproductive filter, progressively refining investment decisions to determine the final fruit set.
器官脱落是最佳生殖的必要条件，但其在多年生木本植物物种中的调控机制尚不清楚。为研究樱花（Prunus × yedoensis, Somei-Yoshino）和樱（Prunus sargentii var. verecunda, Bunhong-Beot）在繁殖过程中发生的5个连续脱落事件：花瓣、花萼、花梗、果梗和花梗的脱落。花萼的脱落带是在激活后重新形成的，而其他脱落带是预先形成的，但发育受阻。局部乙烯反应激活了这些区域，促进了脱落区两侧的细胞分裂、残余细胞和分裂细胞的分化，并在某些情况下促进了木质素的沉积。这一过程伴随着活性氧的积累和pH值的变化。我们观察到在早期花脱落过程中的物种特异性差异：紫杉以不依赖授粉的方式迅速脱落花瓣，而马尾草在未授粉的花上保留花瓣，这些花瓣随后随花梗脱落，可能延长受精窗口。这两种植物都采用了受精后的发育门，通过果梗脱落来选择性地消除小的、生长缓慢的果实。这些发现表明，李属植物协调了一个分层分离程序，作为一个多层生殖过滤器，逐步完善投资决策，以确定最终的果实集。
{"title":"A hierarchical abscission program regulates reproductive allocation in Prunus × yedoensis and Prunus sargentii","authors":"Woo-Taek Jeon, Jeong-A Kim, Ahyeon Cheon, Shawn S Y Lee, Joohyun Kang, Jung-Min Lee, Yuree Lee","doi":"10.1093/hr/uhaf317","DOIUrl":"https://doi.org/10.1093/hr/uhaf317","url":null,"abstract":"Organ abscission is essential for optimal reproduction, yet its regulation in perennial woody plant species is poorly understood. To investigate how abscission is spatially and temporally regulated during reproduction, we analyzed five sequential abscission events in the cherry species Prunus × yedoensis (Cerasus × yedoensis, Somei-Yoshino) and Prunus sargentii var. verecunda (Bunhong-Beot): abscission of the petals, calyces, flower pedicels, fruit pedicels, and peduncles. The abscission zone of the calyx formed de novo upon activation, whereas other abscission zones were pre-formed but developmentally arrested. Localized ethylene responsiveness reactivated these zones, promoting cell division, differentiation of residuum and secession cells on either side of the abscission zone, and lignin deposition in some cases. This progression was accompanied by reactive oxygen species accumulation and pH shifts. We observed species-specific differences during early floral abscission: P. yedoensis shed petals rapidly in a pollination-independent manner, whereas P. sargentii retained petals on unpollinated flowers, which later abscised with the pedicel, potentially extending the fertilization window. Both species employed a post-fertilization developmental gate via fruit pedicel abscission to selectively eliminate small, slow-growing fruits. These findings reveal that Prunus species coordinate a hierarchical abscission program functioning as a multilayered reproductive filter, progressively refining investment decisions to determine the final fruit set.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"87 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145509492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yue Yang, Yu Wang, Mingkun Chen, Xilin Zhou, Jun Wei, Jiayao Tang, Houhua Li
Somatic embryogenesis in plants requires the prior formation of embryogenic cells in plants. The remodeling of the cell wall in mature somatic cells is a prerequisite for embryogenic cell formation. However, the mechanism of this process remains unelucidated. In this study, eTM3699, miR3699 and MANNAN7 (MAN7) were identified as key regulators of embryogenic cell formation through whole-transcriptome sequencing. The dual-luciferase reporter assays and GUS histochemical staining assays, were used to identified the regulatory network of eTM3699-miR3699-MdMAN7. The overexpression and CRISPR/Cas9 mediated transgenic assays were used for functional analysis of miR3699 and MdMAN7. MdMAN7 overexpression can enhance the activity of β-mannanase, induce hemicellulose degradation, and reshape the cell wall of highly differentiated somatic cells, relieve the restriction on cell differentiation and division, ultimately positively regulating the embryogenic cell formation. Specifically, the overexpression of MdMAN7 can significantly improve the efficiency and shorten the induction cycle of somatic embryogenesis. miR3699 acted by negatively regulating MdMAN7. In addition, eTM3699 were identified as endogenous target mimics of miR3699 that bind to miR3699 to prevent cleavage of MdMAN7 and thereby positively regulate embryogenic cell formation. In conclusion, our results elucidate the mechanism of eTM-miR3699-MAN7 module regulating embryogenic cell formation during the early stage of somatic embryogenesis in apple.
{"title":"The eTM-miR3699-MAN7 mediated cell wall degradation in regulating embryogenic cell formation during the early stage of somatic embryogenesis in apple","authors":"Yue Yang, Yu Wang, Mingkun Chen, Xilin Zhou, Jun Wei, Jiayao Tang, Houhua Li","doi":"10.1093/hr/uhaf315","DOIUrl":"https://doi.org/10.1093/hr/uhaf315","url":null,"abstract":"Somatic embryogenesis in plants requires the prior formation of embryogenic cells in plants. The remodeling of the cell wall in mature somatic cells is a prerequisite for embryogenic cell formation. However, the mechanism of this process remains unelucidated. In this study, eTM3699, miR3699 and MANNAN7 (MAN7) were identified as key regulators of embryogenic cell formation through whole-transcriptome sequencing. The dual-luciferase reporter assays and GUS histochemical staining assays, were used to identified the regulatory network of eTM3699-miR3699-MdMAN7. The overexpression and CRISPR/Cas9 mediated transgenic assays were used for functional analysis of miR3699 and MdMAN7. MdMAN7 overexpression can enhance the activity of β-mannanase, induce hemicellulose degradation, and reshape the cell wall of highly differentiated somatic cells, relieve the restriction on cell differentiation and division, ultimately positively regulating the embryogenic cell formation. Specifically, the overexpression of MdMAN7 can significantly improve the efficiency and shorten the induction cycle of somatic embryogenesis. miR3699 acted by negatively regulating MdMAN7. In addition, eTM3699 were identified as endogenous target mimics of miR3699 that bind to miR3699 to prevent cleavage of MdMAN7 and thereby positively regulate embryogenic cell formation. In conclusion, our results elucidate the mechanism of eTM-miR3699-MAN7 module regulating embryogenic cell formation during the early stage of somatic embryogenesis in apple.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"55 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145509490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Young Kyoung Oh, Hari Chandana Yadavalli, Christian Møller, Moon Young Ryu, Seok Keun Cho, Bora Lee, Mikyung Chang, Mi Young Byun, Jong Hum Kim, Hyun Ju Jung, Seong Wook Yang
MicroRNAs (miRNAs) are non-coding RNAs, approximately 21–24 nucleotides in length, that play a pivotal role in post-transcriptional gene regulation by inducing cleavage or translational repression of target mRNAs with complementary sequences. In this study, we identified miRNAs expressed during the early developmental stage of mung bean (Vigna radiata), a major legume crop, using small RNA sequencing (small RNA-seq), and analyzed their expression profiles across various mung bean tissues. Mung bean-specific miRNAs were found to be highly expressed in the aerial parts of seedlings, particularly in the leaves. Furthermore, the expression of these miRNAs was effectively validated using Tailed-Hoogsteen triplex DNA-encapsulated silver nanocluster (DNA/AgNC) sensors. The nanosensor enables rapid detection of target miRNAs within 30 minutes and is easy to apply for field-based assessments. The predicted target mRNAs of the identified miRNAs were associated with a range of biological processes relevant to early-stage development. This study highlights the potential of nanosensor-based approaches for the efficient identification of novel miRNAs in staple crops, offering a promising strategy to reduce the cost, time, and labor required during the transition from laboratory research to field applications.
{"title":"Identification of specific miRNAs in early-stage mung bean ( Vigna radiata ) using DNA/AgNCs sensors and miRNAtome analysis","authors":"Young Kyoung Oh, Hari Chandana Yadavalli, Christian Møller, Moon Young Ryu, Seok Keun Cho, Bora Lee, Mikyung Chang, Mi Young Byun, Jong Hum Kim, Hyun Ju Jung, Seong Wook Yang","doi":"10.1093/hr/uhaf312","DOIUrl":"https://doi.org/10.1093/hr/uhaf312","url":null,"abstract":"MicroRNAs (miRNAs) are non-coding RNAs, approximately 21–24 nucleotides in length, that play a pivotal role in post-transcriptional gene regulation by inducing cleavage or translational repression of target mRNAs with complementary sequences. In this study, we identified miRNAs expressed during the early developmental stage of mung bean (Vigna radiata), a major legume crop, using small RNA sequencing (small RNA-seq), and analyzed their expression profiles across various mung bean tissues. Mung bean-specific miRNAs were found to be highly expressed in the aerial parts of seedlings, particularly in the leaves. Furthermore, the expression of these miRNAs was effectively validated using Tailed-Hoogsteen triplex DNA-encapsulated silver nanocluster (DNA/AgNC) sensors. The nanosensor enables rapid detection of target miRNAs within 30 minutes and is easy to apply for field-based assessments. The predicted target mRNAs of the identified miRNAs were associated with a range of biological processes relevant to early-stage development. This study highlights the potential of nanosensor-based approaches for the efficient identification of novel miRNAs in staple crops, offering a promising strategy to reduce the cost, time, and labor required during the transition from laboratory research to field applications.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"50 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145498285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qingdong Wang, Shuting Su, Yarui Sheng, Mengli Xu, Baohong Tang, Yonggui Ma, Yuhua Shi
Alfalfa (Medicago sativa L.) is a globally pivotal legume forage. Selenium (Se), an essential trace element for humans and animals, can significantly enhance the growth and development of alfalfa. Chlorophyll is the central pigment of plant photosynthesis. Previous research on chlorophyll synthesis in alfalfa has mainly focused on transcriptional regulation, environmental factors (light, nutrient availability), and phytohormone signaling, while fewer studies have been conducted at the post-transcriptional level. Through whole transcriptome sequencing analysis, microRNAs (miRNAs) were identified as positively responsive to selenium. This study focused on the regulation of chlorophyll synthesis by the miR171-SCL6 module in alfalfa. β-glucuronidase (GUS) staining and dual-luciferase assays revealed that MsmiR171 negatively regulated the transcript levels of the SCARECROW-LIKE 6 transcription factor MsSCL6. Subcellular localization analysis revealed that MsSCL6 was mainly in the cell nucleus. Functional analyses demonstrated that MsmiR171 promoted chlorophyll synthesis and photosynthesis in alfalfa, while MsSCL6 negatively regulated chlorophyll synthesis. Notably, selenium treatment upregulated MsmiR171 expression, downregulated MsSCL6 expression, and enhanced chlorophyll accumulation. qRT-PCR analysis revealed differential expression of MsPOR in MsmiR171 and MsSCL6 overexpression or silencing plants. Combined yeast one-hybrid and dual-luciferase assays demonstrated that MsSCL6 transcriptionally represses MsPOR through direct promoter binding, suppressing chlorophyll accumulation. In summary, this study for the first time revealed the mechanism of the MsmiR171-MsSCL6-MsPOR module mediating selenium-regulated chlorophyll biosynthesis in alfalfa. These findings provide a theoretical foundation and technical guidance for alfalfa breeding and the production of selenium-enriched forage.
{"title":"MsmiR171 targets MsSCL6 to mediate selenium-regulated chlorophyll biosynthesis in alfalfa","authors":"Qingdong Wang, Shuting Su, Yarui Sheng, Mengli Xu, Baohong Tang, Yonggui Ma, Yuhua Shi","doi":"10.1093/hr/uhaf305","DOIUrl":"https://doi.org/10.1093/hr/uhaf305","url":null,"abstract":"Alfalfa (Medicago sativa L.) is a globally pivotal legume forage. Selenium (Se), an essential trace element for humans and animals, can significantly enhance the growth and development of alfalfa. Chlorophyll is the central pigment of plant photosynthesis. Previous research on chlorophyll synthesis in alfalfa has mainly focused on transcriptional regulation, environmental factors (light, nutrient availability), and phytohormone signaling, while fewer studies have been conducted at the post-transcriptional level. Through whole transcriptome sequencing analysis, microRNAs (miRNAs) were identified as positively responsive to selenium. This study focused on the regulation of chlorophyll synthesis by the miR171-SCL6 module in alfalfa. β-glucuronidase (GUS) staining and dual-luciferase assays revealed that MsmiR171 negatively regulated the transcript levels of the SCARECROW-LIKE 6 transcription factor MsSCL6. Subcellular localization analysis revealed that MsSCL6 was mainly in the cell nucleus. Functional analyses demonstrated that MsmiR171 promoted chlorophyll synthesis and photosynthesis in alfalfa, while MsSCL6 negatively regulated chlorophyll synthesis. Notably, selenium treatment upregulated MsmiR171 expression, downregulated MsSCL6 expression, and enhanced chlorophyll accumulation. qRT-PCR analysis revealed differential expression of MsPOR in MsmiR171 and MsSCL6 overexpression or silencing plants. Combined yeast one-hybrid and dual-luciferase assays demonstrated that MsSCL6 transcriptionally represses MsPOR through direct promoter binding, suppressing chlorophyll accumulation. In summary, this study for the first time revealed the mechanism of the MsmiR171-MsSCL6-MsPOR module mediating selenium-regulated chlorophyll biosynthesis in alfalfa. These findings provide a theoretical foundation and technical guidance for alfalfa breeding and the production of selenium-enriched forage.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"20 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145498286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kai Luo, Mingchao Li, Man Liu, Xitao Jia, Zhou Li, Xuechun Zhao, Jihui Chen, Xinyao Gu, Jin He, Chao Chen, Rui Dong
Nuclear factor-Y (NF-Y), evolutionarily conserved heterotrimeric transcription factors (TFs), are found throughout eukaryotic organisms. Comprising the NF-YA, NF-YB, and NF-YC subfamilies, this family is established as playing critical roles in plant growth and development. While earlier research has mainly centered on the functional and evolutionary characteristics of NF-Y within individual plant species, large-scale analyses and evolutionary patterns of these genes across major plant lineages remain largely unexplored. Here, we systematically identified 15,392 nonredundant genes of NF-Y family from 320 horticultural and representative plant species. Our findings showed that this gene family originated from charophytes. In bryophytes, pteridophytes, and gymnosperms, dispersed duplication served as the predominant mode of NF-Y gene expansion, whereas in angiosperms, their expansion was driven by WGD/segmental, dispersed, and tandem duplication. Conserved motif analysis revealed that highly conserved motifs are present within each NF-Y subfamily across eight representative plant species. However, some NF-Y genes in higher plants exhibited motif loss, indicating sequence variations during their evolutionary history. Transcriptomic profiling analysis of NF-Y genes in Arabidopsis thaliana under various conditions, including hormonal treatments, abiotic/biotic stresses, as well as various developmental stages, revealed their functional versatility. Furthermore, an interaction network comprising 36 NF-Y genes along with 2,473 downstream and 261 upstream genes was constructed in A. thaliana. Enrichment analysis revealed interactions between NF-Y genes and other TFs, particularly those from the Myb_DNA-binding and APETALA2 (AP2) families, which were consistently enriched among both upstream and downstream regulatory genes. This work provides the first comprehensive and large-scale investigation into the evolutionary dynamics of NF-Y genes, encompassing taxa from basal algae to advanced horticultural plants, thereby offering novel insights into their evolutionary and lineage-specific expansion.
核因子- y （NF-Y）是进化上保守的异三聚体转录因子（tf），在真核生物中广泛存在。该家族包括NF-YA、NF-YB和NF-YC亚家族，在植物生长发育中起着关键作用。虽然早期的研究主要集中在单个植物物种中NF-Y的功能和进化特征，但这些基因在主要植物谱系中的大规模分析和进化模式仍未被探索。本研究系统地从320种园艺和代表性植物中鉴定出NF-Y家族的15392个非冗余基因。研究结果表明，该基因家族起源于蕨类植物。在苔藓植物、蕨类植物和裸子植物中，分散复制是NF-Y基因扩增的主要方式，而在被子植物中，它们的扩增主要由WGD/节段复制、分散复制和串联复制驱动。保守基序分析表明，在8种代表性植物中，NF-Y亚族中存在高度保守的基序。然而，在高等植物中，一些NF-Y基因出现了基序丢失，这表明它们在进化过程中序列发生了变化。对拟南芥（Arabidopsis thaliana）不同条件下（包括激素处理、非生物/生物胁迫以及不同发育阶段）NF-Y基因的转录组学分析揭示了其功能的多功能性。此外，还构建了一个包含36个NF-Y基因、2473个下游基因和261个上游基因的互作网络。富集分析显示NF-Y基因与其他tf之间存在相互作用，特别是来自myb_dna结合家族和APETALA2 （AP2）家族的tf，这些tf在上游和下游调控基因中都持续富集。这项工作为NF-Y基因的进化动力学提供了第一次全面和大规模的研究，涵盖了从基础藻类到高级园艺植物的分类群，从而为它们的进化和谱系特异性扩展提供了新的见解。
{"title":"Large-Scale Comparative Analysis of the Nuclear Factor-Y transcription Factors Across 320 Horticultural and Other Plants","authors":"Kai Luo, Mingchao Li, Man Liu, Xitao Jia, Zhou Li, Xuechun Zhao, Jihui Chen, Xinyao Gu, Jin He, Chao Chen, Rui Dong","doi":"10.1093/hr/uhaf304","DOIUrl":"https://doi.org/10.1093/hr/uhaf304","url":null,"abstract":"Nuclear factor-Y (NF-Y), evolutionarily conserved heterotrimeric transcription factors (TFs), are found throughout eukaryotic organisms. Comprising the NF-YA, NF-YB, and NF-YC subfamilies, this family is established as playing critical roles in plant growth and development. While earlier research has mainly centered on the functional and evolutionary characteristics of NF-Y within individual plant species, large-scale analyses and evolutionary patterns of these genes across major plant lineages remain largely unexplored. Here, we systematically identified 15,392 nonredundant genes of NF-Y family from 320 horticultural and representative plant species. Our findings showed that this gene family originated from charophytes. In bryophytes, pteridophytes, and gymnosperms, dispersed duplication served as the predominant mode of NF-Y gene expansion, whereas in angiosperms, their expansion was driven by WGD/segmental, dispersed, and tandem duplication. Conserved motif analysis revealed that highly conserved motifs are present within each NF-Y subfamily across eight representative plant species. However, some NF-Y genes in higher plants exhibited motif loss, indicating sequence variations during their evolutionary history. Transcriptomic profiling analysis of NF-Y genes in Arabidopsis thaliana under various conditions, including hormonal treatments, abiotic/biotic stresses, as well as various developmental stages, revealed their functional versatility. Furthermore, an interaction network comprising 36 NF-Y genes along with 2,473 downstream and 261 upstream genes was constructed in A. thaliana. Enrichment analysis revealed interactions between NF-Y genes and other TFs, particularly those from the Myb_DNA-binding and APETALA2 (AP2) families, which were consistently enriched among both upstream and downstream regulatory genes. This work provides the first comprehensive and large-scale investigation into the evolutionary dynamics of NF-Y genes, encompassing taxa from basal algae to advanced horticultural plants, thereby offering novel insights into their evolutionary and lineage-specific expansion.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"171 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145492090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Flavonoids are important secondary metabolites that regulate plant growth and development and confer resistance against biotic and abiotic stress. As natural polyphenol substances, flavonoids determine the quality traits of commercial fruits, such as color, flavor, and nutrition. In the past few decades, research on the regulation of flavonoid biosynthesis in plants has made significant progress. However, a deep understanding of this aspect in flavonoid-rich horticultural crops is lacking. This review aims to systematically summarize the current knowledge in the regulation of flavonoid biosynthesis in fruits, including the transcriptional, post-transcriptional, epigenetic, and post-translational regulation mechanisms as well as the composite regulation cascades. Our analysis shows that direct transcriptional regulation involves the actions of different transcription factor families, such as MYB, WRKY, bZIP, AP2/ERF, and MADS, by directly targeting the key synthase genes in flavonoid biosynthetic pathway. Indirect regulation involves specific transcription factors and microRNAs that target the downstream regulators, as well as the regulation modules triggered for degradation of activators or repressors in response to environmental signals or plant hormones. In addition, epigenetic regulation, associated with methylation level in the gene promoter regions or the insertion or deletion of specific sequences therein, plays an important role in controlling anthocyanin accumulation. Based on the diverse regulation mechanisms of the flavonoid biosynthetic pathway, more molecular design targets can be applied in the future, facilitating the production of more stress-tolerant and quality-elevated crop varieties.
{"title":"Molecular insights into the regulation of flavonoid biosynthesis in fruits","authors":"Lili Chen, Yuan Cheng, Gaojie Hong","doi":"10.1093/hr/uhaf306","DOIUrl":"https://doi.org/10.1093/hr/uhaf306","url":null,"abstract":"Flavonoids are important secondary metabolites that regulate plant growth and development and confer resistance against biotic and abiotic stress. As natural polyphenol substances, flavonoids determine the quality traits of commercial fruits, such as color, flavor, and nutrition. In the past few decades, research on the regulation of flavonoid biosynthesis in plants has made significant progress. However, a deep understanding of this aspect in flavonoid-rich horticultural crops is lacking. This review aims to systematically summarize the current knowledge in the regulation of flavonoid biosynthesis in fruits, including the transcriptional, post-transcriptional, epigenetic, and post-translational regulation mechanisms as well as the composite regulation cascades. Our analysis shows that direct transcriptional regulation involves the actions of different transcription factor families, such as MYB, WRKY, bZIP, AP2/ERF, and MADS, by directly targeting the key synthase genes in flavonoid biosynthetic pathway. Indirect regulation involves specific transcription factors and microRNAs that target the downstream regulators, as well as the regulation modules triggered for degradation of activators or repressors in response to environmental signals or plant hormones. In addition, epigenetic regulation, associated with methylation level in the gene promoter regions or the insertion or deletion of specific sequences therein, plays an important role in controlling anthocyanin accumulation. Based on the diverse regulation mechanisms of the flavonoid biosynthetic pathway, more molecular design targets can be applied in the future, facilitating the production of more stress-tolerant and quality-elevated crop varieties.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"54 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145492093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Brassica juncea var. tumida, commonly known as Zha Cai, is a pickled stem mustard widely cultivated in southern China. Its most distinctive trait is the swollen stem, which serves as the primary economic organ for harvest. However, the origin and domestication history of tumida remain unclear, hindering genetic improvement and molecular breeding efforts. Here, we assembled a chromosome-level genome of the landrace 'YAXY' from Chongqing—the center of tumida diversity—totaling 909.1 Mb with a contig N50 of 4.17 Mb. We also collected and resequenced 203 tumida accessions across southern China. By integrating the 'YAXY' reference genome with population data, we generated the first comprehensive tumida variation dataset, comprising 1.38 million single-nucleotide polymorphisms (SNPs) and 0.27 million insertions and deletions (InDels). Joint analysis of the newly sequenced tumida population and 504 public B. juncea datasets revealed that tumida and leafy types from southern China share a common origin from local oilseed mustard. Tumida domestication was accompanied by a strong genetic bottleneck. Additionally, we conducted genome-wide association studies (GWAS) for 21 agronomic traits and identified candidate genes linked to key domestication traits in tumida. For the swollen stem trait, selective sweep and GWAS analyses jointly identified candidate genes likely involved in lignification. Transcriptome data showed consistent differential expression of BjuA05g15010, the Arabidopsis SAGL1 ortholog, across all swelling stages, suggesting a key role in stem morphogenesis. Collectively, our findings shed light on tumida evolution and provide valuable genomic resources and candidate genes to support genetic research and breeding in B. juncea.
芥菜（Brassica juncea var. tumida），俗称刺菜，是中国南方广泛种植的一种腌茎芥。其最显著的特征是膨胀的茎，这是收获的主要经济器官。然而，由于其起源和驯化历史尚不清楚，阻碍了遗传改良和分子育种的努力。在这里，我们组装了来自重庆的地方品种“YAXY”的染色体水平基因组，总长度为909.1 Mb， N50为4.17 Mb。我们还收集了中国南方203份tuma材料并对其进行了重新测序。通过整合“YAXY”参考基因组与群体数据，我们生成了第一个综合的tumida变异数据集，包括138万个单核苷酸多态性（snp）和27万个插入和缺失（InDels）。对新测序的tumida群体和504个公开的juncea数据集的联合分析表明，中国南方的tumida和叶型具有共同的起源，来自当地的油籽芥。Tumida的驯化伴随着很强的遗传瓶颈。此外，我们对21个农艺性状进行了全基因组关联研究（GWAS），并确定了与tumida关键驯化性状相关的候选基因。对于茎膨大性状，选择性扫描和GWAS分析共同确定了可能参与木质素化的候选基因。转录组数据显示，拟南芥SAGL1同源基因BjuA05g15010在所有肿胀阶段的差异表达一致，表明其在茎形态发生中起关键作用。总之，我们的发现揭示了tumida的进化，并为juncea的遗传研究和育种提供了宝贵的基因组资源和候选基因。
{"title":"Population genomic insights into the domestication of Brassica juncea var. tumida","authors":"Hao Wang, Xu Cai, Zhongrong Guan, Jian Wu, Lisha Peng, Wenping Li, Ling Rao, Shiwei Yang, Zhaorong Zhang, Xingxing Zhang, Yonghong Fan, Xiaowu Wang, Jinjuan Shen","doi":"10.1093/hr/uhaf298","DOIUrl":"https://doi.org/10.1093/hr/uhaf298","url":null,"abstract":"Brassica juncea var. tumida, commonly known as Zha Cai, is a pickled stem mustard widely cultivated in southern China. Its most distinctive trait is the swollen stem, which serves as the primary economic organ for harvest. However, the origin and domestication history of tumida remain unclear, hindering genetic improvement and molecular breeding efforts. Here, we assembled a chromosome-level genome of the landrace 'YAXY' from Chongqing—the center of tumida diversity—totaling 909.1 Mb with a contig N50 of 4.17 Mb. We also collected and resequenced 203 tumida accessions across southern China. By integrating the 'YAXY' reference genome with population data, we generated the first comprehensive tumida variation dataset, comprising 1.38 million single-nucleotide polymorphisms (SNPs) and 0.27 million insertions and deletions (InDels). Joint analysis of the newly sequenced tumida population and 504 public B. juncea datasets revealed that tumida and leafy types from southern China share a common origin from local oilseed mustard. Tumida domestication was accompanied by a strong genetic bottleneck. Additionally, we conducted genome-wide association studies (GWAS) for 21 agronomic traits and identified candidate genes linked to key domestication traits in tumida. For the swollen stem trait, selective sweep and GWAS analyses jointly identified candidate genes likely involved in lignification. Transcriptome data showed consistent differential expression of BjuA05g15010, the Arabidopsis SAGL1 ortholog, across all swelling stages, suggesting a key role in stem morphogenesis. Collectively, our findings shed light on tumida evolution and provide valuable genomic resources and candidate genes to support genetic research and breeding in B. juncea.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"20 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145472864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
s Stress sensitivity and tolerance are the consequences of coordinated regulation by multiple genes. Existing genetic tools can identify key genes that mediate metabolic and physiological processes sensing and perceiving stresses. However, it has become increasingly clear that the end-point phenotype of stress response resulting from these intermediate processes involves intricate but well-coordinated networks constituted by a large array of genes. Here, we describe an emerging functional game-graph theory to coalesce all genes from mapping or association studies into genetic interaction networks. These networks enable geneticists to trace, visualize, and interrogate the precise roadmap of how each gene acts and interacts with every other gene to mediate stress response. By shifting a reductionist thinking to a holistic, systems-oriented thinking, this theory overcomes a major challenge of elucidating the detailed genetic architecture of stress response.
{"title":"Network stress: A wiring diagram of whole stress genes","authors":"Yu Wang, Rongling Wu","doi":"10.1093/hr/uhaf302","DOIUrl":"https://doi.org/10.1093/hr/uhaf302","url":null,"abstract":"s Stress sensitivity and tolerance are the consequences of coordinated regulation by multiple genes. Existing genetic tools can identify key genes that mediate metabolic and physiological processes sensing and perceiving stresses. However, it has become increasingly clear that the end-point phenotype of stress response resulting from these intermediate processes involves intricate but well-coordinated networks constituted by a large array of genes. Here, we describe an emerging functional game-graph theory to coalesce all genes from mapping or association studies into genetic interaction networks. These networks enable geneticists to trace, visualize, and interrogate the precise roadmap of how each gene acts and interacts with every other gene to mediate stress response. By shifting a reductionist thinking to a holistic, systems-oriented thinking, this theory overcomes a major challenge of elucidating the detailed genetic architecture of stress response.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"28 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145472808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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