Hannah Rae Thomas, Alice Gevorgyan, Alexandra Hermanson, Samantha Yanders, Lindsay Erndwein, Matthew Norman-Ariztía, Erin E Sparks, Margaret H Frank
Graft compatibility is the capacity of two plants to form cohesive vascular connections. Tomato and pepper are incompatible graft partners; however, the underlying cause of graft rejection between these two species remains unknown. We diagnosed graft incompatibility between tomato and diverse pepper varieties based on weakened biophysical stability, decreased growth, and persistent cell death using viability stains. Transcriptomic analysis of the junction was performed using RNA-sequencing, and molecular signatures for incompatible graft response were characterized based on meta-transcriptomic comparisons with other biotic processes. We show that tomato is broadly incompatible with diverse pepper cultivars. These incompatible graft partners activate prolonged transcriptional changes that are highly enriched for defense processes. Amongst these processes was broad nucleotide-binding and leucine-rich repeat receptors (NLR) upregulation and genetic signatures indicative of an immune response. Using transcriptomic datasets for a variety of biotic stress treatments, we identified a significant overlap in the genetic profile of incompatible grafting and plant parasitism. In addition, we found over 1000 genes that are uniquely upregulated in incompatible grafts. Based on NLR overactivity, DNA damage, and prolonged cell death we hypothesize that tomato and pepper graft incompatibility is characterized by an immune response that triggers cell death which interferes with junction formation.
{"title":"Graft incompatibility between pepper and tomato elicits an immune response and triggers localized cell death","authors":"Hannah Rae Thomas, Alice Gevorgyan, Alexandra Hermanson, Samantha Yanders, Lindsay Erndwein, Matthew Norman-Ariztía, Erin E Sparks, Margaret H Frank","doi":"10.1093/hr/uhae255","DOIUrl":"https://doi.org/10.1093/hr/uhae255","url":null,"abstract":"Graft compatibility is the capacity of two plants to form cohesive vascular connections. Tomato and pepper are incompatible graft partners; however, the underlying cause of graft rejection between these two species remains unknown. We diagnosed graft incompatibility between tomato and diverse pepper varieties based on weakened biophysical stability, decreased growth, and persistent cell death using viability stains. Transcriptomic analysis of the junction was performed using RNA-sequencing, and molecular signatures for incompatible graft response were characterized based on meta-transcriptomic comparisons with other biotic processes. We show that tomato is broadly incompatible with diverse pepper cultivars. These incompatible graft partners activate prolonged transcriptional changes that are highly enriched for defense processes. Amongst these processes was broad nucleotide-binding and leucine-rich repeat receptors (NLR) upregulation and genetic signatures indicative of an immune response. Using transcriptomic datasets for a variety of biotic stress treatments, we identified a significant overlap in the genetic profile of incompatible grafting and plant parasitism. In addition, we found over 1000 genes that are uniquely upregulated in incompatible grafts. Based on NLR overactivity, DNA damage, and prolonged cell death we hypothesize that tomato and pepper graft incompatibility is characterized by an immune response that triggers cell death which interferes with junction formation.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"9 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142170885","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}
Illuminating the phenotype–genotype black box under complex traits is an ambitious goal for researchers. The generation of temporally or spatially phenotypic data today has far outpaced its interpretation, due to their highly dynamic nature depending on the environment and developmental stages. Here we propose an integrated enviro-pheno-geno functional approach to pinpoint the major challenges of decomposing physiological traits. The strategy first features high-throughput functional physiological phenotyping (FPP) to efficiently acquire phenotypic and environmental data. It then features functional mapping (FM) and the extended systems mapping (SM) to tackle trait dynamics. FM, by modeling traits as continuous functions, can increase the power and efficiency in dissecting the spatiotemporal effects of QTLs. SM could enable reconstruction of a genotype–phenotype map from developmental pathways. We present a recent case study that combines FPP and SM to dissect complex physiological traits. This integrated approach will be an important engine to drive the translation of phenomic big data into genetic gain.
阐明复杂性状下的表型-基因型黑箱是研究人员的一个宏伟目标。由于表型数据受环境和发育阶段的影响而具有高度动态性，因此当今生成的时间或空间表型数据远远超过了对其的解释。在此，我们提出了一种综合的环境-表型-基因功能方法，以精确定位分解生理性状所面临的主要挑战。该策略首先以高通量功能生理表型（FPP）为特色，高效获取表型和环境数据。然后，以功能图谱（FM）和扩展系统图谱（SM）为特色，解决性状动态问题。功能图谱将性状建模为连续函数，可提高剖析 QTL 时空效应的能力和效率。SM可以通过发育途径重建基因型-表型图谱。我们介绍了最近的一项案例研究，该研究结合了 FPP 和 SM 来剖析复杂的生理性状。这种综合方法将成为推动表型组大数据转化为遗传增益的重要引擎。
{"title":"Converging functional phenotyping with systems mapping to illuminate the genotype–phenotype associations","authors":"Ting Sun, Zheng Shi, Rujia Jiang, Menachem Moshelion, Pei Xu","doi":"10.1093/hr/uhae256","DOIUrl":"https://doi.org/10.1093/hr/uhae256","url":null,"abstract":"Illuminating the phenotype–genotype black box under complex traits is an ambitious goal for researchers. The generation of temporally or spatially phenotypic data today has far outpaced its interpretation, due to their highly dynamic nature depending on the environment and developmental stages. Here we propose an integrated enviro-pheno-geno functional approach to pinpoint the major challenges of decomposing physiological traits. The strategy first features high-throughput functional physiological phenotyping (FPP) to efficiently acquire phenotypic and environmental data. It then features functional mapping (FM) and the extended systems mapping (SM) to tackle trait dynamics. FM, by modeling traits as continuous functions, can increase the power and efficiency in dissecting the spatiotemporal effects of QTLs. SM could enable reconstruction of a genotype–phenotype map from developmental pathways. We present a recent case study that combines FPP and SM to dissect complex physiological traits. This integrated approach will be an important engine to drive the translation of phenomic big data into genetic gain.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"148 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142160466","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}
Soluble sugars contribute to the taste and flavor of citrus fruit. Potassium (K), known as a quality element, plays key roles in improving sugar accumulation and fruit quality, but the mechanism is largely unknown. This study aims to elucidate how K improves sugar accumulation by regulating carbon flow from source leaves to fruit in Newhall navel orange. We found that optimal fruit K concentrations around 1.5% improved sugar accumulation and fruit quality in citrus. K application increased the strength of both sink and source, as indicated by the increased fruit growth rate, enzymes activities and expression levels of key genes involved in sucrose (Suc) metabolism in fruit and leaf. K application also facilitated Suc transport from source leaves to fruit, as confirmed by the enhanced 13C-Suc level in fruit. Furthermore, we found that navel orange used symplastic pathway for transporting Suc from source leaves to fruits, and K application enhanced symplastic loading, as demonstrated by the intensified CF signal and increased plasmodesmata density in leaves. The findings reveal that K stimulates fruit sugar accumulation by increasing carbon flow from source leaves to fruit in Newhall navel orange.
{"title":"Potassium stimulates fruit sugar accumulation by increasing carbon flow in Citrus sinensis","authors":"Kongjie Wu, Chengxiao Hu, Peiyu Liao, Yinlong Hu, Xuecheng Sun, Qiling Tan, Zhiyong Pan, Shoujun Xu, Zhihao Dong, Songwei Wu","doi":"10.1093/hr/uhae240","DOIUrl":"https://doi.org/10.1093/hr/uhae240","url":null,"abstract":"Soluble sugars contribute to the taste and flavor of citrus fruit. Potassium (K), known as a quality element, plays key roles in improving sugar accumulation and fruit quality, but the mechanism is largely unknown. This study aims to elucidate how K improves sugar accumulation by regulating carbon flow from source leaves to fruit in Newhall navel orange. We found that optimal fruit K concentrations around 1.5% improved sugar accumulation and fruit quality in citrus. K application increased the strength of both sink and source, as indicated by the increased fruit growth rate, enzymes activities and expression levels of key genes involved in sucrose (Suc) metabolism in fruit and leaf. K application also facilitated Suc transport from source leaves to fruit, as confirmed by the enhanced 13C-Suc level in fruit. Furthermore, we found that navel orange used symplastic pathway for transporting Suc from source leaves to fruits, and K application enhanced symplastic loading, as demonstrated by the intensified CF signal and increased plasmodesmata density in leaves. The findings reveal that K stimulates fruit sugar accumulation by increasing carbon flow from source leaves to fruit in Newhall navel orange.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"16 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142160802","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}
Woohyeon Cho, Woojong Jang, Hyeonah Shim, Jiseok Kim, Youngju Oh, Jee Young Park, Young Chang Kim, Jung-Woo Lee, Ick-Hyun Jo, Misun Lee, Jinsu Gil, Martin Mascher, Murukarthick Jayakodi, Xuejiao Liao, Jiang Xu, Deqiang Dou, Yi Lee, Tae-Jin Yang
Ginseng (Panax ginseng) renowned as the king of medicinal plants. Ginseng grows slowly under shade conditions, requiring at least four years to produce a limited number of seeds. Molecular breeding of ginseng faces challenges due to its the tetraploid genome and the absence of an efficient molecular marker system. To overcome these obstacles, we adopted genotyping-by-sequencing to delve into genetic mapping and survey genetic diversity. We constructed a comprehensive genetic map comprising 24 linkage groups, each corresponding to one of the 24 chromosomes in the ginseng genome, based on 1216 non-redundant SNPs obtained from an F2 mapping population. Additionally, 431 103 SNPs were identified from 119 diverse ginseng genotypes. From these, 192 informative subgenome-specific single copy SNPs were selected to develop a SNP chip. The SNP chip was used to genotype a large ginseng collection, encompassing registered cultivars, breeding lines, wild-simulated ginseng, and wild ginseng from various countries and regions. We evaluated the utility of the assay for molecular breeding with 919 ginseng genotypes. This breeder-friendly SNP chip promises versatility, enabling purity assessments of seeds and products, the authentication of species and cultivars, and the determination of homozygosity and homogeneity rates for breeding lines. Genotype data for 1200 ginseng genotypes are now stored in our database. This SNP chip lays the foundation for a molecular breeding in ginseng and will facilitate the breeding process in this medicinal crop.
人参被誉为药用植物之王。人参在荫蔽条件下生长缓慢，至少需要四年才能结出数量有限的种子。由于人参的基因组为四倍体，且缺乏高效的分子标记系统，因此人参的分子育种面临挑战。为了克服这些障碍，我们采用了基因分型测序技术来深入研究遗传图谱和调查遗传多样性。我们基于从一个F2作图群体中获得的1216个非冗余SNP，构建了一个由24个连锁群组成的综合遗传图谱，每个连锁群对应人参基因组中的24条染色体之一。此外，还从 119 种不同的人参基因型中鉴定出 431 103 个 SNPs。从中筛选出 192 个信息丰富的亚基因组特异性单拷贝 SNPs，开发出 SNP 芯片。SNP 芯片被用于对大量人参进行基因分型，其中包括来自不同国家和地区的注册栽培品种、育种品系、野生模拟人参和野生人参。我们用 919 个人参基因型评估了该检测方法在分子育种方面的实用性。这种便于育种的 SNP 芯片具有多功能性，可用于种子和产品的纯度评估、品种和栽培品种的鉴定，以及育种品系的同源性和同质性测定。目前，我们的数据库中已存储了 1200 种人参基因型的基因型数据。这种 SNP 芯片为人参的分子育种奠定了基础，并将促进这种药用作物的育种进程。
{"title":"High-resolution genetic map and SNP chip for molecular breeding in Panax ginseng, a tetraploid medicinal plant","authors":"Woohyeon Cho, Woojong Jang, Hyeonah Shim, Jiseok Kim, Youngju Oh, Jee Young Park, Young Chang Kim, Jung-Woo Lee, Ick-Hyun Jo, Misun Lee, Jinsu Gil, Martin Mascher, Murukarthick Jayakodi, Xuejiao Liao, Jiang Xu, Deqiang Dou, Yi Lee, Tae-Jin Yang","doi":"10.1093/hr/uhae257","DOIUrl":"https://doi.org/10.1093/hr/uhae257","url":null,"abstract":"Ginseng (Panax ginseng) renowned as the king of medicinal plants. Ginseng grows slowly under shade conditions, requiring at least four years to produce a limited number of seeds. Molecular breeding of ginseng faces challenges due to its the tetraploid genome and the absence of an efficient molecular marker system. To overcome these obstacles, we adopted genotyping-by-sequencing to delve into genetic mapping and survey genetic diversity. We constructed a comprehensive genetic map comprising 24 linkage groups, each corresponding to one of the 24 chromosomes in the ginseng genome, based on 1216 non-redundant SNPs obtained from an F2 mapping population. Additionally, 431 103 SNPs were identified from 119 diverse ginseng genotypes. From these, 192 informative subgenome-specific single copy SNPs were selected to develop a SNP chip. The SNP chip was used to genotype a large ginseng collection, encompassing registered cultivars, breeding lines, wild-simulated ginseng, and wild ginseng from various countries and regions. We evaluated the utility of the assay for molecular breeding with 919 ginseng genotypes. This breeder-friendly SNP chip promises versatility, enabling purity assessments of seeds and products, the authentication of species and cultivars, and the determination of homozygosity and homogeneity rates for breeding lines. Genotype data for 1200 ginseng genotypes are now stored in our database. This SNP chip lays the foundation for a molecular breeding in ginseng and will facilitate the breeding process in this medicinal crop.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"10 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142160468","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}
Jordan R Brock, Kevin A Bird, Adrian E Platts, Fabio Gomez-Cano, Suresh Kumar Gupta, Kyle Palos, Caylyn E Railey, Scott J Teresi, Yun Sun Lee, Maria Magallanes-Lundback, Emily G Pawlowski, Andrew D L Nelson, Erich Grotewold, Patrick P Edger
Camelina (Camelina sativa), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, alongside and understanding of the genetic diversity and population structure of material present within breeding programs. We conducted population genetic analyses of a C. sativa diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs. Our analyses confirm that C. sativa has relatively low genetic diversity, and show that the SG3 subgenome has substantially lower genetic diversity compared to the other two subgenomes. Despite the low genetic diversity, our analyses identified thirteen distinct subpopulations including two distinct wild populations and others putatively representing founders in existing breeding populations. When analyzing for subgenome composition of long non-coding RNAs, which are known to play important roles in (a)biotic stress tolerance, we found that the SG3 subgenome contained significantly more lincRNAs compared to other subgenomes. Similarly, transcriptome analyses revealed that expression dominance of SG3 is not as strong as previously reported, and may not be universal across all organ-types. From a global analysis, SG3 was only significant higher expressed in flower, flower bud, and fruit organs, which is an important discovery given that the crop yield is associated with these organs. Collectively, these results will be valuable for guiding future breeding efforts in camelina.
{"title":"Exploring genetic diversity, population structure, and subgenome differences in the allopolyploid Camelina sativa: implications for future breeding and research studies","authors":"Jordan R Brock, Kevin A Bird, Adrian E Platts, Fabio Gomez-Cano, Suresh Kumar Gupta, Kyle Palos, Caylyn E Railey, Scott J Teresi, Yun Sun Lee, Maria Magallanes-Lundback, Emily G Pawlowski, Andrew D L Nelson, Erich Grotewold, Patrick P Edger","doi":"10.1093/hr/uhae247","DOIUrl":"https://doi.org/10.1093/hr/uhae247","url":null,"abstract":"Camelina (Camelina sativa), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, alongside and understanding of the genetic diversity and population structure of material present within breeding programs. We conducted population genetic analyses of a C. sativa diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs. Our analyses confirm that C. sativa has relatively low genetic diversity, and show that the SG3 subgenome has substantially lower genetic diversity compared to the other two subgenomes. Despite the low genetic diversity, our analyses identified thirteen distinct subpopulations including two distinct wild populations and others putatively representing founders in existing breeding populations. When analyzing for subgenome composition of long non-coding RNAs, which are known to play important roles in (a)biotic stress tolerance, we found that the SG3 subgenome contained significantly more lincRNAs compared to other subgenomes. Similarly, transcriptome analyses revealed that expression dominance of SG3 is not as strong as previously reported, and may not be universal across all organ-types. From a global analysis, SG3 was only significant higher expressed in flower, flower bud, and fruit organs, which is an important discovery given that the crop yield is associated with these organs. Collectively, these results will be valuable for guiding future breeding efforts in camelina.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"23 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142160482","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}
Woody bamboo (Bambusoideae) is renowned for its polyploidy and rare flowering. Bambusa odashimae is one of the bamboo species with the highest chromosome count (104) in the subfamily and has the highest heterozygosity of all sequenced bamboo genomes so far. Compared with other bamboo species, it can efficiently utilize exogenous hormones to regulate in vitro flowering, providing valuable insights into the hormonal regulation of bamboo flowering. Here, we generated the haplotype-resolved genome assembly of B. odashimae, despite the complexity and high chromosome number, supplemented by thirty-three transcriptomes from eleven developmental periods using a tissue culture system. The assembled genome can be divided into Haplotype I, Haplotype II, and Haplotype III, each containing A, B, and C subgenomes. Haplotype I may be derived from Dendrocalamus whereas Haplotypes II and III are closely related to Bambusa, indicating that B. odashimae has an origin involving both intergeneric and interspecific hybridizations. The high heterozygosity renders the possibility to detect abundant allele-specific expression (ASE), with ASE genes enriched in cytokinin-related pathways, likely associated with efficient cytokinin-promoted flowering. Notably, we found that the CONSTANS (CO) genes were potentially key regulators of in vitro flowering in B. odashimae. Overall, our study, based on the in vitro system combined with a high-quality reference genome, provides critical insights into the origin of this nonaploid bamboo and links hybridization and in vitro flowering in bamboo.
木竹（Bambusoideae）以其多倍体和罕见的开花而闻名。木竹（Bambusa odashimae）是竹亚科中染色体数（104）最高的竹种之一，也是迄今为止所有竹子基因组测序中杂合度最高的竹种。与其他竹类相比，它能有效地利用外源激素调节离体开花，为研究竹类开花的激素调控提供了宝贵的资料。在此，我们利用组织培养系统，在染色体数目复杂且较多的情况下，生成了单倍型解析的B. odashimae基因组组装，并补充了来自11个发育时期的33个转录组。组装的基因组可分为单倍型 I、单倍型 II 和单倍型 III，每个单倍型都包含 A、B 和 C 亚基因组。单倍型 I 可能来源于 Dendrocalamus，而单倍型 II 和 III 与簕杜鹃关系密切，这表明 B. odashimae 的起源涉及属间杂交和种间杂交。高杂合度使我们有可能检测到丰富的等位基因特异性表达（ASE），ASE基因富集于细胞分裂素相关途径，可能与细胞分裂素高效促进开花有关。值得注意的是，我们发现 CONSTANS（CO）基因可能是 B. odashimae 离体开花的关键调控因子。总之，我们的研究以离体系统为基础，结合高质量的参考基因组，为这种非单倍体竹子的起源提供了重要的见解，并将竹子的杂交和离体开花联系起来。
{"title":"Haplotype-resolved nonaploid genome provides insights into in vitro flowering in bamboo","authors":"Yu-Jiao Wang, Cen Guo, Zhao Lei, Ling Mao, Xiang-Zhou Hu, Yi-Zhou Yang, Ke-Cheng Qian, Peng-Fei Ma, Zhen-Hua Guo, De-Zhu Li","doi":"10.1093/hr/uhae250","DOIUrl":"https://doi.org/10.1093/hr/uhae250","url":null,"abstract":"Woody bamboo (Bambusoideae) is renowned for its polyploidy and rare flowering. Bambusa odashimae is one of the bamboo species with the highest chromosome count (104) in the subfamily and has the highest heterozygosity of all sequenced bamboo genomes so far. Compared with other bamboo species, it can efficiently utilize exogenous hormones to regulate in vitro flowering, providing valuable insights into the hormonal regulation of bamboo flowering. Here, we generated the haplotype-resolved genome assembly of B. odashimae, despite the complexity and high chromosome number, supplemented by thirty-three transcriptomes from eleven developmental periods using a tissue culture system. The assembled genome can be divided into Haplotype I, Haplotype II, and Haplotype III, each containing A, B, and C subgenomes. Haplotype I may be derived from Dendrocalamus whereas Haplotypes II and III are closely related to Bambusa, indicating that B. odashimae has an origin involving both intergeneric and interspecific hybridizations. The high heterozygosity renders the possibility to detect abundant allele-specific expression (ASE), with ASE genes enriched in cytokinin-related pathways, likely associated with efficient cytokinin-promoted flowering. Notably, we found that the CONSTANS (CO) genes were potentially key regulators of in vitro flowering in B. odashimae. Overall, our study, based on the in vitro system combined with a high-quality reference genome, provides critical insights into the origin of this nonaploid bamboo and links hybridization and in vitro flowering in bamboo.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"9 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142142440","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}
Next-generation sequencing (NGS) library construction often requires high-quality DNA extraction, precise adjustment of DNA concentration, and restriction enzyme digestion to reduce genome complexity, which results in increased time and cost in sample preparation and processing. To address these challenges, a PCR-based method for rapid NGS library preparation, named dpMIG-seq, has been developed and proven effective for high-throughput genotyping. However, the application of dpMIG-seq has been limited to diploid and polyploid species with disomic inheritance. In this study, we obtained genome-wide single nucleotide polymorphism (SNP) markers for tetraploid blueberry to evaluate genotyping and downstream analysis outcomes. Comparison of genotyping qualities inferred across samples with different DNA concentrations and multiple bioinformatics approaches revealed high accuracy and reproducibility of dpMIG-seq-based genotyping, with Pearson’s correlation coefficients between replicates in the range of 0.91 to 0.98. Furthermore, we demonstrated that dpMIG-seq enables accurate genotyping of samples with low DNA concentrations. Subsequently, we applied dpMIG-seq to a tetraploid F1 population to examine the inheritance probability of parental alleles. Pairing configuration analysis supported the random meiotic pairing of homologous chromosomes on a genome-wide level. On the other hand, preferential pairing was observed on chr-11, suggesting that there may be an exception to the random pairing. Genotypic data suggested quadrivalent formation within the population, although the frequency of quadrivalent formation varied by chromosome and cultivar. Collectively, the results confirmed applicability of dpMIG-seq for allele dosage genotyping and are expected to catalyze the adoption of this cost-effective and rapid genotyping technology in polyploid studies.
下一代测序（NGS）文库的构建通常需要高质量的 DNA 提取、精确的 DNA 浓度调整和限制性酶消化以降低基因组的复杂性，这就增加了样品制备和处理的时间和成本。为了应对这些挑战，一种基于 PCR 的快速 NGS 文库制备方法（名为 dpMIG-seq）已被开发出来，并被证明对高通量基因分型有效。然而，dpMIG-seq 的应用仅限于二倍体和多倍体物种，而且是非组遗传。在本研究中，我们获得了四倍体蓝莓的全基因组单核苷酸多态性（SNP）标记，以评估基因分型和下游分析结果。通过比较不同DNA浓度样本和多种生物信息学方法推断出的基因分型质量，发现基于dpMIG-seq的基因分型具有很高的准确性和可重复性，重复样本之间的皮尔逊相关系数在0.91至0.98之间。此外，我们还证明了 dpMIG-seq 能够对 DNA 浓度较低的样本进行准确的基因分型。随后，我们将 dpMIG-seq 应用于四倍体 F1 群体，研究亲本等位基因的遗传概率。配对构型分析支持同源染色体在全基因组水平上的随机减数分裂配对。另一方面，在 chr-11 上观察到了优先配对，这表明随机配对可能存在例外。基因型数据表明，虽然四价形成的频率因染色体和栽培品种而异，但在种群中仍有四价形成。总之，这些结果证实了 dpMIG-seq 在等位基因剂量基因分型方面的适用性，并有望促进这种经济高效的快速基因分型技术在多倍体研究中的应用。
{"title":"A low-cost dpMIG-seq method for elucidating complex inheritance in polysomic crops: A case study in tetraploid blueberry","authors":"Kyoka Nagasaka, Kazusa Nishimura, Ko Motoki, Keigo Yamagata, Soichiro Nishiyama, Hisayo Yamane, Ryutaro Tao, Ryohei Nakano, Tetsuya Nakazaki","doi":"10.1093/hr/uhae248","DOIUrl":"https://doi.org/10.1093/hr/uhae248","url":null,"abstract":"Next-generation sequencing (NGS) library construction often requires high-quality DNA extraction, precise adjustment of DNA concentration, and restriction enzyme digestion to reduce genome complexity, which results in increased time and cost in sample preparation and processing. To address these challenges, a PCR-based method for rapid NGS library preparation, named dpMIG-seq, has been developed and proven effective for high-throughput genotyping. However, the application of dpMIG-seq has been limited to diploid and polyploid species with disomic inheritance. In this study, we obtained genome-wide single nucleotide polymorphism (SNP) markers for tetraploid blueberry to evaluate genotyping and downstream analysis outcomes. Comparison of genotyping qualities inferred across samples with different DNA concentrations and multiple bioinformatics approaches revealed high accuracy and reproducibility of dpMIG-seq-based genotyping, with Pearson’s correlation coefficients between replicates in the range of 0.91 to 0.98. Furthermore, we demonstrated that dpMIG-seq enables accurate genotyping of samples with low DNA concentrations. Subsequently, we applied dpMIG-seq to a tetraploid F1 population to examine the inheritance probability of parental alleles. Pairing configuration analysis supported the random meiotic pairing of homologous chromosomes on a genome-wide level. On the other hand, preferential pairing was observed on chr-11, suggesting that there may be an exception to the random pairing. Genotypic data suggested quadrivalent formation within the population, although the frequency of quadrivalent formation varied by chromosome and cultivar. Collectively, the results confirmed applicability of dpMIG-seq for allele dosage genotyping and are expected to catalyze the adoption of this cost-effective and rapid genotyping technology in polyploid studies.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"7 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142142441","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}
Yunpeng Cao, Jiayi Hong, Yun Zhao, Xiaoxu Li, Xiaofeng Feng, Han Wang, Lin Zhang, Mengfei Lin, Yongping Cai, Yuepeng Han
De novo genes can evolve 'from scratch' from non-coding sequences, acquiring novel functions in organisms and integrating into regulatory networks during evolution to drive innovations in important phenotypes and traits. However, identifying de novo genes is challenging, as it requires high-quality genomes from closely related species. According to the comparison with nine closely related Prunus genomes, we determined at least 178 de novo genes in P. persica ‘baifeng’. The distinct differences were observed between de novo and conserved genes in gene characteristics and expression patterns. Gene ontology (GO) enrichment analysis suggested that Type I de novo genes originated from sequences related to plastid modification functions, while Type II genes were inferred to have derived from sequences related to reproductive functions. Finally, transcriptome sequencing across different tissues and developmental stages suggested that de novo genes have been evolutionarily recruited into existing regulatory networks, playing important roles in plant growth and development, which was also supported by WGCNA analysis and quantitative trait loci data. This study lays the groundwork for future research on the origins and functions of genes in Prunus and related taxa.
{"title":"De novo gene integration into regulation networks via interaction with conserved genes in peach","authors":"Yunpeng Cao, Jiayi Hong, Yun Zhao, Xiaoxu Li, Xiaofeng Feng, Han Wang, Lin Zhang, Mengfei Lin, Yongping Cai, Yuepeng Han","doi":"10.1093/hr/uhae252","DOIUrl":"https://doi.org/10.1093/hr/uhae252","url":null,"abstract":"De novo genes can evolve 'from scratch' from non-coding sequences, acquiring novel functions in organisms and integrating into regulatory networks during evolution to drive innovations in important phenotypes and traits. However, identifying de novo genes is challenging, as it requires high-quality genomes from closely related species. According to the comparison with nine closely related Prunus genomes, we determined at least 178 de novo genes in P. persica ‘baifeng’. The distinct differences were observed between de novo and conserved genes in gene characteristics and expression patterns. Gene ontology (GO) enrichment analysis suggested that Type I de novo genes originated from sequences related to plastid modification functions, while Type II genes were inferred to have derived from sequences related to reproductive functions. Finally, transcriptome sequencing across different tissues and developmental stages suggested that de novo genes have been evolutionarily recruited into existing regulatory networks, playing important roles in plant growth and development, which was also supported by WGCNA analysis and quantitative trait loci data. This study lays the groundwork for future research on the origins and functions of genes in Prunus and related taxa.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"21 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142142443","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}
Zihao Li, Lin Yang, Yanni Wu, Ran Zhang, Sen Yu, Liwen Fu
The target of rapamycin (TOR) kinase is a central signaling hub that plays a crucial role in precisely orchestrating plant growth, development, and stress responses. This suggests that TOR is intricately involved in maintaining the balance between plant growth and stress responses. Nevertheless, despite the observed effects, the specific mechanisms through which TOR operates in these processes remain obscure. In this study, we investigated how the tomato (Solanum lycopersicum) TOR (SlTOR) affects plant growth and cold responses. We demonstrated that SlTOR inhibition transcriptionally primes cold stress responses, consequently enhancing tomato cold tolerance. A widely targeted metabolomics analysis revealed the disruption of amino acid metabolism homeostasis under cold stress upon SlTOR inhibition, which led to the accumulation of two important cryoprotective metabolites: salicylic acid (SA) and putrescine (Put). Next, we discovered SlPGH1 (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) as a direct substrate of SlTOR. Inhibiting SlTOR led to increased SlCBF1 (C-REPEAT-BINDING FACTOR 1) expression via SlPGH1, potentially triggering the activation of cold-responsive genes and subsequent metabolic alterations. Our study provides a mechanistic framework that elucidates how SlTOR modulates amino acid-related metabolism to enhance tomato cold tolerance, which sheds light on the complex interplay between growth and stress responses orchestrated by TOR.
雷帕霉素靶蛋白激酶（TOR）是一个中心信号枢纽，在精确协调植物生长、发育和胁迫响应方面发挥着至关重要的作用。这表明 TOR 密切参与了维持植物生长和胁迫反应之间的平衡。然而，尽管观察到了这些影响，但 TOR 在这些过程中的具体作用机制仍然模糊不清。在本研究中，我们研究了番茄（Solanum lycopersicum）TOR（SlTOR）如何影响植物生长和冷反应。我们证明，抑制 SlTOR 可使冷胁迫反应转录激活，从而增强番茄的耐寒性。一项广泛的靶向代谢组学分析表明，在抑制 SlTOR 后，冷胁迫下的氨基酸代谢平衡被破坏，导致两种重要的低温保护性代谢产物：水杨酸（SA）和腐胺（Put）的积累。接着，我们发现 SlPGH1（2-PHOSPHO-D-GLYCERATE HYDRO-LYASE）是 SlTOR 的直接底物。抑制 SlTOR 会导致 SlCBF1（C-REPEAT-BINDING FACTOR 1）通过 SlPGH1 表达增加，从而可能引发冷反应基因的激活和随后的代谢改变。我们的研究提供了一个机理框架，阐明了 SlTOR 如何调节氨基酸相关代谢以提高番茄的耐寒性，从而揭示了 TOR 协调的生长和胁迫响应之间复杂的相互作用。
{"title":"TOR balances plant growth and cold tolerance by orchestrating amino acid-derived metabolism in tomato","authors":"Zihao Li, Lin Yang, Yanni Wu, Ran Zhang, Sen Yu, Liwen Fu","doi":"10.1093/hr/uhae253","DOIUrl":"https://doi.org/10.1093/hr/uhae253","url":null,"abstract":"The target of rapamycin (TOR) kinase is a central signaling hub that plays a crucial role in precisely orchestrating plant growth, development, and stress responses. This suggests that TOR is intricately involved in maintaining the balance between plant growth and stress responses. Nevertheless, despite the observed effects, the specific mechanisms through which TOR operates in these processes remain obscure. In this study, we investigated how the tomato (Solanum lycopersicum) TOR (SlTOR) affects plant growth and cold responses. We demonstrated that SlTOR inhibition transcriptionally primes cold stress responses, consequently enhancing tomato cold tolerance. A widely targeted metabolomics analysis revealed the disruption of amino acid metabolism homeostasis under cold stress upon SlTOR inhibition, which led to the accumulation of two important cryoprotective metabolites: salicylic acid (SA) and putrescine (Put). Next, we discovered SlPGH1 (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) as a direct substrate of SlTOR. Inhibiting SlTOR led to increased SlCBF1 (C-REPEAT-BINDING FACTOR 1) expression via SlPGH1, potentially triggering the activation of cold-responsive genes and subsequent metabolic alterations. Our study provides a mechanistic framework that elucidates how SlTOR modulates amino acid-related metabolism to enhance tomato cold tolerance, which sheds light on the complex interplay between growth and stress responses orchestrated by TOR.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"9 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142142442","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}
Soluble sugars are not only an important contributor to fruit quality, but also serve as the osmotic regulators in response to abiotic stresses. Early drought stress promotes sugar accumulation, while specific sugar transporters govern the cellular distribution of the sugars. Here, we show that apple plantlets accumulate soluble sugars in leaf tissues under drought stress. Transcriptional profiling of stressed and control plantlets revealed differential expression of several plasma membrane- or vacuolar membrane-localized sugar transporter genes. Among these, four previously identified vacuolar sugar transporter (VST) genes (MdERDL6–1, MdERDL6–2, MdTST1 and MdTST2) showed higher expression under drought, suggesting their roles in response to drought stress. Promoter cis-elements analyses, yeast one-hybrid and dual-luciferase tests confirmed that the drought-induced transcription factor MdDREB2A could promote the expression of MdERDL6–1/−2 and MdTST1/2 by binding to their promoter regions. Moreover, overexpressing of each of these four MdVSTs alone in transgenic apple or Arabidopsis plants accumulated more soluble sugars and abscisic acid, and enhanced drought resistance. Furthermore, apple plants overexpressing MdERDL6–1 also showed reduced water potential, facilitated stomatal closure and reactive oxygen species scavenging under drought condition compared to control plants. Overall, our results suggest a potential strategy to enhance drought resistance and sugar accumulation in fruits through manipulating the genes involved in vacuolar sugar transport.
{"title":"Apple vacuolar sugar transporters regulated by MdDREB2A enhance drought resistance by promoting accumulation of soluble sugars and activating ABA signaling","authors":"Lingcheng Zhu, Chunxia Zhang, Nanxiang Yang, Wenjing Cao, Yanzhen Li, Yunjing Peng, Xiaoyu Wei, Baiquan Ma, Fengwang Ma, Yong-Ling Ruan, Mingjun Li","doi":"10.1093/hr/uhae251","DOIUrl":"https://doi.org/10.1093/hr/uhae251","url":null,"abstract":"Soluble sugars are not only an important contributor to fruit quality, but also serve as the osmotic regulators in response to abiotic stresses. Early drought stress promotes sugar accumulation, while specific sugar transporters govern the cellular distribution of the sugars. Here, we show that apple plantlets accumulate soluble sugars in leaf tissues under drought stress. Transcriptional profiling of stressed and control plantlets revealed differential expression of several plasma membrane- or vacuolar membrane-localized sugar transporter genes. Among these, four previously identified vacuolar sugar transporter (VST) genes (MdERDL6–1, MdERDL6–2, MdTST1 and MdTST2) showed higher expression under drought, suggesting their roles in response to drought stress. Promoter cis-elements analyses, yeast one-hybrid and dual-luciferase tests confirmed that the drought-induced transcription factor MdDREB2A could promote the expression of MdERDL6–1/−2 and MdTST1/2 by binding to their promoter regions. Moreover, overexpressing of each of these four MdVSTs alone in transgenic apple or Arabidopsis plants accumulated more soluble sugars and abscisic acid, and enhanced drought resistance. Furthermore, apple plants overexpressing MdERDL6–1 also showed reduced water potential, facilitated stomatal closure and reactive oxygen species scavenging under drought condition compared to control plants. Overall, our results suggest a potential strategy to enhance drought resistance and sugar accumulation in fruits through manipulating the genes involved in vacuolar sugar transport.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"20 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131010","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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