Plant GenomePub Date : 2024-03-01Epub Date: 2024-02-10DOI: 10.1002/tpg2.20406
{"title":"Erratum to: Fertilization of grapevine based on gene expression.","authors":"","doi":"10.1002/tpg2.20406","DOIUrl":"10.1002/tpg2.20406","url":null,"abstract":"","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139713222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-03-01Epub Date: 2024-03-13DOI: 10.1002/tpg2.20445
Rajeev K Varshney, Rutwik Barmukh, Alison Bentley, Henry T Nguyen
{"title":"Exploring the genomics of abiotic stress tolerance and crop resilience to climate change.","authors":"Rajeev K Varshney, Rutwik Barmukh, Alison Bentley, Henry T Nguyen","doi":"10.1002/tpg2.20445","DOIUrl":"10.1002/tpg2.20445","url":null,"abstract":"","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140121141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-03-01Epub Date: 2023-12-21DOI: 10.1002/tpg2.20422
Xiaomeng Liu, Weiwei Zhang, Ning Tang, Zexiong Chen, Shen Rao, Hua Cheng, Chengrong Luo, Jiabao Ye, Shuiyuan Cheng, Feng Xu
{"title":"Genomic-wide identification and expression analysis of AP2/ERF transcription factors in Zanthoxylum armatum reveals the candidate genes for the biosynthesis of terpenoids.","authors":"Xiaomeng Liu, Weiwei Zhang, Ning Tang, Zexiong Chen, Shen Rao, Hua Cheng, Chengrong Luo, Jiabao Ye, Shuiyuan Cheng, Feng Xu","doi":"10.1002/tpg2.20422","DOIUrl":"10.1002/tpg2.20422","url":null,"abstract":"<p><p>Terpenoids are the main active components in the Zanthoxylum armatum leaves, which have extensive medicinal value. The Z. armatum leaf is the main by-product in the Z. armatum industry. However, the transcription factors involved in the biosynthesis of terpenoids are rarely reported. This study was performed to identify and classify the APETALA2/ethylene-responsive factor (AP2/ERF) gene family of Z. armatum. The chromosome distribution, gene structure, conserved motifs, and cis-acting elements of the promoter of the species were also comprehensively analyzed. A total of 214 ZaAP2/ERFs were identified. From the obtained transcriptome and terpenoid content data, four candidate ZaAP2/ERFs involved in the biosynthesis of terpenoids were selected via correlation and weighted gene co-expression network analysis. A phylogenetic tree was constructed using 13 AP2/ERFs related to the biosynthesis of terpenoids in other plants. ZaERF063 and ZaERF166 showed close evolutionary relationships with the ERFs in other plant species and shared a high AP2-domain sequence similarity with the two closest AP2/ERF proteins, namelySmERF8 from Salvia miltiorrhiza and AaERF4 from Artemisia annua. Further investigation into the effects of methyl jasmonate (MeJA) treatment on the content of terpenoids in Z. armatum leaves revealed that MeJA significantly induced the upregulation of ZaERF166 and led to a significant increase in the terpenoids content in Z. armatum leaves, indicating that ZaERF166 might be involved in the accumulation of terpenoids of Z. armatum. Results will be beneficial for the functional characterization of AP2/ERFs in Z. armatum and establishment of the theoretical foundation to increase the production of terpenoids via the manipulation of the regulatory elements and strengthen the development and utilization of Z. armatum leaves.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138832558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-03-01Epub Date: 2024-01-18DOI: 10.1002/tpg2.20427
Samiullah Naik, Jebi Sudan, Uneeb Urwat, Mohammad Maqbool Pakhtoon, Basharat Bhat, Varun Sharma, Parvaze A Sofi, Asif B Shikari, Bilal A Bhat, Najeebul Rehman Sofi, P V Vara Prasad, Sajad Majeed Zargar
{"title":"Genome-wide SNP discovery and genotyping delineates potential QTLs underlying major yield-attributing traits in buckwheat.","authors":"Samiullah Naik, Jebi Sudan, Uneeb Urwat, Mohammad Maqbool Pakhtoon, Basharat Bhat, Varun Sharma, Parvaze A Sofi, Asif B Shikari, Bilal A Bhat, Najeebul Rehman Sofi, P V Vara Prasad, Sajad Majeed Zargar","doi":"10.1002/tpg2.20427","DOIUrl":"10.1002/tpg2.20427","url":null,"abstract":"<p><p>Buckwheat (Fagopyrum spp.) is an important nutritional and nutraceutical-rich pseudo-cereal crop. Despite its obvious potential as a functional food, buckwheat has not been fully harnessed due to its low yield, self-incompatibility, increased seed cracking, limited seed set, lodging, and frost susceptibility. The inadequate availability of genomics resources in buckwheat is one of the major reasons for this. In the present study, genome-wide association mapping (GWAS) was conducted to identify loci associated with various morphological and yield-related traits in buckwheat. High throughput genotyping by sequencing led to the identification of 34,978 single nucleotide polymorphisms that were distributed across eight chromosomes. Population structure analysis grouped the genotypes into three sub-populations. The genotypes were also characterized for various qualitative and quantitative traits at two diverse locations, the analysis of which revealed a significant difference in the mean values. The association analysis revealed a total of 71 significant marker-trait associations across eight chromosomes. The candidate genes were identified near 100 Kb of quantitative trait loci (QTLs), providing insights into several metabolic and biosynthetic pathways. The integration of phenology and GWAS in the present study is useful to uncover the consistent genomic regions, related markers associated with various yield-related traits, and potential candidate genes having implications for being utilized in molecular breeding for the improvement of economically important traits in buckwheat. Moreover, the identified QTLs will assist in tracking the desirable alleles of target genes within the buckwheat breeding populations/germplasm.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139492374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat.","authors":"Roopali Bhoite, Yong Han, Alamuru Krishna Chaitanya, Rajeev K Varshney, Darshan Lal Sharma","doi":"10.1002/tpg2.20358","DOIUrl":"10.1002/tpg2.20358","url":null,"abstract":"<p><p>Climate change is varying the availability of resources, soil physicochemical properties, and rainfall events, which collectively determines soil physical and chemical properties. Soil constraints-acidity (pH < 6), salinity (pH ≤ 8.5), sodicity, and dispersion (pH > 8.5)-are major causes of wheat yield loss in arid and semiarid cropping systems. To cope with changing environments, plants employ adaptive strategies such as phenotypic plasticity, a key multifaceted trait, to promote shifts in phenotypes. Adaptive strategies for constrained soils are complex, determined by key functional traits and genotype × environment × management interactions. The understanding of the molecular basis of stress tolerance is particularly challenging for plasticity traits. Advances in sequencing and high-throughput genomics technologies have identified functional alleles in gene-rich regions, haplotypes, candidate genes, mechanisms, and in silico gene expression profiles at various growth developmental stages. Our review focuses on favorable alleles for enhanced gene expression, quantitative trait loci, and epigenetic regulation of plant responses to soil constraints, including heavy metal stress and nutrient limitations. A strategy is then described for quantitative traits in wheat by investigating significant alleles and functional characterization of variants, followed by gene validation using advanced genomic tools, and marker development for molecular breeding and genome editing. Moreover, the review highlights the progress of gene editing in wheat, multiplex gene editing, and novel alleles for smart control of gene expression. Application of these advanced genomic technologies to enhance plasticity traits along with soil management practices will be an effective tool to build yield, stability, and sustainability on constrained soils in the face of climate change.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9933970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-03-01Epub Date: 2023-05-18DOI: 10.1002/tpg2.20343
Sina Nouraei, Md Sultan Mia, Hui Liu, Neil C Turner, Javed M Khan, Guijun Yan
{"title":"Proteomic analysis of near-isogenic lines reveals key biomarkers on wheat chromosome 4B conferring drought tolerance.","authors":"Sina Nouraei, Md Sultan Mia, Hui Liu, Neil C Turner, Javed M Khan, Guijun Yan","doi":"10.1002/tpg2.20343","DOIUrl":"10.1002/tpg2.20343","url":null,"abstract":"<p><p>Drought is a major constraint for wheat production that is receiving increased attention due to global climate change. This study conducted isobaric tags for relative and absolute quantitation proteomic analysis on near-isogenic lines to shed light on the underlying mechanism of qDSI.4B.1 quantitative trait loci (QTL) on the short arm of chromosome 4B conferring drought tolerance in wheat. Comparing tolerant with susceptible isolines, 41 differentially expressed proteins were identified to be responsible for drought tolerance with a p-value of < 0.05 and fold change >1.3 or <0.7. These proteins were mainly enriched in hydrogen peroxide metabolic activity, reactive oxygen species metabolic activity, photosynthetic activity, intracellular protein transport, cellular macromolecule localization, and response to oxidative stress. Prediction of protein interactions and pathways analysis revealed the interaction between transcription, translation, protein export, photosynthesis, and carbohydrate metabolism as the most important pathways responsible for drought tolerance. The five proteins, including 30S ribosomal protein S15, SRP54 domain-containing protein, auxin-repressed protein, serine hydroxymethyltransferase, and an uncharacterized protein with encoding genes on 4BS, were suggested as candidate proteins responsible for drought tolerance in qDSI.4B.1 QTL. The gene coding SRP54 protein was also one of the differentially expressed genes in our previous transcriptomic study.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9534477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-03-01Epub Date: 2022-10-26DOI: 10.1002/tpg2.20273
Michael Ackah, Xin Jin, Qiaonan Zhang, Frank Kwarteng Amoako, Lei Wang, Thomas Attaribo, Mengdi Zhao, Feng Yuan, Richard Ansah Herman, Changyu Qiu, Qiang Lin, Zhi Yin, Weiguo Zhao
{"title":"Long noncoding RNA transcriptome analysis reveals novel lncRNAs in Morus alba 'Yu-711' response to drought stress.","authors":"Michael Ackah, Xin Jin, Qiaonan Zhang, Frank Kwarteng Amoako, Lei Wang, Thomas Attaribo, Mengdi Zhao, Feng Yuan, Richard Ansah Herman, Changyu Qiu, Qiang Lin, Zhi Yin, Weiguo Zhao","doi":"10.1002/tpg2.20273","DOIUrl":"10.1002/tpg2.20273","url":null,"abstract":"<p><p>Drought stress has been a key environmental factor affecting plant growth and development. The plant genome is capable of producing long noncoding RNAs (lncRNAs). To better understand white mulberry (Morus alba L.) drought response mechanism, we conducted a comparative transcriptome study comparing two treatments: drought-stressed (EG) and well-watered (CK) plants. A total of 674 differentially expressed lncRNAs (DElncRNAs) were identified. In addition, 782 differentially expressed messenger RNAs (DEmRNAs) were identified. We conducted Gene Ontology (GO) and KEGG enrichment analyses focusing on the differential lncRNAs cis-target genes. The target genes of the DElncRNAs were most significantly involved in the biosynthesis of secondary metabolites. Gene regulatory networks of the target genes involving DElncRNAs-mRNAs-DEmRNAs and DElncRNA-miRNA-DEmRNA were constructed. In the DElncRNAs-DEmRNAs network, 30 DEmRNAs involved in the biosynthesis of secondary metabolites are collocated with 46 DElncRNAs. The interaction between DElncRNAs and candidate genes was identified using LncTar. In summary, quantitative real-time polymerase chain reaction (qRT-PCR) validated nine candidate genes and seven target lncRNAs including those identified by LncTar. We predicted that the DElncRNAs-DEmRNAs might recruit microRNAs (miRNAs) to interact with gene regulatory networks under the drought stress response in mulberry. The findings will contribute to our understanding of the regulatory functions of lncRNAs under drought stress and will shed new light on the mulberry-drought stress interactions.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43042296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-03-01Epub Date: 2023-11-14DOI: 10.1002/tpg2.20409
Dongli He, Yifan Li, Cheng Yuan, Xiaoxiong Pei, Rebecca N Damaris, Haiqin Yu, Bao Qian, Yong Liu, Bin Yi, Changjun Huang, Jianmin Zeng
{"title":"Characterization of the CMS genetic regulation through comparative complete mitochondrial genome sequencing in Nicotiana tabacum.","authors":"Dongli He, Yifan Li, Cheng Yuan, Xiaoxiong Pei, Rebecca N Damaris, Haiqin Yu, Bao Qian, Yong Liu, Bin Yi, Changjun Huang, Jianmin Zeng","doi":"10.1002/tpg2.20409","DOIUrl":"10.1002/tpg2.20409","url":null,"abstract":"<p><p>Mitochondrial genomes (mitogenomes) of flowering plants vary greatly in structure and size, which can lead to frequent gene mutation, rearrangement, or recombination, then result in the cytoplasmic male sterile (CMS) mutants. In tobacco (Nicotiana tabacum), suaCMS lines are widely used in heterosis breeding; however, the related genetic regulations are not very clear. In this study, the cytological observation indicated that the pollen abortion of tobacco suaCMS(HD) occurred at the very early stage of the stamen primordia differentiation. In this study, the complete mitochondrial genomes of suaCMS(HD) and its maintainer HD were sequenced using the PacBio and Illumina Hiseq technology. The total length of the assembled mitogenomes of suaCMS(HD) and HD was 494,317 bp and 430,694 bp, respectively. Comparative analysis indicated that the expanded 64 K bases in suaCMS(HD) were mainly located in noncoding regions, and 23 and 21 big syntenic blocks (>5000 bp) were found in suaCMS(HD) and HD with a series of repeats. Electron transport chain-related genes were highly conserved in two mitogenomes, except five genes (ATP4, ATP6, COX2, CcmFC, and SDH3) with substantial substitutions. Three suaCMS(HD)-specific genes, orf261, orf291, and orf433, were screened. Sequence analysis and RT-PCR verification showed that they were unique to suaCMS(HD). Further gene location analysis and protein property prediction indicated that all the three genes were likely candidates for suaCMS(HD). This study provides new insight into understanding the suaCMS mechanism and is useful for improving tobacco breeding.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92157069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Durum wheat heat tolerance loci defined via a north-south gradient.","authors":"Amadou Tidiane Sall, Hafssa Kabbaj, Sidi Ould Ely Menoum, Madiama Cisse, Mulatu Geleta, Rodomiro Ortiz, Filippo M Bassi","doi":"10.1002/tpg2.20414","DOIUrl":"10.1002/tpg2.20414","url":null,"abstract":"<p><p>The global production of durum wheat (Triticum durum Desf.) is hindered by a constant rise in the frequency of severe heat stress events. To identify heat-tolerant germplasm, three different germplasm panels (\"discovery,\" \"investigation,\" and \"validation\") were studied under a range of heat-stressed conditions. Grain yield (GY) and its components were recorded at each site and a heat stress susceptibility index was calculated, confirming that each 1°C temperature rise corresponds to a GY reduction in durum wheat of 4.6%-6.3%. A total of 2552 polymorphic single nucleotide polymorphisms (SNPs) defined the diversity of the first panel, while 5642 SNPs were polymorphic in the \"investigation panel.\" The use of genome-wide association studies revealed that 36 quantitative trait loci were associated with the target traits in the discovery panel, of which five were confirmed in a \"subset\" tested imposing heat stress by plastic tunnels, and in the investigation panel. A study of allelic combinations confirmed that Q.icd.Heat.003-1A, Q.icd.Heat.007-1B, and Q.icd.Heat.016-3B are additive in nature and the positive alleles at all three loci resulted in a 16% higher GY under heat stress. The underlying SNPs were converted into kompetitive allele specific PCR markers and tested on the validation panel, confirming that each explained up to 9% of the phenotypic variation for GY under heat stress. These markers can now be used for breeding to improve resilience to climate change and increase productivity in heat-stressed areas.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138499950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-03-01Epub Date: 2023-07-06DOI: 10.1002/tpg2.20365
Carlos A Robles-Zazueta, Leonardo A Crespo-Herrera, Francisco J Piñera-Chavez, Carolina Rivera-Amado, Gudbjorg I Aradottir
{"title":"Climate change impacts on crop breeding: Targeting interacting biotic and abiotic stresses for wheat improvement.","authors":"Carlos A Robles-Zazueta, Leonardo A Crespo-Herrera, Francisco J Piñera-Chavez, Carolina Rivera-Amado, Gudbjorg I Aradottir","doi":"10.1002/tpg2.20365","DOIUrl":"10.1002/tpg2.20365","url":null,"abstract":"<p><p>Wheat (Triticum aestivum L.) as a staple crop is closely interwoven into the development of modern society. Its influence on culture and economic development is global. Recent instability in wheat markets has demonstrated its importance in guaranteeing food security across national borders. Climate change threatens food security as it interacts with a multitude of factors impacting wheat production. The challenge needs to be addressed with a multidisciplinary perspective delivered across research, private, and government sectors. Many experimental studies have identified the major biotic and abiotic stresses impacting wheat production, but fewer have addressed the combinations of stresses that occur simultaneously or sequentially during the wheat growth cycle. Here, we argue that biotic and abiotic stress interactions, and the genetics and genomics underlying them, have been insufficiently addressed by the crop science community. We propose this as a reason for the limited transfer of practical and feasible climate adaptation knowledge from research projects into routine farming practice. To address this gap, we propose that novel methodology integration can align large volumes of data available from crop breeding programs with increasingly cheaper omics tools to predict wheat performance under different climate change scenarios. Underlying this is our proposal that breeders design and deliver future wheat ideotypes based on new or enhanced understanding of the genetic and physiological processes that are triggered when wheat is subjected to combinations of stresses. By defining this to a trait and/or genetic level, new insights can be made for yield improvement under future climate conditions.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":null,"pages":null},"PeriodicalIF":4.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9755806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}