The Plant Genome最新文献

{"title":"Transcriptome‐wide expression landscape and starch synthesis pathway co‐expression network in sorghum","authors":"Zhenbin Hu, Junhao Chen, Marcus O. Olatoye, Hengyou Zhang, Zhenguo Lin","doi":"10.1002/tpg2.20448","DOIUrl":"https://doi.org/10.1002/tpg2.20448","url":null,"abstract":"The gene expression landscape across different tissues and developmental stages reflects their biological functions and evolutionary patterns. Integrative and comprehensive analyses of all transcriptomic data in an organism are instrumental to obtaining a comprehensive picture of gene expression landscape. Such studies are still very limited in sorghum, which limits the discovery of the genetic basis underlying complex agricultural traits in sorghum. We characterized the genome‐wide expression landscape for sorghum using 873 RNA‐sequencing (RNA‐seq) datasets representing 19 tissues. Our integrative analysis of these RNA‐seq data provides the most comprehensive transcriptomic atlas for sorghum, which will be valuable for the sorghum research community for functional characterizations of sorghum genes. Based on the transcriptome atlas, we identified 595 housekeeping genes (HKGs) and 2080 tissue‐specific expression genes (TEGs) for the 19 tissues. We identified different gene features between HKGs and TEGs, and we found that HKGs have experienced stronger selective constraints than TEGs. Furthermore, we built a transcriptome‐wide co‐expression network (TW‐CEN) comprising 35 modules with each module enriched in specific Gene Ontology terms. High‐connectivity genes in TW‐CEN tend to express at high levels while undergoing intensive selective pressure. We also built global and seed‐preferential co‐expression networks of starch synthesis pathways, which indicated that photosynthesis and microtubule‐based movement play important roles in starch synthesis. The global transcriptome atlas of sorghum generated by this study provides an important functional genomics resource for trait discovery and insight into starch synthesis regulation in sorghum.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140574195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"History and current status of embryogenic culture‐based tissue culture, transformation and gene editing of maize (Zea mays L.)","authors":"Frank L. McFarland, Heidi F. Kaeppler","doi":"10.1002/tpg2.20451","DOIUrl":"https://doi.org/10.1002/tpg2.20451","url":null,"abstract":"The production of embryogenic callus and somatic embryos is integral to the genetic improvement of crops via genetic transformation and gene editing. Regenerable embryogenic cultures also form the backbone of many micro‐propagation processes for crop species. In many species, including maize, the ability to produce embryogenic cultures is highly genotype dependent. While some modern transformation and genome editing methods reduce genotype dependence, these efforts ultimately fall short of producing truly genotype‐independent tissue culture methods. Recalcitrant genotypes are still identified in these genotype‐flexible processes, and their presence is magnified by the stark contrast with more amenable lines, which may respond more efficiently by orders of magnitude. This review aims to describe the history of research into somatic embryogenesis, embryogenic tissue cultures, and plant transformation, with particular attention paid to maize. Contemporary research into genotype‐flexible morphogenic gene‐based transformation and genome engineering is also covered in this review. The rapid evolution of plant biotechnology from nascent technologies in the latter half of the 20th century to well‐established, work‐horse production processes has, and will continue to, fundamentally changed agriculture and plant genetics research.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"152 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140574196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic mapping of dynamic control of leaf angle across multiple canopy levels in maize","authors":"Matthew J. Dzievit, Xianran Li, Jianming Yu","doi":"10.1002/tpg2.20423","DOIUrl":"https://doi.org/10.1002/tpg2.20423","url":null,"abstract":"Optimizing leaf angle and other canopy architecture traits has helped modern maize (<i>Zea mays</i> L.) become adapted to higher planting densities over the last 60 years. Traditional investigations into genetic control of leaf angle have focused on one leaf or the average of multiple leaves; as a result, our understanding of genetic control across multiple canopy levels is still limited. To address this, genetic mapping across four canopy levels was conducted in the present study to investigate the genetic control of leaf angle across the canopy. We developed two populations of doubled haploid lines derived from three inbreds with distinct leaf angle phenotypes. These populations were genotyped with genotyping-by-sequencing and phenotyped for leaf angle at four different canopy levels over multiple years. To understand how leaf angle changes across the canopy, the four measurements were used to derive three additional traits. Composite interval mapping was conducted with the leaf-specific measurements and the derived traits. A set of 59 quantitative trait loci (QTLs) were uncovered for seven traits, and two genomic regions were consistently detected across multiple canopy levels. Additionally, seven genomic regions were found to contain consistent QTLs with either relatively stable or dynamic effects at different canopy levels. Prioritizing the selection of QTLs with dynamic effects across the canopy will aid breeders in selecting maize hybrids with the ideal canopy architecture that continues to maximize yield on a per area basis under increasing planting densities.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138823644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Plant Genome special section: Epigenome and epitranscriptome in plant–environment interactions","authors":"Wai-Shing Yung, Ting-Fung Chan, Fanjiang Kong, Hon-Ming Lam","doi":"10.1002/tpg2.20404","DOIUrl":"https://doi.org/10.1002/tpg2.20404","url":null,"abstract":"<p>Understanding how plants interact with the external environment is critical for improving crops' adaptation to environmental stresses and restoring marginal lands to fulfill food demand under the changing climate. In response to environmental cues, plants utilize the dynamic epigenome to modulate and fine-tune the temporal gene expression for development and stress adaptation (Lloyd &amp; Lister, <span>2022</span>). During long-term adaptation, certain epigenetic modifications can even be retained during aging and transmitted to the progenies (Lamke &amp; Baurle, <span>2017</span>). Over the past decades, technological advances have allowed researchers to have enriched knowledge about the dynamic changes in epigenetic modifications at the genomic level in different plant species (Perrone &amp; Martinelli, <span>2020</span>). Considering the emerging number of epigenomic studies in plants, there is a need to effectively integrate the epigenomic information obtained to generate a holistic understanding of epigenetic regulations in plant responses to the external environment. In moving forward to the investigation of crops, revisiting the concepts and focuses of epigenetic studies would pave the way to potential applications to tackle the challenges posed by the changing environment on crop production. Besides, the epitranscriptome featured by numerous types of RNA modifications is also an important regulatory layer of gene expression (Meyer &amp; Jaffrey, <span>2014</span>). The revolutionary development of third-generation sequencing technologies has enabled comprehensive analyses of plant epitranscriptome and greatly benefited the deciphering of gene regulation to provide novel mechanistic insights and strategies for crop improvement (Zhao et al., <span>2019</span>). This special issue has collected eight articles surrounding the described themes and the highlights are summarized here.</p>\u0000<p>Flowering is a developmental process well known to be regulated by epigenetic mechanisms in plants (He et al., <span>2003</span>). The accurate perception of external environmental conditions enables flowering at the right time. As one of the major pathways controlling flowering time, the photoperiod pathway integrates the signal of day length into the regulation of <i>CONSTANS</i> (<i>CO</i>) and thus <i>FLOWERING LOCUS T</i> (<i>FT</i>) expression which induces flowering. Liu et al. (<span>2023</span>) reviewed the current knowledge on the histone-modifying enzymes responsible for altering the chromatin statuses of the important regulatory genes of photoperiodic flowering, including <i>FT</i>, <i>CO</i>, and GIGANTEA, and reiterated the lack of evidence showing concrete relationships between photoperiodic control and other epigenetic features such as DNA methylation and chromatin remodeling in <i>Arabidopsis</i>. While rice displays photoperiodic regulation similar to <i>Arabidopsis</i>, the pathway in soybean involves regulatory components specific to ","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138823994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Plant Genome special section: Grain quality and nutritional genomics for breeding next-generation crops","authors":"Manish K. Pandey, Reyazul Rouf Mir, Nese Sreenivasulu","doi":"10.1002/tpg2.20396","DOIUrl":"https://doi.org/10.1002/tpg2.20396","url":null,"abstract":"<p>By 2050, the world's population is expected to reach 9.8 billion according to United Nations predictions (https://www.un.org/en/desa/world-population-projected-reach-98-billion-2050-and-112-billion-2100). As a result, crop yields must roughly double in order to feed an expanding global population while still satisfying consumer demands for grain quality and nutrition. In addition to enhancing the nutritional value of food crops, making available affordable, nutrient-dense food, especially to those who are economically disadvantaged, will be a central pillar to address food and nutritional security. The strategy for improving grain quality and nutritional traits in breeding programs has been prioritized with the recent advancements in phenotyping of seeds and grains (metabolomics, mineral and vitamins, assessing the quality of starch, proteins and lipids, and capturing consumer preferred traits), sequencing technologies to do high-throughput genotyping, functional genomics aided gene discovery, high-resolution trait mapping and superior haplotype discovery, as well deploying genomic selection tools in a variety of crops (Pandey et al., <span>2016</span>; Varshney et al., <span>2019</span>). To improve population dietary patterns, a new generation of foods and ingredients with improved intrinsic nutritional quality and preferred grain quality attributes needs to be generated through advanced breeding methods. This will help to improve public health by increasing nutritional density and optimizing the quality of complex carbohydrates, proteins, and lipids. By utilizing and integrating both modern and traditional breeding techniques, it is possible to hasten the production of new crop types with improved yield, grain, and nutritional quality. This special issue highlights the most significant findings, which cover developments in high-throughput genomics, including genomic prediction of traits related to grain quality, and enhancement of nutritive traits in cereals (rice, wheat, maize, and oat) as well as legume crops like groundnut. Overall, this special issue includes a collection of studies deciphering genetic mechanisms of micronutrients covering minerals such as grain iron (Fe), zinc (Zn), and vitamin enrichment (tocochromanols), pigmented bioactives, amino acids, dietary fiber, fatty acid composition, food safety, and end user grain quality traits in cereals and selected legumes.</p>\u0000<p>The genetic mapping approach for identifying genetic regions controlling key grain quality and nutrition traits has been the most successful approach and has contributed significantly to marker discovery and use in crop breeding programs (Cockram &amp; Mackay, <span>2018</span>). High concentrations of essential amino acid such as lysine and limiting the high concentrations of free asparagine to prevent acrylamide during bread formation enhance the nutritional value of wheat grain. The article by Oddy et al. (<span>2023</span>) used this approach for understa","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138823999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a new Rsg1 allele conferring resistance to multiple greenbug biotypes from barley accessions PI 499276 and PI 566459","authors":"Xiangyang Xu, Dolores Mornhinweg, Guihua Bai, Genqiao Li, Ruolin Bian, Amy Bernardo, J. Scott Armstrong","doi":"10.1002/tpg2.20418","DOIUrl":"https://doi.org/10.1002/tpg2.20418","url":null,"abstract":"Greenbug [<i>Schizaphis graminum</i> (Rondani)] is a major insect pest that significantly affects barley production worldwide. The identification of novel greenbug resistance genes is crucial for sustainable barley production and global food security. To identify greenbug resistance genes from a US breeding line PI 499276 and a Chinese cultivar PI 566459, two F_6:7 recombinant inbred line (RIL) populations developed from crosses Weskan × PI 499276 and Weskan × PI 566459 were phenotyped for responses to greenbug biotype E and genotyped using genotyping-by-sequencing (GBS). Linkage analysis using single nucleotide polymorphism and kompetitive allele-specific polymorphism (KASP) markers delimited the greenbug resistance genes from PI 499276 and PI 566459 to a 1.2 Mb genomic region between 666.5 and 667.7 Mb on the long arm of chromosome 3H in the Morex <i>Hordeum vulgare</i> r1 reference sequence. Allelism tests based on responses of four F₂ populations to greenbug biotype E indicated that the greenbug resistance gene in PI 499276 and PI 566459 is either allelic or very close to <i>Rsg1</i>. Given that PI 499276 and PI 566459 shared the same unique resistance pattern to a set of 14 greenbug biotypes, which is different from those of other <i>Rsg1</i> alleles, they carry a new <i>Rsg1</i> allele. The greenbug resistance genes in Post 90, PI 499276/PI 566459, and WBDC 336 were designated as <i>Rsg1.a1</i>, <i>Rsg1.a2</i>, and <i>Rsg1.a3</i>, respectively. KASP markers KASP-Rsg1a3-1, KASP-Rsg1a3-2, and KASP160 can be used to tag <i>Rsg1.a2</i> in barley breeding.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"236 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138629489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new wild emmer wheat panel allows to map new loci associated with resistance to stem rust at seedling stage","authors":"Anna Maria Mastrangelo, Pablo Roncallo, Oadi Matny, Čegan Radim, Brian Steffenson, Viviana Echenique, Jan Šafář, Raffaella Battaglia, Delfina Barabaschi, Luigi Cattivelli, Hakan Özkan, Elisabetta Mazzucotelli","doi":"10.1002/tpg2.20413","DOIUrl":"https://doi.org/10.1002/tpg2.20413","url":null,"abstract":"Wheat stem rust, caused by <i>Puccinia graminis</i> f. sp. <i>tritici</i> (<i>Pgt</i>), is a major wheat disease worldwide. A collection of 283 wild emmer wheat [<i>Triticum turgidum</i> L. subsp<i>. dicoccoides</i> (Körn. ex Asch. &amp; Graebn.) Thell] accessions, representative of the entire Fertile Crescent region where wild emmer naturally occurs, was assembled, genotyped, and characterized for population structure, genetic diversity, and rate of linkage disequilibrium (LD) decay. Then, the collection was employed for mapping <i>Pgt</i> resistance genes, as a proof of concept of the effectiveness of genome-wide association studies in wild emmer. The collection was evaluated in controlled conditions for reaction to six common <i>Pgt</i> pathotypes (TPMKC, TTTTF, JRCQC, TRTTF, TTKSK/Ug99, and TKTTF). Most resistant accessions originated from the Southern Levant wild emmer lineage, with some showing a resistance reaction toward three to six tested races. Association analysis was conducted considering a 12K polymorphic single-nucleotide polymorphisms dataset, kinship relatedness between accessions, and population structure. Eleven significant marker–trait associations (MTA) were identified across the genome, which explained from 17% to up to 49% of phenotypic variance with an average 1.5 additive effect (based on the 1–9 scoring scale). The identified loci were either effective against single or multiple races. Some MTAs colocalized with known <i>Pgt</i> resistance genes, while others represent novel resistance loci useful for durum and bread wheat prebreeding. Candidate genes with an annotated function related to plant response to pathogens were identified at the regions linked to the resistance and defined according to the estimated small LD (about 126 kb), as typical of wild species.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"79 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138681311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}