{"title":"Double‐digest restriction‐associated DNA sequencing‐based genotyping and its applications in sesame germplasm management","authors":"Pradeep Ruperao, Prasad Bajaj, Rashmi Yadav, Mahalingam Angamuthu, Rajkumar Subramani, Vandana Rai, Kapil Tiwari, Abhishek Rathore, Kuldeep Singh, Gyanendra Pratap Singh, Ulavappa B. Angadi, Sean Mayes, Parimalan Rangan","doi":"10.1002/tpg2.20447","DOIUrl":"https://doi.org/10.1002/tpg2.20447","url":null,"abstract":"Sesame (<jats:italic>Sesamum indicum</jats:italic> L.) is an ancient oilseed crop belonging to the family <jats:italic>Pedaliaceae</jats:italic> and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR‐National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics‐assisted double‐digest restriction‐associated DNA sequencing (ddRAD‐seq) approach. A total of 64,910 filtered single‐nucleotide polymorphisms (SNPs) were utilized to assess the genome‐scale diversity. Applications of this genome‐scale information (reduced representation using restriction enzymes) are demonstrated through the development of a molecular core collection (CC) representing maximal SNP diversity. This information is also applied in developing a mid‐density panel (MDP) comprising 2515 hyper‐variable SNPs, representing almost equally the genic and non‐genic regions. The sesame CC comprising 384 accessions, a representative set of accessions with maximal diversity, was identified using multiple criteria such as k‐mer (subsequence of length “k” in a sequence read) diversity, observed heterozygosity, CoreHunter3, GenoCore, and genetic differentiation. The coreset constituted around 15% of the total accessions studied, and this small subset had captured >60% SNP diversity of the entire population. In the coreset, the admixture analysis shows reduced genetic complexity, increased nucleotide diversity (π), and is geographically distributed without any repetitiveness in the CC germplasm. Within the CC, India‐originated accessions exhibit higher diversity (as expected based on the center of diversity concept), than those accessions that were procured from various other countries. The identified CC set and the MDP will be a valuable resource for genomics‐assisted accelerated sesame improvement program.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"163 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140609477","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}
Ruifeng Yang, Hongyi Chen, Da Zhang, Qixiang Zhang, Youjun Huang
{"title":"Integrated transcriptomic and lipidomic analysis provides key insights into lipid content changes during pecan (Carya illinoensis) fruit development","authors":"Ruifeng Yang, Hongyi Chen, Da Zhang, Qixiang Zhang, Youjun Huang","doi":"10.1002/tpg2.20449","DOIUrl":"https://doi.org/10.1002/tpg2.20449","url":null,"abstract":"Pecans [<jats:italic>Carya illinoinensis</jats:italic> (Wangenh.) K. Koch] are highly valued for their abundance of quality healthy lipids, positively impacting human health and making themselves a preferred choice for nutritionally rich foods. However, a comprehensive understanding of the high‐resolution characteristics of pecan fruit lipid composition and its dynamic changes, as well as the transfer between embryo and pericarp during development, remains incomplete. In this study, through integrated multi‐omics analysis, we observed significant spatiotemporal heterogeneity in lipid changes between the pericarp and embryo. It showed smaller fluctuations and more stable lipid levels in the pericarp while exhibiting a dynamic pattern of initially increasing and then decreasing lipid content in the embryo. In this study, a total of 52 differentially expressed genes were identified, related to fatty acid synthesis and metabolism pathways in the two tissues, with changes in oleic acid and linoleic acid composition being the primary features of the embryo. This research lays the foundation for further understanding the differential regulation mechanisms of lipid metabolism between embryo and pericarp. Overall, this study filled the knowledge gap regarding dynamic changes in pericarp lipid metabolites, provided crucial insights into the lipid metabolism network during pecan fruit development, and established a scientific basis for the genetic improvement of pecan crops.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140574267","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}
Zhenbin Hu, Junhao Chen, Marcus O. Olatoye, Hengyou Zhang, Zhenguo Lin
{"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":"Genome‐wide identification and functional profile analysis of long non‐coding RNAs in Avicennia marina","authors":"Lingling Wang, Zixin Yuan, Jingyi Wang, Yali Guan","doi":"10.1002/tpg2.20450","DOIUrl":"https://doi.org/10.1002/tpg2.20450","url":null,"abstract":"<jats:italic>Avicennia marina</jats:italic>, known for its remarkable adaptability to the challenging coastal environment, including high salinity, tide, and anaerobic soils, holds pivotal functions in safeguarding the coastal ecosystem. Long non‐coding RNAs (lncRNAs) have emerged as significant players in various natural processes of plants such as development. However, lncRNAs in <jats:italic>A. marina</jats:italic> remain largely unknown and uncharacterized. Here, we employed the transcriptome datasets from multiple tissues, such as root, leaf, and seed, to detect and characterize the lncRNAs of <jats:italic>A. marina</jats:italic>. Analyzing synthetically, we finally identified 6333 lncRNAs in the <jats:italic>A. marina</jats:italic>. These lncRNAs exhibited distinct features compared to messenger RNAs, including larger exons, lower guanine‐cytosine contents, lower expression levels, and higher tissue specificities. Moreover, we identified thousands of tissue‐specific lncRNAs across the examined tissues and further found that these tissue‐specific lncRNAs were significantly enriched in biological processes related to the major functions of their corresponding tissues. For instance, leaf‐specific lncRNAs showed prominent enrichment in photosynthesis, oxidation–reduction processes, and light harvesting. By providing a comprehensive dataset and functional annotations for <jats:italic>A. marina</jats:italic> lncRNAs, this study offers a valuable overview of lncRNAs in <jats:italic>A. marina</jats:italic> and lays the fundamental foundation for further functional exploring of them.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140574199","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 & Lister, <span>2022</span>). During long-term adaptation, certain epigenetic modifications can even be retained during aging and transmitted to the progenies (Lamke & 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 & 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 & 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}
Manish K. Pandey, Reyazul Rouf Mir, Nese Sreenivasulu
{"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 & 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}
Xiangyang Xu, Dolores Mornhinweg, Guihua Bai, Genqiao Li, Ruolin Bian, Amy Bernardo, J. Scott Armstrong
{"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<sub>6:7</sub> 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 F<sub>2</sub> 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}