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Gupta P, Geniza M, Elser J, Al-Bader N, Baschieri R, Phillips JL, Haq E, Preece J, Naithani S, Jaiswal P. Reference genome of the nutrition-rich orphan crop chia ( Salvia hispanica) and its implications for future breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1272966. [PMID: 38162307 PMCID: PMC10757625 DOI: 10.3389/fpls.2023.1272966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Chia (Salvia hispanica L.) is one of the most popular nutrition-rich foods and pseudocereal crops of the family Lamiaceae. Chia seeds are a rich source of proteins, polyunsaturated fatty acids (PUFAs), dietary fibers, and antioxidants. In this study, we present the assembly of the chia reference genome, which spans 303.6 Mb and encodes 48,090 annotated protein-coding genes. Our analysis revealed that ~42% of the chia genome harbors repetitive content, and identified ~3 million single nucleotide polymorphisms (SNPs) and 15,380 simple sequence repeat (SSR) marker sites. By investigating the chia transcriptome, we discovered that ~44% of the genes undergo alternative splicing with a higher frequency of intron retention events. Additionally, we identified chia genes associated with important nutrient content and quality traits, such as the biosynthesis of PUFAs and seed mucilage fiber (dietary fiber) polysaccharides. Notably, this is the first report of in-silico annotation of a plant genome for protein-derived small bioactive peptides (biopeptides) associated with improving human health. To facilitate further research and translational applications of this valuable orphan crop, we have developed the Salvia genomics database (SalviaGDB), accessible at https://salviagdb.org.
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Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Noor Al-Bader
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Rachel Baschieri
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeremy Levi Phillips
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Ebaad Haq
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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Fu YB, Peterson GW, Horbach C. Deleterious and Adaptive Mutations in Plant Germplasm Conserved Ex Situ. Mol Biol Evol 2023; 40:msad238. [PMID: 37931158 PMCID: PMC10724023 DOI: 10.1093/molbev/msad238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023] Open
Abstract
Conserving more than 7 million plant germplasm accessions in 1,750 genebanks worldwide raises the hope of securing the food supply for humanity for future generations. However, there is a genetic cost for such long-term germplasm conservation, which has been largely unaccounted for before. We investigated the extent and variation of deleterious and adaptive mutations in 490 individual plants representing barley, wheat, oat, soybean, maize, rapa, and sunflower collections in a seed genebank using RNA-Seq technology. These collections were found to have a range of deleterious mutations detected from 125 (maize) to 83,695 (oat) with a mean of 13,537 and of the averaged sample-wise mutation burden per deleterious locus from 0.069 to 0.357 with a mean of 0.200. Soybean and sunflower collections showed that accessions acquired earlier had increased mutation burdens. The germplasm with more years of storage in several collections carried more deleterious and fewer adaptive mutations. The samples with more cycles of germplasm regeneration revealed fewer deleterious and more adaptive mutations. These findings are significant for understanding mutational dynamics and genetic cost in conserved germplasm and have implications for long-term germplasm management and conservation.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, Canada
| | - Gregory W Peterson
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, Canada
| | - Carolee Horbach
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, Canada
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3
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Naithani S, Deng CH, Sahu SK, Jaiswal P. Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes. Biomolecules 2023; 13:1403. [PMID: 37759803 PMCID: PMC10527062 DOI: 10.3390/biom13091403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pan-genomes of several crops. The pan-genomes of crops constructed from various cultivars, accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novel genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding to mitigate the impact of global climate change. Here, we summarize the tools used for pan-genome assembly and annotations, web-portals hosting plant pan-genomes, etc. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and future potential of this emerging field of study.
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Affiliation(s)
- Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| | - Cecilia H. Deng
- Molecular & Digital Breeing Group, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand;
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China;
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
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Al-Bader N, Meier A, Geniza M, Gongora YS, Oard J, Jaiswal P. Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 ( WAK91) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance. Genes (Basel) 2023; 14:1673. [PMID: 37761813 PMCID: PMC10530950 DOI: 10.3390/genes14091673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Leaf sheath blight disease (SB) of rice caused by the soil-borne fungus Rhizoctonia solani results in 10-30% global yield loss annually and can reach 50% under severe outbreaks. Many disease resistance genes and receptor-like kinases (RLKs) are recruited early on by the host plant to respond to pathogens. Wall-associated receptor kinases (WAKs), a subfamily of receptor-like kinases, have been shown to play a role in fungal defense. The rice gene WAK91 (OsWAK91), co-located in the major SB resistance QTL region on chromosome 9, was identified by us as a candidate in defense against rice sheath blight. An SNP mutation T/C in the WAK91 gene was identified in the susceptible rice variety Cocodrie (CCDR) and the resistant line MCR010277 (MCR). The consequence of the resistant allele C is a stop codon loss, resulting in an open reading frame with extra 62 amino acid carrying a longer protein kinase domain and additional phosphorylation sites. Our genotype and phenotype analysis of the parents CCDR and MCR and the top 20 individuals of the double haploid SB population strongly correlate with the SNP. The susceptible allele T is present in the japonica subspecies and most tropical and temperate japonica lines. Multiple US commercial rice varieties with a japonica background carry the susceptible allele and are known for SB susceptibility. This discovery opens the possibility of introducing resistance alleles into high-yielding commercial varieties to reduce yield losses incurred by the sheath blight disease.
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Affiliation(s)
- Noor Al-Bader
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (N.A.-B.); (A.M.); (M.G.)
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR 97331, USA
| | - Austin Meier
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (N.A.-B.); (A.M.); (M.G.)
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (N.A.-B.); (A.M.); (M.G.)
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR 97331, USA
| | - Yamid Sanabria Gongora
- Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (Y.S.G.); (J.O.)
| | - James Oard
- Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (Y.S.G.); (J.O.)
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (N.A.-B.); (A.M.); (M.G.)
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Pasitka L, Cohen M, Ehrlich A, Gildor B, Reuveni E, Ayyash M, Wissotsky G, Herscovici A, Kaminker R, Niv A, Bitcover R, Dadia O, Rudik A, Voloschin A, Shimoni M, Cinnamon Y, Nahmias Y. Spontaneous immortalization of chicken fibroblasts generates stable, high-yield cell lines for serum-free production of cultured meat. NATURE FOOD 2023; 4:35-50. [PMID: 37118574 DOI: 10.1038/s43016-022-00658-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/03/2022] [Indexed: 04/30/2023]
Abstract
Cellular agriculture could meet growing demand for animal products, but yields are typically low and regulatory bodies restrict genetic modification for cultured meat production. Here we demonstrate the spontaneous immortalization and genetic stability of fibroblasts derived from several chicken breeds. Cell lines were adapted to grow as single-cell suspensions using serum-free culture medium, reaching densities of 108 × 106 cells per ml in continuous culture, corresponding to yields of 36% w/v. We show that lecithin activates peroxisome proliferator-activated receptor gamma (PPARγ), inducing adipogenesis in immortalized fibroblasts. Blending cultured adipocyte-like cells with extruded soy protein, formed chicken strips in which texture was supported by animal and plant proteins while aroma and flavour were driven by cultured animal fat. Visual and sensory analysis graded the product 4.5/5.0, with 85% of participants extremely likely to replace their food choice with this cultured meat product. Immortalization without genetic modification and high-yield manufacturing are critical for the market realization of cultured meat.
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Affiliation(s)
- L Pasitka
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - M Cohen
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Cell and Developmental Biology, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - A Ehrlich
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | - M Ayyash
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Believer Meats, Rehovot, Israel
| | | | | | | | - A Niv
- Believer Meats, Rehovot, Israel
| | | | - O Dadia
- Believer Meats, Rehovot, Israel
| | - A Rudik
- Believer Meats, Rehovot, Israel
| | | | | | - Y Cinnamon
- Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Y Nahmias
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Department of Cell and Developmental Biology, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Believer Meats, Rehovot, Israel.
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6
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Tello-Ruiz MK, Naithani S, Gupta P, Olson A, Wei S, Preece J, Jiao Y, Wang B, Chougule K, Garg P, Elser J, Kumari S, Kumar V, Contreras-Moreira B, Naamati G, George N, Cook J, Bolser D, D'Eustachio P, Stein LD, Gupta A, Xu W, Regala J, Papatheodorou I, Kersey PJ, Flicek P, Taylor C, Jaiswal P, Ware D. Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res 2021; 49:D1452-D1463. [PMID: 33170273 DOI: 10.1093/nar/gkaa979] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/09/2020] [Indexed: 01/27/2023] Open
Abstract
Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes-over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene-gene interactions. Gramene integrates ontology-based protein structure-function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome.
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Affiliation(s)
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Yinping Jiao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Priyanka Garg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Nancy George
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Justin Cook
- Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto M5G 1L7, Canada
| | - Daniel Bolser
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK.,Current affiliation: Geromics Inc., Cambridge CB1 3NF, UK
| | - Peter D'Eustachio
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Lincoln D Stein
- Adaptive Oncology Program, Ontario Institute for Cancer Research, Toronto M5G 0A3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Amit Gupta
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX 78758, USA
| | - Weijia Xu
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX 78758, USA
| | - Jennifer Regala
- American Society of Plant Biologists, Rockville, MD 20855-2768, USA.,Current affiliation: American Urological Association, Linthicum, MD 21090, USA
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Paul J Kersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK.,Current affiliation: Royal Botanic Gardens, Kew Richmond, Surrey TW9 3AE, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Crispin Taylor
- American Society of Plant Biologists, Rockville, MD 20855-2768, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.,USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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Elevated mutation and selection in wild emmer wheat in response to 28 years of global warming. Proc Natl Acad Sci U S A 2019; 116:20002-20008. [PMID: 31527251 PMCID: PMC6778259 DOI: 10.1073/pnas.1909564116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The realized threats of global warming to biodiversity have catalyzed the search for a solution to protect and conserve extant plant genetic resources. Part of the solution, however, is dependent on the knowledge of how plant populations respond genetically to these threats, which is largely lacking. We conducted a unique genomic characterization of genetic responses in 10 wild emmer wheat populations in Israel that were sampled twice in 1980 and 2008. After the 28 y of global warming, these populations displayed elevated selection, reduced diversity and temporal divergence, and carried increased mutational burdens forward. However, some populations still showed the ability to acquire beneficial alleles for future adaptation. The patterns of genetic response to rainfall and temperature were complex. Global warming has been documented to threaten wild plants with strong selection pressures, but how plant populations respond genetically to the threats remains poorly understood. We characterized the genetic responses of 10 wild emmer wheat (Triticum dicoccoides Koern.; WEW) populations in Israel, sampling them in 1980 and again in 2008, through an exome capture analysis. It was found that these WEW populations were under elevated selection, displayed reduced diversity and temporal divergence, and carried increased mutational burdens forward. However, some populations still showed the ability to acquire beneficial alleles via selection or de novo mutation for future adaptation. Grouping populations with mean annual rainfall and temperature revealed significant differences in most of the 14 genetic estimates in either sampling year or over the 28 y. The patterns of genetic response to rainfall and temperature varied and were complex. In general, temperature groups displayed more temporal differences in genetic response than rainfall groups. The highest temperature group had more deleterious single nucleotide polymorphisms (dSNPs), higher nucleotide diversity, fewer selective sweeps, lower differentiation, and lower mutational burden. The least rainfall group had more dSNPs, higher nucleotide diversity, lower differentiation and higher mutational burden. These characterized genetic responses are significant, allowing not only for better understanding of evolutionary changes in the threatened populations, but also for realistic modeling of plant population adaptability and vulnerability to global warming.
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