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Molitor C, Kurowski TJ, Fidalgo de Almeida PM, Kevei Z, Spindlow DJ, Chacko Kaitholil SR, Iheanyichi JU, Prasanna HC, Thompson AJ, Mohareb FR. A chromosome-level genome assembly of Solanum chilense, a tomato wild relative associated with resistance to salinity and drought. FRONTIERS IN PLANT SCIENCE 2024; 15:1342739. [PMID: 38525148 PMCID: PMC10957597 DOI: 10.3389/fpls.2024.1342739] [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: 11/22/2023] [Accepted: 02/12/2024] [Indexed: 03/26/2024]
Abstract
Introduction Solanum chilense is a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources. Methods In this study we generated a high-quality, chromosome-level, de novo assembly for the S. chilense accession LA1972 using a hybrid assembly strategy with ~180 Gbp of Illumina short reads and ~50 Gbp long PacBio reads. Further scaffolding was performed using Bionano optical maps and 10x Chromium reads. Results The resulting sequences were arranged into 12 pseudomolecules using Hi-C sequencing. This resulted in a 901 Mbp assembly, with a completeness of 95%, as determined by Benchmarking with Universal Single-Copy Orthologs (BUSCO). Sequencing of RNA from multiple tissues resulting in ~219 Gbp of reads was used to annotate the genome assembly with an RNA-Seq guided gene prediction, and for a de novo transcriptome assembly. This chromosome-level, high-quality reference genome for S. chilense accession LA1972 will support future breeding efforts for more sustainable tomato production. Discussion Gene sequences related to drought and salt resistance were compared between S. chilense and S. lycopersicum to identify amino acid variations with high potential for functional impact. These variants were subsequently analysed in 84 resequenced tomato lines across 12 different related species to explore the variant distributions. We identified a set of 7 putative impactful amino acid variants some of which may also impact on fruit development for example the ethylene-responsive transcription factor WIN1 and ethylene-insensitive protein 2. These variants could be tested for their ability to confer functional phenotypes to cultivars that have lost these variants.
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Affiliation(s)
- Corentin Molitor
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - Tomasz J. Kurowski
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | | | - Zoltan Kevei
- Soil, Agrifood and Biosciences, Cranfield University, Wharley End, United Kingdom
| | - Daniel J. Spindlow
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - Steffimol R. Chacko Kaitholil
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - Justice U. Iheanyichi
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - H. C. Prasanna
- Division of Vegetable Crops, ICAR-Indian Institute of Horticultural Research, Bangalore, India
| | - Andrew J. Thompson
- Soil, Agrifood and Biosciences, Cranfield University, Wharley End, United Kingdom
| | - Fady R. Mohareb
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
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Martina M, De Rosa V, Magon G, Acquadro A, Barchi L, Barcaccia G, De Paoli E, Vannozzi A, Portis E. Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family. FRONTIERS IN PLANT SCIENCE 2024; 15:1278760. [PMID: 38375087 PMCID: PMC10875072 DOI: 10.3389/fpls.2024.1278760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.
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Affiliation(s)
- Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
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Doron-Faigenboim A, Moy-Komemi M, Petreikov M, Eselson Y, Sonawane P, Cardenas P, Fei Z, Aharoni A, Schaffer AA. Transcriptomes of developing fruit of cultivated and wild tomato species. MOLECULAR HORTICULTURE 2023; 3:12. [PMID: 37789418 PMCID: PMC10514971 DOI: 10.1186/s43897-023-00060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/30/2023] [Indexed: 10/05/2023]
Affiliation(s)
- Adi Doron-Faigenboim
- Plant Sciences Institute, Agricultural Research Organization-Volcani Center, Rishon LeZion, Israel
| | - Michal Moy-Komemi
- Plant Sciences Institute, Agricultural Research Organization-Volcani Center, Rishon LeZion, Israel
| | - Marina Petreikov
- Plant Sciences Institute, Agricultural Research Organization-Volcani Center, Rishon LeZion, Israel
| | - Yelena Eselson
- Plant Sciences Institute, Agricultural Research Organization-Volcani Center, Rishon LeZion, Israel
| | - Prashant Sonawane
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Pablo Cardenas
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Arthur A. Schaffer
- Plant Sciences Institute, Agricultural Research Organization-Volcani Center, Rishon LeZion, Israel
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4
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Kaur G, Abugu M, Tieman D. The dissection of tomato flavor: biochemistry, genetics, and omics. FRONTIERS IN PLANT SCIENCE 2023; 14:1144113. [PMID: 37346138 PMCID: PMC10281629 DOI: 10.3389/fpls.2023.1144113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/02/2023] [Indexed: 06/23/2023]
Abstract
Flavor and quality are the major drivers of fruit consumption in the US. However, the poor flavor of modern commercial tomato varieties is a major cause of consumer dissatisfaction. Studies in flavor research have informed the role of volatile organic compounds in improving overall liking and sweetness of tomatoes. These studies have utilized and applied the tools of molecular biology, genetics, biochemistry, omics, machine learning, and gene editing to elucidate the compounds and biochemical pathways essential for good tasting fruit. Here, we discuss the progress in identifying the biosynthetic pathways and chemical modifications of important tomato volatile compounds. We also summarize the advances in developing highly flavorful tomato varieties and future steps toward developing a "perfect tomato".
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Affiliation(s)
- Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Modesta Abugu
- Department of Horticulture Science, North Carolina State University, Raleigh, NC, United States
| | - Denise Tieman
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
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5
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Sapkota M, Pereira L, Wang Y, Zhang L, Topcu Y, Tieman D, van der Knaap E. Structural variation underlies functional diversity at methyl salicylate loci in tomato. PLoS Genet 2023; 19:e1010751. [PMID: 37141297 PMCID: PMC10187894 DOI: 10.1371/journal.pgen.1010751] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/16/2023] [Accepted: 04/19/2023] [Indexed: 05/06/2023] Open
Abstract
Methyl salicylate is an important inter- and intra-plant signaling molecule, but is deemed undesirable by humans when it accumulates to high levels in ripe fruits. Balancing the tradeoff between consumer satisfaction and overall plant health is challenging as the mechanisms regulating volatile levels have not yet been fully elucidated. In this study, we investigated the accumulation of methyl salicylate in ripe fruits of tomatoes that belong to the red-fruited clade. We determine the genetic diversity and the interaction of four known loci controlling methyl salicylate levels in ripe fruits. In addition to Non-Smoky Glucosyl Transferase 1 (NSGT1), we uncovered extensive genome structural variation (SV) at the Methylesterase (MES) locus. This locus contains four tandemly duplicated Methylesterase genes and genome sequence investigations at the locus identified nine distinct haplotypes. Based on gene expression and results from biparental crosses, functional and non-functional haplotypes for MES were identified. The combination of the non-functional MES haplotype 2 and the non-functional NSGT1 haplotype IV or V in a GWAS panel showed high methyl salicylate levels in ripe fruits, particularly in accessions from Ecuador, demonstrating a strong interaction between these two loci and suggesting an ecological advantage. The genetic variation at the other two known loci, Salicylic Acid Methyl Transferase 1 (SAMT1) and tomato UDP Glycosyl Transferase 5 (SlUGT5), did not explain volatile variation in the red-fruited tomato germplasm, suggesting a minor role in methyl salicylate production in red-fruited tomato. Lastly, we found that most heirloom and modern tomato accessions carried a functional MES and a non-functional NSGT1 haplotype, ensuring acceptable levels of methyl salicylate in fruits. Yet, future selection of the functional NSGT1 allele could potentially improve flavor in the modern germplasm.
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Affiliation(s)
- Manoj Sapkota
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Lara Pereira
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Yanbing Wang
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Lei Zhang
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Yasin Topcu
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Denise Tieman
- Horticultural Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Esther van der Knaap
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, Georgia, United States of America
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6
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Frick EM, Sapkota M, Pereira L, Wang Y, Hermanns A, Giovannoni JJ, van der Knaap E, Tieman DM, Klee HJ. A family of methyl esterases converts methyl salicylate to salicylic acid in ripening tomato fruit. PLANT PHYSIOLOGY 2023; 191:110-124. [PMID: 36315067 PMCID: PMC9806648 DOI: 10.1093/plphys/kiac509] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Methyl salicylate imparts a potent flavor and aroma described as medicinal and wintergreen that is undesirable in tomato (Solanum lycopersicum) fruit. Plants control the quantities of methyl salicylate through a variety of biosynthetic pathways, including the methylation of salicylic acid to form methyl salicylate and subsequent glycosylation to prevent methyl salicylate emission. Here, we identified a subclade of tomato methyl esterases, SALICYLIC ACID METHYL ESTERASE1-4, responsible for demethylation of methyl salicylate to form salicylic acid in fruits. This family was identified by proximity to a highly significant methyl salicylate genome-wide association study locus on chromosome 2. Genetic mapping studies in a biparental population confirmed a major methyl salicylate locus on chromosome 2. Fruits from SlMES1 knockout lines emitted significantly (P < 0,05, t test) higher amounts of methyl salicylate than wild-type fruits. Double and triple mutants of SlMES2, SlMES3, and SlMES4 emitted even more methyl salicylate than SlMES1 single knockouts-but not at statistically distinguishable levels-compared to the single mutant. Heterologously expressed SlMES1 and SlMES3 acted on methyl salicylate in vitro, with SlMES1 having a higher affinity for methyl salicylate than SlMES3. The SlMES locus has undergone major rearrangement, as demonstrated by genome structure analysis in the parents of the biparental population. Analysis of accessions that produce high or low levels of methyl salicylate showed that SlMES1 and SlMES3 genes expressed the highest in the low methyl salicylate lines. None of the MES genes were appreciably expressed in the high methyl salicylate-producing lines. We concluded that the SlMES gene family encodes tomato methyl esterases that convert methyl salicylate to salicylic acid in ripe tomato fruit. Their ability to decrease methyl salicylate levels by conversion to salicylic acid is an attractive breeding target to lower the level of a negative contributor to flavor.
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Affiliation(s)
- Elizabeth M Frick
- Horticultural Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Manoj Sapkota
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602, USA
- Department of Horticulture, University of Georgia, Athens, Georgia 30602, USA
| | - Lara Pereira
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602, USA
- Department of Horticulture, University of Georgia, Athens, Georgia 30602, USA
| | - Yanbing Wang
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602, USA
- Department of Horticulture, University of Georgia, Athens, Georgia 30602, USA
| | - Anna Hermanns
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - James J Giovannoni
- United States Department of Agriculture-Agricultural Research Service and Boyce Thompson Institute, Cornell University campus, Ithaca, New York 14853, USA
| | - Esther van der Knaap
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia 30602, USA
- Department of Horticulture, University of Georgia, Athens, Georgia 30602, USA
| | - Denise M Tieman
- Horticultural Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Harry J Klee
- Horticultural Sciences, University of Florida, Gainesville, Florida 32611, USA
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7
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Singh J, van der Knaap E. Unintended Consequences of Plant Domestication. PLANT & CELL PHYSIOLOGY 2022; 63:1573-1583. [PMID: 35715986 DOI: 10.1093/pcp/pcac083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/12/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Human selection on wild populations mostly favored a common set of plant traits during domestication. This process of direct selection also altered other independent traits that were not directly perceived or desired during crop domestication and improvement. A deeper knowledge of the inadvertent and undesirable phenotypic effects and their underlying genetic causes can help design strategies to mitigate their effects and improve genetic gain in crop plants. We review different factors explaining the negative consequences of plant domestication at the phenotypic and genomic levels. We further describe the genetic causes of undesirable effects that originate from the selection of favorable alleles during plant domestication. In addition, we propose strategies that could be useful in attenuating such effects for crop improvement. With novel -omics and genome-editing tools, it is relatively approachable to understand and manipulate the genetic and biochemical mechanisms responsible for the undesirable phenotypes in domesticated plants.
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Affiliation(s)
- Jugpreet Singh
- Center for Applied Genetic Technologies, 111 Riverbend Road, University of Georgia, Athens, GA 30602, USA
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, 111 Riverbend Road, University of Georgia, Athens, GA 30602, USA
- Institute for Plant Breeding, Genetics and Genomics, 111 Riverbend Road, University of Georgia, Athens, GA 30602, USA
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
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8
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Wang S, Qiang Q, Xiang L, Fernie AR, Yang J. Targeted approaches to improve tomato fruit taste. HORTICULTURE RESEARCH 2022; 10:uhac229. [PMID: 36643745 PMCID: PMC9832879 DOI: 10.1093/hr/uhac229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/30/2022] [Indexed: 06/17/2023]
Abstract
Tomato (Solanum lycopersicum) is the most valuable fruit and horticultural crop species worldwide. Compared with the fruits of their progenitors, those of modern tomato cultivars are, however, often described as having unsatisfactory taste or lacking flavor. The flavor of a tomato fruit arises from a complex mix of tastes and volatile metabolites, including sugars, acids, amino acids, and various volatiles. However, considerable differences in fruit flavor occur among tomato varieties, resulting in mixed consumer experiences. While tomato breeding has traditionally been driven by the desire for continual increases in yield and the introduction of traits that provide a long shelf-life, consumers are prepared to pay a reasonable premium for taste. Therefore, it is necessary to characterize preferences of tomato flavor and to define its underlying genetic basis. Here, we review recent conceptual and technological advances that have rendered this more feasible, including multi-omics-based QTL and association analyses, along with the use of trained testing panels, and machine learning approaches. This review proposes how the comprehensive datasets compiled to date could allow a precise rational design of tomato germplasm resources with improved organoleptic quality for the future.
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Affiliation(s)
- Shouchuang Wang
- To whom correspondence should be addressed. E-mail: , or . Tel: 86-0898-66184571. Fax number: 0898-66184571
| | | | - Lijun Xiang
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Alisdair R Fernie
- To whom correspondence should be addressed. E-mail: , or . Tel: 86-0898-66184571. Fax number: 0898-66184571
| | - Jun Yang
- To whom correspondence should be addressed. E-mail: , or . Tel: 86-0898-66184571. Fax number: 0898-66184571
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Qing Y, Zheng Y, Mlotshwa S, Smith HN, Wang X, Zhai X, van der Knaap E, Wang Y, Fei Z. Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic changes during tomato domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1536-1550. [PMID: 35514123 DOI: 10.1111/tpj.15798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/23/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, we performed comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions. We demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nucleotide heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nucleotide hc-siRNAs likely contribute to the alteration of mRNA gene expression in cis during tomato domestication, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families. Our data highlight different selection pressures on miRNAs compared to phasiRNAs and 24-nucleotide hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato.
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Affiliation(s)
- You Qing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | | | - Heather N Smith
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA
| | - Xin Wang
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Xuyang Zhai
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Horticulture, University of Georgia, Athens, GA, 30602, USA
| | - Ying Wang
- Department of Molecular Genetics, Ohio State University, Columbus, OH, 43210, USA
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
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10
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Tay Fernandez CG, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. Int J Mol Sci 2022; 23:2671. [PMID: 35269811 PMCID: PMC8910360 DOI: 10.3390/ijms23052671] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia; (C.G.T.F.); (B.J.N.); (M.F.D.); (M.G.); (J.P.); (P.E.B.); (P.M.F.); (J.B.)
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