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Xu F, Chen H, Chen C, Liu J, Song Z, Ding C. The mutagenic effect of cold plasma on Medicago sativa L. Free Radic Biol Med 2024; 223:18-29. [PMID: 39053862 DOI: 10.1016/j.freeradbiomed.2024.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/13/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
To explore the feasibility of using cold plasma as a mutagenesis breeding technology for forage crops, in this study we used the Medicago sativa L. cultivar, Zhongcao No. 3, as the experimental material. The effects of plasma treatments on Medicago sativa L. were analyzed through the use of plasma and activated water. Treatments with plasma and activated water inhibited plant height but promoted root growth. By creating a closed environment, adding a dielectric barrier plate, and combining these two treatment methods, the greatest impact can be had on the growth of Medicago sativa L. seeds. After treatment, the plant heights were approximately half those of the control group, and the root lengths were approximately 1.6 times those of the control group. Through emission spectroscopy, it was found that active particles such as O, NO2, and N2* were present and could be considered to have produced plasma-activated water through contact with the water surface, thus affecting the survival and growth of the seeds. Whole-genome resequencing (WGRS) was performed on the wild-type and selected mutants after treatment, with an average sequencing depth of 115.93×, an average genome alignment rate of 91.72 %, and an average genome coverage rate of 91.85 %. Various types of mutations were detected and annotated. After filtering, 7,822,324 SNP (single nucleotide polymorphisms) sites, 2,161,917 indel sites, 200,544 SV sites, 238 CNV (copy number variation) sites. The SNPs, indels (insertions/deletions), and SVs (structural variations) were mainly heterozygous, with heterozygosity rates of 87.13 %, 92.16 %, and 83.49 %, respectively. The CNVs were dominated by low copy numbers, accounting for 53.77 %. These results indicate that plasma treatment has significant effects on plant growth and genome of Medicago sativa L.
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Affiliation(s)
- Fei Xu
- College of Science, Inner Mongolia University of Technology, Hohhot, 010051, China; Discharge Plasma and Functional Materials Application Laboratory, Inner Mongolia University of Technology, Hohhot, 010051, China
| | - Hao Chen
- College of Science, Inner Mongolia University of Technology, Hohhot, 010051, China; Discharge Plasma and Functional Materials Application Laboratory, Inner Mongolia University of Technology, Hohhot, 010051, China.
| | - Chan Chen
- College of Science, Inner Mongolia University of Technology, Hohhot, 010051, China; Discharge Plasma and Functional Materials Application Laboratory, Inner Mongolia University of Technology, Hohhot, 010051, China
| | - Jiaqi Liu
- College of Science, Inner Mongolia University of Technology, Hohhot, 010051, China; Discharge Plasma and Functional Materials Application Laboratory, Inner Mongolia University of Technology, Hohhot, 010051, China
| | - Zhiqing Song
- College of Science, Inner Mongolia University of Technology, Hohhot, 010051, China; Discharge Plasma and Functional Materials Application Laboratory, Inner Mongolia University of Technology, Hohhot, 010051, China
| | - Changjiang Ding
- College of Science, Inner Mongolia University of Technology, Hohhot, 010051, China; Discharge Plasma and Functional Materials Application Laboratory, Inner Mongolia University of Technology, Hohhot, 010051, China
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2
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Pancaldi F, Gulisano A, Severing EI, van Kaauwen M, Finkers R, Kodde L, Trindade LM. The genome of Lupinus mutabilis: Evolution and genetics of an emerging bio-based crop. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39264984 DOI: 10.1111/tpj.17021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 08/02/2024] [Accepted: 08/23/2024] [Indexed: 09/14/2024]
Abstract
Lupinus mutabilis is an under-domesticated legume species from the Andean region of South America. It belongs to the New World lupins clade, which groups several lupin species displaying large genetic variation and adaptability to highly different environments. L. mutabilis is attracting interest as a potential multipurpose crop to diversify the European supply of plant proteins, increase agricultural biodiversity, and fulfill bio-based applications. This study reports the first high-quality L. mutabilis genome assembly, which is also the first sequenced assembly of a New World lupin species. Through comparative genomics and phylogenetics, the evolution of L. mutabilis within legumes and lupins is described, highlighting both genomic similarities and patterns specific to L. mutabilis, potentially linked to environmental adaptations. Furthermore, the assembly was used to study the genetics underlying important traits for the establishment of L. mutabilis as a novel crop, including protein and quinolizidine alkaloids contents in seeds, genomic patterns of classic resistance genes, and genomic properties of L. mutabilis mycorrhiza-related genes. These analyses pointed out copy number variation, differential genomic gene contexts, and gene family expansion through tandem duplications as likely important drivers of the genomic diversity observed for these traits between L. mutabilis and other lupins and legumes. Overall, the L. mutabilis genome assembly will be a valuable resource to conduct genetic research and enable genomic-based breeding approaches to turn L. mutabilis into a multipurpose legume crop.
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Affiliation(s)
- Francesco Pancaldi
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Agata Gulisano
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Edouard I Severing
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Martijn van Kaauwen
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
- Gennovation B.V, Agro Business Park 10, 6708PW, Wageningen, The Netherlands
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
- Gennovation B.V, Agro Business Park 10, 6708PW, Wageningen, The Netherlands
| | - Linda Kodde
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Luisa M Trindade
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
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Massa AN, Sobolev VS, Faustinelli PC, Tallury SP, Stalker HT, Lamb MC, Arias RS. Genetic diversity, disease resistance, and environmental adaptation of Arachis duranensis L.: New insights from landscape genomics. PLoS One 2024; 19:e0299992. [PMID: 38625995 PMCID: PMC11020403 DOI: 10.1371/journal.pone.0299992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/19/2024] [Indexed: 04/18/2024] Open
Abstract
The genetic diversity that exists in natural populations of Arachis duranensis, the wild diploid donor of the A subgenome of cultivated tetraploid peanut, has the potential to improve crop adaptability, resilience to major pests and diseases, and drought tolerance. Despite its potential value for peanut improvement, limited research has been focused on the association between allelic variation, environmental factors, and response to early (ELS) and late leaf spot (LLS) diseases. The present study implemented a landscape genomics approach to gain a better understanding of the genetic variability of A. duranensis represented in the ex-situ peanut germplasm collection maintained at the U.S. Department of Agriculture, which spans the entire geographic range of the species in its center of origin in South America. A set of 2810 single nucleotide polymorphism (SNP) markers allowed a high-resolution genome-wide characterization of natural populations. The analysis of population structure showed a complex pattern of genetic diversity with five putative groups. The incorporation of bioclimatic variables for genotype-environment associations, using the latent factor mixed model (LFMM2) method, provided insights into the genomic signatures of environmental adaptation, and led to the identification of SNP loci whose allele frequencies were correlated with elevation, temperature, and precipitation-related variables (q < 0.05). The LFMM2 analysis for ELS and LLS detected candidate SNPs and genomic regions on chromosomes A02, A03, A04, A06, and A08. These findings highlight the importance of the application of landscape genomics in ex situ collections of peanut and other crop wild relatives to effectively identify favorable alleles and germplasm for incorporation into breeding programs. We report new sources of A. duranensis germplasm harboring adaptive allelic variation, which have the potential to be utilized in introgression breeding for a single or multiple environmental factors, as well as for resistance to leaf spot diseases.
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Affiliation(s)
- Alicia N. Massa
- National Peanut Research Laboratory, USDA-ARS, Dawson, Georgia, United States of America
| | - Victor S. Sobolev
- National Peanut Research Laboratory, USDA-ARS, Dawson, Georgia, United States of America
| | - Paola C. Faustinelli
- National Peanut Research Laboratory, USDA-ARS, Dawson, Georgia, United States of America
| | - Shyamalrau P. Tallury
- Plant Genetic Resources Conservation Unit, USDA-ARS, Griffin, Georgia, United States of America
| | - H. Thomas Stalker
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Marshall C. Lamb
- National Peanut Research Laboratory, USDA-ARS, Dawson, Georgia, United States of America
| | - Renee S. Arias
- National Peanut Research Laboratory, USDA-ARS, Dawson, Georgia, United States of America
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Lim I, Park YJ, Ha J. Evolutionary and synteny analysis of HIS1, BADH2, GBSS1, and GBSS2 in rice: insights for effective introgression breeding strategies. Sci Rep 2024; 14:5226. [PMID: 38433262 PMCID: PMC10909864 DOI: 10.1038/s41598-024-55581-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024] Open
Abstract
The key genes BADH2, GBSS1, GBSS2, and HIS1 regulate the fragrance, starch synthesis, and herbicide resistance in rice. Although the molecular functions of four genes have been investigated in the Oryza sativa species, little is known regarding their evolutionary history in the Oryza genus. Here, we studied the evolution of four focal genes in 10 Oryza species using phylogenetic and syntenic approaches. The HIS1 family underwent several times of tandem duplication events in the Oryza species, resulting in copy number variation ranging from 2 to 7. At most one copy of BADH2, GBSS1, and GBSS2 orthologs were identified in each Oryza species, and gene loss events of BADH2 and GBSS2 were identified in three Oryza species. Gene transfer analysis proposed that the functional roles of GBSS1 and GBSS2 were developed in the Asian and African regions, respectively, and most allelic variations of BADH2 in japonica rice emerged after the divergence between the Asian and African rice groups. These results provide clues to determine the origin and evolution of the key genes in rice breeding as well as valuable information for molecular breeders and scientists to develop efficient strategies to simultaneously improve grain quality and yield potential in rice.
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Affiliation(s)
- Insu Lim
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea
| | - Yong-Jin Park
- Department of Plant Sciences, Kongju National University, Yesan, 340-702, Korea
| | - Jungmin Ha
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea.
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5
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Deng CH, Naithani S, Kumari S, Cobo-Simón I, Quezada-Rodríguez EH, Skrabisova M, Gladman N, Correll MJ, Sikiru AB, Afuwape OO, Marrano A, Rebollo I, Zhang W, Jung S. Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Database (Oxford) 2023; 2023:baad088. [PMID: 38079567 PMCID: PMC10712715 DOI: 10.1093/database/baad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]
Abstract
Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.
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Affiliation(s)
- Cecilia H Deng
- Molecular and Digital Breeding, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland 1025, New Zealand
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
| | - Irene Cobo-Simón
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Institute of Forest Science (ICIFOR-INIA, CSIC), Madrid, Spain
| | - Elsa H Quezada-Rodríguez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maria Skrabisova
- Department of Biochemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Nick Gladman
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA
| | - Melanie J Correll
- Agricultural and Biological Engineering Department, University of Florida, 1741 Museum Rd, Gainesville, FL 32611, USA
| | | | | | - Annarita Marrano
- Phoenix Bioinformatics, 39899 Balentine Drive, Suite 200, Newark, CA 94560, USA
| | | | - Wentao Zhang
- National Research Council Canada, 110 Gymnasium Pl, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sook Jung
- Department of Horticulture, Washington State University, 303c Plant Sciences Building, Pullman, WA 99164-6414, USA
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Caccialupi G, Milc J, Caradonia F, Nasar MF, Francia E. The Triticeae CBF Gene Cluster-To Frost Resistance and Beyond. Cells 2023; 12:2606. [PMID: 37998341 PMCID: PMC10670769 DOI: 10.3390/cells12222606] [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: 09/26/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
The pivotal role of CBF/DREB1 transcriptional factors in Triticeae crops involved in the abiotic stress response has been highlighted. The CBFs represent an important hub in the ICE-CBF-COR pathway, which is one of the most relevant mechanisms capable of activating the adaptive response to cold and drought in wheat, barley, and rye. Understanding the intricate mechanisms and regulation of the cluster of CBF genes harbored by the homoeologous chromosome group 5 entails significant potential for the genetic improvement of small grain cereals. Triticeae crops seem to share common mechanisms characterized, however, by some peculiar aspects of the response to stress, highlighting a combined landscape of single-nucleotide variants and copy number variation involving CBF members of subgroup IV. Moreover, while chromosome 5 ploidy appears to confer species-specific levels of resistance, an important involvement of the ICE factor might explain the greater tolerance of rye. By unraveling the genetic basis of abiotic stress tolerance, researchers can develop resilient varieties better equipped to withstand extreme environmental conditions. Hence, advancing our knowledge of CBFs and their interactions represents a promising avenue for improving crop resilience and food security.
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Affiliation(s)
- Giovanni Caccialupi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy; (J.M.); (F.C.); (M.F.N.); (E.F.)
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7
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Zhang C, Johnson NA, Hall N, Tian X, Yu Q, Patterson EL. Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica. Nat Commun 2023; 14:4865. [PMID: 37567866 PMCID: PMC10421919 DOI: 10.1038/s41467-023-40407-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Genomic structural variation (SV) has profound effects on organismal evolution; often serving as a source of novel genetic variation. Gene copy number variation (CNV), one type of SV, has repeatedly been associated with adaptive evolution in eukaryotes, especially with environmental stress. Resistance to the widely used herbicide, glyphosate, has evolved through target-site CNV in many weedy plant species, including the economically important grass, Eleusine indica (goosegrass); however, the origin and mechanism of these CNVs remain elusive in many weed species due to limited genetic and genomic resources. To study this CNV in goosegrass, we present high-quality reference genomes for glyphosate-susceptible and -resistant goosegrass lines and fine-assembles of the duplication of glyphosate's target site gene 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). We reveal a unique rearrangement of EPSPS involving chromosome subtelomeres. This discovery adds to the limited knowledge of the importance of subtelomeres as genetic variation generators and provides another unique example for herbicide resistance evolution.
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Affiliation(s)
- Chun Zhang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, P.R. China
| | - Nicholas A Johnson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Nathan Hall
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Xingshan Tian
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, P.R. China.
| | - Qin Yu
- Australian Herbicide Resistance Initiative (AHRI), School of Agriculture and Environment, University of Western Australia (UWA), Perth, Australia.
| | - Eric L Patterson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
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Krug AS, B. M. Drummond E, Van Tassel DL, Warschefsky EJ. The next era of crop domestication starts now. Proc Natl Acad Sci U S A 2023; 120:e2205769120. [PMID: 36972445 PMCID: PMC10083606 DOI: 10.1073/pnas.2205769120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Current food systems are challenged by relying on a few input-intensive, staple crops. The prioritization of yield and the loss of diversity during the recent history of domestication has created contemporary crops and cropping systems that are ecologically unsustainable, vulnerable to climate change, nutrient poor, and socially inequitable. For decades, scientists have proposed diversity as a solution to address these challenges to global food security. Here, we outline the possibilities for a new era of crop domestication, focused on broadening the palette of crop diversity, that engages and benefits the three elements of domestication: crops, ecosystems, and humans. We explore how the suite of tools and technologies at hand can be applied to renew diversity in existing crops, improve underutilized crops, and domesticate new crops to bolster genetic, agroecosystem, and food system diversity. Implementing the new era of domestication requires that researchers, funders, and policymakers boldly invest in basic and translational research. Humans need more diverse food systems in the Anthropocene-the process of domestication can help build them.
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Affiliation(s)
| | - Emily B. M. Drummond
- Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
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Du Y, Wang M, Chen Y, Deng Y, Zhang L, Bai T, Ji M. Occurrence and mechanism of target-site resistance to bensulfuron-methyl in Monochoria korsakowii from China. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 191:105379. [PMID: 36963949 DOI: 10.1016/j.pestbp.2023.105379] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/18/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Monochoria korsakowii is an increasingly significant threat to rice production across China, particularly in Liaoning province. Few studies have reported herbicide resistance in M. korsakowii, and resistance status and mechanisms are poorly understood. Here, thirty field populations of M. korsakowii were collected from 11 rice-growing regions of Liaoning, and 97% of populations had evolved resistance to bensulfuron-methyl (BM), with majority (24 of 28) showing high resistance levels (RI > 10). The first in-depth analysis of molecular features of AHAS1 and AHAS2 in BM-resistant populations showed that four Pro197 mutations (Pro197 to His, Ala, Leu or Ser) in AHAS1 and one mutation (Pro197Ser) in AHAS2 were identified. Notably, novel double Pro197Ser mutations co-occurred in both AHAS1 and AHAS2 in the most resistant line LN-20. Furthermore, resistant mutants were used to investigate the effect of Pro197 mutations on AHAS functionality, binding modes, gene expression and cross-resistance in M. korsakowii. All the detected Pro197 mutations considerably reduced in vitro AHAS sensitivity to BM by weakening hydrogen bonds and hydrophobic interactions in the predicted BM-AHAS complexes, especially the double Pro197Ser mutations. This novel resistance mutation combination slightly impacted the extractable AHAS activity, and increased the affinity and catalytic rate of pyruvate. Also, the AHAS expression level was significantly up-regulated. Moreover, all mutations provided resistance only to other sulfonylureas herbicides but not triazolopyrimidine or pyrimidinyl-benzoates herbicides. In conclusion, bensulfuron-methyl resistance in M. korsakowii was grim in Liaoning, China, and amino acid mutations on AHAS isozymes were the primary resistance mechanism. Double Pro197Ser mutations in both AHAS1 and AHAS2 confer higher herbicide resistance than single mutations in AHAS1. Thus, this work deepens our understanding of resistance status and mechanisms of M. korsakowii.
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Affiliation(s)
- Ying Du
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Minlong Wang
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yan Chen
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Yunyan Deng
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Lulu Zhang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Tianlang Bai
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Mingshan Ji
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
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10
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Xie Y, Nachappa P, Nalam VJ, Pearce S. Genomic and Molecular Characterization of Wheat Streak Mosaic Virus Resistance Locus 2 ( Wsm2) in Common Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:928949. [PMID: 35845691 PMCID: PMC9285007 DOI: 10.3389/fpls.2022.928949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Wheat streak mosaic virus (WSMV) is an economically important viral pathogen that threatens global wheat production, particularly in the Great Plains of the United States. The Wsm2 locus confers resistance to WSMV and has been widely deployed in common wheat varieties adapted to this region. Characterizing the underlying causative genetic variant would contribute to our understanding of viral resistance mechanisms in wheat and aid the development of perfect markers for breeding. In this study, linkage mapping in a doubled-haploid (DH) mapping population confirmed Wsm2 as a major locus conferring WSMV resistance in wheat. The Wsm2 flanking markers were mapped to a 4.0 Mbp region at the distal end of chromosome 3BS containing 142 candidate genes. Eight haplotypes were identified from seventeen wheat genotypes collected from different agroecological zones, indicating that Wsm2 lies in a dynamic region of the genome with extensive structural variation and that it is likely a rare allele in most available genome assemblies of common wheat varieties. Exome sequencing of the variety "Snowmass", which carries Wsm2, revealed several loss-of-function mutations and copy number variants in the 142 candidate genes within the Wsm2 interval. Six of these genes are differentially expressed in "Snowmass" compared to "Antero," a variety lacking Wsm2, including a gene that encodes a nucleotide-binding site leucine-rich repeat (NBS-LRR) type protein with homology to RPM1. A de novo assembly of unmapped RNA-seq reads identified nine transcripts expressed only in "Snowmass," three of which are also induced in response to WSMV inoculation. This study sheds light on the variation underlying Wsm2 and provides a list of candidate genes for subsequent validation.
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Affiliation(s)
- Yucong Xie
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Punya Nachappa
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Vamsi J. Nalam
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
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Pincot DDA, Feldmann MJ, Hardigan MA, Vachev MV, Henry PM, Gordon TR, Bjornson M, Rodriguez A, Cobo N, Famula RA, Cole GS, Coaker GL, Knapp SJ. Novel Fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2121-2145. [PMID: 35583656 PMCID: PMC9205853 DOI: 10.1007/s00122-022-04102-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/11/2022] [Indexed: 05/05/2023]
Abstract
Several Fusarium wilt resistance genes were discovered, genetically and physically mapped, and rapidly deployed via marker-assisted selection to develop cultivars resistant to Fusarium oxysporum f. sp. fragariae, a devastating soil-borne pathogen of strawberry. Fusarium wilt, a soilborne disease caused by Fusarium oxysporum f. sp. fragariae, poses a significant threat to strawberry (Fragaria [Formula: see text] ananassa) production in many parts of the world. This pathogen causes wilting, collapse, and death in susceptible genotypes. We previously identified a dominant gene (FW1) on chromosome 2B that confers resistance to race 1 of the pathogen, and hypothesized that gene-for-gene resistance to Fusarium wilt was widespread in strawberry. To explore this, a genetically diverse collection of heirloom and modern cultivars and octoploid ecotypes were screened for resistance to Fusarium wilt races 1 and 2. Here, we show that resistance to both races is widespread in natural and domesticated populations and that resistance to race 1 is conferred by partially to completely dominant alleles among loci (FW1, FW2, FW3, FW4, and FW5) found on three non-homoeologous chromosomes (1A, 2B, and 6B). The underlying genes have not yet been cloned and functionally characterized; however, plausible candidates were identified that encode pattern recognition receptors or other proteins known to confer gene-for-gene resistance in plants. High-throughput genotyping assays for SNPs in linkage disequilibrium with FW1-FW5 were developed to facilitate marker-assisted selection and accelerate the development of race 1 resistant cultivars. This study laid the foundation for identifying the genes encoded by FW1-FW5, in addition to exploring the genetics of resistance to race 2 and other races of the pathogen, as a precaution to averting a Fusarium wilt pandemic.
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Affiliation(s)
- Dominique D. A. Pincot
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Mitchell J. Feldmann
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Michael A. Hardigan
- Horticultural Crops Research Unit, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR 97331 USA
| | - Mishi V. Vachev
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Peter M. Henry
- United States Department of Agriculture Agricultural Research Service, 1636 East Alisal Street, Salinas, CA 93905 USA
| | - Thomas R. Gordon
- Department of Plant Pathology, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Marta Bjornson
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Alan Rodriguez
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Nicolas Cobo
- Departamento de Producción, Agropecuaria Universidad de La Frontera, Temuco, Chile
| | - Randi A. Famula
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Glenn S. Cole
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Gitta L. Coaker
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
| | - Steven J. Knapp
- Department of Plant Sciences, One Shields Avenue, University of California, Davis, CA 95616 USA
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Li WJ, Wu N, Chen C, Zhao YP, Hou YX. Identification and expression analysis of arabinogalactan protein genes in cotton reveal the function of GhAGP15 in Verticillium dahliae resistance. Gene 2022; 822:146336. [PMID: 35182675 DOI: 10.1016/j.gene.2022.146336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/13/2022] [Accepted: 02/11/2022] [Indexed: 11/04/2022]
Abstract
Verticillium wilt, primarily caused by the fungal pathogen Verticillium dahliae, is a serious disease in cotton. Arabinogalactan proteins (AGPs), a class of hydroxyproline-rich glycoproteins, have been widely implicated in plant growth and environmental adaptation. The purpose of this study is to identify and characterize AGP members in cotton plants and explore their roles in responding to environmental stressors. In total, 65 GhAGP members were identified in upland cotton (Gossypium hirsutum), along with 43, 35, and 37 AGP members that were also identified in G. barbadense, G. arboreum, and G. raimondii, respectively. According to gene structure and protein domains analysis, GhAGP genes in upland cotton are highly conserved. Meanwhile, tandem duplication events have occurred frequently throughout cotton's evolutionary history. Expression analysis showed that GhAGP genes were widely expressed during growth and development and in response to abiotic stressors. Many cis-elements related to hormonal responses and environmental stressors were detected in GhAGP promoter regions. GhAGP genes participate in responding to cold, drought, and salt stress, and were sensitive to ET signaling. Furthermore, the expression level of GhAGP15 was elevated during V. dahliae infection and resistance against V. dahliae in upland cotton was significantly weakened by silencing GhAGP15 using a virus-induced gene silencing (VIGS) approach. Our results further suggest that the function of GhAGP15 in V. dahliae resistance might be involved in regulation of the JA, SA, and reactive oxygen species (ROS) pathways. The comprehensive analysis of AGP genes in cotton performed in this study provides a basic framework for further functional research of these genes.
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Affiliation(s)
- Wen-Jie Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, Zhengzhou 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Na Wu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, Zhengzhou 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Chen Chen
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, Zhengzhou 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yan-Peng Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, Zhengzhou 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yu-Xia Hou
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Henan, Zhengzhou 450001, China; College of Science, China Agricultural University, Beijing 100193, China.
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13
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Canaguier A, Guilbaud R, Denis E, Magdelenat G, Belser C, Istace B, Cruaud C, Wincker P, Le Paslier MC, Faivre-Rampant P, Barbe V. Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection. BMC Genomics 2022; 23:317. [PMID: 35448948 PMCID: PMC9026655 DOI: 10.1186/s12864-022-08499-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 03/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Structural Variations (SVs) are genomic rearrangements derived from duplication, deletion, insertion, inversion, and translocation events. In the past, SVs detection was limited to cytological approaches, then to Next-Generation Sequencing (NGS) short reads and partitioned assemblies. Nowadays, technologies such as DNA long read sequencing and optical mapping have revolutionized the understanding of SVs in genomes, due to the enhancement of the power of SVs detection. This study aims to investigate performance of two techniques, 1) long-read sequencing obtained with the MinION device (Oxford Nanopore Technologies) and 2) optical mapping obtained with Saphyr device (Bionano Genomics) to detect and characterize SVs in the genomes of the two ecotypes of Arabidopsis thaliana, Columbia-0 (Col-0) and Landsberg erecta 1 (Ler-1). RESULTS We described the SVs detected from the alignment of the best ONT assembly and DLE-1 optical maps of A. thaliana Ler-1 against the public reference genome Col-0 TAIR10.1. After filtering (SV > 1 kb), 1184 and 591 Ler-1 SVs were retained from ONT and Bionano technologies respectively. A total of 948 Ler-1 ONT SVs (80.1%) corresponded to 563 Bionano SVs (95.3%) leading to 563 common locations. The specific locations were scrutinized to assess improvement in SV detection by either technology. The ONT SVs were mostly detected near TE and gene features, and resistance genes seemed particularly impacted. CONCLUSIONS Structural variations linked to ONT sequencing error were removed and false positives limited, with high quality Bionano SVs being conserved. When compared with the Col-0 TAIR10.1 reference genome, most of the detected SVs discovered by both technologies were found in the same locations. ONT assembly sequence leads to more specific SVs than Bionano one, the latter being more efficient to characterize large SVs. Even if both technologies are complementary approaches, ONT data appears to be more adapted to large scale populations studies, while Bionano performs better in improving assembly and describing specificity of a genome compared to a reference.
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Affiliation(s)
- Aurélie Canaguier
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000 Evry-Courcouronnes, France
| | - Romane Guilbaud
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000 Evry-Courcouronnes, France
| | - Erwan Denis
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Ghislaine Magdelenat
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Corinne Cruaud
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Marie-Christine Le Paslier
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000 Evry-Courcouronnes, France
| | - Patricia Faivre-Rampant
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000 Evry-Courcouronnes, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Raboanatahiry N, Chao H, He J, Li H, Yin Y, Li M. Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:862363. [PMID: 35360294 PMCID: PMC8963808 DOI: 10.3389/fpls.2022.862363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 06/12/2023]
Abstract
Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.
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Affiliation(s)
- Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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15
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Dolatabadian A, Fernando WGD. Genomic Variations and Mutational Events Associated with Plant-Pathogen Interactions. BIOLOGY 2022; 11:421. [PMID: 35336795 PMCID: PMC8945218 DOI: 10.3390/biology11030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/23/2022]
Abstract
Phytopathologists are actively researching the molecular basis of plant-pathogen interactions. The mechanisms of responses to pathogens have been studied extensively in model crop plant species and natural populations. Today, with the rapid expansion of genomic technologies such as DNA sequencing, transcriptomics, proteomics, and metabolomics, as well as the development of new methods and protocols, data analysis, and bioinformatics, it is now possible to assess the role of genetic variation in plant-microbe interactions and to understand the underlying molecular mechanisms of plant defense and microbe pathogenicity with ever-greater resolution and accuracy. Genetic variation is an important force in evolution that enables organisms to survive in stressful environments. Moreover, understanding the role of genetic variation and mutational events is essential for crop breeders to produce improved cultivars. This review focuses on genetic variations and mutational events associated with plant-pathogen interactions and discusses how these genome compartments enhance plants' and pathogens' evolutionary processes.
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Affiliation(s)
- Aria Dolatabadian
- Department of Plant Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
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16
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Rajendram A, Mostaffa NH, Dumin W, Oke MA, Simarani K, Somasundram C, Razali Z, Rejab NA, Al-Idrus A. Dual activity of Meloidogyne incognita-regulated Musa acuminata Pathogenesis-related-10 (MaPR-10) gene. Gene 2022; 809:146041. [PMID: 34710526 DOI: 10.1016/j.gene.2021.146041] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/24/2021] [Accepted: 10/21/2021] [Indexed: 12/01/2022]
Abstract
Plant immunity to pathogen infections is a dynamic response that involves multiple organelles and defence signalling systems such as hypersensitive response (HR) and systemic acquired resistance (SAR). The latter requires the function of Pathogenesis-related (PR) proteins, a common plant protein family with diverse roles in plant innate immunity. Our previous proteomics study showed that a PR gene (ITC1587_Bchr9_P26466_MUSBA) was differentially regulated during a compatible banana-M. incognita interaction, substantiating the isolation of this gene in the current study. Here, we successfully isolated and characterised Pathogenesis-related-10 (PR10) gene with β-1,3-glucanase and ribonuclease (RNase) activities from two Musa acuminata cultivars (denoted as MaPR10) namely Berangan and Grand Naine (ITC1256). We found that MaPR10 cloned sequences possess glycine-rich loop domain and shared conserved motifs specific to PR10 gene group, confirming its identity as a member of this group. Interestingly, we also found a catalytic domain sequence for glycoside hydrolase family 16 (EXDXXE), unique only to MaPR10 cloned sequences. Two peptide variants closely related to the reference sequence ITC1587_Bchr9_P26466_MUSBA namely MaPR10-BeB5 and MaPR10-GNA5 were overexpressed and purified to test for their functionality. Here, we confirmed that both protein variants possess β-1,3-glucanase and ribonuclease (RNase) activities, and inhibit the growth of Aspergillus fumigatus, a human opportunistic pathogen. To our knowledge, this is the first PR10 plant proteins with such properties to be reported thus far.
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Affiliation(s)
- Arullthevan Rajendram
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Nur Hikmah Mostaffa
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Walftor Dumin
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development, Wanju 55365, Republic of Korea
| | - Mushafau Adebayo Oke
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Khanom Simarani
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Chandran Somasundram
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Zuliana Razali
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Nur Ardiyana Rejab
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Aisyafaznim Al-Idrus
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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17
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Zhang X, Zhu Y, Kremling KAG, Romay MC, Bukowski R, Sun Q, Gao S, Buckler ES, Lu F. Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:273-290. [PMID: 34661697 DOI: 10.1007/s00122-021-03965-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Two read depth methods were jointly used in next-generation sequencing data to identify deletions in maize population. GWAS by deletions were analyzed for gene expression pattern and classical traits, respectively. Many studies have confirmed that structural variation (SV) is pervasive throughout the maize genome. Deletion is one type of SV that may impact gene expression and cause phenotypic changes in quantitative traits. In this study, two read count approaches were used to analyze the deletions in the whole-genome sequencing data of 270 maize inbred lines. A total of 19,754 deletion windows overlapped 12,751 genes, which were unevenly distributed across the genome. The deletions explained population structure well and correlated with genomic features. The deletion proportion of genes was determined to be negatively correlated with its expression. The detection of gene expression quantitative trait loci (eQTL) indicated that local eQTL were fewer but had larger effects than distant ones. The common associated genes were related to basic metabolic processes, whereas unique associated genes with eQTL played a role in the stress or stimulus responses in multiple tissues. Compared with the eQTL detected by SNPs derived from the same sequencing data, 89.4% of the associated genes could be detected by both markers. The effect of top eQTL detected by SNPs was usually larger than that detected by deletions for the same gene. A genome-wide association study (GWAS) on flowering time and plant height illustrated that only a few loci could be consistently captured by SNPs, suggesting that combining deletion and SNP for GWAS was an excellent strategy to dissect trait architecture. Our findings will provide insights into characteristic and biological function of genome-wide deletions in maize.
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Affiliation(s)
- Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China.
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA.
| | - Yonghui Zhu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Karl A G Kremling
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
| | - Robert Bukowski
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Qi Sun
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Shibin Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
- USDA-ARS, R. W. Holley Center, Cornell University, Ithaca, NY, USA
| | - Fei Lu
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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18
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Yu J, Hulse-Kemp AM, Babiker E, Staton M. High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii). HORTICULTURE RESEARCH 2021; 8:228. [PMID: 34719668 PMCID: PMC8558335 DOI: 10.1038/s41438-021-00641-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/22/2021] [Accepted: 07/13/2021] [Indexed: 05/07/2023]
Abstract
Vaccinium darrowii Camp (2n = 2x = 24) is a native North American blueberry species and an important source of traits such as low chill requirement in commercial southern highbush blueberry breeding (Vaccinium corymbosum, 2n = 4x = 48). We present a chromosomal-scale genome of V. darrowii generated by the combination of PacBio sequencing and high throughput chromatin conformation capture (Hi-C) scaffolding technologies, yielding a total length of 1.06 Gigabases (Gb). Over 97.8% of the genome sequences are scaffolded into 24 chromosomes representing the two haplotypes. The primary haplotype assembly of V. darrowii contains 34,809 protein-coding genes. Comparison to a V. corymbosum haplotype assembly reveals high collinearity between the two genomes with small intrachromosomal rearrangements in eight chromosome pairs. With small RNA sequencing, the annotation was further expanded to include more than 200,000 small RNA loci and 638 microRNAs expressed in berry tissues. Transcriptome analysis across fruit development stages indicates that genes involved in photosynthesis are downregulated, while genes involved in flavonoid and anthocyanin biosynthesis are significantly increased at the late stage of berry ripening. A high-quality reference genome and accompanying annotation of V. darrowii is a significant new resource for assessing the evergreen blueberry contribution to the breeding of southern highbush blueberries.
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Affiliation(s)
- Jiali Yu
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, 37996, USA
| | - Amanda M Hulse-Kemp
- USDA-ARS Genomics and Bioinformatics Research Unit, Raleigh, NC, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA
| | - Ebrahiem Babiker
- USDA-ARS Thad Cochran Southern Horticultural Laboratory, Poplarville, MS, USA.
| | - Margaret Staton
- Genome Science and Technology Program, University of Tennessee, Knoxville, TN, 37996, USA.
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
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19
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Yuan Y, Bayer PE, Batley J, Edwards D. Current status of structural variation studies in plants. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2153-2163. [PMID: 34101329 PMCID: PMC8541774 DOI: 10.1111/pbi.13646] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 05/23/2023]
Abstract
Structural variations (SVs) including gene presence/absence variations and copy number variations are a common feature of genomes in plants and, together with single nucleotide polymorphisms and epigenetic differences, are responsible for the heritable phenotypic diversity observed within and between species. Understanding the contribution of SVs to plant phenotypic variation is important for plant breeders to assist in producing improved varieties. The low resolution of early genetic technologies and inefficient methods have previously limited our understanding of SVs in plants. However, with the rapid expansion in genomic technologies, it is possible to assess SVs with an ever-greater resolution and accuracy. Here, we review the current status of SV studies in plants, examine the roles that SVs play in phenotypic traits, compare current technologies and assess future challenges for SV studies.
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Affiliation(s)
- Yuxuan Yuan
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
- School of Life Sciences and State Key Laboratory for AgrobiotechnologyThe Chinese University of Hong KongHong Kong SARChina
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
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20
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Yakimowski SB, Teitel Z, Caruso CM. Defence by duplication: The relation between phenotypic glyphosate resistance and EPSPS gene copy number variation in Amaranthus palmeri. Mol Ecol 2021; 30:5328-5342. [PMID: 34662479 DOI: 10.1111/mec.16231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 12/12/2022]
Abstract
Gene copy number variation (CNV) has been increasingly associated with organismal responses to environmental stress, but we know little about the quantitative relation between CNV and phenotypic variation. In this study we quantify the relation between variation in EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) copy number using digital drop PCR and variation in phenotypic glyphosate resistance in 22 populations of Amaranthus palmeri (Palmer Amaranth), a range-expanding agricultural weed. Overall, we detected a significant positive relation between population mean copy number and resistance. The majority of populations exhibited high glyphosate resistance yet maintained low-resistance individuals, resulting in bimodality in many populations. We also investigated threshold models for the relation between copy number and resistance, and found evidence for a threshold of ~15 EPSPS copies: there was a steep increase in resistance below the threshold, followed by a much shallower increase. Across 924 individuals, as copy number increased the range of variation in resistance decreased, yielding an increasing frequency of high phenotypic resistance individuals. Among populations we detected a decline in variation (s.d.) as mean phenotypic resistance increased from moderate to high, consistent with the prediction that as phenotypic resistance increases in populations, stabilizing selection decreases variation in the trait. Our study demonstrates that populations of A. palmeri can harbour wide variation in EPSPS copy number and phenotypic glyphosate resistance, reflecting the history of, and template for future, resistance evolution.
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Affiliation(s)
| | - Zachary Teitel
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Christina M Caruso
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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21
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Trick AY, Chen FE, Schares JA, Freml BE, Lor P, Yun Y, Wang TH. High resolution estimates of relative gene abundance with quantitative ratiometric regression PCR (qRR-PCR). Analyst 2021; 146:6463-6469. [PMID: 34605831 PMCID: PMC8627783 DOI: 10.1039/d1an01397a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Quantification of the relative abundance of genetic traits has broad applications for biomarker discovery, diagnostics, and assessing gene expression in biological research. Relative quantification of genes is traditionally done with the 2-ΔΔCT method using quantitative real-time polymerase chain reaction (qPCR) data, which is often limited in resolution beyond orders of magnitude difference. The latest techniques for quantification of nucleic acids employ digital PCR or microarrays which involve lengthy sample preparation and complex instrumentation. In this work, we describe a quantitative ratiometric regression PCR (qRR-PCR) method for computing relative abundance of genetic traits in a sample with high resolution from a single duplexed real-time quantitative PCR assay. Instead of comparing the individual cycle threshold (Ct) values as is done for the 2-ΔΔCT method, our qRR-PCR algorithm leverages the innate relationship of co-amplified PCR targets to measure their relative quantities using characteristic curves derived from the normalized ratios of qPCR fluorescence curves. We demonstrate the utility of this technique for discriminating the fractional abundance of mixed alleles with resolution below 5%.
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Affiliation(s)
- Alexander Y Trick
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | | | | | - Pa Lor
- Corteva Agriscience, Johnston, IA 50131, USA
| | - Yue Yun
- Corteva Agriscience, Johnston, IA 50131, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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22
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Cheng YH, Liu CFJ, Yu YH, Jhou YT, Fujishima M, Tsai IJ, Leu JY. Genome plasticity in Paramecium bursaria revealed by population genomics. BMC Biol 2020; 18:180. [PMID: 33250052 PMCID: PMC7702705 DOI: 10.1186/s12915-020-00912-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 10/29/2020] [Indexed: 11/25/2022] Open
Abstract
Background Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains of Paramecium bursaria, a highly divergent species of the genus Paramecium which can stably establish endosymbioses with green algae. Results We assembled a high-quality macronuclear genome of P. bursaria and further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways. Conclusions We report programmed DNA rearrangements in the P. bursaria macronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments. Supplementary information The online version contains supplementary material available at 10.1186/s12915-020-00912-2.
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Affiliation(s)
- Yu-Hsuan Cheng
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan.,Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Chien-Fu Jeff Liu
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Yen-Hsin Yu
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Yu-Ting Jhou
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Masahiro Fujishima
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8512, Japan
| | - Isheng Jason Tsai
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Jun-Yi Leu
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan. .,Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
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23
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Islam MS, Coronejo S, Subudhi PK. Whole-genome sequencing reveals uniqueness of black-hulled and straw-hulled weedy rice genomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2461-2475. [PMID: 32488303 DOI: 10.1007/s00122-020-03611-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/13/2020] [Indexed: 05/22/2023]
Abstract
Both SH and BHA weedy rice genotypes evolved independently and have distinct genomic composition. Different genetic mechanisms may be responsible for their competitiveness and adaptation to diverse environmental conditions. Two major types of weedy rice are recognized in the USA based on morphology: straw-hull (SH) and black-hull awned (BHA) weedy rice. We performed whole-genome resequencing of a SH weedy rice 'PSRR-1', a BHA weedy rice 'BHA1115', and a japonica cultivar 'Cypress' to delineate genome-wide differences and their relevance to genetics and evolution of weedy attributes. The high-quality reads were uniformly distributed with 82-88% genome coverage. The number of genotype-specific SNPs and InDels was highest in Cypress, followed by BHA1115 and PSRR-1. However, more genes were affected in BHA1115 compared with other two genotypes which is evident from the number of high-impact SNPs and InDels. Haplotype analysis of selected genes involved in domestication, adaptation, and agronomic performance not only differentiated SH from BHA weedy rice and supported evolution of weedy rice through de-domestication, but also validated the function of several genes such as qAn-1, qAn-2, Bh4, Rc, SD1, OsLG1, and OsC1. Several candidate genes were identified for previously reported seed dormancy and seed shattering QTLs. The SH and BHA weedy rice have distinct genomic composition, and the BHA weedy rice likely diverged earlier than SH weedy rice. The accumulation of plant development, reproduction, and defense-related genes in weedy rice possibly helped them to compete, survive, and spread under a wide range of environmental conditions by employing novel and diverse mechanisms. The genomic resources will be useful for both weed management and rice improvement by exploring the molecular basis of key agronomic, adaptive, and domestication attributes.
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Affiliation(s)
- Md Shofiqul Islam
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Sapphire Coronejo
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Prasanta Kumar Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
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24
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Mareri L, Milc J, Laviano L, Buti M, Vautrin S, Cauet S, Mascagni F, Natali L, Cavallini A, Bergès H, Pecchioni N, Francia E. Influence of CNV on transcript levels of HvCBF genes at Fr-H2 locus revealed by resequencing in resistant barley cv. 'Nure' and expression analysis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110305. [PMID: 31779917 DOI: 10.1016/j.plantsci.2019.110305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/18/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Resequencing in resistant cultivar 'Nure' and structural comparison with the same region of susceptible 'Morex' was performed in order to gain a better insight into barley Frost-resistance-H2 locus. Accurate annotation showed copy number variation (CNV) in the proximal part of the locus. In 'Nure', two exact copies of the HvCBF4-HvCBF2A region and one of the HvCBF4-HvCBF2B segment were observed, while in 'Morex' the corresponding region harboured a single HvCBF4-HvCBF2A (22 kb) segment. Abundance and diversity of repetitive element classes, gene function gain/losses, regulatory motifs and SNPs in gene sequences were identified. An expression study of key HvCBFs with/without CNV on selected genotypes contrasting for frost resistance and estimated HvCBF4-HvCBF2B copy number (2-10 copies) was also performed. Under light stimulus at warm temperature (23 °C), CNV of HvCBF2A and HvCBF4 correlated with their expression levels and reported frost resistance of genotypes; moreover, expression levels of HvCBF2A and HvCBF14 were strongly correlated (r = 0.908, p < 0.01). On the other hand, frost resistance correlated to HvCBF14 expression (r = 0.871, p < 0.01) only after cold induction (6°C) in the dark. A complex interplay of HvCBFs expression levels under different light/temperature stimuli is discussed in light of CNV and presence/number of regulatory elements that integrate different signal transduction pathways.
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Affiliation(s)
- Lavinia Mareri
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Justyna Milc
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Luca Laviano
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Matteo Buti
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Sonia Vautrin
- Centre National de Ressources Génomiques Végétales (CNRGV), Chemin de Borde Rouge 24-Auzeville CS 52627, Castanet Tolosan Cedex, F-31326, France
| | - Stéphane Cauet
- Centre National de Ressources Génomiques Végétales (CNRGV), Chemin de Borde Rouge 24-Auzeville CS 52627, Castanet Tolosan Cedex, F-31326, France
| | - Flavia Mascagni
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, via del Borghetto 80, Pisa, I-56124, Italy
| | - Lucia Natali
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, via del Borghetto 80, Pisa, I-56124, Italy
| | - Andrea Cavallini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, via del Borghetto 80, Pisa, I-56124, Italy
| | - Hélène Bergès
- Centre National de Ressources Génomiques Végétales (CNRGV), Chemin de Borde Rouge 24-Auzeville CS 52627, Castanet Tolosan Cedex, F-31326, France
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops (CREA-CI), S.S. 673, Km 25,200, Foggia, I-71122, Italy; Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy
| | - Enrico Francia
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, Reggio Emilia, I-42122, Italy.
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25
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Golicz AA, Bayer PE, Bhalla PL, Batley J, Edwards D. Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications. Trends Genet 2019; 36:132-145. [PMID: 31882191 DOI: 10.1016/j.tig.2019.11.006] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/09/2019] [Accepted: 11/12/2019] [Indexed: 02/01/2023]
Abstract
The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single individual; the sequence can be core, present in all individuals, or accessory (variable or dispensable), found in a subset of individuals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely stemming from divergent evolutionary histories, but also surprising similarities.
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Affiliation(s)
- Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, Australia.
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia.
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26
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Wilkinson SW, Magerøy MH, López Sánchez A, Smith LM, Furci L, Cotton TEA, Krokene P, Ton J. Surviving in a Hostile World: Plant Strategies to Resist Pests and Diseases. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:505-529. [PMID: 31470772 DOI: 10.1146/annurev-phyto-082718-095959] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
As primary producers, plants are under constant pressure to defend themselves against potentially deadly pathogens and herbivores. In this review, we describe short- and long-term strategies that enable plants to cope with these stresses. Apart from internal immunological strategies that involve physiological and (epi)genetic modifications at the cellular level, plants also employ external strategies that rely on recruitment of beneficial organisms. We discuss these strategies along a gradient of increasing timescales, ranging from rapid immune responses that are initiated within seconds to (epi)genetic adaptations that occur over multiple plant generations. We cover the latest insights into the mechanistic and evolutionary underpinnings of these strategies and present explanatory models. Finally, we discuss how knowledge from short-lived model species can be translated to economically and ecologically important perennials to exploit adaptive plant strategies and mitigate future impacts of pests and diseases in an increasingly interconnected and changing world.
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Affiliation(s)
- Samuel W Wilkinson
- Plant Production and Protection Institute and Department of Animal and Plant Sciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom;
- Department of Molecular Plant Biology, Division for Biotechnology and Plant Health, Norwegian Institute for Bioeconomy Research, 1431 Ås, Norway
| | - Melissa H Magerøy
- Department of Molecular Plant Biology, Division for Biotechnology and Plant Health, Norwegian Institute for Bioeconomy Research, 1431 Ås, Norway
| | - Ana López Sánchez
- Plant Production and Protection Institute and Department of Animal and Plant Sciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom;
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Campus de Cantoblanco, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lisa M Smith
- Plant Production and Protection Institute and Department of Animal and Plant Sciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom;
| | - Leonardo Furci
- Plant Production and Protection Institute and Department of Animal and Plant Sciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom;
| | - T E Anne Cotton
- Plant Production and Protection Institute and Department of Animal and Plant Sciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom;
| | - Paal Krokene
- Department of Molecular Plant Biology, Division for Biotechnology and Plant Health, Norwegian Institute for Bioeconomy Research, 1431 Ås, Norway
| | - Jurriaan Ton
- Plant Production and Protection Institute and Department of Animal and Plant Sciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom;
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27
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Mwathi MW, Schiessl SV, Batley J, Mason AS. "Doubled-haploid" allohexaploid Brassica lines lose fertility and viability and accumulate genetic variation due to genomic instability. Chromosoma 2019; 128:521-532. [PMID: 31377850 DOI: 10.1007/s00412-019-00720-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 01/01/2023]
Abstract
Microspore culture stimulates immature pollen grains to develop into plants via tissue culture and is used routinely in many crop species to produce "doubled haploids": homozygous, true-breeding lines. However, microspore culture is also often used on material that does not have stable meiosis, such as interspecific hybrids. In this case, the resulting progeny may lose their "doubled haploid" homozygous status as a result of chromosome missegregation and homoeologous exchanges. However, little is known about the frequency of these effects. We assessed fertility, meiosis and genetic variability in self-pollinated progeny sets (the MDL2 population) resulting from first-generation plants (the MDL1 population) derived from microspores of a near-allohexaploid interspecific hybrid from the cross (Brassica napus × B. carinata) × B. juncea. Allelic inheritance and copy number variation were predicted using single nucleotide polymorphism marker data from the Illumina Infinium 60K Brassica array. Seed fertility and viability decreased substantially from the MDL1 to the MDL2 generation. In the MDL2 population, 87% of individuals differed genetically from their MDL1 parent. These genetic differences resulted from novel homoeologous exchanges between chromosomes, chromosome loss and gain, and segregation and instability of pre-existing karyotype abnormalities. Novel karyotype change was extremely common, with 2.2 new variants observed per MDL2 individual. Significant differences between progeny sets in the number of novel genetic variants were also observed. Meiotic instability clearly has the potential to dramatically change karyotypes (often without detectable effects on the presence or absence of alleles) in putatively homozygous, microspore-derived lines, resulting in loss of fertility and viability.
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Affiliation(s)
- Margaret W Mwathi
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,School of Biological Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Sarah V Schiessl
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,School of Biological Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Annaliese S Mason
- Department of Plant Breeding, Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
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28
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Würschum T, Rapp M, Miedaner T, Longin CFH, Leiser WL. Copy number variation of Ppd-B1 is the major determinant of heading time in durum wheat. BMC Genet 2019; 20:64. [PMID: 31357926 PMCID: PMC6664704 DOI: 10.1186/s12863-019-0768-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/17/2019] [Indexed: 11/13/2022] Open
Abstract
Background Heading time is an important adaptive trait in durum wheat. In hexaploid wheat, Photoperiod-1 (Ppd) loci are essential regulators of heading time, with Ppd-B1 conferring photoperiod insensitivity through copy number variations (CNV). In tetraploid wheat, the D-genome Ppd-D1 locus is absent and generally, our knowledge on the genetic architecture underlying heading time lacks behind that of bread wheat. Results In this study, we employed a panel of 328 diverse European durum genotypes that were evaluated for heading time at five environments. Genome-wide association mapping identified six putative QTL, with a major QTL on chromosome 2B explaining 26.2% of the genotypic variance. This QTL was shown to correspond to copy number variation at Ppd-B1, for which two copy number variants appear to be present. The higher copy number confers earlier heading and was more frequent in the heat and drought prone countries of lower latitude. In addition, two other QTL, corresponding to Vrn-B3 (TaFT) and Ppd-A1, were found to explain 9.5 and 5.3% of the genotypic variance, respectively. Conclusions Our results revealed the yet unknown role of copy number variation of Ppd-B1 as the major source underlying the variation in heading time in European durum wheat. The observed geographic patterns underline the adaptive value of this polymorphism and suggest that it is already used in durum breeding to tailor cultivars to specific target environments. In a broader context our findings provide further support for a more widespread role of copy number variation in mediating abiotic and biotic stress tolerance in plants. Electronic supplementary material The online version of this article (10.1186/s12863-019-0768-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Würschum
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany.
| | - Matthias Rapp
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
| | - Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
| | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
| | - Willmar L Leiser
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
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29
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Lye ZN, Purugganan MD. Copy Number Variation in Domestication. TRENDS IN PLANT SCIENCE 2019; 24:352-365. [PMID: 30745056 DOI: 10.1016/j.tplants.2019.01.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 05/22/2023]
Abstract
Domesticated plants have long served as excellent models for studying evolution. Many genes and mutations underlying important domestication traits have been identified, and most causal mutations appear to be SNPs. Copy number variation (CNV) is an important source of genetic variation that has been largely neglected in studies of domestication. Ongoing work demonstrates the importance of CNVs as a source of genetic variation during domestication, and during the diversification of domesticated taxa. Here, we review how CNVs contribute to evolutionary processes underlying domestication, and review examples of domestication traits caused by CNVs. We draw from examples in plant species, but also highlight cases in animal systems that could illuminate the roles of CNVs in the domestication process.
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Affiliation(s)
- Zoe N Lye
- Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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30
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Xie M, Chung CYL, Li MW, Wong FL, Wang X, Liu A, Wang Z, Leung AKY, Wong TH, Tong SW, Xiao Z, Fan K, Ng MS, Qi X, Yang L, Deng T, He L, Chen L, Fu A, Ding Q, He J, Chung G, Isobe S, Tanabata T, Valliyodan B, Nguyen HT, Cannon SB, Foyer CH, Chan TF, Lam HM. A reference-grade wild soybean genome. Nat Commun 2019; 10:1216. [PMID: 30872580 PMCID: PMC6418295 DOI: 10.1038/s41467-019-09142-9] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/22/2019] [Indexed: 01/01/2023] Open
Abstract
Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs.
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Affiliation(s)
- Min Xie
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Claire Yik-Lok Chung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Man-Wah Li
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Fuk-Ling Wong
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Xin Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Ailin Liu
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Zhili Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Alden King-Yung Leung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Tin-Hang Wong
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Suk-Wah Tong
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Zhixia Xiao
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Kejing Fan
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Ming-Sin Ng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Xinpeng Qi
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Linfeng Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Tianquan Deng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Lijuan He
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Lu Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Aisi Fu
- Wuhan Institute of Biotechnology, Wuhan, 430075, Hubei, China
| | - Qiong Ding
- Wuhan Institute of Biotechnology, Wuhan, 430075, Hubei, China
| | - Junxian He
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Gwangju, 550-749, Jeonnam, South Korea
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, 292-0818, Chiba, Japan
| | - Takanari Tanabata
- Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, 292-0818, Chiba, Japan
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, 65211, USA
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, 65211, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Ames, Iowa, 50011-4014, USA
| | - Christine H Foyer
- Faculty of Biological Sciences, Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, Yorkshire, UK
| | - Ting-Fung Chan
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.
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Lyra DH, Galli G, Alves FC, Granato ÍSC, Vidotti MS, Bandeira E Sousa M, Morosini JS, Crossa J, Fritsche-Neto R. Modeling copy number variation in the genomic prediction of maize hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:273-288. [PMID: 30382311 DOI: 10.1007/s00122-018-3215-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 10/20/2018] [Indexed: 06/08/2023]
Abstract
Our study indicates that copy variants may play an essential role in the phenotypic variation of complex traits in maize hybrids. Moreover, predicting hybrid phenotypes by combining additive-dominance effects with copy variants has the potential to be a viable predictive model. Non-additive effects resulting from the actions of multiple loci may influence trait variation in single-cross hybrids. In addition, complementation of allelic variation could be a valuable contributor to hybrid genetic variation, especially when crossing inbred lines with higher contents of copy gains. With this in mind, we aimed (1) to study the association between copy number variation (CNV) and hybrid phenotype, and (2) to compare the predictive ability (PA) of additive and additive-dominance genomic best linear unbiased prediction model when combined with the effects of CNV in two datasets of maize hybrids (USP and HELIX). In the USP dataset, we observed a significant negative phenotypic correlation of low magnitude between copy number loss and plant height, revealing a tendency that more copy losses lead to lower plants. In the same set, when CNV was combined with the additive plus dominance effects, the PA significantly increased only for plant height under low nitrogen. In this case, CNV effects explicitly capture relatedness between individuals and add extra information to the model. In the HELIX dataset, we observed a pronounced difference in PA between additive (0.50) and additive-dominance (0.71) models for predicting grain yield, suggesting a significant contribution of dominance. We conclude that copy variants may play an essential role in the phenotypic variation of complex traits in maize hybrids, although the inclusion of CNVs into datasets does not return significant gains concerning PA.
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Affiliation(s)
- Danilo Hottis Lyra
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil.
- Department of Computational and Analytical Sciences, Rothamsted Research, West Common, Harpenden, AL52JQ, UK.
| | - Giovanni Galli
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Filipe Couto Alves
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Ítalo Stefanine Correia Granato
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Miriam Suzane Vidotti
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Massaine Bandeira E Sousa
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - Júlia Silva Morosini
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
| | - José Crossa
- Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), 06600, Texcoco, D.F, Mexico
| | - Roberto Fritsche-Neto
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, São Paulo, Brazil
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32
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Nelson TC, Monnahan PJ, McIntosh MK, Anderson K, MacArthur-Waltz E, Finseth FR, Kelly JK, Fishman L. Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers. Mol Ecol 2018; 28:1460-1475. [PMID: 30346101 DOI: 10.1111/mec.14904] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/03/2018] [Accepted: 10/08/2018] [Indexed: 12/15/2022]
Abstract
Copy number variation (CNV) is a major part of the genetic diversity segregating within populations, but remains poorly understood relative to single nucleotide variation. Here, we report on a tRNA ligase gene (Migut.N02091; RLG1a) exhibiting unprecedented, and fitness-relevant, CNV within an annual population of the yellow monkeyflower Mimulus guttatus. RLG1a variation was associated with multiple traits in pooled population sequencing (PoolSeq) scans of phenotypic and phenological cohorts. Resequencing of inbred lines revealed intermediate-frequency three-copy variants of RLG1a (trip+; 5/35 = 14%), and trip+ lines exhibited elevated RLG1a expression under multiple conditions. trip+ carriers, in addition to being over-represented in late-flowering and large-flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment (p < 0.05). In wild population samples, we discovered an additional rare RLG1a variant (high+) that carries 250-300 copies of RLG1a totalling ~5.7 Mb (20-40% of a chromosome). In the progeny of a high+ carrier, Mendelian segregation of diagnostic alleles and qPCR-based copy counts indicate that high+ is a single tandem array unlinked to the single-copy RLG1a locus. In the wild, high+ carriers had highest fitness in two particularly dry and/or hot years (2015 and 2017; both p < 0.01), while single-copy individuals were twice as fecund as either CNV type in a lush year (2016: p < 0.005). Our results demonstrate fluctuating selection on CNVs affecting phenological traits in a wild population, suggest that plant tRNA ligases mediate stress-responsive life-history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.
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Affiliation(s)
- Thomas C Nelson
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | - Patrick J Monnahan
- Department of Ecology and Evolution, University of Kansas, Lawrence, Kansas
| | - Mariah K McIntosh
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | - Kayli Anderson
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | | | - Findley R Finseth
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | - John K Kelly
- Department of Ecology and Evolution, University of Kansas, Lawrence, Kansas
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana
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Gabur I, Chawla HS, Liu X, Kumar V, Faure S, von Tiedemann A, Jestin C, Dryzska E, Volkmann S, Breuer F, Delourme R, Snowdon R, Obermeier C. Finding invisible quantitative trait loci with missing data. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:2102-2112. [PMID: 29729219 PMCID: PMC6230954 DOI: 10.1111/pbi.12942] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/26/2018] [Accepted: 04/28/2018] [Indexed: 05/21/2023]
Abstract
Evolutionary processes during plant polyploidization and speciation have led to extensive presence-absence variation (PAV) in crop genomes, and there is increasing evidence that PAV associates with important traits. Today, high-resolution genetic analysis in major crops frequently implements simple, cost-effective, high-throughput genotyping from single nucleotide polymorphism (SNP) hybridization arrays; however, these are normally not designed to distinguish PAV from failed SNP calls caused by hybridization artefacts. Here, we describe a strategy to recover valuable information from single nucleotide absence polymorphisms (SNaPs) by population-based quality filtering of SNP hybridization data to distinguish patterns associated with genuine deletions from those caused by technical failures. We reveal that including SNaPs in genetic analyses elucidate segregation of small to large-scale structural variants in nested association mapping populations of oilseed rape (Brassica napus), a recent polyploid crop with widespread structural variation. Including SNaP markers in genomewide association studies identified numerous quantitative trait loci, invisible using SNP markers alone, for resistance to two major fungal diseases of oilseed rape, Sclerotinia stem rot and blackleg disease. Our results indicate that PAV has a strong influence on quantitative disease resistance in B. napus and that SNaP analysis using cost-effective SNP array data can provide extensive added value from 'missing data'. This strategy might also be applicable for improving the precision of genetic mapping in many important crop species.
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Affiliation(s)
- Iulian Gabur
- Department of Plant BreedingJustus Liebig UniversityGiessenGermany
| | | | - Xiwei Liu
- Department of Plant BreedingJustus Liebig UniversityGiessenGermany
| | - Vinod Kumar
- IGEPP, INRA, AGROCAMPUS OUESTUniv RennesLe RheuFrance
| | | | - Andreas von Tiedemann
- Section of General Plant Pathology and Crop ProtectionGeorg August UniversityGöttingenGermany
| | | | | | | | | | | | - Rod Snowdon
- Department of Plant BreedingJustus Liebig UniversityGiessenGermany
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Lauer S, Avecilla G, Spealman P, Sethia G, Brandt N, Levy SF, Gresham D. Single-cell copy number variant detection reveals the dynamics and diversity of adaptation. PLoS Biol 2018; 16:e3000069. [PMID: 30562346 PMCID: PMC6298651 DOI: 10.1371/journal.pbio.3000069] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022] Open
Abstract
Copy number variants (CNVs) are a pervasive source of genetic variation and evolutionary potential, but the dynamics and diversity of CNVs within evolving populations remain unclear. Long-term evolution experiments in chemostats provide an ideal system for studying the molecular processes underlying CNV formation and the temporal dynamics with which they are generated, selected, and maintained. Here, we developed a fluorescent CNV reporter to detect de novo gene amplifications and deletions in individual cells. We used the CNV reporter in Saccharomyces cerevisiae to study CNV formation at the GAP1 locus, which encodes the general amino acid permease, in different nutrient-limited chemostat conditions. We find that under strong selection, GAP1 CNVs are repeatedly generated and selected during the early stages of adaptive evolution, resulting in predictable dynamics. Molecular characterization of CNV-containing lineages shows that the CNV reporter detects different classes of CNVs, including aneuploidies, nonreciprocal translocations, tandem duplications, and complex CNVs. Despite GAP1's proximity to repeat sequences that facilitate intrachromosomal recombination, breakpoint analysis revealed that short inverted repeat sequences mediate formation of at least 50% of GAP1 CNVs. Inverted repeat sequences are also found at breakpoints at the DUR3 locus, where CNVs are selected in urea-limited chemostats. Analysis of 28 CNV breakpoints indicates that inverted repeats are typically 8 nucleotides in length and separated by 40 bases. The features of these CNVs are consistent with origin-dependent inverted-repeat amplification (ODIRA), suggesting that replication-based mechanisms of CNV formation may be a common source of gene amplification. We combined the CNV reporter with barcode lineage tracking and found that 102-104 independent CNV-containing lineages initially compete within populations, resulting in extreme clonal interference. However, only a small number (18-21) of CNV lineages ever constitute more than 1% of the CNV subpopulation, and as selection progresses, the diversity of CNV lineages declines. Our study introduces a novel means of studying CNVs in heterogeneous cell populations and provides insight into their dynamics, diversity, and formation mechanisms in the context of adaptive evolution.
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Affiliation(s)
- Stephanie Lauer
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Biology, New York University, New York, New York, United States of America
| | - Grace Avecilla
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Biology, New York University, New York, New York, United States of America
| | - Pieter Spealman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Biology, New York University, New York, New York, United States of America
| | - Gunjan Sethia
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Biology, New York University, New York, New York, United States of America
| | - Nathan Brandt
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Biology, New York University, New York, New York, United States of America
| | - Sasha F. Levy
- Joint Initiative for Metrology in Biology, National Institute of Standards and Technology, Stanford University, Stanford, California, United States of America
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Department of Biology, New York University, New York, New York, United States of America
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35
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Foster TM, Aranzana MJ. Attention sports fans! The far-reaching contributions of bud sport mutants to horticulture and plant biology. HORTICULTURE RESEARCH 2018; 5:44. [PMID: 30038785 PMCID: PMC6046048 DOI: 10.1038/s41438-018-0062-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/06/2018] [Indexed: 05/08/2023]
Abstract
A bud sport is a lateral shoot, inflorescence or single flower/fruit with a visibly different phenotype from the rest of the plant. The new phenotype is often caused by a stable somatic mutation in a single cell that is passed on to its clonal descendants and eventually populates part or all of a meristem. In many cases, a bud sport can be vegetatively propagated, thereby preserving the novel phenotype without sexual reproduction. Bud sports provide new characteristics while retaining the desirable qualities of the parent plant, which is why many bud sports have been developed into popular cultivars. We present an overview of the history of bud sports, the causes and methods of detecting somaclonal variation, and the types of mutant phenotypes that have arisen spontaneously. We focus on examples where the molecular or cytological changes causing the phenotype have been identified. Analysis of these sports has provided valuable insight into developmental processes, gene function and regulation, and in some cases has revealed new information about layer-specific roles of some genes. Examination of the molecular changes causing a phenotype and in some cases reversion back to the original state has contributed to our understanding of the mechanisms that drive genomic evolution.
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Affiliation(s)
- Toshi M. Foster
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North, 4474 New Zealand
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
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