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Lo T, Coombe L, Gagalova KK, Marr A, Warren RL, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I, Thomson A. Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response. G3 (BETHESDA, MD.) 2023; 14:jkad247. [PMID: 37875130 PMCID: PMC10755193 DOI: 10.1093/g3journal/jkad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/17/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]
Abstract
Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.
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Affiliation(s)
- Theodora Lo
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Lauren Coombe
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Kristina K Gagalova
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Alex Marr
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - René L Warren
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Heather Kirk
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Pawan Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Richard A Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Carol Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Steven J M Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Joerg Bohlmann
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Inanç Birol
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Ashley Thomson
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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Lasa AV, Guevara MÁ, Villadas PJ, Vélez MD, Fernández-González AJ, de María N, López-Hinojosa M, Díaz L, Cervera MT, Fernández-López M. Correlating the above- and belowground genotype of Pinus pinaster trees and rhizosphere bacterial communities under drought conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 832:155007. [PMID: 35381249 DOI: 10.1016/j.scitotenv.2022.155007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Increasing temperatures along with severe droughts are factors that may jeopardize the survival of the forests in the Mediterranean basin. In this region, Pinus pinaster is a common conifer species, that has been used as a model species in evolutionary studies due to its adaptive response to changing environments. Although its drought tolerance mechanisms are already known, knowledge about the dynamics of its root microbiota is still scarce. We aimed to decipher the structural (bacterial abundance), compositional, functional and associative changes of the P. pinaster rhizosphere bacterial communities in spring and summer, at DNA and RNA level (environmental DNA, live and dead cells, and those synthesizing proteins). A fundamental aspect of root microbiome-based approaches is to guarantee the correct origin of the samples. Thus, we assessed the genotype of host needles and roots from which rhizosphere samples were obtained. For more than 50% of the selected trees, genotype discrepancies were found and in three cases the plant species could not be determined. Rhizosphere bacterial communities were homogeneous with respect to diversity and structural levels regardless of the host genotype in both seasons. Nonetheless, significant changes were seen in the taxonomic profiles depending on the season. Seasonal changes were also evident in the bacterial co-occurrence patterns, both in DNA and RNA libraries. While spring communities switched to more complex networks, summer populations resulted in more compartmentalized networks, suggesting that these communities were facing a disturbance. These results may mirror the future status of bacterial communities in a context of climate change. A keystone hub was ascribed to the genus Phenylobacterium in the functional network calculated for summer. Overall, it is important to validate the origin and identity of plant samples in any plant-microbiota study so that more reliable ecological analyses are performed.
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Affiliation(s)
- Ana V Lasa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 Granada, Spain.
| | - M Ángeles Guevara
- Dept. Forest Ecology and Genetics, Centro de Investigación Forestal, INIA-CSIC, Carretera de La Coruña Km 7,5, 28040 Madrid, Spain; Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPM, Spain.
| | - Pablo J Villadas
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 Granada, Spain.
| | - María Dolores Vélez
- Dept. Forest Ecology and Genetics, Centro de Investigación Forestal, INIA-CSIC, Carretera de La Coruña Km 7,5, 28040 Madrid, Spain; Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPM, Spain.
| | - Antonio J Fernández-González
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 Granada, Spain.
| | - Nuria de María
- Dept. Forest Ecology and Genetics, Centro de Investigación Forestal, INIA-CSIC, Carretera de La Coruña Km 7,5, 28040 Madrid, Spain; Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPM, Spain.
| | - Miriam López-Hinojosa
- Dept. Forest Ecology and Genetics, Centro de Investigación Forestal, INIA-CSIC, Carretera de La Coruña Km 7,5, 28040 Madrid, Spain; Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPM, Spain
| | - Luis Díaz
- Dept. Forest Ecology and Genetics, Centro de Investigación Forestal, INIA-CSIC, Carretera de La Coruña Km 7,5, 28040 Madrid, Spain; Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPM, Spain.
| | - María Teresa Cervera
- Dept. Forest Ecology and Genetics, Centro de Investigación Forestal, INIA-CSIC, Carretera de La Coruña Km 7,5, 28040 Madrid, Spain; Mixed Unit of Forest Genomics and Ecophysiology, INIA/UPM, Spain.
| | - Manuel Fernández-López
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 Granada, Spain.
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Hurel A, de Miguel M, Dutech C, Desprez‐Loustau M, Plomion C, Rodríguez‐Quilón I, Cyrille A, Guzman T, Alía R, González‐Martínez SC, Budde KB. Genetic basis of growth, spring phenology, and susceptibility to biotic stressors in maritime pine. Evol Appl 2021; 14:2750-2772. [PMID: 34950227 PMCID: PMC8674897 DOI: 10.1111/eva.13309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/03/2021] [Indexed: 11/30/2022] Open
Abstract
Forest ecosystems are increasingly challenged by extreme events, for example, drought, storms, pest attacks, and fungal pathogen outbreaks, causing severe ecological and economic losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems, as genetic variation in a trait (i.e., heritability) determines its potential for human-mediated or evolutionary change. Maritime pine (Pinus pinaster Aiton), a conifer widely distributed in southwestern Europe and northwestern Africa, grows under contrasted environmental conditions promoting local adaptation. Genetic variation at adaptive phenotypes, including height, spring phenology, and susceptibility to two fungal pathogens (Diplodia sapinea and Armillaria ostoyae) and an insect pest (Thaumetopoea pityocampa), was assessed in a range-wide clonal common garden of maritime pine. Broad-sense heritability was significant for height (0.219), spring phenology (0.165-0.310), and pathogen susceptibility (necrosis length caused by D. sapinea, 0.152; and by A. ostoyae, 0.021, measured on inoculated, excised branches under controlled conditions), but not for pine processionary moth incidence in the common garden. The correlations of trait variation among populations revealed contrasting trends for pathogen susceptibility to D. sapinea and A. ostoyae with respect to height. Taller trees showed longer necrosis length caused by D. sapinea while shorter trees were more affected by A. ostoyae. Moreover, maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to D. sapinea but more susceptible to A. ostoyae. Finally, an association study using 4227 genome-wide SNPs revealed several loci significantly associated with each trait (range of 3-26), including a possibly disease-induced translation initiation factor, eIF-5, associated with needle discoloration caused by D. sapinea. This study provides important insights to develop genetic conservation and breeding strategies integrating species responses to biotic stressors.
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Affiliation(s)
- Agathe Hurel
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
| | - Marina de Miguel
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
- EGFV, INRAEUniversity of BordeauxVillenave‐d'OrnonFrance
| | - Cyril Dutech
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
| | | | | | | | | | | | | | | | - Katharina B. Budde
- BIOGECO, INRAEUniversity of BordeauxCestasFrance
- Büsgen‐InstituteGeorg‐August University GöttingenGöttingenGermany
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5
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Mohammadi Alaghuz R, Darvishzadeh R, Alijanpour A, Razi M. Toward the identification of molecular markers associated with phytochemical traits in the Iranian sumac ( Rhus coriaria L.) population. Food Sci Nutr 2021; 9:3142-3154. [PMID: 34136179 PMCID: PMC8194943 DOI: 10.1002/fsn3.2273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/09/2021] [Accepted: 03/14/2021] [Indexed: 02/04/2023] Open
Abstract
Sumac (Rhus coriaria L.) is one of the important forest species dispersed in the northwest of Iran. It is one of the important spice in Iran and the Middle East because of active components containing organic acids, phenolic acids, flavonoids, anthocyanins, tannins and terpenoids. This study aimed to investigate population structure and linkage disequilibrium (LD) extent within Rhus coriaria L. genotypes using ISSR markers and identify molecular markers associated with phytochemical traits using association analysis. In the molecular part of the experiment, the genetic diversity of 75 sumac genotypes from five different areas of northwest Iran was assessed by 18 ISSR primers. In the phenotypic assessment, the fruits of the sumac genotypes were analyzed using HPLC-LC/MSMS for determining phytochemical components including maleic acid, ellagic acid, maleic acid hexoside, gallic acid, coumaric acid, quercetin, caftaric acid, and linoleic acid. The phenotypic data analysis revealed the great phenotypic diversity among and within Iranian sumac populations for the studied phytochemical traits. The studied sumac genotypes were divided into two subpopulations based on molecular marker-based structure analysis. A significant level of LD was observed in 11.64% of the ISSR marker pairs (p < .05). The mixed linear model procedure showed that 12 loci had a significant association with investigated traits. The ISSR loci identified in this study can be potentially used in marker-assisted selection in sumac breeding programs.
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Affiliation(s)
- Rasoul Mohammadi Alaghuz
- Agricultural BiotechnologyDepartment of Plant Production and GeneticsFaculty of Agriculture and Natural ResourcesUrmia UniversityUrmiaIran
| | - Reza Darvishzadeh
- Department of Plant Production and GeneticsFaculty of Agriculture and Natural ResourcesUrmia UniversityUrmiaIran
| | - Ahmad Alijanpour
- Department of ForestryFaculty of Agriculture and Natural ResourcesUrmia UniversityUrmiaIran
| | - Mitra Razi
- Department of Plant Production and GeneticsFaculty of Agriculture and Natural ResourcesUrmia UniversityUrmiaIran
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6
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Valledor L, Guerrero S, García-Campa L, Meijón M. Proteometabolomic characterization of apical bud maturation in Pinus pinaster. TREE PHYSIOLOGY 2021; 41:508-521. [PMID: 32870277 DOI: 10.1093/treephys/tpaa111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/30/2020] [Accepted: 08/22/2020] [Indexed: 05/03/2023]
Abstract
Bud maturation is a physiological process that implies a set of morphophysiological changes that lead to the transition of growth patterns from young to mature. This transition defines tree growth and architecture, and in consequence traits such as biomass production and wood quality. In Pinus pinaster Aiton, a conifer of great timber value, bud maturation is closely related to polycyclism (multiple growth periods per year). This process causes a lack of apical dominance, and consequently increased branching that reduces its timber quality and value. However, despite its importance, little is known about bud maturation. In this work, proteomics and metabolomics were employed to study apical and basal sections of young and mature buds in P. pinaster. Proteins and metabolites in samples were described and quantified using (n)UPLC-LTQ-Orbitrap. The datasets were analyzed employing an integrative statistical approach, which allowed the determination of the interactions between proteins and metabolites and the different bud sections and ages. Specific dynamics of proteins and metabolites such as histones H3 and H4, ribosomal proteins L15 and L12, chaperonin TCP1, 14-3-3 protein gamma, gibberellins A1, A3 and A8, strigolactones and abscisic acid, involved in epigenetic regulation, proteome remodeling, hormonal signaling and abiotic stress pathways showed their potential role during bud maturation. Candidates and pathways were validated employing interaction databases and targeted transcriptomics. These results increase our understanding of the molecular processes behind bud maturation, a key step towards improving timber production and natural pine forests management in a future scenario of climate change. However, further studies are necessary using different P. pinaster populations that show contrasting wood quality and stress tolerance in order to generalize the results.
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Affiliation(s)
- Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, C/Catedrático Rodrigo Uría, University of Oviedo, Oviedo 33071, Asturias, Spain
| | - Sara Guerrero
- Plant Physiology, Department of Organisms and Systems Biology, C/Catedrático Rodrigo Uría, University of Oviedo, Oviedo 33071, Asturias, Spain
| | - Lara García-Campa
- Plant Physiology, Department of Organisms and Systems Biology, C/Catedrático Rodrigo Uría, University of Oviedo, Oviedo 33071, Asturias, Spain
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology, C/Catedrático Rodrigo Uría, University of Oviedo, Oviedo 33071, Asturias, Spain
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7
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Obala J, Saxena RK, Singh VK, Kumar CVS, Saxena KB, Tongoona P, Sibiya J, Varshney RK. Development of sequence-based markers for seed protein content in pigeonpea. Mol Genet Genomics 2018; 294:57-68. [PMID: 30173295 DOI: 10.1007/s00438-018-1484-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F2 population of the cross ICP 5529 (high SPC) × ICP 11605 (low SPC), resulted in four of the CAPS/dCAPS markers significantly (P < 0.05) co-segregated with SPC. In summary, four markers derived from mutations in four genes will be useful for enhancing/regulating SPC in pigeonpea crop improvement programs.
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Affiliation(s)
- Jimmy Obala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Pangirayi Tongoona
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Julia Sibiya
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
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Bartholomé J, Bink MCAM, van Heerwaarden J, Chancerel E, Boury C, Lesur I, Isik F, Bouffier L, Plomion C. Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness. PLoS One 2016; 11:e0165323. [PMID: 27806077 PMCID: PMC5091878 DOI: 10.1371/journal.pone.0165323] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/10/2016] [Indexed: 01/26/2023] Open
Abstract
Background Increasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches. Results The populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait. Conclusions This study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program.
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Affiliation(s)
| | - Marco CAM Bink
- Biometris, Wageningen University and Research Centre, NL-6700 AC, Wageningen, Netherlands
| | - Joost van Heerwaarden
- Biometris, Wageningen University and Research Centre, NL-6700 AC, Wageningen, Netherlands
| | | | | | - Isabelle Lesur
- BIOGECO, INRA, Univ. Bordeaux, 33610, Cestas, France
- HelixVenture, Mérignac, France
| | - Fikret Isik
- North Carolina State University, Department of Forestry and Environmental Resources, Raleigh, NC, United States of America
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9
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Plomion C, Bartholomé J, Lesur I, Boury C, Rodríguez-Quilón I, Lagraulet H, Ehrenmann F, Bouffier L, Gion JM, Grivet D, de Miguel M, de María N, Cervera MT, Bagnoli F, Isik F, Vendramin GG, González-Martínez SC. High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster). Mol Ecol Resour 2015; 16:574-87. [PMID: 26358548 DOI: 10.1111/1755-0998.12464] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 08/28/2015] [Accepted: 09/03/2015] [Indexed: 12/18/2022]
Abstract
Maritime pine provides essential ecosystem services in the south-western Mediterranean basin, where it covers around 4 million ha. Its scattered distribution over a range of environmental conditions makes it an ideal forest tree species for studies of local adaptation and evolutionary responses to climatic change. Highly multiplexed single nucleotide polymorphism (SNP) genotyping arrays are increasingly used to study genetic variation in living organisms and for practical applications in plant and animal breeding and genetic resource conservation. We developed a 9k Illumina Infinium SNP array and genotyped maritime pine trees from (i) a three-generation inbred (F2) pedigree, (ii) the French breeding population and (iii) natural populations from Portugal and the French Atlantic coast. A large proportion of the exploitable SNPs (2052/8410, i.e. 24.4%) segregated in the mapping population and could be mapped, providing the densest ever gene-based linkage map for this species. Based on 5016 SNPs, natural and breeding populations from the French gene pool exhibited similar level of genetic diversity. Population genetics and structure analyses based on 3981 SNP markers common to the Portuguese and French gene pools revealed high levels of differentiation, leading to the identification of a set of highly differentiated SNPs that could be used for seed provenance certification. Finally, we discuss how the validated SNPs could facilitate the identification of ecologically and economically relevant genes in this species, improving our understanding of the demography and selective forces shaping its natural genetic diversity, and providing support for new breeding strategies.
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Affiliation(s)
- C Plomion
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - J Bartholomé
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - I Lesur
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,HelixVenture, F-33700, Mérignac, France
| | - C Boury
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | | | - H Lagraulet
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - F Ehrenmann
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - L Bouffier
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - J M Gion
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,UMR AGAP, CIRAD, F-33612, Cestas, France
| | - D Grivet
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - M de Miguel
- BIOGECO, UMR 1202, INRA, F-33610, Cestas, France.,BIOGECO, UMR 1202, University of Bordeaux, F-33400, Talence, France
| | - N de María
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - M T Cervera
- Forest Research Centre, INIA, E-28040, Madrid, Spain
| | - F Bagnoli
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy
| | - F Isik
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - G G Vendramin
- Institute of Biosciences and Bioresources, National Research Council, Sesto Fiorentino (FI), Italy
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