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Li J, West JB, Hart A, Wegrzyn JL, Smith MA, Domec JC, Loopstra CA, Casola C. Extensive Variation in Drought-Induced Gene Expression Changes Between Loblolly Pine Genotypes. Front Genet 2021; 12:661440. [PMID: 34140968 PMCID: PMC8203665 DOI: 10.3389/fgene.2021.661440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/07/2021] [Indexed: 01/22/2023] Open
Abstract
Drought response is coordinated through expression changes in a large suite of genes. Interspecific variation in this response is common and associated with drought-tolerant and -sensitive genotypes. The extent to which different genetic networks orchestrate the adjustments to water deficit in tolerant and sensitive genotypes has not been fully elucidated, particularly in non-model or woody plants. Differential expression analysis via RNA-seq was evaluated in root tissue exposed to simulated drought conditions in two loblolly pine (Pinus taeda L.) clones with contrasting tolerance to drought. Loblolly pine is the prevalent conifer in southeastern U.S. and a major commercial forestry species worldwide. Significant changes in gene expression levels were found in more than 4,000 transcripts [drought-related transcripts (DRTs)]. Genotype by environment (GxE) interactions were prevalent, suggesting that different cohorts of genes are influenced by drought conditions in the tolerant vs. sensitive genotypes. Functional annotation categories and metabolic pathways associated with DRTs showed higher levels of overlap between clones, with the notable exception of GO categories in upregulated DRTs. Conversely, both differentially expressed transcription factors (TFs) and TF families were largely different between clones. Our results indicate that the response of a drought-tolerant loblolly pine genotype vs. a sensitive genotype to water limitation is remarkably different on a gene-by-gene level, although it involves similar genetic networks. Upregulated transcripts under drought conditions represent the most diverging component between genotypes, which might depend on the activation and repression of substantially different groups of TFs.
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Affiliation(s)
- Jingjia Li
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States
| | - Jason B West
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States
| | - Alexander Hart
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Matthew A Smith
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Jean-Christophe Domec
- Bordeaux Sciences Agro, UMR 1391 INRA ISPA, Gradignan, France.,Nicholas School of the Environment, Duke University, Durham, NC, United States
| | - Carol A Loopstra
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States
| | - Claudio Casola
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, United States
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Lu M, Krutovsky KV, Loopstra CA. Predicting Adaptive Genetic Variation of Loblolly Pine (Pinus taeda L.) Populations Under Projected Future Climates Based on Multivariate Models. J Hered 2019; 110:857-865. [DOI: 10.1093/jhered/esz065] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 10/25/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Greenhouse gas emission and global warming are likely to cause rapid climate change within the natural range of loblolly pine over the next few decades, thus bringing uncertainty to their adaptation to the environment. Here, we studied adaptive genetic variation of loblolly pine and correlated genetic variation with bioclimatic variables using multivariate modeling methods—Redundancy Analysis, Generalized Dissimilarity Modeling, and Gradient Forests. Studied trees (N = 299) were originally sampled from their native range across eight states on the east side of the Mississippi River. Genetic variation was calculated using a total of 44,317 single-nucleotide polymorphisms acquired by exome target sequencing. The fitted models were used to predict the adaptive genetic variation on a large spatial and temporal scale. We observed east-to-west spatial genetic variation across the range, which presented evidence of isolation by distance. Different key factors drive adaptation of loblolly pine from different geographical regions. Trees residing near the northeastern edge of the range, spanning across Delaware and Maryland and mountainous areas of Virginia, North Carolina, South Carolina, and northern Georgia, were identified to be most likely impacted by climate change based on the large difference in genetic composition under current and future climate conditions. This study provides new perspectives on adaptive genetic variation of loblolly pine in response to different climate scenarios, and the results can be used to target particular populations while developing adaptive forest management guidelines.
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Affiliation(s)
- Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August-University of Göttingen, Göttingen, Germany
- Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX
- Molecular and Environmental Plant Sciences Program, Texas A&M University, College Station, TX
| | - Carol A Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX
- Molecular and Environmental Plant Sciences Program, Texas A&M University, College Station, TX
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Lu M, Loopstra CA, Krutovsky KV. Detecting the genetic basis of local adaptation in loblolly pine ( Pinus taeda L.) using whole exome-wide genotyping and an integrative landscape genomics analysis approach. Ecol Evol 2019; 9:6798-6809. [PMID: 31380016 PMCID: PMC6662259 DOI: 10.1002/ece3.5225] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/17/2019] [Accepted: 04/08/2019] [Indexed: 01/04/2023] Open
Abstract
In the Southern United States, the widely distributed loblolly pine contributes greatly to lumber and pulp production, as well as providing many important ecosystem services. Climate change may affect the productivity and range of loblolly pine. Nevertheless, we have insufficient knowledge of the adaptive potential and the genetics underlying the adaptability of loblolly pine. To address this, we tested the association of 2.8 million whole exome-based single nucleotide polymorphisms (SNPs) with climate and geographic variables, including temperature, precipitation, latitude, longitude, and elevation data. Using an integrative landscape genomics approach by combining multiple environmental association and outlier detection analyses, we identified 611 SNPs associated with 56 climate and geographic variables. Longitude, maximum temperature of the warm months and monthly precipitation associated with most SNPs, indicating their importance and complexity in shaping the genetic variation in loblolly pine. Functions of candidate genes related to terpenoid synthesis, pathogen defense, transcription factors, and abiotic stress response. We provided evidence that environment-associated SNPs also composed the genetic structure of adaptive phenotypic traits including height, diameter, metabolite levels, and gene transcript abundance. Our study promotes understanding of the genetic basis of local adaptation in loblolly pine and provides promising tools for selecting genotypes adapted to local environments in a changing climate.
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Affiliation(s)
- Mengmeng Lu
- Department of Ecosystem Science and ManagementTexas A&M UniversityCollege StationTexas
- Molecular and Environmental Plant Sciences ProgramTexas A&M UniversityCollege StationTexas
- Present address:
Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Carol A. Loopstra
- Department of Ecosystem Science and ManagementTexas A&M UniversityCollege StationTexas
- Molecular and Environmental Plant Sciences ProgramTexas A&M UniversityCollege StationTexas
| | - Konstantin V. Krutovsky
- Department of Ecosystem Science and ManagementTexas A&M UniversityCollege StationTexas
- Molecular and Environmental Plant Sciences ProgramTexas A&M UniversityCollege StationTexas
- Department of Forest Genetics and Forest Tree BreedingGeorg‐August‐University of GöttingenGöttingenGermany
- Laboratory of Population Genetics, N. I. Vavilov Institute of General GeneticsRussian Academy of SciencesMoscowRussia
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and BiotechnologySiberian Federal UniversityKrasnoyarskRussia
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Lu M, Seeve CM, Loopstra CA, Krutovsky KV. Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network construction. BMC Genet 2018; 19:100. [PMID: 30400815 PMCID: PMC6219081 DOI: 10.1186/s12863-018-0687-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 10/26/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Identifying genetic variations that shape important complex traits is fundamental to the genetic improvement of important forest tree species, such as loblolly pine (Pinus taeda L.), which is one of the most commonly planted forest tree species in the southern U.S. Gene transcripts and metabolites are important regulatory intermediates that link genetic variations to higher-order complex traits such as wood development and drought response. A few prior studies have associated intermediate phenotypes including mRNA expression and metabolite levels with a limited number of molecular markers, but the identification of genetic variations that regulate intermediate phenotypes needs further investigation. RESULTS We identified 1841 single nucleotide polymorphisms (SNPs) associated with 191 gene expression mRNA phenotypes and 524 SNPs associated with 53 metabolite level phenotypes using 2.8 million exome-derived SNPs. The identified SNPs reside in genes with a wide variety of functions. We further integrated the identified SNPs and the associated expressed genes and metabolites into networks. We described the SNP-SNP interactions that significantly impacted the gene transcript abundance and metabolite level in the networks. Key loci and genes in the wood development and drought response networks were identified and analyzed. CONCLUSIONS This work provides new candidate genes for research on the genetic basis of gene expression and metabolism linked to wood development and drought response in loblolly pine and highlights the efficiency of using association-mapping-based networks to discover candidate genes with important roles in complex biological processes.
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Affiliation(s)
- Mengmeng Lu
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA.,Department of Biological Sciences, University of Calgary, 507 Campus Drive NW, Calgary, AB, T2N 4S8, Canada
| | | | - Carol A Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA
| | - Konstantin V Krutovsky
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA. .,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA. .,Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077, Göttingen, Germany. .,Laboratory of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Str. 3, Moscow, 119333, Russia. .,Laboratory of Forest Genomics, Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk, 660036, Russia.
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Gonzalez-Ibeas D, Martinez-Garcia PJ, Famula RA, Delfino-Mix A, Stevens KA, Loopstra CA, Langley CH, Neale DB, Wegrzyn JL. Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana). G3 (Bethesda) 2016; 6:3787-3802. [PMID: 27799338 PMCID: PMC5144951 DOI: 10.1534/g3.116.032805] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 07/13/2016] [Indexed: 02/06/2023]
Abstract
Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers.
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Affiliation(s)
- Daniel Gonzalez-Ibeas
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | | | - Randi A Famula
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Annette Delfino-Mix
- United States Department of Agriculture Forest Service, Institute of Forest Genetics, Placerville, California 95667
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Carol A Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas 77843
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
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Lu M, Krutovsky KV, Nelson CD, Koralewski TE, Byram TD, Loopstra CA. Erratum to: Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.). BMC Genomics 2016; 17:869. [PMID: 27814686 PMCID: PMC5097424 DOI: 10.1186/s12864-016-3220-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/28/2016] [Indexed: 11/10/2022] Open
Affiliation(s)
- Mengmeng Lu
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA
| | - Konstantin V Krutovsky
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA. .,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA. .,Department of Forest Genetics and Forest Tree Breeding, Georg-August-University of Göttingen, Göttingen, 37077, Germany. .,N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Str, Moscow, 119333, Russia. .,Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk, 660036, Russia.
| | - C Dana Nelson
- USDA Forest Service, Southern Research Station, Southern Institute of Forest Genetics, 23332 Success Road, Saucier, MS, 39574, USA.,University of Kentucky, Forest Health Research and Education Center, 730 Rose Street, Lexington, KY, 40546, USA
| | - Tomasz E Koralewski
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA
| | - Thomas D Byram
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Texas A&M Forest Service, 2585 TAMU, College Station, TX, 77843-2585, USA
| | - Carol A Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA
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Lu M, Krutovsky KV, Nelson CD, Koralewski TE, Byram TD, Loopstra CA. Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.). BMC Genomics 2016; 17:730. [PMID: 27624183 PMCID: PMC5022155 DOI: 10.1186/s12864-016-3081-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/09/2016] [Indexed: 01/06/2023] Open
Abstract
Background Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated single nucleotide polymorphisms (SNPs) and to genotype the sampled trees. Results The exons were captured in the ADEPT2 association mapping population of 375 clonally-propagated loblolly pine trees using NimbleGen oligonucleotide hybridization probes, and then exome-enriched genomic DNA fragments were sequenced using the Illumina HiSeq 2500 platform. Oligonucleotide probes were designed based on 199,723 exons (≈49 Mbp) partitioned from the loblolly pine reference genome (PineRefSeq v. 1.01). The probes covered 90.2 % of the target regions. Capture efficiency was high; on average, 67 % of the sequence reads generated for each tree could be mapped to the capture target regions, and more than 70 % of the captured target bases had at least 10X sequencing depth per tree. A total of 972,720 high quality SNPs were identified after filtering. Among them, 53 % were located in coding regions (CDS), 5 % in 5’ or 3’ untranslated regions (UTRs) and 42 % in non-target and non-coding regions, such as introns and adjacent intergenic regions collaterally captured. We found that linkage disequilibrium (LD) decayed very rapidly, with the correlation coefficient (r2) between pairs of SNPs linked within single scaffolds decaying to half maximum (r2 = 0.22) within 55 bp, to r2 = 0.1 within 192 bp, and to r2 = 0.05 within 451 bp. Population structure analysis using unlinked SNPs demonstrated the presence of two main distinct clusters representing western and eastern parts of the loblolly pine range included in our sample of trees. Conclusions The obtained results demonstrated the efficiency of exome capture for genotyping species such as loblolly pine with a large and complex genome. The highly diverse genetic variation reported in this study will be a valuable resource for future genetic and genomic research in loblolly pine. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3081-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mengmeng Lu
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA
| | - Konstantin V Krutovsky
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA. .,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA. .,Department of Forest Genetics and Forest Tree Breeding, Georg-August-University of Göttingen, Göttingen, 37077, Germany. .,N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Str, Moscow, 119333, Russia. .,Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk, 660036, Russia.
| | - C Dana Nelson
- USDA Forest Service, Southern Research Station, Southern Institute of Forest Genetics, 23332 Success Road, Saucier, MS, 39574, USA.,University of Kentucky, Forest Health Research and Education Center, 730 Rose Street, Lexington, KY, 40546, USA
| | - Tomasz E Koralewski
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA
| | - Thomas D Byram
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Texas A&M Forest Service, 2585 TAMU, College Station, TX, 77843-2585, USA
| | - Carol A Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA
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Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JFD, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg SL, Langley CH. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol 2014; 15:R59. [PMID: 24647006 PMCID: PMC4053751 DOI: 10.1186/gb-2014-15-3-r59] [Citation(s) in RCA: 274] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 03/04/2014] [Indexed: 11/30/2022] Open
Abstract
Background The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination. Results We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome. Conclusions In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied.
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Palle SR, Seeve CM, Eckert AJ, Wegrzyn JL, Neale DB, Loopstra CA. Association of loblolly pine xylem development gene expression with single-nucleotide polymorphisms. Tree Physiol 2013; 33:763-74. [PMID: 23933831 DOI: 10.1093/treephys/tpt054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Variation in the expression of genes with putative roles in wood development was associated with single-nucleotide polymorphisms (SNPs) using a population of loblolly pine (Pinus taeda L.) that included individuals from much of the native range. Association studies were performed using 3938 SNPs and expression data obtained using quantitative real-time polymerase chain reaction (PCR) (qRT-PCR) for 106 xylem development genes in 400 clonally replicated loblolly pine individuals. A general linear model (GLM) approach, which takes the underlying population structure into consideration, was used to discover significant associations. After adjustment for multiple testing using a false discovery rate correction, 88 statistically significant associations (Q<0.05) were observed for 80 SNPs with the expression data of 33 xylem development genes. Thirty SNPs caused nonsynonymous mutations, 18 resulted in synonymous mutations, 11 were in 3' untranslated regions (UTRs), 1 was in a 5' UTR and 20 were in introns. Using AraNet, we found that Arabidopsis genes with high similarity to the loblolly pine genes involved in 21 of the 88 statistically significant associations are connected in functional gene networks. Comparisons of gene expression values revealed that in most cases the average expression in plants homozygous for the rare SNP allele was lower than that of plants that were heterozygous or homozygous for the abundant allele. Although there are association studies of SNPs and expression profiles for humans, Arabidopsis and white spruce, to the best of our knowledge, this is the first example of such an association genetic study in pines. Functional validation of these associations will lead to a deeper understanding of the molecular basis of phenotypic differences in wood development among individuals in conifer populations.
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Affiliation(s)
- Sreenath R Palle
- Department of Ecosystem Science and Management, Molecular and Environmental Plant Sciences, Texas A&M University, TAMU 2138, College Station, TX 77843, USA
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Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics 2010; 11:420. [PMID: 20609256 PMCID: PMC2996948 DOI: 10.1186/1471-2164-11-420] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 07/07/2010] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND In today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24). The size and complexity of these genomes have prompted much speculation as to the feasibility of completing a conifer genome sequence. Conifer genomes are reputed to be highly repetitive, but there is little information available on the nature and identity of repetitive units in gymnosperms. The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda. RESULTS We present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS) sequences representing 7.5% of the genome. Computational annotation of ten BACs predicts three putative protein-coding genes and at least fifteen likely pseudogenes in nearly one megabase of sequence. We found three conifer-specific LTR retroelements in the BACs, and tentatively identified at least 15 others based on evidence from the distantly related angiosperms. Alignment of WGS sequences to the BACs indicates that 80% of BAC sequences have similar copies (> or = 75% nucleotide identity) elsewhere in the genome, but only 23% have identical copies (99% identity). The three most common repetitive elements in the genome were identified and, when combined, represent less than 5% of the genome. CONCLUSIONS This study indicates that the majority of repeats in the P. taeda genome are 'novel' and will therefore require additional BAC or genomic sequencing for accurate characterization. The pine genome contains a very large number of diverged and probably defunct repetitive elements. This study also provides new evidence that sequencing a pine genome using a WGS approach is a feasible goal.
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Affiliation(s)
- Allen Kovach
- Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Jill L Wegrzyn
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Genis Parra
- Genome Center, Division of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Carson Holt
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - George E Bruening
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Carol A Loopstra
- Department of Ecological Science and Management, Texas A&M University, College Station, TX 77843, USA
| | - James Hartigan
- Beckman Coulter Genomics (formerly Agencourt Biosciences), Danvers, MA 01923, USA
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Charles H Langley
- Section of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ian Korf
- Genome Center, Division of Biological Sciences, University of California, Davis, CA 95616, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Institute of Forest Genetics, USDA Forest Service, Davis, CA, 95616, USA
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11
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Abstract
In developing xylem, gene expression levels vary in different genotypes, at different stages of development, throughout a growing season, and in response to stresses. Commercially important characteristics such as wood-specific gravity are known to differ with seed source. For example, when grown on a common site, the specific gravity of Arkansas loblolly pine (Pinus taeda L.) trees is greater than that of Louisiana loblolly pine, and Texas loblolly pines have a greater specific gravity than loblolly pines from the Atlantic coast. A microarray analysis was performed to examine variation in gene expression among trees from different geographical sources when grown on a common site, and seasonal variation in gene expression in each seed source. We used microarrays containing 2171 expressed sequence tags (ESTs) with putative functions of interest, selected from several loblolly pine xylem partial cDNA libraries and a shoot tip library. Genes with significant variation in expression for each factor were identified. Many genes preferentially expressed in latewood compared with earlywood were for proteins involved in cell wall biosynthesis. Variation in gene expression among trees from the two seed sources in each growing season suggests that there may be more differences between South Arkansas trees and South Louisiana trees in latewood than in earlywood. Variation in gene expression among trees from different regions may reflect adaptation to different environments.
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Affiliation(s)
- Suk-Hwan Yang
- Institute for Plant Genomics and Biotechnology and The Department of Forest Science, Molecular and Environmental Plant Science, Texas A&M University, College Station, TX 77843-2123, USA
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12
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Zhang Y, Brown G, Whetten R, Loopstra CA, Neale D, Kieliszewski MJ, Sederoff RR. An arabinogalactan protein associated with secondary cell wall formation in differentiating xylem of loblolly pine. Plant Mol Biol 2003; 52:91-102. [PMID: 12825692 DOI: 10.1023/a:1023978210001] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Arabinogalactan proteins (AGPs) are abundant plant proteoglycans implicated in plant growth and development. Here, we report the genetic characterization, partial purification and immunolocalization of a classical AGP (PtaAGP6, accession number AF101785) in loblolly pine (Pinus taeda L.). A PtaAGP6 full-length cDNA clone was expressed in bacteria. PtaAGP6 resembles tomato LeAGP-1 and Arabidopsis AtAGP17-19 in that they all possess a subdomain composed of basic amino acids. The accessibility of this domain in the glycoprotein makes it possible to label the PtaAGP6 epitopes on the cell surface or in the cell wall with polyclonal antibodies raised against this subdomain. The antibodies recognize the peptide of the basic subdomain and bind to the intact protein molecule. A soluble protein-containing fraction was purified from the differentiating xylem of pine trees by using beta-glucosyl Yariv reagent (beta-glcY) and was recognized by antibodies against the basic subdomain. Immunolocalization studies showed that the PtaAGP6 epitopes are restricted to a file of cells that just precede secondary cell wall thickening, suggesting roles in xylem differentiation and wood formation. The location of apparent labeling of the PtaAGP6 epitopes is separated from the location of lignin deposition. Multiple single nucleotide polymorphisms (SNPs) were detected in EST variants. Denaturing HPLC analysis of PCR products suggests that PtaAGP6 is encoded by a single gene. Mobility variation in denaturing gel electrophoresis was used to map PtaAGP6 SNPs to a site on linkage group 5.
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Affiliation(s)
- Yi Zhang
- Forest Biotechnology Group, 2500 Partners II, Centennial Campus, Box 7247, North Carolina State University, Raleigh, NC 27695-7247, USA
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13
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Abstract
An arabinogalactan-protein (AGP) was purified from differentiating xylem of loblolly pine (Pinus taeda L.) and the N-terminal sequence used to identify a cDNA clone. The protein, PtaAGP3, was not coded for by any previously identified AGP-like genes. Moreover, PtaAGP3 was abundantly and preferentially expressed in differentiating xylem. The encoded protein contains four domains, a signal peptide, a cleaved hydrophilic region, a region rich in serine, alanine, and proline/hydroxyproline, and a hydrophobic C-terminus. It is postulated to contain a GPI (glycosylphosphatidylinositol) anchor site. If the protein is cleaved at the putative GPI anchor site, as has been observed in other classical AGPs, all but the Ser-Ala-Pro/Hyp-rich domain may be missing from the mature protein. Xylem-specific AGPs are hypothesized to be involved in xylem development.
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Affiliation(s)
- C A Loopstra
- Department of Forest Science and Crop Biotechnology Center, Texas A&M University, College Station 77843, USA
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14
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Loopstra CA, Mouradov A, Vivian-Smith A, Glassick TV, Gale BV, Southerton SG, Marshall H, Teasdale RD. Two pine endo-beta-1,4-glucanases are associated with rapidly growing reproductive structures. Plant Physiol 1998; 116:959-67. [PMID: 9501128 PMCID: PMC35097 DOI: 10.1104/pp.116.3.959] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/1997] [Accepted: 12/05/1997] [Indexed: 05/20/2023]
Abstract
Two cDNA clones encoding endo-beta-1,4-glucanases (EGases) were isolated from a radiata pine (Pinus radiata) cDNA library prepared from immature female strobili. The cDNAs PrCel1 (inus adiata cellulase ) and PrCel2 encode proteins 509 and 515 amino acids in length, respectively, including putative signal peptides. Both proteins contain domains conserved in plant and bacterial EGases. The proteins PRCEL1 and PRCEL2 showed strong similarity to each other (76% amino acid identity), and higher similarity to TPP18 (73 and 67%, respectively), an EGase cloned from tomato (Lycopersicon esculentum) pistils, than to any other reported EGases. Northern-blot analyses indicated that both genes displayed a similar pattern of expression. The only significant difference was in the level of expression. In situ hybridizations were used to demonstrate that, within differentiating pine reproductive structures, PrCel1 expression was greatest in microsporangia in pollen strobili and near the developing ovule in the seed strobili. Expression was also found in vegetative tissues, especially in regions experiencing cell elongation, such as the elongating region of root tips. Both proteins have an ability to degrade carboxymethylcellulose in vitro. Genomic-blot analysis indicated the presence of a family of EGase genes in the radiata pine genome, and that PrCel1 and PrCel2 are transcribed from distinct one-copy genes.
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Affiliation(s)
- C A Loopstra
- Department of Forest Science, Texas A&M University, College Station, Texas 77843-2135, USA
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15
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Abstract
Two genes preferentially expressed in differentiating xylem of loblolly pine (Pinus taeda L.) were cloned from cDNA and genomic libraries and designated PtX3H6 and PtX14A9. Transcripts of PtX3H6 and PtX14A9 are very abundant in differentiating xylem, less abundant in needles, and very low or non-detectable in embryos and megagametophytes. PtX3H6 contains a putative signal peptide, a threonine-rich region, a proline-rich region, and a hydrophobic tail. Repeats of Pro-Pro-Pro-Val-X-X are similar to repeats found in proline-rich cell wall proteins. The amino acid compositions of PtX3H6 and PtX14A9 are similar to those of arabinogalactan proteins (AGPs). PtX14A9 contains an 8 amino acid sequence similar to amino terminal sequences of ryegrass, carrot and rose AGPs. Upstream sequences have been determined from genomic clones encoding PtX3H6 and PtX14A9. A 7 bp sequence found in the 5' flanking regions of both genes has previously been shown to be involved in the vascular-specific expression of GRP 1.8, a glycine-rich protein found in bean. The sequence is also present upstream of another glycine-rich protein from bean, GRP 1.0, and may be partially responsible for the xylem-specific expression of pTx3H6 and PtX14A9.
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Affiliation(s)
- C A Loopstra
- Department of Forestry, North Carolina State University, Raleigh 27695-8008
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16
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Abstract
DNA transfer using Agrobacterium tumefaciens has been demonstrated in sugar pine, Pinus lambertiana Dougl. Shoots derived from cytokinin-treated cotyledons formed galls after inoculation with A. tumefaciens strains containing the plasmid pTiBo542. A selectable marker, neomycin phosphotransferase II, conferring resistance to kanamycin, was transferred into sugar pine using a binary armed vector system. Callus proliferated from the galls grew without hormones and in some cases, kanamycin-resistant callus could be cultured. Southern blots provided evidence of physical transfer of T-DNA and the nptII gene. Expression of the nptII gene under control of the nos promoter was demonstrated by neomycin phosphotransferase assays. Several aspects of DNA transfer were similar to those previously observed in angiosperms transformed by A. tumefaciens. This is the first evidence for DNA transfer by Agrobacterium in this species and the first physical evidence for transfer in any pine. These results bring us closer to genetic engineering in this commercially important genus of forest trees.
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Affiliation(s)
- C A Loopstra
- Institute of Forest Genetics, Pacific Southwest Forest Experiment Station, USDA Forest Service, Berkeley, CA 94701
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