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Gaur VS, Sood S, Guzmán C, Olsen KM. Molecular insights on the origin and development of waxy genotypes in major crop plants. Brief Funct Genomics 2024; 23:193-213. [PMID: 38751352 DOI: 10.1093/bfgp/elad035] [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: 04/01/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 06/14/2024] Open
Abstract
Starch is a significant ingredient of the seed endosperm with commercial importance in food and industry. Crop varieties with glutinous (waxy) grain characteristics, i.e. starch with high amylopectin and low amylose, hold longstanding cultural importance in some world regions and unique properties for industrial manufacture. The waxy character in many crop species is regulated by a single gene known as GBSSI (or waxy), which encodes the enzyme Granule Bound Starch Synthase1 with null or reduced activity. Several allelic variants of the waxy gene that contribute to varying levels of amylose content have been reported in different crop plants. Phylogenetic analysis of protein sequences and the genomic DNA encoding GBSSI of major cereals and recently sequenced millets and pseudo-cereals have shown that GBSSI orthologs form distinct clusters, each representing a separate crop lineage. With the rapidly increasing demand for waxy starch in food and non-food applications, conventional crop breeding techniques and modern crop improvement technologies such as gene silencing and genome editing have been deployed to develop new waxy crop cultivars. The advances in research on waxy alleles across different crops have unveiled new possibilities for modifying the synthesis of amylose and amylopectin starch, leading to the potential creation of customized crops in the future. This article presents molecular lines of evidence on the emergence of waxy genes in various crops, including their genesis and evolution, molecular structure, comparative analysis and breeding innovations.
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Affiliation(s)
- Vikram S Gaur
- Raja Bhoj College of Agriculture, Balaghat, JNKVV, Jabalpur, Madhya Pradesh, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Shimla- 171001, Himachal Pradesh, India
| | - Carlos Guzmán
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Campus de Rabanales, Universidad de Córdoba, CeiA3, ES-14071, Córdoba, Spain
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John D, Sureshkumar S, Raman M. Type‐2 diabetes and identification of major genetic determinants of glycemic index in rice‐ A review. STARCH-STARKE 2022. [DOI: 10.1002/star.202100277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Deepa John
- Department of Biotechnology Faculty of Ocean Science and Technology Kerala University of Fisheries and Ocean Studies Cochin Kerala 682506 India
| | - S Sureshkumar
- Faculty of Ocean Science and Technology Kerala University of Fisheries and Ocean Studies Cochin Kerala 682506 India
| | - Maya Raman
- Department of Food Science and Technology Faculty of Ocean Science and Technology Kerala University of Fisheries and Ocean Studies Cochin Kerala 682506 India
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Tanaka N, Shenton M, Kawahara Y, Kumagai M, Sakai H, Kanamori H, Yonemaru JI, Fukuoka S, Sugimoto K, Ishimoto M, Wu J, Ebana K. Investigation of the Genetic Diversity of a Rice Core Collection of Japanese Landraces using Whole-Genome Sequencing. PLANT & CELL PHYSIOLOGY 2021; 61:2087-2096. [PMID: 33539537 PMCID: PMC7861467 DOI: 10.1093/pcp/pcaa125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/22/2020] [Indexed: 06/12/2023]
Abstract
The Rice Core Collection of Japanese Landraces (JRC) consisting of 50 accessions was developed by the genebank at the National Agriculture and Food Research Organization (NARO) in 2008. As a Japanese landrace core collection, the JRC has been used for many research projects, including screening for different phenotypes and allele mining for target genes. To understand the genetic diversity of Japanese Landraces, we performed whole-genome resequencing of these 50 accessions and obtained a total of 2,145,095 single nucleotide polymorphism (SNPs) and 317,832 insertion-deletions (indels) by mapping against the Oryza sativa ssp. japonica Nipponbare genome. A JRC phylogenetic tree based on 1,394 representative SNPs showed that JRC accessions were divided into two major groups and one small group. We used the multiple genome browser, TASUKE+, to examine the haplotypes of flowering genes and detected new mutations in these genes. Finally, we performed genome-wide association studies (GWAS) for agronomical traits using the JRC and another core collection, the World Rice Core Collection (WRC), comprising 69 accessions also provided by the NARO genebank. In leaf blade width, a strong peak close to NAL1, a key gene for the regulation of leaf width, and, in heading date, a peak near HESO1 involved in flowering regulation were observed in GWAS using the JRC. They were also detected in GWAS using the combined JRC + WRC. Thus, JRC and JRC + WRC are suitable populations for GWAS of particular traits.
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Affiliation(s)
- Nobuhiro Tanaka
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Matthew Shenton
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Yoshihiro Kawahara
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Masahiko Kumagai
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Hiroaki Sakai
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Jun-ichi Yonemaru
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Shinichi Fukuoka
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Kazuhiko Sugimoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Masao Ishimoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Jianzhong Wu
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Kaworu Ebana
- Genetic Resources Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
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Roy S, Banerjee A, Basak N, Bagchi TB, Mandal NP, Patra BC, Misra AK, Singh SK, Rathi RS, Pattanayak A. Genetic diversity analysis of specialty glutinous and low-amylose rice (Oryza sativa L.) landraces of Assam based on Wx locus and microsatellite diversity. J Biosci 2020. [DOI: 10.1007/s12038-020-00059-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Jiménez-Ruiz J, Ramírez-Tejero JA, Fernández-Pozo N, Leyva-Pérez MDLO, Yan H, Rosa RDL, Belaj A, Montes E, Rodríguez-Ariza MO, Navarro F, Barroso JB, Beuzón CR, Valpuesta V, Bombarely A, Luque F. Transposon activation is a major driver in the genome evolution of cultivated olive trees (Olea europaea L.). THE PLANT GENOME 2020; 13:e20010. [PMID: 33016633 DOI: 10.1002/tpg2.20010] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/15/2020] [Indexed: 05/25/2023]
Abstract
The primary domestication of olive (Olea europaea L.) in the Levant dates back to the Neolithic period, around 6,000-5,500 BC, as some archeological remains attest. Cultivated olive trees are reproduced clonally, with sexual crosses being the sporadic events that drive the development of new varieties. In order to determine the genomic changes which have occurred in a modern olive cultivar, the genome of the Picual cultivar, one of the most popular olive varieties, was sequenced. Additional 40 cultivated and 10 wild accessions were re-sequenced to elucidate the evolution of the olive genome during the domestication process. It was found that the genome of the 'Picual' cultivar contains 79,667 gene models, of which 78,079 were protein-coding genes and 1,588 were tRNA. Population analyses support two independent events in olive domestication, including an early possible genetic bottleneck. Despite genetic bottlenecks, cultivated accessions showed a high genetic diversity driven by the activation of transposable elements (TE). A high TE gene expression was observed in presently cultivated olives, which suggests a current activity of TEs in domesticated olives. Several TEs families were expanded in the last 5,000 or 6,000 years and produced insertions near genes that may have been involved in selected traits during domestication as reproduction, photosynthesis, seed development, and oil production. Therefore, a great genetic variability has been found in cultivated olive as a result of a significant activation of TEs during the domestication process.
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Affiliation(s)
- Jaime Jiménez-Ruiz
- Center for Advanced Studies in Olive Grove and Olive Oils, Department of Experimental Biology, University. Jaén, Jaén, 23071, Spain
| | - Jorge A Ramírez-Tejero
- Center for Advanced Studies in Olive Grove and Olive Oils, Department of Experimental Biology, University. Jaén, Jaén, 23071, Spain
| | - Noé Fernández-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - María de la O Leyva-Pérez
- Center for Advanced Studies in Olive Grove and Olive Oils, Department of Experimental Biology, University. Jaén, Jaén, 23071, Spain
| | - Haidong Yan
- School of Plants and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Raúl de la Rosa
- Centro de Investigación y Formación Agraria de Alameda del Obispo, Instituto de Investigación y Formación Agraria y Pesquera (IFAPA), Córdoba, Spain
| | - Angjelina Belaj
- Centro de Investigación y Formación Agraria de Alameda del Obispo, Instituto de Investigación y Formación Agraria y Pesquera (IFAPA), Córdoba, Spain
| | - Eva Montes
- Instituto Universitario de Investigación en Arqueología Ibérica, University. Jaén, Jaén, 23071, Spain
| | - Mª Oliva Rodríguez-Ariza
- Instituto Universitario de Investigación en Arqueología Ibérica, University. Jaén, Jaén, 23071, Spain
| | - Francisco Navarro
- Center for Advanced Studies in Olive Grove and Olive Oils, Department of Experimental Biology, University. Jaén, Jaén, 23071, Spain
| | - Juan Bautista Barroso
- Center for Advanced Studies in Olive Grove and Olive Oils, Department of Experimental Biology, University. Jaén, Jaén, 23071, Spain
| | - Carmen R Beuzón
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - Victoriano Valpuesta
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - Aureliano Bombarely
- School of Plants and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- present address, Department of Bioscience, Universita degli Studi di Milano, Milan, 20133, Italy
| | - Francisco Luque
- Center for Advanced Studies in Olive Grove and Olive Oils, Department of Experimental Biology, University. Jaén, Jaén, 23071, Spain
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Zhang H, Zhou L, Xu H, Wang L, Liu H, Zhang C, Li Q, Gu M, Wang C, Liu Q, Zhu Y. The qSAC3 locus from indica rice effectively increases amylose content under a variety of conditions. BMC PLANT BIOLOGY 2019; 19:275. [PMID: 31234778 PMCID: PMC6591921 DOI: 10.1186/s12870-019-1860-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 05/31/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Amylose content (AC) is a critical factor for the quality of rice. It is determined by the biosynthesis gene Waxy (Wx) and a variety of quantitative trait loci (QTLs). Although many QTLs have been reported to affect rice AC, few of them have been investigated under varying growth conditions, especially various temperatures, which are known to greatly influence the AC. RESULTS We analyzed the AC at different temperatures and planting seasons in a set of chromosome segment substitution lines (CSSLs) which were derived from a cross between the indica variety 9311 and the japonica variety Nipponbare carrying the same Wxb allele. A joint analysis detected a single locus, qSAC3, with a high logarithm of odds (LOD) score in four different conditions. The qSAC3 from indica 9311 (qSAC3ind) substantially increased the AC in japonica Nipponbare under all tested growth conditions. Furthermore, introducing the qSAC3ind into the soft rice variety Nangeng9108 with Wxmq, a mutant allele of Wxb, also moderately increased its AC and improved its appearance quality significantly by reducing the chalkiness of the polished rice. CONCLUSIONS Our results indicate that the qSAC3ind could increase the AC of japonica rice in different environments as well as in the background of different Wx alleles and that qSAC3 is a valuable locus for fine-tuning the rice AC and ameliorating the dull endosperm in rice varieties with the Wxmq allele.
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Affiliation(s)
- Hua Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Lihui Zhou
- Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Provincial Key Laboratory of Agrobiology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu China
| | - Heng Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Liangchao Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Huijie Liu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Qianfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Cailin Wang
- Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Provincial Key Laboratory of Agrobiology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Ying Zhu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
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Shaping Plant Adaptability, Genome Structure and Gene Expression through Transposable Element Epigenetic Control: Focus on Methylation. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8090180] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In plants, transposable elements (TEs) represent a large fraction of the genome, with potential to alter gene expression and produce genomic rearrangements. Epigenetic control of TEs is often used to stop unrestricted movement of TEs that would result in detrimental effects due to insertion in essential genes. The current review focuses on the effects of methylation on TEs and their genomic context, and how this type of epigenetic control affects plant adaptability when plants are faced with different stresses and changes. TEs mobilize in response to stress elicitors, including biotic and abiotic cues, but also developmental transitions and ‘genome shock’ events like polyploidization. These events transitionally lift TE repression, allowing TEs to move to new genomic locations. When TEs fall close to genes, silencing through methylation can spread to nearby genes, resulting in lower gene expression. The presence of TEs in gene promoter regions can also confer stress inducibility modulated through alternative methylation and demethylation of the TE. Bursts of transposition triggered by events of genomic shock can increase genome size and account for differences seen during polyploidization or species divergence. Finally, TEs have evolved several mechanisms to suppress their own repression, including the use of microRNAs to control genes that promote methylation. The interplay between silencing, transient TE activation, and purifying selection allows the genome to use TEs as a reservoir of potential beneficial modifications but also keeps TEs under control to stop uncontrolled detrimental transposition.
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The Functional Impact of Transposable Elements on the Diversity of Plant Genomes. DIVERSITY 2018. [DOI: 10.3390/d10020018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Ogawa D, Yamamoto E, Ohtani T, Kanno N, Tsunematsu H, Nonoue Y, Yano M, Yamamoto T, Yonemaru JI. Haplotype-based allele mining in the Japan-MAGIC rice population. Sci Rep 2018. [PMID: 29531264 PMCID: PMC5847589 DOI: 10.1038/s41598-018-22657-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multi-parent advanced generation inter-cross (MAGIC) lines have broader genetic variation than bi-parental recombinant inbred lines. Genome-wide association study (GWAS) using high number of DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) is a popular tool for allele mining in MAGIC populations, in which the associations of phenotypes with SNPs are investigated; however, the effects of haplotypes from multiple founders on phenotypes are not considered. Here, we describe an improved method of allele mining using the newly developed Japan-MAGIC (JAM) population, which is derived from eight high-yielding rice cultivars in Japan. To obtain information on the haplotypes in the JAM lines, we predicted the haplotype blocks in the whole chromosomes using 16,345 SNPs identified via genotyping-by-sequencing analysis. Using haplotype-based GWAS, we clearly detected the loci controlling the glutinous endosperm and culm length traits. Information on the alleles of the eight founders, which was based on the effects of mutations revealed by the analysis of next-generation sequencing data, was used to narrow down the candidate genes and reveal the associations between alleles and phenotypes. The haplotype-based allele mining (HAM) proposed in this study is a promising approach to the detection of allelic variation in genes controlling agronomic traits in MAGIC populations.
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Affiliation(s)
- Daisuke Ogawa
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Eiji Yamamoto
- Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Toshikazu Ohtani
- Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Noriko Kanno
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Hiroshi Tsunematsu
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Yasunori Nonoue
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Masahiro Yano
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Toshio Yamamoto
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan. .,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan.
| | - Jun-Ichi Yonemaru
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan. .,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan.
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Fan X, Zhu J, Dong W, Sun Y, Lv C, Guo B, Xu R. Comparative Mapping and Candidate Gene Analysis of SSIIa Associated with Grain Amylopectin Content in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1531. [PMID: 28928763 PMCID: PMC5591850 DOI: 10.3389/fpls.2017.01531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
Amylopectin concentration in barley endosperm has important effects on grain quality and end-use. In this study, quantitative trait locus (QTL) analysis together with genome-wide association studies (GWAS) were performed to identify markers linked to grain amylopectin content respectively using a doubled haploid (DH) population of 178 lines and a collection of 185 diverse barley germplasms both genotyped by genotyping-by-sequencing (GBS). A stable QTL on chromosome 7H and 11 associated single nucleotide polymorphisms (SNPs) were detected. In the co-localized region, the SSIIa (SSII-3) gene was predicted as the candidate gene. Then we isolated and characterized biparental SSIIa alleles of the DH population, investigated the expression pattern by quantitative real-time PCR (qRT-PCR), and revealed that a 33-bp deletion in exon 2 is responsible for reducing SSIIa transcript, thus resulting in a reduced amylopectin content. A sequence-based molecular marker was developed for the SSIIa allele and validated the effectivity, which would provide help for barley breeding.
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Abstract
LTR retrotransposons are the most abundant group of transposable elements (TEs) in plants. These elements can fall inside or close to genes, and therefore influence their expression and evolution. This review aims to examine how LTR retrotransposons, especially Ty1-copia elements, mediate gene regulation and evolution. Various stimuli, including polyploidization and biotic and abiotic elicitors, result in the transcription and movement of these retrotransposons, and can facilitate adaptation. The presence of cis-regulatory motifs in the LTRs are central to their stress-mediated responses and are shared with host stress-responsive genes, showing a complex evolutionary history in which TEs provide new regulatory units to genes. The presence of retrotransposon remnants in genes that are necessary for normal gene function, demonstrates the importance of exaptation and co-option, and is also a consequence of the abundance of these elements in plant genomes. Furthermore, insertions of LTR retrotransposons in and around genes provide potential for alternative splicing, epigenetic control, transduction, duplication and recombination. These characteristics can become an active part of the evolution of gene families as in the case of resistance genes (R-genes). The character of TEs as exclusively selfish is now being re-evaluated. Since genome-wide reprogramming via TEs is a long evolutionary process, the changes we can examine are case-specific and their fitness advantage may not be evident until TE-derived motifs and domains have been completely co-opted and fixed. Nevertheless, the presence of LTR retrotransposons inside genes and as part of gene promoter regions is consistent with their roles as engines of plant genome evolution.
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Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions. BMC Genomics 2016; 17:1002. [PMID: 27927184 PMCID: PMC5142383 DOI: 10.1186/s12864-016-3337-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/23/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Initial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity. Flax, where accessions are bred mainly for seed nutritional properties or for fibers, constitutes a good model for studying the relationship of transpositional activity with diversification and breeding. In this study, we estimated copy number and used a type of transposon display known as Sequence-Specific Amplification Polymorphisms (SSAPs), to characterize six families of Ty1-copia elements across 14 flax accessions. Polymorphic insertion sites were sequenced to find insertions that could potentially alter gene expression, and a preliminary test was performed with selected genes bearing transposable element (TE) insertions. RESULTS Quantification of six families of Ty1-copia elements indicated different abundances among TE families and between flax accessions, which suggested diverse transpositional histories. SSAPs showed a high level of polymorphism in most of the evaluated retrotransposon families, with a trend towards higher levels of polymorphism in low-copy number families. Ty1-copia insertion polymorphisms among cultivars allowed a general distinction between oil and fiber types, and between spring and winter types, demonstrating their utility in diversity studies. Characterization of polymorphic insertions revealed an overwhelming association with genes, with insertions disrupting exons, introns or within 1 kb of coding regions. A preliminary test on the potential transcriptional disruption by TEs of four selected genes evaluated in three different tissues, showed one case of significant impact of the insertion on gene expression. CONCLUSIONS We demonstrated that specific Ty1-copia families have been active since breeding commenced in flax. The retrotransposon-derived polymorphism can be used to separate flax types, and the close association of many insertions with genes defines a good source of potential mutations that could be associated with phenotypic changes, resulting in diversification processes.
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Hsu YC, Wang CS, Lin YR, Wu YP. Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza. Evol Bioinform Online 2016; 12:29-40. [PMID: 26819544 PMCID: PMC4718150 DOI: 10.4137/ebo.s35158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/08/2015] [Accepted: 11/16/2015] [Indexed: 11/16/2022] Open
Abstract
Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named RTPOSON primarily occurs in the genus Oryza and in several species of the Poaceae family. RTPOSON has been identified in the Ty1-copia group of retrotransposons because two of its open reading frames encode an uncharacterized protein and UBN2_2 and zinc knuckle, respectively. More than 700 RTPOSONs were identified in Oryza genomes; 127 RTPOSONs with LTRs and gag-pol elements were classified into three subgroups. The subgroup RTPOSON_sub3 had the smallest DNA size and 97% (32/33) of RTPOSON elements from Oryza punctata are classified in this group. The insertion time of these RTPOSONs varied and their proliferation occurred within the last 8 Mya, with two bursting periods within the last 1.5–5.0 Mya. A total of 37 different orthologous insertions of RTPOSONs, with different nested transposable elements and gene fragments, were identified by comparing the genomes of ssp. japonica cv. Nipponbare and ssp. indica cv. 93–11. A part of intact RTPOSON elements was evolved independently after the divergence of indica and japonica. In addition, intact RTPOSONs and homologous fragments were preferentially retained or integrated in genic regions. This novel LTR retrotransposon, RTPOSON, might have an impact on genome evolution, genic innovation, and genetic variation.
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Affiliation(s)
- Yu-Chia Hsu
- Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yong-Pei Wu
- Department of Agronomy, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
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Wei L, Cao X. The effect of transposable elements on phenotypic variation: insights from plants to humans. SCIENCE CHINA-LIFE SCIENCES 2016; 59:24-37. [PMID: 26753674 DOI: 10.1007/s11427-015-4993-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/16/2015] [Indexed: 11/25/2022]
Abstract
Transposable elements (TEs), originally discovered in maize as controlling elements, are the main components of most eukaryotic genomes. TEs have been regarded as deleterious genomic parasites due to their ability to undergo massive amplification. However, TEs can regulate gene expression and alter phenotypes. Also, emerging findings demonstrate that TEs can establish and rewire gene regulatory networks by genetic and epigenetic mechanisms. In this review, we summarize the key roles of TEs in fine-tuning the regulation of gene expression leading to phenotypic plasticity in plants and humans, and the implications for adaption and natural selection.
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Affiliation(s)
- Liya Wei
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center (Beijing), CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China.
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15
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The Hairless Stem Phenotype of Cotton (Gossypium barbadense) Is Linked to a Copia-Like Retrotransposon Insertion in a Homeodomain-Leucine Zipper Gene (HD1). Genetics 2015; 201:143-54. [PMID: 26133897 DOI: 10.1534/genetics.115.178236] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 06/25/2015] [Indexed: 02/03/2023] Open
Abstract
Cotton (Gossypium) stem trichomes are mostly single cells that arise from stem epidermal cells. In this study, a homeodomain-leucine zipper gene (HD1) was found to cosegregate with the dominant trichome locus previously designated as T1 and mapped to chromosome 6. Characterization of HD1 orthologs revealed that the absence of stem trichomes in modern Gossypium barbadense varieties is linked to a large retrotransposon insertion in the ninth exon, 2565 bp downstream from the initial codon in the At subgenome HD1 gene (At-GbHD1). In both the At and Dt subgenomes, reduced transcription of GbHD1 genes is caused by this insertion. The disruption of At-HD1 further affects the expression of downstream GbMYB25 and GbHOX3 genes. Analyses of primitive cultivated accessions identified another retrotransposon insertion event in the sixth exon of At-GbHD1 that might predate the previously identified retrotransposon in modern varieties. Although both retrotransposon insertions results in similar phenotypic changes, the timing of these two retrotransposon insertion events fits well with our current understanding of the history of cotton speciation and dispersal. Taken together, the results of genetics mapping, gene expression and association analyses suggest that GbHD1 is an important component that controls stem trichome development and is a promising candidate gene for the T1 locus. The interspecific phenotypic difference in stem trichome traits also may be attributable to HD1 inactivation associated with retrotransposon insertion.
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16
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Luo Y, Zakaria S, Basyah B, Ma T, Li Z, Yang J, Yin Z. Marker-assisted breeding of Indonesia local rice variety Siputeh for semi-dwarf phonetype, good grain quality and disease resistance to bacterial blight. RICE (NEW YORK, N.Y.) 2014; 7:33. [PMID: 26224562 PMCID: PMC4884010 DOI: 10.1186/s12284-014-0033-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND Rice is one of the most important staple food crops in Asia. Since the first green revolution beginning in 1960s, high-yield semidwarf modern rice varieties have been widely planted; however, traditional rice varieties with tall plant type are still grown in many countries due to their good grain quality and adaptation to local climate and environment. Siputeh, a local rice variety mainly planted in Java and Sumatra islands of Indonesia, produces long grain rice with good cooking and eating quality. However, the variety has low yield with tall plant type and long growth duration and is highly susceptible to biotic and abiotic stress. RESULTS Siputeh as the recurrent female was crossed with the donor line WH421, an elite paternal line of hybrid rice containing the sd1, Wx (b), Xa4 and Xa21 genes, followed by backcrossing and self-pollination. TS4, a BC3F4 line derived from the breeding program, was obtained through marker-assisted selection for the sd1, Wx (b), Xa4 and Xa21 loci. TS4 has semi-dwarf phenotype and short growth duration. TS4 conferred disease resistance to multiple Xanthomonas oryzae pv. oryzae (Xoo) strains collected from different countries around the world. TS4 achieved higher grain yield than Siputeh in two field trials conducted in Banda Aceh, Indonesia and Lingshui, China, respectively. Finally, TS4 has better grain quality than Siputeh in terms of degree of chalkiness and amylose content. CONCLUSION An improved rice line, designed as TS4, has been developed to contain semi-dwarf gene sd1, low amylase content gene Wx (b) and bacterial light resistance genes Xa4 and Xa21 through marker-assisted selection. TS4 has semi-dwarf phenotype with reduced growth duration, produces high yield with good grain quality and provides broad-spectrum resistance to Xoo strains. The development of TS4 enriches the diversity of local rice varieties with high yield potential and good grain quality.
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Affiliation(s)
- Yanchang Luo
- />Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604 Republic of Singapore
- />Rice Research institute, Anhui Academy of Agricultrural Sciences, Hefei, 230031 China
| | - Sabaruddin Zakaria
- />Department of Agrotechnology, Agriculture Faculty, Syiah Kuala University, Darussalam-Banda, 23111 Aceh, Indonesia
| | - Bakhtiar Basyah
- />Department of Agrotechnology, Agriculture Faculty, Syiah Kuala University, Darussalam-Banda, 23111 Aceh, Indonesia
| | - Tingchen Ma
- />Rice Research institute, Anhui Academy of Agricultrural Sciences, Hefei, 230031 China
| | - Zefu Li
- />Rice Research institute, Anhui Academy of Agricultrural Sciences, Hefei, 230031 China
| | - Jianbo Yang
- />Rice Research institute, Anhui Academy of Agricultrural Sciences, Hefei, 230031 China
| | - Zhongchao Yin
- />Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604 Republic of Singapore
- />Department of Biological Sciences, 14 Science Drive, National University of Singapore, Singapore 117543 Republic of Singapore
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17
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Oliver KR, McComb JA, Greene WK. Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol Evol 2014; 5:1886-901. [PMID: 24065734 PMCID: PMC3814199 DOI: 10.1093/gbe/evt141] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are a dominant feature of most flowering plant genomes. Together with other accepted facilitators of evolution, accumulating data indicate that TEs can explain much about their rapid evolution and diversification. Genome size in angiosperms is highly correlated with TE content and the overwhelming bulk (>80%) of large genomes can be composed of TEs. Among retro-TEs, long terminal repeats (LTRs) are abundant, whereas DNA-TEs, which are often less abundant than retro-TEs, are more active. Much adaptive or evolutionary potential in angiosperms is due to the activity of TEs (active TE-Thrust), resulting in an extraordinary array of genetic changes, including gene modifications, duplications, altered expression patterns, and exaptation to create novel genes, with occasional gene disruption. TEs implicated in the earliest origins of the angiosperms include the exapted Mustang, Sleeper, and Fhy3/Far1 gene families. Passive TE-Thrust can create a high degree of adaptive or evolutionary potential by engendering ectopic recombination events resulting in deletions, duplications, and karyotypic changes. TE activity can also alter epigenetic patterning, including that governing endosperm development, thus promoting reproductive isolation. Continuing evolution of long-lived resprouter angiosperms, together with genetic variation in their multiple meristems, indicates that TEs can facilitate somatic evolution in addition to germ line evolution. Critical to their success, angiosperms have a high frequency of polyploidy and hybridization, with resultant increased TE activity and introgression, and beneficial gene duplication. Together with traditional explanations, the enhanced genomic plasticity facilitated by TE-Thrust, suggests a more complete and satisfactory explanation for Darwin's "abominable mystery": the spectacular success of the angiosperms.
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Affiliation(s)
- Keith R Oliver
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
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18
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Vitte C, Fustier MA, Alix K, Tenaillon MI. The bright side of transposons in crop evolution. Brief Funct Genomics 2014; 13:276-95. [PMID: 24681749 DOI: 10.1093/bfgp/elu002] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The past decades have revealed an unexpected yet prominent role of so-called 'junk DNA' in the regulation of gene expression, thereby challenging our view of the mechanisms underlying phenotypic evolution. In particular, several mechanisms through which transposable elements (TEs) participate in functional genome diversity have been depicted, bringing to light the 'TEs bright side'. However, the relative contribution of those mechanisms and, more generally, the importance of TE-based polymorphisms on past and present phenotypic variation in crops species remain poorly understood. Here, we review current knowledge on both issues, and discuss how analyses of massively parallel sequencing data combined with statistical methodologies and functional validations will help unravelling the impact of TEs on crop evolution in a near future.
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19
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Zhang H, Duan L, Dai JS, Zhang CQ, Li J, Gu MH, Liu QQ, Zhu Y. Major QTLs reduce the deleterious effects of high temperature on rice amylose content by increasing splicing efficiency of Wx pre-mRNA. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:273-82. [PMID: 24162153 DOI: 10.1007/s00122-013-2216-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 10/14/2013] [Indexed: 05/12/2023]
Abstract
We discovered four QTLs that maintain proper rice amylose content at high temperature by increasing the splicing efficiency of Wx gene. Amylose content mainly controlled by Wx gene is a key physicochemical property for eating and cooking quality in rice. During the grain filling stage, high temperature can harm rice grain quality by significantly reducing the amylose content in many rice varieties. Here, we provide genetic evidences between Wx gene expression and rice amylose content at high temperature, and identified several quantitative trait loci (QTLs) in this pathway. We performed a genome-wide survey on a set of chromosome segment substitution lines (CSSLs) which carried chromosomal segments from the heat resistant indica 9311 in the heat-sensitive japonica Nipponbare background. Four QTLs, qHAC4, qHAC8a, qHAC8b and qHAC10, which can reduce the deleterious effects of amylose content at high temperature, were identified and mapped to chromosome 4, 8, 8 and 10, respectively. The major QTL qHAC8a, with the highest LOD score of 6.196, was physically mapped to a small chromosome segment (~300 kb). The CSSLs carrying the qHAC8a, qHAC8b and/or qHAC4 from 9311 have the high pre-mRNA splicing efficiency of Wx gene and likely lead to stable amylose content at high temperature. Thus, increasing pre-mRNA processing efficiency of Wx gene could be an important regulation mechanism for maintaining stable amylose content in rice seeds at high temperature. In addition, our results provide a theoretical basis for breeding heat-stable grain in rice.
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Affiliation(s)
- Hua Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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20
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Ii Y, Adachi S. DNA Markers Detecting Non-glutinous Rice in Glutinous Rice Processed Food. J JPN SOC FOOD SCI 2013. [DOI: 10.3136/nskkk.60.705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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21
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Kishine M, Okunishi T. Detection of Japanese Glutinous Rice Cultivars by DNA Markers for Identifying wx Mutations. J JPN SOC FOOD SCI 2011. [DOI: 10.3136/nskkk.58.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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22
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Ma J, Jiang QT, Wei YM, Andre L, Lu ZX, Chen GY, Liu YX, Zheng YL. Molecular characterization and comparative analysis of two waxy alleles in barley. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0062-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Hu G, Hawkins JS, Grover CE, Wendel JF. The history and disposition of transposable elements in polyploid Gossypium. Genome 2010; 53:599-607. [PMID: 20725147 DOI: 10.1139/g10-038] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transposable elements (TEs) are a major component of plant genomes. It is of particular interest to explore the potential activation of TE proliferation, especially in hybrids and polyploids, which often are associated with rapid genomic and epigenetic restructuring. Here we explore the consequences of genomic merger and doubling on copia and gypsy-like Gorge3 long terminal repeat (LTR) retrotransposons as well as on non-LTR long interspersed nuclear elements (LINEs) in allotetraploid cotton, Gossypium hirsutum. Using phylogenetic and quantitative methods, we describe the composition and genomic origin of TEs in polyploid Gossypium. In addition, we present information on ancient and recent transposition activities of the three TE types and demonstrate the absence of an impressive proliferation of TEs following polyploidization in Gossypium. Further, we provide evidence for present-day transcription of LINEs, a relatively minor component of Gossypium genomes, whereas the more abundant LTR retrotransposons display limited expression and only under stressed conditions.
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Affiliation(s)
- Guanjing Hu
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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24
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Izawa T, Konishi S, Shomura A, Yano M. DNA changes tell us about rice domestication. CURRENT OPINION IN PLANT BIOLOGY 2009; 12:185-92. [PMID: 19185529 DOI: 10.1016/j.pbi.2009.01.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Revised: 01/06/2009] [Accepted: 01/06/2009] [Indexed: 05/08/2023]
Abstract
Crop domestication can be considered a model system of plant evolution. Genome analyses of rice have revealed the fine population structure of this major crop associated with local origins of landraces. Recent cloning of rice domestication-related genes and identification of the responsible functional nucleotide polymorphisms in landraces, while taking into account their population structures, have revealed the existence of historical signatures of the DNA involved in the domestication process. These signatures imply the importance of multiple selection steps wherein natural variants were combined to improve crop performance during domestication. These analyses will provide new insights into the relationship between Darwinian selection for agronomical phenotypes and DNA changes in terms of plant evolution.
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Affiliation(s)
- Takeshi Izawa
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.
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25
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Jeng TL, Wang CS, Tseng TH, Wu MT, Sung JM. Nucleotide polymorphisms in the waxy gene of NaN3-induced waxy rice mutants. J Cereal Sci 2009. [DOI: 10.1016/j.jcs.2008.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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26
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Hawkins JS, Hu G, Rapp RA, Grafenberg JL, Wendel JF. Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium. Genome 2008; 51:11-8. [PMID: 18356935 DOI: 10.1139/g07-099] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transposable elements contribute significantly to plant genome evolution in myriad ways, ranging from local insertional mutations to global effects exerted on genome size through accumulation. Differential accumulation and deletion of transposable elements may profoundly affect genome size, even among members of the same genus. One example is that of Gossypium (cotton), where much of the 3-fold genome size variation is due to differential accumulation of one gypsy-like LTR retrotransposon, Gorge3. Copia and non-LTR LINE retrotransposons are also major components of the Gossypium genome, but unlike Gorge3, their extant copy numbers do not correlate with genome size. In the present study, we describe the nature and timing of transposition for copia and LINE retrotransposons in Gossypium. Our findings indicate that copia retrotransposons have been active in each lineage since divergence from a common ancestor, and that they have proliferated in a punctuated manner. However, the evolutionary history of LINEs contrasts markedly with that of the copia retrotransposons. Although LINEs have also been active in each lineage, they have accumulated in a stochastically regular manner, and phylogenetic analysis suggests that extant LINE populations in Gossypium are dominated by ancient insertions. Interestingly, the magnitude of transpositional bursts in each lineage corresponds directly with extant estimated copy number.
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Affiliation(s)
- Jennifer S Hawkins
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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