1
|
Yu S, Li T, Teng X, Yang F, Ma X, Han J, Zhou L, Bian Z, Wei H, Deng H, Zhu Y, Yu X. Autotetraploidy of rice does not potentiate the tolerance to drought stress in the seedling stage. RICE (NEW YORK, N.Y.) 2024; 17:40. [PMID: 38888627 PMCID: PMC11189374 DOI: 10.1186/s12284-024-00716-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024]
Abstract
Polyploid is considered an advantage that has evolved to be more environmentally adaptable than its diploid. To understand if doubled chromosome of diploid rice can improve drought tolerance, we evaluated the diploid (2X) and autotetraploid (4X) plants of three indica and three japonica varieties. Drought stress in the plastic bucket of four-leaf stage revealed that the drought tolerance of 4X plants was lower than that of its diploid donor plants. The assay of photosynthetic rate of all varieties showed that all 4X varieties had lower rates than their diploid donors. The capacity for reactive oxygen species production and scavenging varied among different 2X and 4X varieties. Further, transcriptomic analysis of 2X and 4X plants of four varieties under normal and drought condition showed that the wide variation of gene expression was caused by difference of varieties, not by chromosome ploidy. However, weighted gene co-expression network analysis (WGCNA) revealed that the severe interference of photosynthesis-related genes in tetraploid plants under drought stress is the primary reason for the decrease of drought tolerance in autotetraploid lines. Consistently, new transcripts analysis in autotetraploid revealed that the gene transcription related with mitochondrion and plastid of cell component was influenced most significantly. The results indicated that chromosome doubling of diploid rice weakened their drought tolerance, primarily due to disorder of photosynthesis-related genes in tetraploid plants under drought stress. Maintain tetraploid drought tolerance through chromosome doubling breeding in rice needs to start with the selection of parental varieties and more efforts.
Collapse
Affiliation(s)
- Shunwu Yu
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Tianfei Li
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Xiaoying Teng
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Fangwen Yang
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Jing Han
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Li Zhou
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Zhijuan Bian
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | - Haibin Wei
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China
| | - Hui Deng
- Institute of Crop Sciences, Wuhan Acadamy of Agricultual Sciences, Wuhan, 430345, China
| | - Yongsheng Zhu
- Institute of Crop Sciences, Wuhan Acadamy of Agricultual Sciences, Wuhan, 430345, China.
| | - Xinqiao Yu
- Shanghai Agrobiological Gene Center, Shanghai, 201106, China.
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China.
| |
Collapse
|
2
|
Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
Collapse
Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| |
Collapse
|
3
|
Hersh EW, Medina ARL, Whitton J. Dispersal and establishment traits provide a colonization advantage for a polyploid apomictic plant. AMERICAN JOURNAL OF BOTANY 2023; 110:e16149. [PMID: 36857315 DOI: 10.1002/ajb2.16149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Apomictic plants (reproducing asexually through seed) often have larger ranges and occur at higher latitudes than closely related sexuals, a pattern known as geographical parthenogenesis (GP). Explanations for GP include differences in colonizing ability due to reproductive assurance and direct/indirect effects of polyploidy (most apomicts are polyploid) on ecological tolerances. While life history traits associated with dispersal and establishment also contribute to the potential for range expansion, few studies compare these traits in related apomicts and sexuals. METHODS We investigated differences in early life history traits between diploid-sexual and polyploid-apomictic Townsendia hookeri (Asteraceae), which displays a classic pattern of GP. Using lab and greenhouse experiments, we measured seed dispersal traits, germination success, and seedling size and survival in sexual and apomictic populations from across the range of the species. RESULTS While theory predicts that trade-offs between dispersal and establishment traits should be common, this was largely not the case in T. hookeri. Apomictic seeds had both lower terminal velocity (staying aloft longer when dropped) and higher germination success than sexual seeds. While there were no differences in seedling size between reproductive types, apomicts did, however, have slightly lower seedling survival than sexuals. CONCLUSIONS These differences in early life history traits, combined with reproductive assurance conferred by apomixis, suggest that apomicts achieve a greater range through advantages in their ability to both spread and establish.
Collapse
Affiliation(s)
- Evan Whitney Hersh
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Alberto Ruiz-Larrea Medina
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Jeannette Whitton
- Department of Botany and Biodiversity Research Centre, The University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada, V6T 1Z4
| |
Collapse
|
4
|
Shimizu-Inatsugi R, Morishima A, Mourato B, Shimizu KK, Sato Y. Phenotypic variation of a new synthetic allotetraploid Arabidopsis kamchatica enhanced in natural environment. FRONTIERS IN PLANT SCIENCE 2023; 13:1058522. [PMID: 36684772 PMCID: PMC9846130 DOI: 10.3389/fpls.2022.1058522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The phenotypic variation of vegetative organs and reproductive organs of newly synthesized and natural Arabidopsis kamchatica genotypes was investigated in both a controlled environment and a natural environment in an experimental garden. When we compared the variation of their leaf shape as a vegetative organ, the synthetic A. kamchatica individuals grown in the garden showed larger variation compared with the individuals incubated in a growth chamber, suggesting enhanced phenotypic variation in a natural fluctuating environment. In contrast, the natural A. kamchatica genotypes did not show significant change in variation by growth condition. The phenotypic variation of floral organs by growth condition was much smaller in both synthetic and natural A. kamchatica genotypes, and the difference in variation width between the growth chamber and the garden was not significant in each genotype as well as among genotypes. The higher phenotypic variation in synthetic leaf may imply flexible transcriptomic regulation of a newly synthesized polyploid compared with a natural polyploid.
Collapse
Affiliation(s)
- Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Aki Morishima
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Beatriz Mourato
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Yasuhiro Sato
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| |
Collapse
|
5
|
Lai H, Zhou Y, Chen W, Deng Y, Qiu Y, Chen X, Guo J. Changes in sucrose metabolism patterns affect the early maturation of Cassava sexual tetraploid roots. BMC PLANT BIOLOGY 2022; 22:574. [PMID: 36496357 PMCID: PMC9738016 DOI: 10.1186/s12870-022-03969-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Cassava (Manihot esculenta Crantz) is an important multiuse crop grown for economic and energy purposes. Its vegetative organs are storage roots, in which the main storage material is starch. The accumulation characteristics of starch in cassava roots can directly affect the yield, starch content and maturation of cassava storage roots. In this study, we used a cassava sexual tetraploid (ST), which showed early maturation heterosis in previous work, as the main test material. We analyzed the sucrose metabolism and starch accumulation characteristics of the ST and its parents from the leaf "source" to the storage root "sink" during different developmental stages and explored the regulatory mechanisms of ST storage root early maturation by combining the transcriptome data of the storage roots during the expansion period. RESULTS The results showed that the trends in sucrose, glucose and fructose contents in the ST leaves were similar to those of the two parents during different stages of development, but the trends in the ST storage roots were significantly different from those of their parents, which showed high sucrose utilization rates during the early stage of development and decreased utilization capacity in the late developmental stage. Transcriptome data showed that the genes that were expressed differentially between ST and its parents were mainly involved in the degradation and utilization of sucrose in the storage roots, and four key enzyme genes were significantly upregulated (Invertase MeNINV8/MeVINV3, Sucrose synthase MeSuSy2, Hexokinase MeHXK2), while the expressions of key enzyme genes involved in starch synthesis were not significantly different. CONCLUSIONS The results revealed that the pattern of sucrose degradation and utilization in the cassava ST was different from that of its parents and promoted early maturation in its tuberous roots. Starch accumulation in the ST from sucrose mainly occurred during the early expansion stage of the storage roots, and the starch content during this period was higher than that of both parents, mainly due to the regulation of invertase and hexokinase activities during sucrose metabolism. This study provides a basis for further genetic improvements to cassava traits and for breeding varieties that mature early and are adapted well to provide starch supply requirements.
Collapse
Affiliation(s)
- Hanggui Lai
- Tropical Crops College of Hainan University, Haikou, 571104, China
| | - Yangjiao Zhou
- Tropical Crops College of Hainan University, Haikou, 571104, China
| | - Weiwen Chen
- Hainan Forest Tree Seeds (Saplings) Terminal, Haikou, 570203, China
| | - Yajie Deng
- Tropical Crops College of Hainan University, Haikou, 571104, China
| | - Yue Qiu
- Tropical Crops College of Hainan University, Haikou, 571104, China
| | - Xia Chen
- College of Jiyang, Zhejiang A&F University, Zhuji, 311800, China.
| | - Jianchun Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| |
Collapse
|
6
|
Islam MM, Deepo DM, Nasif SO, Siddique AB, Hassan O, Siddique AB, Paul NC. Cytogenetics and Consequences of Polyploidization on Different Biotic-Abiotic Stress Tolerance and the Potential Mechanisms Involved. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202684. [PMID: 36297708 PMCID: PMC9609754 DOI: 10.3390/plants11202684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 06/12/2023]
Abstract
The application of polyploidy in sustainable agriculture has already brought much appreciation among researchers. Polyploidy may occur naturally or can be induced in the laboratory using chemical or gaseous agents and results in complete chromosome nondisjunction. This comprehensive review described the potential of polyploidization on plants, especially its role in crop improvement for enhanced production and host-plant resistance development against pests and diseases. An in-depth investigation on techniques used in the induction of polyploidy, cytogenetic evaluation methods of different ploidy levels, application, and current research trends is also presented. Ongoing research has mainly aimed to bring the recurrence in polyploidy, which is usually detected by flow cytometry, chromosome counting, and cytogenetic techniques such as fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). Polyploidy can bring about positive consequences in the growth and yield attributes of crops, making them more tolerant to abiotic and biotic stresses. However, the unexpected change in chromosome set and lack of knowledge on the mechanism of stress alleviation is hindering the application of polyploidy on a large scale. Moreover, a lack of cost-benefit analysis and knowledge gaps on the socio-economic implication are predominant. Further research on polyploidy coupling with modern genomic technologies will help to bring real-world market prospects in the era of changing climate. This review on polyploidy provides a solid foundation to do next-generation research on crop improvement.
Collapse
Affiliation(s)
- Md Mazharul Islam
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
- Research and Development, Horticultural Crop Breeding, Quality Feeds Limited, Dhaka 1230, Bangladesh
| | - Deen Mohammad Deepo
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
| | - Saifullah Omar Nasif
- Global Centre for Environmental Remediation (GCER), College of Engineering Science and Environment, The University of Newcastle, Newcastle, NSW 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), ATC Building, The University of Newcastle, Newcastle, NSW 2308, Australia
| | - Abu Bakar Siddique
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, 90736 Umeå, Sweden
| | - Oliul Hassan
- Department of Ecology and Environmental System, College of Ecology and Environmental Sciences, Kyungpook National University, Sangju 37224, Korea
| | - Abu Bakar Siddique
- Department of Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Narayan Chandra Paul
- Kumho Life Science Laboratory, Department of Integrative Food Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea
| |
Collapse
|
7
|
Boza Espinoza TE, Kessler M. A monograph of the genus Polylepis (Rosaceae). PHYTOKEYS 2022; 203:1-274. [PMID: 36761034 PMCID: PMC9849045 DOI: 10.3897/phytokeys.203.83529] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
We present a monograph of the high Andean tree genus Polylepis (Rosaceae), based on a species concept considering morphological, climatic and biogeographic distinctness as indicators of evolutionary independence. In total, we recognize 45 species of Polylepis, grouped in five sections. Polylepissect.Sericeae is represented by 15 species in four subsections, P.sect.Reticulatae by seven species, P.sect.Subsericantes by three species, P.sect.Australes by two species and P.sect.Incanaee by three subsections with 18 species. We describe seven new species, one from Colombia (P.frontinensis), one from Ecuador (P.simpsoniae) and five from Peru (P.acomayensis, P.fjeldsaoi, P.occidentalis, P.pilosissima and P.sacra). Three species from Peru (P.albicans, P.pallidistigma and P.serrata) are re-instated as valid species. Two taxa from Bolivia (P.incanoides and P.nana) are elevated from subspecies to species rank. The morphology, habitat, distribution, ecology and conservation status of each species are documented. We also provide an identification key to the species of the genus and general introductions on taxonomic history, morphology, evolution, ecology and conservation.
Collapse
Affiliation(s)
- Tatiana Erika Boza Espinoza
- Institute for Nature, Earth and Energy (INTE), Pontificia Universidad Católica del Perú (PUCP), Av. Universitaria 1801, Lima 15088, PeruPontificia Universidad Católica del Perú (PUCP)LimaPeru
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, SwitzerlandUniversity of ZurichZürichSwitzerland
| |
Collapse
|
8
|
Chen T, Sheng Y, Hao Z, Long X, Fu F, Liu Y, Tang Z, Ali A, Peng Y, Liu Y, Lu L, Hu X, Shi J, Chen J. Transcriptome and proteome analysis suggest enhanced photosynthesis in tetraploid Liriodendron sino-americanum. TREE PHYSIOLOGY 2021; 41:1953-1971. [PMID: 33791793 PMCID: PMC8498940 DOI: 10.1093/treephys/tpab039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 02/17/2021] [Indexed: 06/01/2023]
Abstract
Polyploidy generally provides an advantage in phenotypic variation and growth vigor. However, the underlying mechanisms remain poorly understood. The tetraploid Liriodendron sino-americanum (Liriodendron × sinoamericanum P.C Yieh ex C.B. Shang & Zhang R.Wang) exhibits altered morphology compared with its diploid counterpart, including larger, thicker and deeper green leaves, bigger stomata, thicker stems and increased tree height. Such characteristics can be useful in ornamental and industrial applications. To elucidate the molecular mechanisms behind this variation, we performed a comparative transcriptome and proteome analysis. Our transcriptome data indicated that some photosynthesis genes and pathways were differentially altered and enriched in tetraploid L. sino-americanum, mainly related to F-type ATPase, the cytochrome b6/f complex, photosynthetic electron transport, the light harvesting chlorophyll protein complexes, and photosystem I and II. Most of the differentially expressed proteins we could identify are also involved in photosynthesis. Our physiological results showed that tetraploids have an enhanced photosynthetic capacity, concomitant with great levels of sugar and starch in leaves. This suggests that tetraploid L. sino-americanum might experience comprehensive transcriptome reprogramming of genes related to photosynthesis. This study has especially emphasized molecular changes involved in photosynthesis that accompany polyploidy, and provides a possible explanation for the altered phenotype of polyploidy plants in comparison with their diploid form.
Collapse
Affiliation(s)
- Tingting Chen
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Yu Sheng
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Xiaofei Long
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Fangfang Fu
- College of Forestry, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Yang Liu
- School of Forestry, Northeast Forestry University, 26 Hexing Rd, Xiangfang District, Harbin 150040, China
| | - Zhonghua Tang
- College of Chemistry, Chemical Engineer and Resource Utilization, Northeast Forestry University, 26 Hexing Rd, Xiangfang District, Harbin 150040, China
| | - Asif Ali
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Ye Peng
- College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Yang Liu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Lu Lu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Xiangyang Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, 266 Jufeng Rd, Baoshan, Shanghai 201900, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Rd, Xuanwu, Nanjing 210037, China
| |
Collapse
|
9
|
Hao Y, Mabry ME, Edger PP, Freeling M, Zheng C, Jin L, VanBuren R, Colle M, An H, Abrahams RS, Washburn JD, Qi X, Barry K, Daum C, Shu S, Schmutz J, Sankoff D, Barker MS, Lyons E, Pires JC, Conant GC. The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. Genome Res 2021; 31:799-810. [PMID: 33863805 PMCID: PMC8092008 DOI: 10.1101/gr.270033.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/05/2021] [Indexed: 01/08/2023]
Abstract
The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica, a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.
Collapse
Affiliation(s)
- Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Makenzie E Mabry
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
- Genetics and Genome Sciences, Michigan State University, East Lansing, Michigan 48824, USA
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Lingling Jin
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824, USA
| | - Marivi Colle
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Hong An
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - R Shawn Abrahams
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Jacob D Washburn
- Plant Genetics Research Unit, USDA-ARS, Columbia, Missouri 65211, USA
| | - Xinshuai Qi
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
- Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA
- Program in Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| |
Collapse
|
10
|
Qi X, An H, Hall TE, Di C, Blischak PD, McKibben MTW, Hao Y, Conant GC, Pires JC, Barker MS. Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. THE NEW PHYTOLOGIST 2021; 230:372-386. [PMID: 33452818 DOI: 10.1111/nph.17194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication. In order to test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crop varieties of Brassica rapa. Like all 'diploid' flowering plants, B. rapa has a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than 100 cultivated B. rapa accessions. Using a combination of approaches, we identified > 3000 candidate genes associated with the domestication of four major B. rapa crop varieties. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs were significantly more diverse than non-paleologs. Our analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication of B. rapa and provide support for its importance in the success of modern agriculture.
Collapse
Affiliation(s)
- Xinshuai Qi
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Tara E Hall
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Chenlu Di
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Paul D Blischak
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael T W McKibben
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| |
Collapse
|
11
|
Boza Espinoza TE, Popp V, Kessler M. Guard cell sizes and ploidy levels in Polylepis (Rosaceae). NEOTROPICAL BIODIVERSITY 2020. [DOI: 10.1080/23766808.2020.1844992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Tatiana Erika Boza Espinoza
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Universidad Nacional de San Antonio Abad del Cusco, Herbario Vargas CUZ, Cusco, Perú
| | | | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| |
Collapse
|
12
|
Behling AH, Shepherd LD, Cox MP. The importance and prevalence of allopolyploidy in Aotearoa New Zealand. J R Soc N Z 2019. [DOI: 10.1080/03036758.2019.1676797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Anna H. Behling
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Murray P. Cox
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| |
Collapse
|
13
|
Holmes RS. Polyploidy among salmonid aldehyde dehydrogenase genes and proteins. Chem Biol Interact 2019; 303:22-26. [PMID: 30776359 DOI: 10.1016/j.cbi.2019.01.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/17/2019] [Accepted: 01/25/2019] [Indexed: 01/22/2023]
Abstract
Bioinformatic analyses of salmon (Salmo salar) ALDH amino acid sequences supported the presence of at least 30 ALDH genes, which is more than for any other higher vertebrate and is greater than the 19 human ALDH genes currently reported. These included 8 polyploid ALDH genes and proteins: ALDH1A2 (chromosomes 11 and 26); ALDH1L2 (chromosomes 7 and 17); ALDH2, encoding mitochondrial ALDH2 (chromosomes 2 and 5); ALDH3A2 (chromosomes 4, 9 and 20), for which evidence for 5 genes was obtained; ALDH3B1 (chromosomes 3, 6 and 24); ALDH4A1 (chromosomes 12 and 22); ALDH6A1 (chromosomes 1, 6 and 15); and ALDH18A1 (chromosomes 19 and 28). In contrast, 7 salmon ALDH gene families (ALDH1A1, ALDH1A3, ALDH5, ALDH7, ALDH8, ALDH9 and ALDH16) possessed only one gene family member. Phylogenetic studies of salmon and rainbow trout ALDH3A2 genes and proteins suggested that salmonid gene tetraploidy has occurred in at least 2 distinct stages of ALDH3A2 gene evolution.
Collapse
Affiliation(s)
- Roger S Holmes
- Griffith Institute for Drug Discovery and School of Environment and Science, Griffith University, Nathan, 4111, QLD, Australia.
| |
Collapse
|
14
|
Jones DM, Wells R, Pullen N, Trick M, Irwin JA, Morris RJ. Spatio-temporal expression dynamics differ between homologues of flowering time genes in the allopolyploid Brassica napus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:103-118. [PMID: 29989238 PMCID: PMC6175450 DOI: 10.1111/tpj.14020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/18/2018] [Accepted: 06/19/2018] [Indexed: 05/20/2023]
Abstract
Polyploidy is a recurrent feature of eukaryotic evolution and has been linked to increases in complexity, adaptive radiation and speciation. Within angiosperms such events have occurred repeatedly in many plant lineages. Here we investigate the retention and spatio-temporal expression dynamics of duplicated genes predicted to regulate the floral transition in Brassica napus (oilseed rape, OSR). We show that flowering time genes are preferentially retained relative to other genes in the OSR genome. Using a transcriptome time series in two tissues (leaf and shoot apex) across development we show that 67% of these retained flowering time genes are expressed. Furthermore, between 64% (leaf) and 74% (shoot apex) of the retained gene homologues show diverged expression patterns relative to each other across development, suggesting neo- or subfunctionalization. A case study of homologues of the shoot meristem identity gene TFL1 reveals differences in cis-regulatory elements that could explain this divergence. Such differences in the expression dynamics of duplicated genes highlight the challenges involved in translating gene regulatory networks from diploid model systems to more complex polyploid crop species.
Collapse
Affiliation(s)
- D. Marc Jones
- Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Computational and Systems BiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Rachel Wells
- Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Nick Pullen
- Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Martin Trick
- Computational and Systems BiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Judith A. Irwin
- Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Richard J. Morris
- Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Computational and Systems BiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| |
Collapse
|
15
|
Ferrão LFV, Benevenuto J, Oliveira IDB, Cellon C, Olmstead J, Kirst M, Resende MFR, Munoz P. Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00107] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
16
|
Samans B, Chalhoub B, Snowdon RJ. Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species Brassica napus. THE PLANT GENOME 2017; 10. [PMID: 29293818 DOI: 10.3835/plantgenome2017.02.0013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyploidization has played a major role in crop plant evolution, leading to advantageous traits that have been selected by humans. Here, we describe restructuring patterns in the genome of L., a recent allopolyploid species. Widespread segmental deletions, duplications, and homeologous chromosome exchanges were identified in diverse genome sequences from 32 natural and 20 synthetic accessions, indicating that homeologous exchanges are a major driver of postpolyploidization genome diversification. Breakpoints of genomic rearrangements are rich in microsatellite sequences that are known to interact with the meiotic recombination machinery. In both synthetic and natural , a subgenome bias was observed toward exchanges replacing larger chromosome segments from the C-subgenome by their smaller, homeologous A-subgenome segments, driving postpolyploidization genome size reduction. Selection in natural favored segmental deletions involving genes associated with immunity, reproduction, and adaptation. Deletions affecting mismatch repair system genes, which are assumed to control homeologous recombination, were also found to be under selection. Structural exchanges between homeologous subgenomes appear to be a major source of novel genetic diversity in de novo allopolyploids. Documenting the consequences of genomic collision by genomic resequencing gives insights into the adaptive processes accompanying allopolyploidization.
Collapse
|
17
|
Griswold CK, Williamson MW. A two-locus model of selection in autotetraploids: Chromosomal gametic disequilibrium and selection for an adaptive epistatic gene combination. Heredity (Edinb) 2017; 119:314-327. [PMID: 28832578 PMCID: PMC5637366 DOI: 10.1038/hdy.2017.44] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 06/23/2017] [Accepted: 06/23/2017] [Indexed: 11/08/2022] Open
Abstract
In this paper, we present a two-locus model of selection for an autotetraploid population. We also investigate a measure of disequilibrium that occurs between homologous chromosomes in the diploid gametes of autotetraploids, namely chromosomal gametic disequilibrium. We apply the model and measure of disequilibrium to compare how an adaptive epistatic gene combination is inherited and selected for in an autotetraploid versus diploid population. Autotetraploids are expected to have higher genomic mutation and recombination rates relative to diploids, due to a greater ploidy level. These two processes can work in opposition in terms of selection for adaptive epistatic gene combinations. While a higher genomic mutation rate can generate the alleles that confer an epistatic combination more quickly, a higher recombination rate is expected to break the combination down more quickly. We show that chromosomal gametic disequilibrium in autotetraploids can potentially compensate for less linkage disequilibrium in autotetraploids. We also explore how double reduction affects the inheritance of and selection for an epistatic gene combination. Over all, our analysis provides theoretical evidence that adaptive epistatic combinations can be selected for more efficiently in autotetraploids versus diploids. This may provide insight into empirical work that finds epistasis has a role in causing population differentiation between autotetraploid plant populations.
Collapse
Affiliation(s)
- C K Griswold
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - M W Williamson
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
18
|
Roy Choudhury S, Pandey S. Recently duplicated plant heterotrimeric Gα proteins with subtle biochemical differences influence specific outcomes of signal-response coupling. J Biol Chem 2017; 292:16188-16198. [PMID: 28827312 PMCID: PMC5625049 DOI: 10.1074/jbc.m117.793380] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/10/2017] [Indexed: 12/31/2022] Open
Abstract
Heterotrimeric G-proteins, comprising Gα, Gβ, and Gγ subunits, regulate key signaling processes in eukaryotes. The Gα subunit determines the status of signaling by switching between inactive GDP-bound and active GTP-bound forms. Unlike animal systems, in which multiple Gα proteins with variable biochemical properties exist, plants have fewer, highly similar Gα subunits that have resulted from recent genome duplications. These proteins exhibit subtle differences in their GTP-binding, GDP/GTP-exchange, and GTP-hydrolysis activities, but the extent to which these differences contribute to affect plant signaling and development remains unknown. To evaluate this, we expressed native and engineered Gα proteins from soybean in an Arabidopsis Gα-null background and studied their effects on modulating a range of developmental and hormonal signaling phenotypes. Our results indicated that inherent biochemical differences in these highly similar Gα proteins are biologically relevant, and some proteins are more flexible than others in influencing the outcomes of specific signals. These observations suggest that alterations in the rate of the G-protein cycle itself may contribute to the specificity of response regulation in plants by affecting the duration of active signaling and/or by the formation of distinct protein-protein complexes. In species such as Arabidopsis having a single canonical Gα, this rate could be affected by regulatory proteins in the presence of specific signals, whereas in plants with multiple Gα proteins, an even more complex regulation may exist, which likely contributes to the specificity of signal-response coupling.
Collapse
Affiliation(s)
| | - Sona Pandey
- From the Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| |
Collapse
|
19
|
Lv Y, Xiao J, Liu J, Xing F. E2F8 is a Potential Therapeutic Target for Hepatocellular Carcinoma. J Cancer 2017; 8:1205-1213. [PMID: 28607595 PMCID: PMC5463435 DOI: 10.7150/jca.18255] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/11/2017] [Indexed: 12/15/2022] Open
Abstract
E2F transcriptional factors are widely expressed in a number of tissues and organs, possessing many regulatory functions related to cellular proliferation, differentiation, DNA repair, cell-cycle and cell apoptosis. E2F8 is a recently identified member of the E2F family with a duplicated DNA-binding domain feature discriminated from E2F1-6, controlling gene expression in a dimerization partner-independent manner. It is indispensable for angiogenesis, lymphangiogenesis and embryonic development. Although E2F8 and E2F7 perform complementary and overlapping functions in many cell metabolisms, E2F8, but not E2F7, overexpresses remarkably in hepatocellular carcinoma (HCC) to facilitate the HCC occurrence and development via activating a E2F1/ Cyclin D1 signaling pathway to regulate the G1- to S-phase transition of cell cycle progression or transcriptionally suppressing CDK1 to induce hepatocyte polyploidization. It also involves closely a variety of cellular physiological functions and pathological processes, which may bring a new breakthrough for the treatment of certain diseases, especially the HCC. Here, we summarize the latest progress of E2F8 on its relevant functions and mechanisms as well as potential application.
Collapse
Affiliation(s)
- Yi Lv
- Department of Immunobiology, Institute of Tissue Transplantation and Immunology, Jinan University, Guangzhou, China.,Key Laboratory of Functional Protein Research of Guangdong, Higher Education Institutes, Jinan University, Guangzhou, China
| | - Jia Xiao
- Department of Immunobiology, Institute of Tissue Transplantation and Immunology, Jinan University, Guangzhou, China
| | - Jing Liu
- Department of Stomatology, Jinan University, Guangzhou, China
| | - Feiyue Xing
- Department of Immunobiology, Institute of Tissue Transplantation and Immunology, Jinan University, Guangzhou, China.,Key Laboratory of Functional Protein Research of Guangdong, Higher Education Institutes, Jinan University, Guangzhou, China
| |
Collapse
|
20
|
Braynen J, Yang Y, Wei F, Cao G, Shi G, Tian B, Zhang X, Jia H, Wei X, Wei Z. Transcriptome Analysis of Floral Buds Deciphered an Irregular Course of Meiosis in Polyploid Brassica rapa. FRONTIERS IN PLANT SCIENCE 2017; 8:768. [PMID: 28553302 PMCID: PMC5427127 DOI: 10.3389/fpls.2017.00768] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 04/24/2017] [Indexed: 05/21/2023]
Abstract
Polyploidy is a fundamental process in plant evolution. Understanding the polyploidy-associated effects on plant reproduction is essential for polyploid breeding program. In the present study, our cytological analysis firstly demonstrated that an overall course of meiosis was apparently distorted in the synthetic polyploid Brassica rapa in comparison with its diploid progenitor. To elucidate genetic basis of this irregular meiosis at a molecular level, the comparative RNA-seq analysis was further used to investigate differential genetic regulation of developing floral buds identified at meiosis between autotetraploid and diploid B. rapa. In total, compared to its diploid counterparts, among all 40,927 expressed genes revealed, 4,601 differentially expressed genes (DEGs) were identified in the floral buds of autotetraploid B. rapa, among which 288 DEGs annotated were involved in meiosis. Notably, DMC1 identified as one previously known meiosis-specific gene involved in inter-homologous chromosome dependent repair of DNA double stranded breaks (DSBs), was significantly down-regulated in autotetraploid B. rapa, which presumably contributed to abnormal progression during meiosis I. Although certain DEGs associated with RNA helicase, cell cycling, and somatic DNA repair were up-regulated after genome duplication, genes associated with meiotic DSB repair were significantly down-regulated. Furthermore, the expression of randomly selected DEGs by RNA-seq analysis was confirmed by quantitative real-time PCR analysis in both B. rapa and Arabidopsis thaliana. Our results firstly account for adverse effects of polyploidy on an entire course of meiosis at both cytological and transcriptomic levels, and allow for a comprehensive understanding of the uniformity and differences in the transcriptome of floral buds at meiosis between diploid and polyploid B. rapa as well.
Collapse
Affiliation(s)
- Janeen Braynen
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
- Institute of Horticultural Research, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Yan Yang
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
| | - Fang Wei
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
- *Correspondence: Fang Wei
| | - Gangqiang Cao
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
| | - Gongyao Shi
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
| | - Baoming Tian
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
- Baoming Tian
| | - Xiaowei Zhang
- Institute of Horticultural Research, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Hao Jia
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
- Institute of Horticultural Research, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Xiaochun Wei
- Institute of Horticultural Research, Henan Academy of Agricultural SciencesZhengzhou, China
- Xiaochun Wei
| | - Zhenzhen Wei
- School of Life Sciences, Zhengzhou UniversityZhengzhou, China
- Institute of Horticultural Research, Henan Academy of Agricultural SciencesZhengzhou, China
| |
Collapse
|
21
|
Salman-Minkov A, Sabath N, Mayrose I. Whole-genome duplication as a key factor in crop domestication. NATURE PLANTS 2016; 2:16115. [PMID: 27479829 DOI: 10.1038/nplants.2016.115] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/30/2016] [Indexed: 05/21/2023]
Abstract
Polyploidy is commonly thought to be associated with the domestication process because of its concurrence with agriculturally favourable traits and because it is widespread among the major plant crops(1-4). Furthermore, the genetic consequences of polyploidy(5-7) might have increased the adaptive plasticity of those plants, enabling successful domestication(6-8). Nevertheless, a detailed phylogenetic analysis regarding the association of polyploidy with the domestication process, and the temporal order of these distinct events, has been lacking(3). Here, we have gathered a comprehensive data set including dozens of genera, each containing one or more major crop species and for which sufficient sequence and chromosome number data exist. Using probabilistic inference of ploidy levels conducted within a phylogenetic framework, we have examined the incidence of polyploidization events within each genus. We found that domesticated plants have gone through more polyploidy events than their wild relatives, with monocots exhibiting the most profound difference: 54% of the crops are polyploids versus 40% of the wild species. We then examined whether the preponderance of polyploidy among crop species is the result of two, non-mutually-exclusive hypotheses: (1) polyploidy followed by domestication, and (2) domestication followed by polyploidy. We found support for the first hypothesis, whereby polyploid species were more likely to be domesticated than their wild relatives, suggesting that the genetic consequences of polyploidy have conferred genetic preconditions for successful domestication on many of these plants.
Collapse
Affiliation(s)
- Ayelet Salman-Minkov
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Niv Sabath
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
22
|
Sattler MC, Carvalho CR, Clarindo WR. The polyploidy and its key role in plant breeding. PLANTA 2016; 243:281-96. [PMID: 26715561 DOI: 10.1007/s00425-015-2450-x] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 12/16/2015] [Indexed: 05/19/2023]
Abstract
This article provides an up-to-date review concerning from basic issues of polyploidy to aspects regarding the relevance and role of both natural and artificial polyploids in plant breeding programs. Polyploidy is a major force in the evolution of both wild and cultivated plants. Polyploid organisms often exhibit increased vigor and, in some cases, outperform their diploid relatives in several aspects. This remarkable superiority of polyploids has been the target of many plant breeders in the last century, who have induced polyploidy and/or used natural polyploids in many ways to obtain increasingly improved plant cultivars. Some of the most important consequences of polyploidy for plant breeding are the increment in plant organs ("gigas" effect), buffering of deleterious mutations, increased heterozygosity, and heterosis (hybrid vigor). Regarding such features as tools, cultivars have been generated with higher yield levels, improving the product quality and increasing the tolerance to both biotic and abiotic stresses. In some cases, when the crossing between two species is not possible because of differences in ploidy level, polyploids can be used as a bridge for gene transferring between them. In addition, polyploidy often results in reduced fertility due to meiotic errors, allowing the production of seedless varieties. On the other hand, the genome doubling in a newly formed sterile hybrid allows the restoration of its fertility. Based on these aspects, the present review initially concerns the origin, frequency and classification of the polyploids, progressing to show the revolution promoted by the discovery of natural polyploids and polyploidization induction in the breeding program status of distinct crops.
Collapse
Affiliation(s)
- Mariana Cansian Sattler
- Laboratório de Citogenética, Departamento de Biologia, Centro de Ciências Agrárias, Universidade Federal do Espírito Santo, Alegre, ES, CEP: 29.500-000, Brazil
| | - Carlos Roberto Carvalho
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa, MG, CEP: 36.570-000, Brazil
| | - Wellington Ronildo Clarindo
- Laboratório de Citogenética, Departamento de Biologia, Centro de Ciências Agrárias, Universidade Federal do Espírito Santo, Alegre, ES, CEP: 29.500-000, Brazil.
| |
Collapse
|
23
|
Han Y, Xin M, Huang K, Xu Y, Liu Z, Hu Z, Yao Y, Peng H, Ni Z, Sun Q. Altered expression of TaRSL4 gene by genome interplay shapes root hair length in allopolyploid wheat. THE NEW PHYTOLOGIST 2016; 209:721-32. [PMID: 26334764 DOI: 10.1111/nph.13615] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/22/2015] [Indexed: 05/23/2023]
Abstract
Polyploidy is a major driving force in plant evolution and speciation. Phenotypic changes often arise with the formation, natural selection and domestication of polyploid plants. However, little is known about the consequence of hybridization and polyploidization on root hair development. Here, we report that root hair length of synthetic and natural allopolyploid wheats is significantly longer than those of their diploid progenitors, whereas no difference is observed between allohexaploid and allotetraploid wheats. The expression of wheat gene TaRSL4, an orthologue of AtRSL4 controlling the root hair development in Arabidopsis, was positively correlated with the root hair length in diploid and allotetraploid wheats. Moreover, transcript abundance of TaRSL4 homoeologue from A genome (TaRSL4-A) was much higher than those of other genomes in natural allopolyploid wheat. Notably, increased root hair length by overexpression of the TaRSL4-A in wheat led to enhanced shoot fresh biomass under nutrient-poor conditions. Our observations indicate that increased root hair length in allohexaploid wheat originated in the allotetraploid progenitors and altered expression of TaRSL4 gene by genome interplay shapes root hair length in allopolyploid wheat.
Collapse
Affiliation(s)
- Yao Han
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Ke Huang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Yuyun Xu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Zhenshan Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Yuanmingyuan Xi Road No. 2, Haidian District, Beijing, 100193, China
| |
Collapse
|
24
|
Clevenger J, Chavarro C, Pearl SA, Ozias-Akins P, Jackson SA. Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations. MOLECULAR PLANT 2015; 8:831-46. [PMID: 25676455 DOI: 10.1016/j.molp.2015.02.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/21/2015] [Accepted: 02/01/2015] [Indexed: 05/23/2023]
Abstract
Understanding the relationship between genotype and phenotype is a major biological question and being able to predict phenotypes based on molecular genotypes is integral to molecular breeding. Whole-genome duplications have shaped the history of all flowering plants and present challenges to elucidating the relationship between genotype and phenotype, especially in neopolyploid species. Although single nucleotide polymorphisms (SNPs) have become popular tools for genetic mapping, discovery and application of SNPs in polyploids has been difficult. Here, we summarize common experimental approaches to SNP calling, highlighting recent polyploid successes. To examine the impact of software choice on these analyses, we called SNPs among five peanut genotypes using different alignment programs (BWA-mem and Bowtie 2) and variant callers (SAMtools, GATK, and Freebayes). Alignments produced by Bowtie 2 and BWA-mem and analyzed in SAMtools shared 24.5% concordant SNPs, and SAMtools, GATK, and Freebayes shared 1.4% concordant SNPs. A subsequent analysis of simulated Brassica napus chromosome 1A and 1C genotypes demonstrated that, of the three software programs, SAMtools performed with the highest sensitivity and specificity on Bowtie 2 alignments. These results, however, are likely to vary among species, and we therefore propose a series of best practices for SNP calling in polyploids.
Collapse
Affiliation(s)
- Josh Clevenger
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Tifton, GA 31793, USA
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Stephanie A Pearl
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Tifton, GA 31793, USA.
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA.
| |
Collapse
|
25
|
Hu G, Koh J, Yoo MJ, Pathak D, Chen S, Wendel JF. Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.). PLANTA 2014; 240:1237-1251. [PMID: 25156487 DOI: 10.1007/s00425-014-2146-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/07/2014] [Indexed: 06/03/2023]
Abstract
Comparative proteomic analyses were performed to detail the evolutionary consequences of strong directional selection for enhanced fiber traits in modern upland cotton (Gossypium hirsutum L.). Using two complementary proteomic approaches, 2-DE and iTRAQ LC-MS/MS, fiber proteomes were examined for four representative stages of fiber development. Approximately 1,000 protein features were characterized using each strategy, collectively resulting in the identification and functional categorization of 1,223 proteins. Unequal contributions of homoeologous proteins were detected for over a third of the fiber proteome, but overall expression was balanced with respect to the genome-of-origin in the allopolyploid G. hirsutum. About 30% of the proteins were differentially expressed during fiber development within wild and domesticated cotton. Notably, domestication was accompanied by a doubling of protein developmental dynamics for the period between 10 and 20 days following pollination. Expression levels of 240 iTRAQ proteins and 293 2-DE spots were altered by domestication, collectively representing multiple cellular and metabolic processes, including metabolism, energy, protein synthesis and destination, defense and stress response. Analyses of homoeolog-specific expression indicate that duplicated gene products in cotton fibers can be differently regulated in response to selection. These results demonstrate the power of proteomics for the analysis of crop domestication and phenotypic evolution.
Collapse
Affiliation(s)
- Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | | | | | | | | | | |
Collapse
|
26
|
Renny-Byfield S, Wendel JF. Doubling down on genomes: polyploidy and crop plants. AMERICAN JOURNAL OF BOTANY 2014; 101:1711-25. [PMID: 25090999 DOI: 10.3732/ajb.1400119] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyploidy, or whole genome multiplication, is ubiquitous among angiosperms. Many crop species are relatively recent allopolyploids, resulting from interspecific hybridization and polyploidy. Thus, an appreciation of the evolutionary consequences of (allo)polyploidy is central to our understanding of crop plant domestication, agricultural improvement, and the evolution of angiosperms in general. Indeed, many recent insights into plant biology have been gleaned from polyploid crops, including, but not limited to wheat, tobacco, sugarcane, apple, and cotton. A multitude of evolutionary processes affect polyploid genomes, including rapid and substantial genome reorganization, transgressive gene expression alterations, gene fractionation, gene conversion, genome downsizing, and sub- and neofunctionalization of duplicate genes. Often these genomic changes are accompanied by heterosis, robustness, and the improvement of crop yield, relative to closely related diploids. Historically, however, the genome-wide analysis of polyploid crops has lagged behind those of diploid crops and other model organisms. This lag is partly due to the difficulties in genome assembly, resulting from the genomic complexities induced by combining two or more evolutionarily diverged genomes into a single nucleus and by the significant size of polyploid genomes. In this review, we explore the role of polyploidy in angiosperm evolution, the domestication process and crop improvement. We focus on the potential of modern technologies, particularly next-generation sequencing, to inform us on the patterns and processes governing polyploid crop improvement and phenotypic change subsequent to domestication.
Collapse
Affiliation(s)
- Simon Renny-Byfield
- Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011 USA
| | - Jonathan F Wendel
- Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011 USA
| |
Collapse
|
27
|
Fuentes I, Stegemann S, Golczyk H, Karcher D, Bock R. Horizontal genome transfer as an asexual path to the formation of new species. Nature 2014; 511:232-5. [PMID: 24909992 DOI: 10.1038/nature13291] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/31/2014] [Indexed: 11/08/2022]
Abstract
Allopolyploidization, the combination of the genomes from two different species, has been a major source of evolutionary innovation and a driver of speciation and environmental adaptation. In plants, it has also contributed greatly to crop domestication, as the superior properties of many modern crop plants were conferred by ancient allopolyploidization events. It is generally thought that allopolyploidization occurred through hybridization events between species, accompanied or followed by genome duplication. Although many allopolyploids arose from closely related species (congeners), there are also allopolyploid species that were formed from more distantly related progenitor species belonging to different genera or even different tribes. Here we have examined the possibility that allopolyploidization can also occur by asexual mechanisms. We show that upon grafting--a mechanism of plant-plant interaction that is widespread in nature--entire nuclear genomes can be transferred between plant cells. We provide direct evidence for this process resulting in speciation by creating a new allopolyploid plant species from a herbaceous species and a woody species in the nightshade family. The new species is fertile and produces fertile progeny. Our data highlight natural grafting as a potential asexual mechanism of speciation and also provide a method for the generation of novel allopolyploid crop species.
Collapse
Affiliation(s)
- Ignacia Fuentes
- 1] Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany [2]
| | - Sandra Stegemann
- 1] Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany [2]
| | - Hieronim Golczyk
- Department of Molecular Biology, Institute of Biotechnology, John Paul II Catholic University of Lublin, Konstantynow 1I, 20-708 Lublin, Poland
| | - Daniel Karcher
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| |
Collapse
|
28
|
Fopa Fomeju B, Falentin C, Lassalle G, Manzanares-Dauleux MJ, Delourme R. Homoeologous duplicated regions are involved in quantitative resistance of Brassica napus to stem canker. BMC Genomics 2014; 15:498. [PMID: 24948032 PMCID: PMC4082613 DOI: 10.1186/1471-2164-15-498] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 06/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several major crop species are current or ancient polyploids. To better describe the genetic factors controlling traits of agronomic interest (QTL), it is necessary to understand the structural and functional organisation of these QTL regions in relation to genome duplication. We investigated quantitative resistance to the fungal disease stem canker in Brassica napus, a highly duplicated amphidiploid species, to assess the proportion of resistance QTL located at duplicated positions. RESULTS Genome-wide association analysis on a panel of 116 oilseed rape varieties genotyped with 3228 SNP indicated that 321 markers, corresponding to 64 genomic regions, are associated with resistance to stem canker. These genomic regions are relatively equally distributed on the A (53%) and C (47%) genomes of B. napus. Overall, 44% of these regions (28/64) are duplicated homoeologous regions. They are located in duplications of six (E, J, R, T, U and W) of the 24 ancestral blocks that constitute the B. napus genome. Overall, these six ancestral blocks have 34 duplicated copies in the B.napus genome. Almost all of the duplicated copies (82% of the 34 regions) harboured resistance associated markers for stem canker resistance, which suggests structural and functional conservation of genetic factors involved in this trait in B. napus. CONCLUSIONS Our study provides information on the involvement of duplicated loci in the control of stem canker resistance in B. napus. Further investigation of the similarity/divergence in sequence and gene content of these duplicated regions will provide insight into the conservation and allelic diversity of the underlying genes.
Collapse
|
29
|
|
30
|
Polyploidy, body size, and opportunities for genetic enhancement and fixation of heterozygosity in plants. THE NUCLEUS 2013. [DOI: 10.1007/s13237-013-0075-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
|
31
|
Olsen KM, Wendel JF. Crop plants as models for understanding plant adaptation and diversification. FRONTIERS IN PLANT SCIENCE 2013; 4:290. [PMID: 23914199 PMCID: PMC3729982 DOI: 10.3389/fpls.2013.00290] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/13/2013] [Indexed: 05/19/2023]
Abstract
Since the time of Darwin, biologists have understood the promise of crop plants and their wild relatives for providing insight into the mechanisms of phenotypic evolution. The intense selection imposed by our ancestors during plant domestication and subsequent crop improvement has generated remarkable transformations of plant phenotypes. Unlike evolution in natural settings, descendent and antecedent conditions for crop plants are often both extant, providing opportunities for direct comparisons through crossing and other experimental approaches. Moreover, since domestication has repeatedly generated a suite of "domestication syndrome" traits that are shared among crops, opportunities exist for gaining insight into the genetic and developmental mechanisms that underlie parallel adaptive evolution. Advances in our understanding of the genetic architecture of domestication-related traits have emerged from combining powerful molecular technologies with advanced experimental designs, including nested association mapping, genome-wide association studies, population genetic screens for signatures of selection, and candidate gene approaches. These studies may be combined with high-throughput evaluations of the various "omics" involved in trait transformation, revealing a diversity of underlying causative mutations affecting phenotypes and their downstream propagation through biological networks. We summarize the state of our knowledge of the mutational spectrum that generates phenotypic novelty in domesticated plant species, and our current understanding of how domestication can reshape gene expression networks and emergent phenotypes. An exploration of traits that have been subject to similar selective pressures across crops (e.g., flowering time) suggests that a diversity of targeted genes and causative mutational changes can underlie parallel adaptation in the context of crop evolution.
Collapse
Affiliation(s)
- Kenneth M. Olsen
- Biology Department, Washington UniversitySt. Louis, MO, USA
- *Correspondence: Kenneth M. Olsen, Biology Department, Washington University, Campus Box 1137, St. Louis, MO 63130-4899, USA e-mail:
| | - Jonathan F. Wendel
- Ecology, Evolution, and Organismal Biology Department, Iowa State UniversityAmes, IA, USA
| |
Collapse
|
32
|
Olsen KM, Wendel JF. A bountiful harvest: genomic insights into crop domestication phenotypes. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:47-70. [PMID: 23451788 DOI: 10.1146/annurev-arplant-050312-120048] [Citation(s) in RCA: 221] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Human selection during crop domestication has resulted in remarkable transformations of plant phenotypes, providing a window into the genetic basis of morphological evolution. Recent progress in our understanding of the genetic architecture of novel plant traits has emerged from combining advanced molecular technologies with improved experimental designs, including nested association mapping, genome-wide association studies, population genetic screens for signatures of selection, and candidate gene approaches. These studies reveal a diversity of underlying causative mutations affecting phenotypes important in plant domestication and crop improvement, including coding sequence substitutions, presence/absence and copy number variation, transposon activation leading to novel gene structures and expression patterns, diversification following gene duplication, and polyploidy leading to altered combinatorial capabilities. The genomic regions unknowingly targeted by human selection include both structural and regulatory genes, often with results that propagate through the transcriptome as well as to other levels in the biosynthetic and morphogenetic networks.
Collapse
Affiliation(s)
- Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | | |
Collapse
|
33
|
Lerceteau-Köhler E, Moing A, Guérin G, Renaud C, Petit A, Rothan C, Denoyes B. Genetic dissection of fruit quality traits in the octoploid cultivated strawberry highlights the role of homoeo-QTL in their control. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1059-77. [PMID: 22215248 PMCID: PMC3304055 DOI: 10.1007/s00122-011-1769-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 12/08/2011] [Indexed: 05/18/2023]
Abstract
Fruit quality traits are major breeding targets in the Rosaceae. Several of the major Rosaceae species are current or ancient polyploids. To dissect the inheritance of fruit quality traits in polyploid fleshy fruit species, we used a cultivated strawberry segregating population comprising a 213 full-sibling F1 progeny from a cross between the variety 'Capitola' and the genotype 'CF1116'. We previously developed the most comprehensive strawberry linkage map, which displays seven homoeology groups (HG), including each four homoeology linkage groups (Genetics 179:2045-2060, 2008). The map was used to identify quantitative trait loci (QTL) for 19 fruit traits related to fruit development, texture, colour, anthocyanin, sugar and organic acid contents. Analyses were carried out over two or three successive years on field-grown plants. QTL were detected for all the analysed traits. Because strawberry is an octopolyploid species, QTL controlling a given trait and located at orthologous positions on different homoeologous linkage groups within one HG are considered as homoeo-QTL. We found that, for various traits, about one-fourth of QTL were putative homoeo-QTL and were localised on two linkage groups. Several homoeo-QTL could be detected the same year, suggesting that several copies of the gene underlying the QTL are functional. The detection of some other homoeo-QTL was year-dependent. Therefore, changes in allelic expression could take place in response to environmental changes. We believe that, in strawberry as in other polyploid fruit species, the mechanisms unravelled in the present study may play a crucial role in the variations of fruit quality.
Collapse
Affiliation(s)
- E. Lerceteau-Köhler
- Ciref, Maison Jeannette, 24140 Douville, France
- Present Address: Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
| | - A. Moing
- UMR 1332 Biologie du Fruit et Pathologie, INRA, 33140 Villenave d’Ornon, France
| | - G. Guérin
- UMR 1332 Biologie du Fruit et Pathologie, INRA, 33140 Villenave d’Ornon, France
| | - C. Renaud
- UMR 1332 Biologie du Fruit et Pathologie, INRA, 33140 Villenave d’Ornon, France
| | - A. Petit
- Ciref, Maison Jeannette, 24140 Douville, France
| | - C. Rothan
- UMR 1332 Biologie du Fruit et Pathologie, INRA, 33140 Villenave d’Ornon, France
| | - Béatrice Denoyes
- UMR 1332 Biologie du Fruit et Pathologie, INRA, 33140 Villenave d’Ornon, France
| |
Collapse
|
34
|
Fonceka D, Tossim HA, Rivallan R, Vignes H, Faye I, Ndoye O, Moretzsohn MC, Bertioli DJ, Glaszmann JC, Courtois B, Rami JF. Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding. BMC PLANT BIOLOGY 2012; 12:26. [PMID: 22340522 PMCID: PMC3312858 DOI: 10.1186/1471-2229-12-26] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 02/17/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Polyploidy can result in genetic bottlenecks, especially for species of monophyletic origin. Cultivated peanut is an allotetraploid harbouring limited genetic diversity, likely resulting from the combined effects of its single origin and domestication. Peanut wild relatives represent an important source of novel alleles that could be used to broaden the genetic basis of the cultigen. Using an advanced backcross population developed with a synthetic amphidiploid as donor of wild alleles, under two water regimes, we conducted a detailed QTL study for several traits involved in peanut productivity and adaptation as well as domestication. RESULTS A total of 95 QTLs were mapped in the two water treatments. About half of the QTL positive effects were associated with alleles of the wild parent and several QTLs involved in yield components were specific to the water-limited treatment. QTLs detected for the same trait mapped to non-homeologous genomic regions, suggesting differential control in subgenomes as a consequence of polyploidization. The noteworthy clustering of QTLs for traits involved in seed and pod size and in plant and pod morphology suggests, as in many crops, that a small number of loci have contributed to peanut domestication. CONCLUSION In our study, we have identified QTLs that differentiated cultivated peanut from its wild relatives as well as wild alleles that contributed positive variation to several traits involved in peanut productivity and adaptation. These findings offer novel opportunities for peanut improvement using wild relatives.
Collapse
Affiliation(s)
- Daniel Fonceka
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| | | | - Ronan Rivallan
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| | - Hélène Vignes
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| | - Issa Faye
- ISRA/Ceraas, Route de Khombole, BP 3320, Thiès Escale, Senegal
| | - Ousmane Ndoye
- ISRA/Ceraas, Route de Khombole, BP 3320, Thiès Escale, Senegal
| | - Márcio C Moretzsohn
- Embrapa Recursos Genéticos e Biotecnologia, C.P. 02372, CEP 70.770-900 Brasilia, DF, Brazil
| | - David J Bertioli
- Universidade de Brasília, Campus Universitário, CEP 70.910-900 Brasília, DF, Brazil
| | | | - Brigitte Courtois
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| | - Jean-François Rami
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| |
Collapse
|
35
|
Ilut DC, Coate JE, Luciano AK, Owens TG, May GD, Farmer A, Doyle JJ. A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species. AMERICAN JOURNAL OF BOTANY 2012; 99:383-96. [PMID: 22301896 DOI: 10.3732/ajb.1100312] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY RNA-seq analysis of plant transcriptomes poses unique challenges due to the highly duplicated nature of plant genomes. We address these challenges in the context of recently formed polyploid species and detail an RNA-seq experiment comparing the leaf transcriptome profile of an allopolyploid relative of soybean with the diploid species that contributed its homoeologous genomes. METHODS RNA-seq reads were obtained from the three species and were aligned against the genome sequence of Glycine max. Transcript levels were estimated for each gene, relative contributions of polyploidy-duplicated loci (homoeologues) in the tetraploid were identified, and comparisons of transcript profiles and individual genes were used to analyze the regulation of transcript levels. KEY RESULTS We present a novel metric developed to address issues arising from high degrees of gene space duplication and a method for dissecting a gene's measured transcript level in a polyploid species into the relative contribution of its homoeologues. We identify the gene family likely contributing to differences in photosynthetic rate between the allotetraploid and its progenitors and show that the tetraploid appears to be using the "redundant" gene copies in novel ways. CONCLUSIONS Given the prevalence of polyploidy events in plants, we believe many of the approaches developed here to be applicable, and often necessary, in most plant RNA-seq experiments. The deep sampling provided by RNA-seq allows us to dissect the genetic underpinnings of specific phenotypes as well as examine complex interactions within polyploid genomes.
Collapse
Affiliation(s)
- Daniel C Ilut
- Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA.
| | | | | | | | | | | | | |
Collapse
|
36
|
|
37
|
Pala I, Schartl M, Brito M, Malta Vacas J, Coelho MM. Gene expression regulation and lineage evolution: the North and South tale of the hybrid polyploid Squalius alburnoides complex. Proc Biol Sci 2010; 277:3519-25. [PMID: 20554543 DOI: 10.1098/rspb.2010.1071] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The evolution of hybrid polyploid vertebrates, their viability and their perpetuation over evolutionary time have always been questions of great interest. However, little is known about the impact of hybridization and polyploidization on the regulatory networks that guarantee the appropriate quantitative and qualitative gene expression programme. The Squalius alburnoides complex of hybrid fish is an attractive system to address these questions, as it includes a wide variety of diploid and polyploid forms, and intricate systems of genetic exchange. Through the study of genome-specific allele expression of seven housekeeping and tissue-specific genes, we found that a gene copy silencing mechanism of dosage compensation exists throughout the distribution range of the complex. Here we show that the allele-specific patterns of silencing vary within the complex, according to the geographical origin and the type of genome involved in the hybridization process. In southern populations, triploids of S. alburnoides show an overall tendency for silencing the allele from the minority genome, while northern population polyploids exhibit preferential biallelic gene expression patterns, irrespective of genomic composition. The present findings further suggest that gene copy silencing and variable expression of specific allele combinations may be important processes in vertebrate polyploid evolution.
Collapse
Affiliation(s)
- Irene Pala
- Centro de Biologia Ambiental, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal.
| | | | | | | | | |
Collapse
|
38
|
Complete switchgrass genetic maps reveal subgenome collinearity, preferential pairing and multilocus interactions. Genetics 2010; 185:745-60. [PMID: 20407132 DOI: 10.1534/genetics.110.113910] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyploidy is an important aspect of the evolution of flowering plants. The potential of gene copies to diverge and evolve new functions is influenced by meiotic behavior of chromosomes leading to segregation as a single locus or duplicated loci. Switchgrass (Panicum virgatum) linkage maps were constructed using a full-sib population of 238 plants and SSR and STS markers to access the degree of preferential pairing and the structure of the tetraploid genome and as a step toward identification of loci underlying biomass feedstock quality and yield. The male and female framework map lengths were 1645 and 1376 cM with 97% of the genome estimated to be within 10 cM of a mapped marker in both maps. Each map coalesced into 18 linkage groups arranged into nine homeologous pairs. Comparative analysis of each homology group to the diploid sorghum genome identified clear syntenic relationships and collinear tracts. The number of markers with PCR amplicons that mapped across subgenomes was significantly fewer than expected, suggesting substantial subgenome divergence, while both the ratio of coupling to repulsion phase linkages and pattern of marker segregation indicated complete or near complete disomic inheritance. The proportion of transmission ratio distorted markers was relatively low, but the male map was more extensively affected by distorted transmission ratios and multilocus interactions, associated with spurious linkages.
Collapse
|
39
|
Abstract
Autopolyploidy is more common in plants than traditionally assumed, but has received little attention compared with allopolyploidy. Hence, the advantages and disadvantages of genome doubling per se compared with genome doubling coupled with hybridizations in allopolyploids remain unclear. Autopolyploids are characterized by genomic redundancy and polysomic inheritance, increasing effective population size. To shed light on the evolutionary consequences of autopolyploidy, we review a broad range of studies focusing on both synthetic and natural autopolyploids encompassing levels of biological organization from genes to evolutionary lineages. The limited evidence currently available suggests that autopolyploids neither experience strong genome restructuring nor wide reorganization of gene expression during the first generations following genome doubling, but that these processes may become more important in the longer term. Biogeographic and ecological surveys point to an association between the formation of autopolyploid lineages and environmental change. We thus hypothesize that polysomic inheritance may provide a short-term evolutionary advantage for autopolyploids compared to diploid relatives when environmental change enforces range shifts. In addition, autopolyploids should possess increased genome flexibility, allowing them to adapt and persist across heterogeneous landscapes in the long run.
Collapse
Affiliation(s)
- Christian Parisod
- National Centre for Biosystematics, University of Oslo, 0318 Oslo, Norway.
| | | | | |
Collapse
|
40
|
Chong YT, Gidda SK, Sanford C, Parkinson J, Mullen RT, Goring DR. Characterization of the Arabidopsis thaliana exocyst complex gene families by phylogenetic, expression profiling, and subcellular localization studies. THE NEW PHYTOLOGIST 2010; 185:401-19. [PMID: 19895414 DOI: 10.1111/j.1469-8137.2009.03070.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
*The exocyst is a complex of eight proteins (Sec3p, Sec5p, Sec6p, Sec8p, Sec10p, Sec15p, Exo70p and Exo84p) involved in tethering vesicles to the plasma membrane during regulated or polarized secretion. Here, the plant exocyst complex was explored in phylogenetic, expression, and subcellular localization studies. *Evolutionary relationships of predicted exocyst subunits were examined in the complete genomes of Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Physcomitrella patens. Furthermore, detailed expression profiling of the A. thaliana microarray databases was performed and subcellular localization patterns were studied. *Several plant exocyst subunit genes appear to have undergone gene expansion in a common ancestor and subsequent duplication events in independent plant lineages. Expression profiling revealed that the A. thaliana Exo70 gene family exhibits dynamic expression patterns, while the remaining exocyst subunit genes displayed more static profiles. Subcellular localization patterns for A. thaliana exocyst subunits ranged from cytosolic to endosomal compartments (with enrichment in the early endosomes and the trans-Golgi network). Interestingly, two endosomal-localized AtExo70 proteins also recruited other exocyst subunits to these compartments. *Overall subcellular localization patterns were observed that were also found in yeast and animal cells, and this, coupled with the evolutionary relationships, suggests that the exocyst may perform similar conserved functions in plants.
Collapse
Affiliation(s)
- Yolanda T Chong
- Department of Cell & Systems Biology and the Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | | | | | | | | | | |
Collapse
|
41
|
Meimberg H, Rice KJ, Milan NF, Njoku CC, McKay JK. Multiple origins promote the ecological amplitude of allopolyploid Aegilops (Poaceae). AMERICAN JOURNAL OF BOTANY 2009; 96:1262-1273. [PMID: 21628275 DOI: 10.3732/ajb.0800345] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Polyploidy has been ubiquitous in plant evolution and is thought to be an important engine of biodiversity that facilitates speciation, adaptation, and range expansion. Polyploid species can exhibit higher ecological tolerance than their progenitor species. For allotetraploid species, this higher tolerance is often attributed to the existence of heterosis resulting from entire genome duplication. However, multiple origins of allopolyploid species may further promote their ecological success by providing genetic variability in ecological traits underlying local adaptation and range expansion. Here we show in a group of allopolyploid species in the genus Aegilops that range size and abundance are correlated with the number of inferred origins. We found that allopolyploid Aegilops spp. contain multiple chloroplast haplotypes, each identical to haplotypes of the diploid progenitor species, indicating multiple origins as the major source of variation. The number of inferred origins in each allopolyploid species was correlated to the total area occupied by the allopolyploid and the tendency for the species to be common. Additionally, we found differences in ecological tolerance among independent origins in Aegilops triuncialis. These results strongly support the hypothesis that the introduction of genetic variability by multiple origins can increase the ecological amplitude and evolutionary success of allopolyploid species.
Collapse
Affiliation(s)
- Harald Meimberg
- CIBIO, University of Porto, Campus Agrario de Vairao, 4485-661 Vairao, Portugal
| | | | | | | | | |
Collapse
|
42
|
Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes. Mol Phylogenet Evol 2009; 51:515-30. [PMID: 19166953 DOI: 10.1016/j.ympev.2008.12.024] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 12/23/2008] [Accepted: 12/29/2008] [Indexed: 12/27/2022]
Abstract
Phylogenetic utility of two nuclear genes (GBSSI-2 and DHAR) was explored in genus Fragaria in order to clarify phylogenetic relationships among taxa and to elucidate the origin of the polyploid species. Orthology of the amplified products was assessed by several methods. Our results strongly suggest the loss of one GBSSI duplicated copy (GBSSI-1) in the Fragariinae subtribe. Phylogenetic analyses provided new insights into the evolutionary history of Fragaria, such as evidence supporting the presence of three main diploid genomic pools in the genus and demonstrating the occurrence of independent events of polyploidisation. In addition, the data provide evidence supporting an allopolyploid origin of the hexaploid F. moschata, and the octoploids F. chiloensis, F. iturupensis and F. virginiana. Accordingly, a new pattern summarizing our present knowledge on the Fragaria evolutionary history is proposed. Additionally, sequence analyses also revealed relaxed constraints on homoeologous copies at high ploidy level, as demonstrated by deletion events within DHAR coding sequences of some allo-octoploid haplotypes.
Collapse
|
43
|
Innes RW, Ameline-Torregrosa C, Ashfield T, Cannon E, Cannon SB, Chacko B, Chen NWG, Couloux A, Dalwani A, Denny R, Deshpande S, Egan AN, Glover N, Hans CS, Howell S, Ilut D, Jackson S, Lai H, Mammadov J, Del Campo SM, Metcalf M, Nguyen A, O'Bleness M, Pfeil BE, Podicheti R, Ratnaparkhe MB, Samain S, Sanders I, Ségurens B, Sévignac M, Sherman-Broyles S, Thareau V, Tucker DM, Walling J, Wawrzynski A, Yi J, Doyle JJ, Geffroy V, Roe BA, Maroof MAS, Young ND. Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. PLANT PHYSIOLOGY 2008; 148:1740-59. [PMID: 18842825 PMCID: PMC2593655 DOI: 10.1104/pp.108.127902] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2008] [Accepted: 10/06/2008] [Indexed: 05/18/2023]
Abstract
The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.
Collapse
Affiliation(s)
- Roger W Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Barbazuk WB, Fu Y, McGinnis KM. Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res 2008; 18:1381-92. [PMID: 18669480 DOI: 10.1101/gr.053678.106] [Citation(s) in RCA: 252] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Alternative splicing (AS) creates multiple mRNA transcripts from a single gene. While AS is known to contribute to gene regulation and proteome diversity in animals, the study of its importance in plants is in its early stages. However, recently available plant genome and transcript sequence data sets are enabling a global analysis of AS in many plant species. Results of genome analysis have revealed differences between animals and plants in the frequency of alternative splicing. The proportion of plant genes that have one or more alternative transcript isoforms is approximately 20%, indicating that AS in plants is not rare, although this rate is approximately one-third of that observed in human. The majority of plant AS events have not been functionally characterized, but evidence suggests that AS participates in important plant functions, including stress response, and may impact domestication and trait selection. The increasing availability of plant genome sequence data will enable larger comparative analyses that will identify functionally important plant AS events based on their evolutionary conservation, determine the influence of genome duplication on the evolution of AS, and discover plant-specific cis-elements that regulate AS. This review summarizes recent analyses of AS in plants, discusses the importance of further analysis, and suggests directions for future efforts.
Collapse
Affiliation(s)
- W Brad Barbazuk
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.
| | | | | |
Collapse
|
45
|
Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry. Genetics 2008; 179:2045-60. [PMID: 18660542 DOI: 10.1534/genetics.107.083840] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Macrosynteny and colinearity between Fragaria (strawberry) species showing extreme levels of ploidy have been studied through comparative genetic mapping between the octoploid cultivated strawberry (F. xananassa) and its diploid relatives. A comprehensive map of the octoploid strawberry, in which almost all linkage groups are ranged into the seven expected homoeologous groups was obtained, thus providing the first reference map for the octoploid Fragaria. High levels of conserved macrosynteny and colinearity were observed between homo(eo)logous linkage groups and between the octoploid homoeologous groups and their corresponding diploid linkage groups. These results reveal that the polyploidization events that took place along the evolution of the Fragaria genus and the more recent juxtaposition of two octoploid strawberry genomes in the cultivated strawberry did not trigger any major chromosomal rearrangements in genomes involved in F. xananassa. They further suggest the existence of a close relationship between the diploid Fragaria genomes. In addition, despite the possible existence of residual levels of polysomic segregation suggested by the observation of large linkage groups in coupling phase only, the prevalence of linkage groups in coupling/repulsion phase clearly demonstrates that the meiotic behavior is mainly disomic in the cultivated strawberry.
Collapse
|
46
|
Albertin W, Alix K, Balliau T, Brabant P, Davanture M, Malosse C, Valot B, Thiellement H. Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization. BMC Genomics 2007; 8:56. [PMID: 17313678 PMCID: PMC1805753 DOI: 10.1186/1471-2164-8-56] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 02/21/2007] [Indexed: 12/24/2022] Open
Abstract
Background Allopolyploidy is a preeminent process in plant evolution that results from the merger of distinct genomes in a common nucleus via inter-specific hybridization. Allopolyploid formation is usually related to genome-wide structural and functional changes though the underlying mechanisms operating during this "genomic shock" still remain poorly known. The aim of the present study was to investigate the modifications occurring at the proteomic level following an allopolyploidization event and to determine whether these changes are related to functional properties of the proteins. In a previous report, we applied comparative proteomics to synthetic amphiploids of Brassica napus and to its diploid progenitors B. rapa and B. oleracea. Although several hundred polypeptides displayed additivity (i.e. mid-parent values) in the amphiploids, many of them showed non-additivity. Here, we report the in silico functional characterization of the "non-additive" proteins (the ones with a non-additive pattern of regulation) in synthetic B. napus. Results The complete set of non-additive proteins (335 in the stem and 205 in the root), as well as a subset of additive polypeptides (200 per organ), was identified by mass spectrometry. Several protein isoforms were found, and most of them (~55%) displayed "different" or "opposite" patterns of regulation in the amphiploids, i.e. isoforms of the same protein showing both up-regulation and down-regulation in the synthetic B. napus compared to the mid-parent value. Components of protein complexes were identified of which ~50% also displayed "different" or "opposite" patterns of regulation in the allotetraploids. In silico functional categorization of the identified proteins was carried out, and showed that neither functional category nor metabolic pathway were systematically affected by non-additivity in the synthetic amphiploids. In addition, no subcellular compartment was found to be over- or under-represented among the proteins displaying non-additive values in the allopolyploids. Conclusion Protein identification showed that functionally related polypeptides (isoforms and complex subunits) could be differentially regulated in synthetic B. napus in comparison to its diploid progenitors while such proteins are usually expected to display co-regulation. The genetic redundancy within an allopolyploid could explain why functionally related proteins could display imbalanced levels of expression. No functional category, no metabolic pathway and no subcellular localization was found to be over- or under-represented within non-additive polypeptides, suggesting that the differential regulation of gene products was not related to functional properties of the proteins. Thus, at the protein level, there is no evidence for the "genomic shock" expected in neo-polyploids and the overall topology of protein networks and metabolic pathways is conserved in synthetic allotetraploids of B. napus in comparison to its diploid progenitors B. rapa and B. oleracea.
Collapse
Affiliation(s)
- Warren Albertin
- UMR de Génétique Végétale, INRA/CNRS/UPSud/INA P-G, La ferme du Moulon, 91190 Gif-sur-Yvette, France
| | - Karine Alix
- UMR de Génétique Végétale, INRA/CNRS/UPSud/INA P-G, La ferme du Moulon, 91190 Gif-sur-Yvette, France
| | - Thierry Balliau
- Plate-forme de Protéomique, La ferme du Moulon, 91190 Gif-sur-Yvette, France
| | - Philippe Brabant
- UMR de Génétique Végétale, INRA/CNRS/UPSud/INA P-G, La ferme du Moulon, 91190 Gif-sur-Yvette, France
| | - Marlène Davanture
- Plate-forme de Protéomique, La ferme du Moulon, 91190 Gif-sur-Yvette, France
| | - Christian Malosse
- Plate-forme de Protéomique de Versailles, INRA, 78026 Versailles, France
| | - Benoît Valot
- Plate-forme de Protéomique, La ferme du Moulon, 91190 Gif-sur-Yvette, France
| | - Hervé Thiellement
- UMR de Génétique Végétale, INRA/CNRS/UPSud/INA P-G, La ferme du Moulon, 91190 Gif-sur-Yvette, France
| |
Collapse
|
47
|
Nelson MN, Lydiate DJ. New evidence from Sinapis alba L. for ancestral triplication in a crucifer genome. Genome 2006; 49:230-8. [PMID: 16604105 DOI: 10.1139/g05-099] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We present clear evidence of ancestral genome triplication in Sinapis alba, a close relative of the cultivated Brassica species. Exceptionally high levels of heterozygosity in the parents of an F1 intercross permitted the mapping of an estimated 87% of all detected restriction fragment length polymorphism (RFLP) loci, with each RFLP probe typically detecting 2 or 3 loci. These duplicated loci were arranged in 8 triplicated homologous linkage blocks and 2 small, duplicated, homologous linkage blocks covering the majority of the S. alba genome. Several large-scale inversions and translocations appear to have rearranged the order of loci within homologous blocks. The role of successive polyploidization events on the evolution of crucifer species is discussed.
Collapse
Affiliation(s)
- Matthew N Nelson
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, University of Western Australia, 35 Stirling Highway, Crawley, 6009 WA, Australia.
| | | |
Collapse
|
48
|
Shoemaker RC, Schlueter J, Doyle JJ. Paleopolyploidy and gene duplication in soybean and other legumes. CURRENT OPINION IN PLANT BIOLOGY 2006; 9:104-9. [PMID: 16458041 DOI: 10.1016/j.pbi.2006.01.007] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 01/23/2006] [Indexed: 05/06/2023]
Abstract
Two of the most important observations from whole-genome sequences have been the high rate of gene birth and death and the prevalence of large-scale duplication events, including polyploidy. There is also a growing appreciation that polyploidy is more than the sum of the gene duplications it creates, in part because polyploidy duplicates the members of entire regulatory networks. Thus, it may be important to distinguish paralogs that are produced by individual gene duplications from the homoeologous sequences produced by (allo)polyploidy. This is not a simple task, for several reasons, including the chromosomally cryptic nature of many duplications and the variable rates of gene evolution. Recent progress has been made in understanding patterns of gene and genome duplication in the legume family, specifically in soybean.
Collapse
Affiliation(s)
- Randy C Shoemaker
- USDA-ARS and Iowa State University, G401 Agronomy Hall, Ames, Iowa 50011, USA.
| | | | | |
Collapse
|
49
|
Abstract
Polyploids - organisms that have multiple sets of chromosomes - are common in certain plant and animal taxa, and can be surprisingly stable. The evidence that has emerged from genome analyses also indicates that many other eukaryotic genomes have a polyploid ancestry, suggesting that both humans and most other eukaryotes have either benefited from or endured polyploidy. Studies of polyploids soon after their formation have revealed genetic and epigenetic interactions between redundant genes. These interactions can be related to the phenotypes and evolutionary fates of polyploids. Here, I consider the advantages and challenges of polyploidy, and its evolutionary potential.
Collapse
Affiliation(s)
- Luca Comai
- Department of Biology, Box 355325, University of Washington, Seattle, Washington 98195, USA.
| |
Collapse
|