1
|
Yu Z, Cui B, Xiao J, Jiao W, Wang H, Wang Z, Sun L, Song Q, Yuan J, Wang X. Dosage effect genes modulating grain development in synthesized Triticum durum-Haynaldia villosa allohexaploid. J Genet Genomics 2024:S1673-8527(24)00081-X. [PMID: 38670432 DOI: 10.1016/j.jgg.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Polyploidization in plants often leads to increased cell size and grain size, which may be affected by the increased genome dosage and transcription abundance. The synthesized Triticum durum (AABB)-Haynaldia villosa (VV) amphiploid (AABBVV) has significantly increased grain size, especially grain length than the tetraploid and diploid parents. To investigate how the polyploidization affects grain development at transcriptional level, we perform transcriptome analysis using the immature seeds of T. durum, H. villosa, and the amphiploid. The dosage effect genes are contributed more by differentially expressed genes (DEGs) from genome V of H. villosa. The dosage effect genes overrepresent grain development related genes. Interestingly, the vernalization gene TaVRN1 is among the positive dosage effect genes in the T. durum‒H. villosa and T. turgidum‒Ae. tauschii amphiploids. The expression levels of TaVRN1 homologs are significantly positively correlated with the grain size and weight. The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence, decreased cell size, grain size, and grain yield. These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development. The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improving wheat yield.
Collapse
Affiliation(s)
- Zhongyu Yu
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Baofeng Cui
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Jin Xiao
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Wu Jiao
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Haiyan Wang
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Zongkuan Wang
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Li Sun
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Qingxin Song
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Jingya Yuan
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China.
| | - Xiue Wang
- State Key Lab of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China.
| |
Collapse
|
2
|
Huwanixi A, Peng Z, Li S, Zhou Y, Zhao S, Wan C. Comparative proteomic analysis of seed germination between allotetraploid cotton Gossypium hirsutum and Gossypium barbadense. J Proteomics 2024; 297:105130. [PMID: 38401592 DOI: 10.1016/j.jprot.2024.105130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/23/2024] [Accepted: 02/18/2024] [Indexed: 02/26/2024]
Abstract
Seed germination, a key initial event in the plant life cycle, directly affects cotton yield and quality. Gossypium barbadense and Gossypium hirsutum gradually evolved through polyploidization, resulting in different characteristics, and this interspecific variation lacks genetic and molecular explanation. This work aimed to compare the proteomes between G. barbadense and G. hirsutum during seed germination. Here, we identified 2740 proteins for G. barbadense and 3758 for G. hirsutum. In the initial state, proteins in two cotton involved similar bioprocess, such as sugar metabolism, DNA repairing, and ABA signaling pathway. However, in the post-germination stage, G. hirsutum expressed more protein related to redox homeostasis, peroxidase activity, and pathogen interactions. Analyzing the different expression patterns of 915 single-copy orthogroups between the two kinds of cotton indicated that most of the differentially expressed proteins in G. barbadense were related to carbon metabolism. In contrast, most proteins in G. hirsutum were associated with stress response. Besides that, by proteogenomic analysis, we found 349 putative non-canonical peptides, which may be involved in plant development. These results will help to understand the different characteristics of these two kinds of cotton, such as fiber quality, yield, and adaptability. SIGNIFICANCE STATEMENT: Cotton is the predominant natural fiber crop worldwide; Gossypium barbadense and Gossypium hirsutum have evolved through polyploidization to produce differing traits. However, given their specific features, the divergence of mechanisms underlying seed germination between G. hirsutum and G. barbadense has not been discussed. Here, we explore what protein contributes to interspecific differences between G. barbadense and G. hirsutum during the seed germination period. This study helps to elucidate the evolution and domestication history of cotton polyploids and may allow breeders to understand their domestication history better and improve fiber quality and adaptability.
Collapse
Affiliation(s)
- Aishuake Huwanixi
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Zhao Peng
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Shenglan Li
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Yutian Zhou
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Sixian Zhao
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Cuihong Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China.
| |
Collapse
|
3
|
Penin AA, Kasianov AS, Klepikova AV, Omelchenko DO, Makarenko MS, Logacheva MD. Origin and diversity of Capsella bursa-pastoris from the genomic point of view. BMC Biol 2024; 22:52. [PMID: 38439107 PMCID: PMC10913212 DOI: 10.1186/s12915-024-01832-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/23/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Capsella bursa-pastoris, a cosmopolitan weed of hybrid origin, is an emerging model object for the study of early consequences of polyploidy, being a fast growing annual and a close relative of Arabidopsis thaliana. The development of this model is hampered by the absence of a reference genome sequence. RESULTS We present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome of Capsella bursa-pastoris. It shows that the subgenomes are mostly colinear, with no massive deletions, insertions, or rearrangements in any of them. A subgenome-aware annotation reveals the lack of genome dominance-both subgenomes carry similar number of genes. While most chromosomes can be unambiguously recognized as derived from either paternal or maternal parent, we also found homeologous exchange between two chromosomes. It led to an emergence of two hybrid chromosomes; this event is shared between distant populations of C. bursa-pastoris. The whole-genome analysis of 119 samples belonging to C. bursa-pastoris and its parental species C. grandiflora/rubella and C. orientalis reveals introgression from C. orientalis but not from C. grandiflora/rubella. CONCLUSIONS C. bursa-pastoris does not show genome dominance. In the earliest stages of evolution of this species, a homeologous exchange occurred; its presence in all present-day populations of C. bursa-pastoris indicates on a single origin of this species. The evidence coming from whole-genome analysis challenges the current view that C. grandiflora/rubella was a direct progenitor of C. bursa-pastoris; we hypothesize that it was an extinct (or undiscovered) species sister to C. grandiflora/rubella.
Collapse
Affiliation(s)
- Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.
| | - Artem S Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Denis O Omelchenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maksim S Makarenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| |
Collapse
|
4
|
Wang M, Li X, Wang C, Zou M, Yang J, Li XD, Guo B. Asymmetric and parallel subgenome selection co-shape common carp domestication. BMC Biol 2024; 22:4. [PMID: 38166816 PMCID: PMC10762839 DOI: 10.1186/s12915-023-01806-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The common carp (Cyprinus carpio) might best represent the domesticated allopolyploid animals. Although subgenome divergence which is well-known to be a key to allopolyploid domestication has been comprehensively characterized in common carps, the link between genetic architecture underlying agronomic traits and subgenome divergence is unknown in the selective breeding of common carps globally. RESULTS We utilized a comprehensive SNP dataset in 13 representative common carp strains worldwide to detect genome-wide genetic variations associated with scale reduction, vibrant skin color, and high growth rate in common carp domestication. We identified numerous novel candidate genes underlie the three agronomically most desirable traits in domesticated common carps, providing potential molecular targets for future genetic improvement in the selective breeding of common carps. We found that independently selective breeding of the same agronomic trait (e.g., fast growing) in common carp domestication could result from completely different genetic variations, indicating the potential advantage of allopolyploid in domestication. We observed that candidate genes associated with scale reduction, vibrant skin color, and/or high growth rate are repeatedly enriched in the immune system, suggesting that domestication of common carps was often accompanied by the disease resistance improvement. CONCLUSIONS In common carp domestication, asymmetric subgenome selection is prevalent, while parallel subgenome selection occurs in selective breeding of common carps. This observation is not due to asymmetric gene retention/loss between subgenomes but might be better explained by reduced pleiotropy through transposable element-mediated expression divergence between ohnologs. Our results demonstrate that domestication benefits from polyploidy not only in plants but also in animals.
Collapse
Affiliation(s)
- Min Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinxin Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chongnv Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ming Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Yang
- Institute of Chinese Sturgeon, China Three Gorges Corporation, Yichang, 443100, Hubei, China
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Institute of Chinese Sturgeon, China Three Gorges Corporation, Yichang, 443100, Hubei, China
| | - Xiang-Dong Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Integrated Management of Insect Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810008, China.
| |
Collapse
|
5
|
Benson CW, Sheltra MR, Maughan PJ, Jellen EN, Robbins MD, Bushman BS, Patterson EL, Hall ND, Huff DR. Homoeologous evolution of the allotetraploid genome of Poa annua L. BMC Genomics 2023; 24:350. [PMID: 37365554 DOI: 10.1186/s12864-023-09456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Poa annua (annual bluegrass) is an allotetraploid turfgrass, an agronomically significant weed, and one of the most widely dispersed plant species on earth. Here, we report the chromosome-scale genome assemblies of P. annua's diploid progenitors, P. infirma and P. supina, and use multi-omic analyses spanning all three species to better understand P. annua's evolutionary novelty. RESULTS We find that the diploids diverged from their common ancestor 5.5 - 6.3 million years ago and hybridized to form P. annua ≤ 50,000 years ago. The diploid genomes are similar in chromosome structure and most notably distinguished by the divergent evolutionary histories of their transposable elements, leading to a 1.7 × difference in genome size. In allotetraploid P. annua, we find biased movement of retrotransposons from the larger (A) subgenome to the smaller (B) subgenome. We show that P. annua's B subgenome is preferentially accumulating genes and that its genes are more highly expressed. Whole-genome resequencing of several additional P. annua accessions revealed large-scale chromosomal rearrangements characterized by extensive TE-downsizing and evidence to support the Genome Balance Hypothesis. CONCLUSIONS The divergent evolutions of the diploid progenitors played a central role in conferring onto P. annua its remarkable phenotypic plasticity. We find that plant genes (guided by selection and drift) and transposable elements (mostly guided by host immunity) each respond to polyploidy in unique ways and that P. annua uses whole-genome duplication to purge highly parasitized heterochromatic sequences. The findings and genomic resources presented here will enable the development of homoeolog-specific markers for accelerated weed science and turfgrass breeding.
Collapse
Affiliation(s)
- Christopher W Benson
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA.
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, USA.
| | - Matthew R Sheltra
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, USA
| | - Peter J Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Logan, UT, USA
| | - Eric N Jellen
- Department of Plant and Wildlife Sciences, Brigham Young University, Logan, UT, USA
| | | | | | - Eric L Patterson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Nathan D Hall
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - David R Huff
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA.
| |
Collapse
|
6
|
Jordon-Thaden IE, Spoelhof JP, Viccini LF, Combs J, Gomez F, Walker I, Soltis DE, Soltis PS. Phenotypic trait variation in the North American Tragopogon allopolyploid complex. Am J Bot 2023. [PMID: 37210744 DOI: 10.1002/ajb2.16189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
PREMISE Recently formed allopolyploids Tragopogon mirus and T. miscellus and their diploid parental species, T. dubius, T. porrifolius, and T. pratensis, offer a rare opportunity to study the earliest stages of allopolyploidy. The allopolyploid species have also been resynthesized, allowing comparisons between the youngest possible allopolyploid lineages and their natural, established counterparts. For the first time we compare phenotypic traits on a large scale in Tragopogon diploids, natural allopolyploids, and three generations of synthetic allopolyploids. METHODS Our large common-garden experiment measured traits in growth, development, physiology, and reproductive fitness and analyzed differences between allopolyploids and their parental species and between synthetic and natural allopolyploids. KEY RESULTS As in many polyploids, the allopolyploid species had some larger physical traits and a higher capacity for photosynthesis than diploid species. Reproductive fitness traits were variable and inconsistent. Allopolyploids had intermediate phenotypes compared to their diploid parents in several traits, but patterns of variation often varied between allopolyploid complexes. Resynthesized and natural allopolyploid lines generally showed minor to non-existent trait differences. CONCLUSIONS In Tragopogon, allopolyploidy results in some typical phenotypic changes, including gigas effects and increased photosynthetic capacity. Being polyploid did not produce a significant reproductive advantage. Comparisons between natural and synthetic T. mirus and T. miscellus are consistent with very limited, idiosyncratic phenotypic evolution following allopolyploidization. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Ingrid E Jordon-Thaden
- Department of Botany, University of Wisconsin - Madison, Madison, 53706, WI, USA
- Florida Museum, University of Florida, Gainesville, 32611, FL, USA
| | | | - Lyderson Facio Viccini
- Department of Biology, Institute of Biological Sciences, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, Juiz de Fora, Minas Gerais, Brazil
| | - Joseph Combs
- The Jackson Laboratory, Bar Harbor, 04609, ME, USA
| | - Francisco Gomez
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, 48824, MI, USA
| | | | - Douglas E Soltis
- Florida Museum, University of Florida, Gainesville, 32611, FL, USA
- Department of Biology, University of Florida, Gainesville, 32611, FL, USA
| | - Pamela S Soltis
- Florida Museum, University of Florida, Gainesville, 32611, FL, USA
| |
Collapse
|
7
|
Bomblies K. Learning to tango with four (or more): the molecular basis of adaptation to polyploid meiosis. Plant Reprod 2023; 36:107-124. [PMID: 36149479 PMCID: PMC9957869 DOI: 10.1007/s00497-022-00448-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/10/2022] [Indexed: 05/29/2023]
Abstract
Polyploidy, which arises from genome duplication, has occurred throughout the history of eukaryotes, though it is especially common in plants. The resulting increased size, heterozygosity, and complexity of the genome can be an evolutionary opportunity, facilitating diversification, adaptation and the evolution of functional novelty. On the other hand, when they first arise, polyploids face a number of challenges, one of the biggest being the meiotic pairing, recombination and segregation of the suddenly more than two copies of each chromosome, which can limit their fertility. Both for developing polyploidy as a crop improvement tool (which holds great promise due to the high and lasting multi-stress resilience of polyploids), as well as for our basic understanding of meiosis and plant evolution, we need to know both the specific nature of the challenges polyploids face, as well as how they can be overcome in evolution. In recent years there has been a dramatic uptick in our understanding of the molecular basis of polyploid adaptations to meiotic challenges, and that is the focus of this review.
Collapse
Affiliation(s)
- Kirsten Bomblies
- Plant Evolutionary Genetics, Institute of Plant Molecular Biology, Department of Biology, ETH Zürich, Zurich, Switzerland.
| |
Collapse
|
8
|
Zhong DL, Li YC, Zhang JQ. Allopolyploid origin and niche expansion of Rhodiola integrifolia (Crassulaceae). Plant Divers 2023; 45:36-44. [PMID: 36876317 PMCID: PMC9975476 DOI: 10.1016/j.pld.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 06/18/2023]
Abstract
Polyploidy after hybridization between species can lead to immediate post-zygotic isolation, causing saltatory origin of new species. Although the incidence of polyploidization in plants is high, it is thought that a new polyploid lineage can succeed only if it establishes a new ecological niche divergent from its progenitor lineages. We tested the hypothesis that Rhodiola integrifolia from North America is an allopolyploid produced by R. rhodantha and R. rosea and determined whether its survival can be explained by the niche divergence hypothesis. To this end, we sequenced two low-copy nuclear genes (ncpGS and rpb2) in a phylogenetic analysis of 42 Rhodiola species and tested for niche equivalency and similarity using Schoener's D as the index of niche overlap. Our phylogeny-based approach showed that R. integrifolia possesses alleles from both R. rhodantha and R. rosea. Dating analysis showed that the hybridization event that led to R. integrifolia occurred ca. 1.67 Mya and niche modeling analysis showed that at this time, both R. rosea and R. rhodantha may have been present in Beringia, providing the opportunity for the hybridization event. We also found that the niche of R. integrifolia differs from that of its progenitors in both niche breadth and optimum. Taken together, these results confirm the hybrid origin of R. integrifolia and support the niche divergence hypothesis for this tetraploid species. Our results underscore the fact that lineages with no current overlapping distribution could produce hybrid descendants in the past, when climate oscillations made their distributions overlap.
Collapse
|
9
|
Li M, Hu M, Xiao Y, Wu X, Wang J. The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus. Hortic Res 2022; 9:uhab075. [PMID: 35043208 PMCID: PMC8923814 DOI: 10.1093/hr/uhab075] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 06/14/2023]
Abstract
Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes occurred in allopolyploids. What evolutionary changes of transcripts have taken place in Brassica napus during the early establishment and subsequent evolution was a fascinating scientific question. Here, we study this issue using a set of materials (natural, resynthesized B. napus and their progenitors/parents) by long-read RNA sequencing technology. The results showed that more genes were up-regulated in resynthesized B. napus compared with its two parents, and more up-regulated expressed genes were observed in natural B. napus compared with resynthesized B. napus. The presence of up-regulation genes in organism may help it adapt to the influence of "genomic shock" and cope with natural environment. Isoforms are produced from precursor mRNAs by alternative splicing (AS) events, and more than 60% of novel isoforms were identified in all materials, which could improve the reference genome information of B. napus. We found that the isoform numbers, the number of genes potentially involved in AS and alternative polyadenylation increased in B. napus after evolution, which may involve in the adaptation of plants to natural environment. In addition, all identified isoforms were functional annotated by searching 7 databases. In general, this study could improve our overall understanding of the full-length transcriptome of B. napus, and help us recognize the significant gene expression changes and isoform abundance changes occurred in allopolyploid B. napus during evolution.
Collapse
Affiliation(s)
- Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, China
| | - Meimei Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yafang Xiao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| |
Collapse
|
10
|
Shamim Z, Armstrong SJ. Using Genome In Situ Hybridization (GISH) to Distinguish the Constituent Genomes of Brassica nigra and B. rapa in the Hybrid B. juncea. Methods Mol Biol 2020; 2061:69-78. [PMID: 31583654 DOI: 10.1007/978-1-4939-9818-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The genome in situ hybridization (GISH) technique has become important for deciphering the organization of the constituent genomes in the allopolyploid plants that comprise many of the crop species. This technique comprises using the nuclear DNA from the constituent genomes as probes that have been labeled separately with different nucleotides that can be identified by using secondary antibodies. The Brassica family includes a range of mustard species with diverse phytochemical and morphological profile, hence making it an important plant family in agriculture. Meiosis is a specialized cellular division which brings the homologous chromosomes together and creates recombinants via pairing and synapsis during its early phase. Transfer of the genetic material within homoelog pairs creates novelty in subsequent generations which hold promise for improving the agriculture sector. This chapter is concerned with developing a GISH technique that discriminates between the constituent genomes in the allopolyploid B. juncea, in order to study meiosis.
Collapse
Affiliation(s)
- Zeeshan Shamim
- School of Biosciences, University of Birmingham, Birmingham, UK.,Department of Biotechnology, Mirpur University of Science and Technology (MUST), Mirpur Azad Kashmir, Pakistan
| | | |
Collapse
|
11
|
Cara N, Piccoli PN, Bolcato L, Marfil CF, Masuelli RW. Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties. Phytochemistry 2020; 180:112516. [PMID: 32949937 DOI: 10.1016/j.phytochem.2020.112516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/25/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Polyploids often display a variety of phenotypic novelties when compared to their diploid progenitors, some of which may represent ecological advantages, especially regarding tolerance to biotic and abiotic factors. Plants cope with environmental factors by producing chemicals such as volatile organic compounds (VOCs) and specific amino acids (AAs). In potato, the third most important food crop in the world, gene introgression from diploid wild relative species into the genetic pool of the cultivated species (tetraploid) would be of great agronomical interest. The consequences of allopolyploidization on the potato VOCs and AAs profiles have not been yet analyzed. In this work, the effects of whole genome duplication on VOCs and AAs contents in leaves of potato allo- and autotetraploids and cultivated varieties were studied. The polyploids were obtained by chromosomal duplication of a genotype of the wild diploid species S. kurtzianum (autopolyploid model), and a diploid interspecific hybrid between the cultivated species S. tuberosum and S. kurtzianum (allopolyploid model). Almost all compounds levels varied greatly among these tetraploid lines; while all tetraploids showed higher contents of non-isoprenoids compounds than diploids, we found either increments or reductions in terpenes and AAs content. The results support the idea that genome duplication is a stochastic source of variability, which might be directly used for introgression in the 4x gene pool of the cultivated potato by sexual hybridization.
Collapse
Affiliation(s)
- Nicolás Cara
- Facultad de Ciencias Agrarias, UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| | - Patricia N Piccoli
- Facultad de Ciencias Agrarias, UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina; Instituto de Biología Agrícola de Mendoza (IBAM), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| | - Leonardo Bolcato
- Instituto de Biología Agrícola de Mendoza (IBAM), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| | - Carlos F Marfil
- Facultad de Ciencias Agrarias, UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina; Instituto de Biología Agrícola de Mendoza (IBAM), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| | - Ricardo W Masuelli
- Facultad de Ciencias Agrarias, UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina; Instituto de Biología Agrícola de Mendoza (IBAM), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| |
Collapse
|
12
|
Dai X, Li X, Huang Y, Liu X. The speciation and adaptation of the polyploids: a case study of the Chinese Isoetes L. diploid-polyploid complex. BMC Evol Biol 2020; 20:118. [PMID: 32928096 PMCID: PMC7490897 DOI: 10.1186/s12862-020-01687-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 09/09/2020] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The Chinese Isoetes L. are distributed in a stairway pattern: diploids in the high altitude and polyploids in the low altitude. The allopolyploid I. sinensis and its diploid parents I. yunguiensis and I. taiwanensis is an ideal system with which to investigate the relationships between polyploid speciation and the ecological niches preferences. RESULTS There were two major clades in the nuclear phylogenetic tree, all of the populations of polyploid were simultaneously located in both clades. The chloroplast phylogenetic tree included two clades with different populations of the polyploid clustered with the diploids separately: I. yunguiensis with partial populations of the I. sinensis and I. taiwanensis with the rest populations of the I. sinensis. The crow node of the I. sinensis allopolyploid system was 4.43 Ma (95% HPD: 2.77-6.97 Ma). The divergence time between I. sinensis and I. taiwanensis was estimated to 0.65 Ma (95% HPD: 0.26-1.91 Ma). The narrower niche breadth in I.sinensis than those of its diploid progenitors and less niche overlap in the pairwise comparisons between the polyploid and its progenitors. CONCLUSIONS Our results elucidate that I. yunguinensis and I. taiwanensis contribute to the speciation of I. sinensis, the diploid parents are the female parents of different populations. The change of altitude might have played an important role in allopolyploid speciation and the pattern of distribution of I. sinensis. Additionally, niche novelty of the allopolyploid population of I. sinensis has been detected, in accordance with the hypothesis that niche shift between the polyploids and its diploid progenitors is important for the establishment and persistence of the polyploids.
Collapse
Affiliation(s)
- Xiaokang Dai
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei People’s Republic of China
| | - Xiang Li
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei People’s Republic of China
| | - Yuqian Huang
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei People’s Republic of China
| | - Xing Liu
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei People’s Republic of China
- College of Sciences, Tibet University, Lhasa, 850012 Tibet People’s Republic of China
| |
Collapse
|
13
|
Zhao Q, Wang Y, Bi Y, Zhai Y, Yu X, Cheng C, Wang P, Li J, Lou Q, Chen J. Oligo-painting and GISH reveal meiotic chromosome biases and increased meiotic stability in synthetic allotetraploid Cucumis ×hytivus with dysploid parental karyotypes. BMC Plant Biol 2019; 19:471. [PMID: 31694540 PMCID: PMC6833230 DOI: 10.1186/s12870-019-2060-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/27/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Meiosis of newly formed allopolyploids frequently encounter perturbations induced by the merging of divergent and hybridizable genomes. However, to date, the meiotic properties of allopolyploids with dysploid parental karyotypes have not been studied in detail. The allotetraploid Cucumis ×hytivus (HHCC, 2n = 38) was obtained from interspecific hybridization between C. sativus (CC, 2n = 14) and C. hystrix (HH, 2n = 24) followed by chromosome doubling. The results of this study thus offer an excellent opportunity to explore the meiotic properties of allopolyploids with dysploid parental karyotypes. RESULTS In this report, we describe the meiotic properties of five chromosomes (C5, C7, H1, H9 and H10) and two genomes in interspecific hybrids and C. ×hytivus (the 4th and 14th inbred family) through oligo-painting and genomic in situ hybridization (GISH). We show that 1) only two translocations carrying C5-oligo signals were detected on the chromosomes C2 and C4 of one 14th individual by the karyotyping of eight 4th and 36 14th plants based on C5- and C7-oligo painting, and possible cytological evidence was observed in meiosis of the 4th generation; 2) individual chromosome have biases for homoeologous pairing and univalent formation in F1 hybrids and allotetraploids; 3) extensive H-chromosome autosyndetic pairings (e.g., H-H, 25.5% PMCs) were observed in interspecific F1 hybrid, whereas no C-chromosome autosyndetic pairings were observed (e.g. C-C); 4) the meiotic properties of two subgenomes have significant biases in allotetraploids: H-subgenome exhibits higher univalent and chromosome lagging frequencies than C-subgenome; and 5) increased meiotic stability in the S14 generation compared with the S4 generation, including synchronous meiosis behavior, reduced incidents of univalent and chromosome lagging. CONCLUSIONS These results suggest that the meiotic behavior of two subgenomes has dramatic biases in response to interspecific hybridization and allopolyploidization, and the meiotic behavior harmony of subgenomes is a key subject of meiosis evolution in C. ×hytivus. This study helps to elucidate the meiotic properties and evolution of nascent allopolyploids with the dysploid parental karyotypes.
Collapse
Affiliation(s)
- Qinzheng Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Yunzhu Wang
- Institue of Horticulture, Zhejiang Academy of Agriculture Sciences, Hangzhou, 310021, China
| | - Yunfei Bi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Yufei Zhai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Xiaqing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Panqiao Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China.
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China.
| |
Collapse
|
14
|
Gordon SP, Levy JJ, Vogel JP. PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution. BMC Genomics 2019; 20:580. [PMID: 31299888 PMCID: PMC6626429 DOI: 10.1186/s12864-019-5828-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Our understanding of polyploid genomes is limited by our inability to definitively assign sequences to a specific subgenome without extensive prior knowledge like high resolution genetic maps or genome sequences of diploid progenitors. In theory, existing methods for assigning sequences to individual species from metagenome samples could be used to separate subgenomes in polyploid organisms, however, these methods rely on differences in coarse genome properties like GC content or sequences from related species. Thus, these approaches do not work for subgenomes where gross features are indistinguishable and related genomes are lacking. Here we describe a method that uses rapidly evolving repetitive DNA to circumvent these limitations. RESULTS By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes from test datasets and subgenomes from two polyploid plants, tobacco and wheat, without any prior knowledge. CONCLUSION This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.
Collapse
Affiliation(s)
- Sean P. Gordon
- DOE Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA 94598 USA
| | - Joshua J. Levy
- DOE Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA 94598 USA
- University of California Berkeley, Berkeley, CA USA
| | - John P. Vogel
- DOE Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA 94598 USA
- University of California Berkeley, Berkeley, CA USA
| |
Collapse
|
15
|
Yew CL, Kakui H, Shimizu KK. Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica. J Plant Res 2018; 131:349-358. [PMID: 29032409 DOI: 10.1007/s10265-017-0982-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/11/2017] [Indexed: 06/07/2023]
Abstract
Polyploidization has played an important role in the speciation and diversification of plant species. However, genetic analyses of polyploids are challenging because the vast majority of the model species are diploids. The allotetraploid Arabidopsis kamchatica, which originated through the hybridization of the diploid Arabidopsis halleri and Arabidopsis lyrata, is an emerging model system for studying various aspects of polyploidy. However, a transgenic method that allows the insertion of a gene of interest into A. kamchatica is still lacking. In this study, we investigated the early development of pistils in A. kamchatica and confirmed the formation of open pistils in young flower buds (stages 8-9), which is important for allowing Agrobacterium to access female reproductive tissues. We established a simple Agrobacterium-mediated floral dip transformation method to transform a gene of interest into A. kamchatica by dipping A. kamchatica inflorescences bearing many young flower buds into a 5% sucrose solution containing 0.05% Silwet L-77 and Agrobacterium harboring the gene of interest. We showed that a screenable marker comprising fluorescence-accumulating seed technology with green fluorescent protein was useful for screening the transgenic seeds of two accessions of A. kamchatica subsp. kamchatica and an accession of A. kamchatica subsp. kawasakiana.
Collapse
Affiliation(s)
- Chow-Lih Yew
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Hiroyuki Kakui
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka-ward, Yokohama, 244-0813, Japan.
| |
Collapse
|
16
|
Yanagi T, Shirasawa K, Terachi M, Isobe S. Sequence analysis of cultivated strawberry ( Fragaria × ananassa Duch.) using microdissected single somatic chromosomes. Plant Methods 2017; 13:91. [PMID: 29118823 PMCID: PMC5663147 DOI: 10.1186/s13007-017-0237-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/08/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Cultivated strawberry (Fragaria × ananassa Duch.) has homoeologous chromosomes because of allo-octoploidy. For example, two homoeologous chromosomes that belong to different sub-genome of allopolyploids have similar base sequences. Thus, when conducting de novo assembly of DNA sequences, it is difficult to determine whether these sequences are derived from the same chromosome. To avoid the difficulties associated with homoeologous chromosomes and demonstrate the possibility of sequencing allopolyploids using single chromosomes, we conducted sequence analysis using microdissected single somatic chromosomes of cultivated strawberry. RESULTS Three hundred and ten somatic chromosomes of the Japanese octoploid strawberry 'Reiko' were individually selected under a light microscope using a microdissection system. DNA from 288 of the dissected chromosomes was successfully amplified using a DNA amplification kit. Using next-generation sequencing, we decoded the base sequences of the amplified DNA segments, and on the basis of mapping, we identified DNA sequences from 144 samples that were best matched to the reference genomes of the octoploid strawberry, F. × ananassa, and the diploid strawberry, F. vesca. The 144 samples were classified into seven pseudo-molecules of F. vesca. The coverage rates of the DNA sequences from the single chromosome onto all pseudo-molecular sequences varied from 3 to 29.9%. CONCLUSION We demonstrated an efficient method for sequence analysis of allopolyploid plants using microdissected single chromosomes. On the basis of our results, we believe that whole-genome analysis of allopolyploid plants can be enhanced using methodology that employs microdissected single chromosomes.
Collapse
Affiliation(s)
- Tomohiro Yanagi
- Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa 761-0795 Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, Chiba Japan
| | - Mayuko Terachi
- Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa 761-0795 Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, Chiba Japan
| |
Collapse
|
17
|
Migdałek G, Nowak J, Saługa M, Cieślak E, Szczepaniak M, Ronikier M, Marcussen T, Słomka A, Kuta E. No evidence of contemporary interploidy gene flow between the closely related European woodland violets Viola reichenbachiana and V. riviniana (sect. Viola, Violaceae). Plant Biol (Stuttg) 2017; 19:542-551. [PMID: 28402054 DOI: 10.1111/plb.12571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
Viola reichenbachiana (2n = 4x = 20) and V. riviniana (2n = 8x = 40) are closely related species widely distributed in Europe, often sharing the same habitat throughout their overlapping ranges. It has been suggested in numerous studies that their high intraspecific morphological variability and plasticity might have been further increased by interspecific hybridisation in contact zones, given the sympatry of the species and the incomplete sterility of their hybrid. The aims of this study were to: (i) confirm that V. reichenbachiana and V. riviniana have one 4x genome in common, and (ii) determine the impact of hybridisation and introgression on genetic variation of these two species in selected European populations. For our study, we used 31 Viola populations from four European countries, which were analysed using AFLP and sequencing of a variable plastid intergenic spacer, trnH-psbA. Our analysis revealed that V. reichenbachiana exhibited larger haplotype diversity, having three species-specific haplotypes versus one in V. riviniana. The relationships among haplotypes suggest transfer of common haplotypes into V. riviniana from both V. reichenbachiana and hypothetically the other, now extinct, parental species. AFLP analysis showed low overall genetic diversity of both species, with V. riviniana showing higher among-population diversity. None of the morphologically designated hybrid populations had additive AFLP polymorphisms that would have indicated recent hybridisation. Also, kinship coefficients between both species did not indicate gene flow. V. riviniana showed significant population subdivision and significant isolation by distance, in contrast to V. reichenbachiana. The results indicate lack of gene flow between species, high influence of selfing on genetic variability, as well as probably only localised introgression toward V. riviniana.
Collapse
Affiliation(s)
- G Migdałek
- Department of Plant Physiology, Pedagogical University of Cracow, Cracow, Poland
| | - J Nowak
- W. Szafer Institute of Botany, Polish Academy of Sciences, Cracow, Poland
| | - M Saługa
- W. Szafer Institute of Botany, Polish Academy of Sciences, Cracow, Poland
| | - E Cieślak
- W. Szafer Institute of Botany, Polish Academy of Sciences, Cracow, Poland
| | - M Szczepaniak
- W. Szafer Institute of Botany, Polish Academy of Sciences, Cracow, Poland
| | - M Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Cracow, Poland
| | - T Marcussen
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - A Słomka
- Department of Plant Cytology and Embryology, Jagiellonian University, Cracow, Poland
| | - E Kuta
- Department of Plant Cytology and Embryology, Jagiellonian University, Cracow, Poland
| |
Collapse
|
18
|
Ma J, Stiller J, Zheng Z, Liu YX, Wei Y, Zheng YL, Liu C. A high-throughput pipeline for detecting locus-specific polymorphism in hexaploid wheat (Triticum aestivum L.). Plant Methods 2015; 11:39. [PMID: 26244051 PMCID: PMC4524443 DOI: 10.1186/s13007-015-0082-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/22/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Bread wheat (Triticum aestivum L., 2n = 6x = 42) is an allohexaploid with a huge genome. Due to the presence of extensive homoeologs and paralogs, generating locus-specific sequences can be challenging, especially when a large number of sequences are required. Traditional methods of generating locus-specific sequences are rather strenuous and time-consuming if large numbers of sequences are to be handled. RESULTS To improve the efficiency of isolating sequences for targeted loci, a time-saving and high-throughput pipeline integrating orthologous sequence alignment, genomic sequence retrieving, and multiple sequence alignment was developed. This pipeline was successfully employed in retrieving and aligning homoeologous sequences and 83% of the primers designed based on the pipeline successfully amplified fragments from the targeted subgenomes. CONCLUSIONS The high-throughput pipeline developed in this study makes it feasible to efficiently identify locus-specific sequences for large numbers of sequences. It could find applications in all research projects where locus-specific sequences are required. In addition to generating locus-specific markers, the pipeline was also used in our laboratory to identify differentially expressed genes among the three subgenomes of bread wheat. Importantly, the pipeline is not only valuable for research in wheat but should also be applicable to other allopolyploid species.
Collapse
Affiliation(s)
- Jian Ma
- />Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 China
- />CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD 4067 Australia
| | - Jiri Stiller
- />CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD 4067 Australia
| | - Zhi Zheng
- />CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD 4067 Australia
- />School of Plant Biology, The University of Western Australia, Perth, WA 6009 Australia
- />National Foxtail Millet Improvement Centre, Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Ya-Xi Liu
- />Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 China
| | - Yuming Wei
- />Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 China
| | - You-Liang Zheng
- />Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 China
| | - Chunji Liu
- />CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD 4067 Australia
- />School of Plant Biology, The University of Western Australia, Perth, WA 6009 Australia
| |
Collapse
|
19
|
Pajarón S, Pangua E, Quintanilla LG, Jiménez A. Influence of water availability on gender determination of gametophytes in a diploid-polyploid complex of a xerophytic fern genus. AoB Plants 2015; 7:plv047. [PMID: 25940203 PMCID: PMC4480211 DOI: 10.1093/aobpla/plv047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 04/21/2015] [Indexed: 05/27/2023]
Abstract
Environmental sex determination (ESD) is present in several animal and plant lineages. Diverse factors such as temperature, light or water availability have been described as sex determinants in these organisms. Among plants, ferns frequently display ESD. This work compares the effect of different levels of water availability in two diploid species of the xerophytic fern genus Cheilanthes and in their derived tetraploid, and if they are sensitive to antheridiogen (i.e. maleness-inducing pheromone). Different watering regimes were applied to isolated gametophyte cultures of the three study species. Gametophyte survival, size, gender and sporophyte production were assessed after 13, 18 and 23 weeks of culture. Cultures combining spores and adult gametophytes were established to test the effect of antheridiogen. Isolated gametophytes had an asexual to female to bisexual sequence that did not depend upon the degree of soil moisture. Both gender expression and growth reduction in response to water scarcity of the allotetraploid were more similar to those of one of the diploid parents. In all watering regimes, survival was higher in the allotetraploid, suggesting hybrid vigour, whereas automixis rate was similar in the three species and reached ∼50 % at high moisture. This breeding system can ensure reproduction in the absence of males. In the three species, female gametophytes produced antheridiogens that enhanced maleness. This promotes a mixed mating system that could be favourable for ferns growing in xeric habitats.
Collapse
Affiliation(s)
- Santiago Pajarón
- Departamento de Biología Vegetal I. Facultad de Biología, Universidad Complutense, C/José Antonio Novais 2, 28040 Madrid, Spain
| | - Emilia Pangua
- Departamento de Biología Vegetal I. Facultad de Biología, Universidad Complutense, C/José Antonio Novais 2, 28040 Madrid, Spain
| | - Luis G Quintanilla
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, C/Tulipán s/n, 28933 Móstoles, Madrid, Spain
| | - Ares Jiménez
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, C/Tulipán s/n, 28933 Móstoles, Madrid, Spain
| |
Collapse
|
20
|
Garmendia A, Ferriol M, Juarez J, Zając A, Kałużny K, Merle H. A rare case of a natural contact zone in Morocco between an autopolyploid and an allopolyploid of Centaurea aspera with sterile tetraploid hybrids. Plant Biol (Stuttg) 2015; 17:746-757. [PMID: 25363815 DOI: 10.1111/plb.12284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/24/2014] [Indexed: 06/04/2023]
Abstract
A new contact zone between Centaurea aspera and Centaurea seridis was found in Morocco. Chromosome counts and flow cytometry showed that both taxa were tetraploid (4x = 44). A literature review and morphometric analysis established that C. aspera corresponds to the autopolyploid C. aspera subsp. gentilii and C. seridis corresponds to the allopolyploid C. seridis var. auriculata. This contact area was compared with the homologous contact zones in Spain formed by the diploid C. aspera subsp. stenophylla and the tetraploid C. seridis subsp. maritima. Natural hybrids between parental species were frequent in both areas. In Spain, hybrids were triploid (from reduced gametes A and gamete AB), highly sterile and exerted a 'triploid block'. In Morocco, cytometry showed that hybrids were tetraploid and, therefore, probably fertile, but all the capitula lacked achenes. It is likely that the resulting genome of the new tetraploid hybrid (AAAB), through the fusion of reduced gametes AA (from subsp. gentilii) and AB (from var. auriculata), could explain irregularities in meiosis through formation of aneuploid gametes and, therefore, infertility of the hybrid. Moroccan sterile tetraploid hybrids develop, but have the identical irregularities to Spanish triploids, probably due to the odd number of homologous chromosomes. The new hybrid is first described as C. x subdecurrens nothosubsp. paucispinus. In addition, distribution and ecological traits are analysed.
Collapse
Affiliation(s)
- A Garmendia
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain
| | | | | | | | | | | |
Collapse
|
21
|
Wang Y, Wang X, Chen Q, Zhang L, Tang H, Luo Y, Liu Z. Phylogenetic insight into subgenera Idaeobatus and Malachobatus (Rubus, Rosaceae) inferring from ISH analysis. Mol Cytogenet 2015; 8:11. [PMID: 25674160 PMCID: PMC4324050 DOI: 10.1186/s13039-015-0114-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/21/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rubus is a large and taxonomically complex genus exhibiting agamospermy, polyploidy and frequent hybridization. The objective of this work was to elucidate rDNA disrtibution pattern and investigate genomic composition of polyploids in 16 Rubus taxa (2n = 2x, 3x, 4x, 8x) of two subgenera Idaeobatus and Malachobatus by ISH method. RESULTS The basic Rubus genome had one 45S rDNA locus, and all the polyploids (except R. setchuenensis) had the expected multiples of this number. Diploid and tetraploid Rubus taxa carried two 5S rDNA, whereas the triploid and octoploid species only had three. The duplicated 45S rDNA sites tended to be conserved, whereas those of 5S rDNA tended to be eliminated after polyploidization. The accession R03-20 was an autotriploid R. parvifolius, while R03-27 and R03-57 were naturally-occurred triploid hybrids between R. parvifolius and R. coreanus. GISH results suggested that R. parvifolius had close relationship with polyploids from Malachobatus. CONCLUSIONS The polyploids from Malachobatus were probable allopolyploid. In addition, Rubus parvifolius might be involved in hybridization, polyploidization and speciation of some Idaeobatus and Malachobatus species.
Collapse
Affiliation(s)
- Yan Wang
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
| | - Xiaorong Wang
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
- />Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, 611130 People’s Republic of China
| | - Qing Chen
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
| | - Li Zhang
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
| | - Haoru Tang
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
| | - Ya Luo
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
| | - Zejing Liu
- />College of Horticulture, Sichuan Agricultural University, Ya’an, 625014 People’s Republic of China
| |
Collapse
|
22
|
Hao M, Chen J, Zhang L, Luo J, Yuan Z, Yan Z, Zhang B, Chen W, Wei Y, Zhang H, Zheng Y, Liu D. The genetic study utility of a hexaploid wheat DH population with non-recombinant A- and B-genomes. Springerplus 2013; 2:131. [PMID: 23577301 PMCID: PMC3618880 DOI: 10.1186/2193-1801-2-131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 03/15/2013] [Indexed: 12/16/2022]
Abstract
To study the D-genome of the wild wheat relative Aegilops tauschii Cosson at the hexaploid level, we developed a synthetic doubled-haploid (DH) hexaploid wheat population, SynDH3. This population was derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from a cross between Triticum turgidum ssp. dicoccon PI377655 and A. tauschii ssp. strangulata AS66 × ssp. tauschii AS87. SynDH3 is a diploidization-hexaploid DH population containing recombinant D chromosomes from two different A. tauschii genotypes, with A and B chromosomes from T. turgidum being homogenous across the entire population. Using this population, we constructed a genetic map. Of the 440 markers used to construct the map, 421 (96%) were assigned to 12 linkage groups; these included 346 Diversity Arrays Technology (DArT) and 75 simple sequence repeat (SSR) markers. The total map length of the seven D chromosomes spanned 916.27 cM, with an average length of 130.90 cM per chromosome and an average distance between markers of 3.47 cM. Seven segregation distortion regions were detected on seven linkage groups. Out of 50 markers shared with those on a common wheat map, 37 showed a consistent order. The utility of the diploidization-hexaploid DH population for mapping qualitative trait genes was confirmed using the dominant glaucousness-inhibiting gene W2 (I) as an example.
Collapse
Affiliation(s)
- Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130 Sichuan P.R. China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|