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He Y, He J, Zhao Y, Zhang S, Rao X, Wang H, Wang Z, Song A, Jiang J, Chen S, Chen F. Divergence of 10 satellite repeats in Artemisia (Asteraceae: Anthemideae) based on sequential fluorescence in situ hybridization analysis: evidence for species identification and evolution. Chromosome Res 2024; 32:5. [PMID: 38502277 DOI: 10.1007/s10577-024-09749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024]
Abstract
Artemisia is a large genus encompassing about 400 diverse species, many of which have considerable medicinal and ecological value. However, complex morphological information and variation in ploidy level and nuclear DNA content have presented challenges for evolution studies of this genus. Consequently, taxonomic inconsistencies within the genus persist, hindering the utilization of such large plant resources. Researchers have utilized satellite DNAs to aid in chromosome identification, species classification, and evolutionary studies due to their significant sequence and copy number variation between species and close relatives. In the present study, the RepeatExplorer2 pipeline was utilized to identify 10 satellite DNAs from three species (Artemisia annua, Artemisia vulgaris, Artemisia viridisquama), and fluorescence in situ hybridization confirmed their distribution on chromosomes in 24 species, including 19 Artemisia species with 5 outgroup species from Ajania and Chrysanthemum. Signals of satellite DNAs exhibited substantial differences between species. We obtained one genus-specific satellite from the sequences. Additionally, molecular cytogenetic maps were constructed for Artemisia vulgaris, Artemisia leucophylla, and Artemisia viridisquama. One species (Artemisia verbenacea) showed a FISH distribution pattern suggestive of an allotriploid origin. Heteromorphic FISH signals between homologous chromosomes in Artemisia plants were observed at a high level. Additionally, the relative relationships between species were discussed by comparing ideograms. The results of the present study provide new insights into the accurate identification and taxonomy of the Artemisia genus using molecular cytological methods.
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Affiliation(s)
- Yanze He
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun He
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Zhao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuangshuang Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinyu Rao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haibin Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Zhenxing Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Aiping Song
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Jiafu Jiang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Sumei Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China
| | - Fadi Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing, 210014, China.
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Yücel G, Senderowicz M, Kolano B. The Use of Ribosomal DNA for Comparative Cytogenetics. Methods Mol Biol 2023; 2672:265-284. [PMID: 37335483 DOI: 10.1007/978-1-0716-3226-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA) sequences provides excellent chromosome markers for comparative cytogenetic analyses, especially in non-model plant species. The tandem repeat nature of a sequence and the presence of a highly conserved genic region make rDNA sequences relatively easy to isolate and clone. In this chapter, we describe the use of rDNA as markers for comparative cytogenetics studies. Traditionally, cloned probes labeled with Nick-translation have been used to detect rDNA loci. Recently, pre-labeled oligonucleotides are also employed quite frequently to detect both 35S and 5S rDNA loci. Ribosomal DNA sequences, together with other DNA probes in FISH/GISH or with fluorochromes such as CMA3 banding or silver staining, are very useful tools in comparative analyses of plant karyotypes.
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Affiliation(s)
- Gülru Yücel
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Türkiye
| | - Magdalena Senderowicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Bożena Kolano
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland.
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Yucel G, Betekhtin A, Cabi E, Tuna M, Hasterok R, Kolano B. The Chromosome Number and rDNA Loci Evolution in Onobrychis (Fabaceae). Int J Mol Sci 2022; 23:ijms231911033. [PMID: 36232345 PMCID: PMC9570107 DOI: 10.3390/ijms231911033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 02/02/2023] Open
Abstract
The evolution of chromosome number and ribosomal DNA (rDNA) loci number and localisation were studied in Onobrychis Mill. Diploid and tetraploid species, as well as two basic chromosome numbers, x = 7 and x = 8, were observed among analysed taxa. The chromosomal distribution of rDNA loci was presented here for the first time using fluorescence in situ hybridisation (FISH) with 5S and 35S rDNA probes. Onobrychis species showed a high polymorphism in the number and localisation of rDNA loci among diploids, whereas the rDNA loci pattern was very similar in polyploids. Phylogenetic relationships among the species, inferred from nrITS sequences, were used as a framework to reconstruct the patterns of basic chromosome number and rDNA loci evolution. Analysis of the evolution of the basic chromosome numbers allowed the inference of x = 8 as the ancestral number and the descending dysploidy and polyploidisation as the major mechanisms of the chromosome number evolution. Analyses of chromosomal patterns of rRNA gene loci in a phylogenetic context resulted in the reconstruction of one locus of 5S rDNA and one locus of 35S rDNA in the interstitial chromosomal position as the ancestral state in this genus.
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Affiliation(s)
- Gulru Yucel
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun 55200, Turkey
- Department of Biology, Institute of Natural and Applied Sciences, Tekirdag Namik Kemal University, Tekirdag 59030, Turkey
| | - Alexander Betekhtin
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Evren Cabi
- Department of Biology, Faculty of Arts and Sciences, Tekirdag Namik Kemal University, Tekirdag 59030, Turkey
| | - Metin Tuna
- Department of Field Crops, Faculty of Agriculture, Tekirdag Namik Kemal University, Tekirdag 59030, Turkey
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Bozena Kolano
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
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Comparative Analyses of Complete Chloroplast Genomes and Karyotypes of Allotetraploid Iris koreana and Its Putative Diploid Parental Species ( Iris Series Chinenses, Iridaceae). Int J Mol Sci 2022; 23:ijms231810929. [PMID: 36142840 PMCID: PMC9504294 DOI: 10.3390/ijms231810929] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 12/16/2022] Open
Abstract
The Iris series Chinenses in Korea comprises four species (I. minutoaurea, I. odaesanensis, I. koreana, and I. rossii), and the group includes some endangered species, owing to their high ornamental, economic, and conservation values. Among them, the putative allotetraploid, Iris koreana (2n = 4x = 50), is hypothesized to have originated from the hybridization of the diploids I. minutoaurea (2n = 2x = 22) and I. odaesanensis (2n = 2x = 28) based on morphological characters, chromosome numbers, and genome size additivity. Despite extensive morphological and molecular phylogenetical studies on the genus Iris, little is known about Korean irises in terms of their complete chloroplast (cp) genomes and molecular cytogenetics that involve rDNA loci evolution based on fluorescence in situ hybridization (FISH). This study reports comparative analyses of the karyotypes of the three Iris species (I. koreana, I. odaesanensis, and I. minutoaurea), with an emphasis on the 5S and 35S rDNA loci number and localization using FISH together with the genome size and chromosome number. Moreover, the cp genomes of the same individuals were sequenced and assembled for comparative analysis. The rDNA loci numbers, which were localized consistently at the same position in all species, and the chromosome numbers and genome size values of tetraploid Iris koreana (four 5S and 35S loci; 2n = 50; 1C = 7.35 pg) were additively compared to its putative diploid progenitors, I. minutoaurea (two 5S and 35S loci; 2n = 22; 1C = 3.71 pg) and I. odaesanensis (two 5S and 35S loci; 2n = 28; 1C = 3.68 pg). The chloroplast genomes were 152,259–155,145 bp in length, and exhibited a conserved quadripartite structure. The Iris cp genomes were highly conserved and similar to other Iridaceae cp genomes. Nucleotide diversity analysis indicated that all three species had similar levels of genetic variation, but the cp genomes of I. koreana and I. minutoaurea were more similar to each other than to I. odaesanensis. Positive selection was inferred for psbK and ycf2 genes of the three Iris species. Phylogenetic analyses consistently recovered I. odaesanensis as a sister to a clade containing I. koreana and I. minutoaurea. Although the phylogenetic relationship, rDNA loci number, and localization, together with the genome size and chromosome number of the three species, allowed for the inference of I. minutoaurea as a putative maternal taxon and I. odaesanensis as a paternal taxon, further analyses involving species-specific molecular cytogenetic markers and genomic in situ hybridization are required to interpret the mechanisms involved in the origin of the chromosomal variation in Iris series Chinenses. This study contributes towards the genomic and chromosomal evolution of the genus Iris.
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Sharbrough J, Conover JL, Gyorfy MF, Grover CE, Miller ER, Wendel JF, Sloan DB. Global Patterns of subgenome evolution in organelle-targeted genes of six allotetraploid angiosperms. Mol Biol Evol 2022; 39:6564157. [PMID: 35383845 PMCID: PMC9040051 DOI: 10.1093/molbev/msac074] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary “mismatches” between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.
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Affiliation(s)
- Joel Sharbrough
- Biology Department, Colorado State University, Fort Collins, CO, USA.,Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Emma R Miller
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Daniel B Sloan
- Biology Department, Colorado State University, Fort Collins, CO, USA
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Molecular and Cytogenetic Analysis of rDNA Evolution in Crepis Sensu Lato. Int J Mol Sci 2022; 23:ijms23073643. [PMID: 35409003 PMCID: PMC8998684 DOI: 10.3390/ijms23073643] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023] Open
Abstract
Although Crepis was the first model plant group in which chromosomal changes were considered to play an important role in speciation, their chromosome structure and evolution have been barely investigated using molecular cytogenetic methods. The aim of the study was to provide a better understanding of the patterns and directions of Crepis chromosome evolution, using comparative analyses of rDNA loci number and localisation. The chromosome base number and chromosomal organisation of 5S and 35S rDNA loci were analysed in the phylogenetic background for 39 species of Crepis, which represent the evolutionary lineages of Crepis sensu stricto and Lagoseris, including Lapsana communis. The phylogenetic relationships among all the species were inferred from nrITS and newly obtained 5S rDNA NTS sequences. Despite high variations in rDNA loci chromosomal organisation, most species had a chromosome with both rDNA loci within the same (usually short) chromosomal arm. The comparative analyses revealed several independent rDNA loci number gains and loci repositioning that accompanied diversification and speciation in Crepis. Some of the changes in rDNA loci patterns were reconstructed for the same evolutionary lineages as descending dysploidy.
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7
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Ansari HA, Ellison N, Stewart AV, Williams WM. Distribution patterns of rDNA loci in the Schedonorus- Lolium complex (Poaceae). COMPARATIVE CYTOGENETICS 2022; 16:39-54. [PMID: 35437460 PMCID: PMC8971122 DOI: 10.3897/compcytogen.v16.i1.79056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
The Schedonorus-Lolium complex of the subtribe Loliinae (Poaceae) includes several economically important forage and turf grasses. This complex encompasses Lolium Linnaeus, 1753, Festuca Linnaeus, 1753 subgenus Schedonorus (P. Beauvois, 1824) Petermann, 1849 and Micropyropsis Romero Zarco et Cabezudo, 1983. New FISH results of 5S and 18S-26S rDNA sequences are presented for three species and the results are interpreted in a review of distribution patterns of 5S and 18S-26S rDNA sequences among other species in the complex. Micropyropsistuberosa Romero Zarco et Cabezudo, 1983 (2n = 2x = 14) displayed a distribution pattern of rDNA sequences identical to that of F.pratensis Hudson, 1762, supporting a close phylogenetic relationship at the bottom of the phylogenetic tree. "Loliummultiflorum" Lamarck, 1779 accessions sourced from Morocco showed a different pattern from European L.multiflorum and could be a unique and previously uncharacterised taxon. North African Festucasimensis Hochstetter ex A. Richard, 1851 had a marker pattern consistent with allotetraploidy and uniparental loss of one 18S-26S rDNA locus. This allotetraploid has previously been suggested to have originated from a hybrid with Festucaglaucescens (Festucaarundinaceavar.glaucescens Boissier, 1844). However, the distribution patterns of the two rDNA sequences in this allotetraploid do not align with F.glaucescens, suggesting that its origin from this species is unlikely. Furthermore, comparisons with other higher alloploids in the complex indicate that F.simensis was a potential donor of two sub-genomes of allohexaploid Festucagigantea (Linnaeus) Villars, 1787. In the overall complex, the proximal locations of both rDNA markers were conserved among the diploid species. Two types of synteny of the two markers could, to a considerable extent, distinguish allo- and autogamous Lolium species. The ancestral parentage of the three Festuca allotetraploids has not yet been determined, but all three appear to have been sub-genome donors to the higher allopolypoids of sub-genus Schedonorus. Terminal locations of both the markers were absent from the diploids but were very frequently observed in the polyploids.
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Affiliation(s)
- Helal Ahmad Ansari
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
| | - Nicholas Ellison
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
| | - Alan Vincent Stewart
- PGG Wrightson Seeds, Kimihia Research Centre, 1375 Springs Road, RD4, Lincoln 7674, New ZealandKimihia Research CentreLincolnNew Zealand
| | - Warren Mervyn Williams
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
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Borowska-Zuchowska N, Senderowicz M, Trunova D, Kolano B. Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060784. [PMID: 35336666 PMCID: PMC8953110 DOI: 10.3390/plants11060784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 05/05/2023]
Abstract
Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome- and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics.
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Zhao P, Li X, Sun H, Zhao X, Wang X, Ran R, Zhao J, Wei Y, Liu X, Chen G. Healthy values and de novo domestication of sand rice ( Agriophyllum squarrosum), a comparative view against Chenopodium quinoa. Crit Rev Food Sci Nutr 2021:1-22. [PMID: 34755571 DOI: 10.1080/10408398.2021.1999202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Sand rice (Agriophyllum squarrosum) is prized for its well-balanced nutritional properties, broad adaptability in Central Asia and highly therapeutic potentials. It has been considered as a potential climate-resilient crop. Its seed has comparable metabolite profile with Chenopodium quinoa and is rich in proteins, essential amino acids, minerals, polyunsaturated fatty acids, and phenolics, but low in carbohydrates. Phenolics like protocatechuic acid and quercetins have been characterized with biological functions on regulation of lipid and glucose metabolism in addition to anti-inflammatory and antioxidant activities. Sand rice is thus an important source for developing functional and nutraceutical products. Though historical consumption has been over 1300 years, sand rice has undergone few agronomic improvements until recently. Breeding by individual selection has been performed and yield of the best genotype can reach up to 1295.5 kg/ha. Furthermore, chemical mutagenesis has been used to modify the undesirable traits and a case study of a dwarf line (dwarf1), which showed the Green Revolution-like phenotypes, is presented. Utilization of both breeding methodologies will accelerate its domestication process. As a novel crop, sand rice research is rather limited compared with quinoa. More scientific input is urgently required if the nutritional and commercial potentials are to be fully realized.
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Affiliation(s)
- Pengshan Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P.R, China.,Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P.R. China
| | - Xiaofeng Li
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P.R, China.,University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Hong Sun
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P.R, China.,University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Xin Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P.R, China
| | - Xiaohua Wang
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P.R. China
| | - Ruilan Ran
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P.R, China.,University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Jiecai Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P.R, China.,Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P.R. China
| | - Yuming Wei
- Animal Husbandry Pasture and Green Agriculture Institute of Gansu Academy of Agricultural Sciences, Lanzhou, P.R. China
| | - Xin Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Guoxiong Chen
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P.R, China.,Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, P.R. China
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Ma Q, Su C, Dong CH. Genome-Wide Transcriptomic and Proteomic Exploration of Molecular Regulations in Quinoa Responses to Ethylene and Salt Stress. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112281. [PMID: 34834644 PMCID: PMC8625574 DOI: 10.3390/plants10112281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 06/02/2023]
Abstract
Quinoa (Chenopodiumquinoa Willd.), originated from the Andean region of South America, shows more significant salt tolerance than other crops. To reveal how the plant hormone ethylene is involved in the quinoa responses to salt stress, 4-week-old quinoa seedlings of 'NL-6' treated with water, sodium chloride (NaCl), and NaCl with ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) were collected and analyzed by transcriptional sequencing and tandem mass tag-based (TMT) quantitative proteomics. A total of 9672 proteins and 60,602 genes was identified. Among them, the genes encoding glutathione S-transferase (GST), peroxidase (POD), phosphate transporter (PT), glucan endonuclease (GLU), beta-galactosidase (BGAL), cellulose synthase (CES), trichome birefringence-like protein (TBL), glycine-rich cell wall structural protein (GRP), glucosyltransferase (GT), GDSL esterase/lipase (GELP), cytochrome P450 (CYP), and jasmonate-induced protein (JIP) were significantly differentially expressed. Further analysis suggested that the genes may mediate through osmotic adjustment, cell wall organization, reactive oxygen species (ROS) scavenging, and plant hormone signaling to take a part in the regulation of quinoa responses to ethylene and salt stress. Our results provide a strong foundation for exploration of the molecular mechanisms of quinoa responses to ethylene and salt stress.
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Affiliation(s)
- Qian Ma
- Correspondence: (Q.M.); (C.-H.D.); Tel.: +86-53258957640 (Q.M.); +86-53258957640 (C.-H.D.)
| | | | - Chun-Hai Dong
- Correspondence: (Q.M.); (C.-H.D.); Tel.: +86-53258957640 (Q.M.); +86-53258957640 (C.-H.D.)
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Mizuno N, Toyoshima M, Fujita M, Fukuda S, Kobayashi Y, Ueno M, Tanaka K, Tanaka T, Nishihara E, Mizukoshi H, Yasui Y, Fujita Y. The genotype-dependent phenotypic landscape of quinoa in salt tolerance and key growth traits. DNA Res 2021; 27:5920640. [PMID: 33051662 PMCID: PMC7566363 DOI: 10.1093/dnares/dsaa022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
Cultivation of quinoa (Chenopodium quinoa), an annual pseudocereal crop that originated in the Andes, is spreading globally. Because quinoa is highly nutritious and resistant to multiple abiotic stresses, it is emerging as a valuable crop to provide food and nutrition security worldwide. However, molecular analyses have been hindered by the genetic heterogeneity resulting from partial outcrossing. In this study, we generated 136 inbred quinoa lines as a basis for the molecular identification and characterization of gene functions in quinoa through genotyping and phenotyping. Following genotyping-by-sequencing analysis of the inbred lines, we selected 5,753 single-nucleotide polymorphisms (SNPs) in the quinoa genome. Based on these SNPs, we show that our quinoa inbred lines fall into three genetic sub-populations. Moreover, we measured phenotypes, such as salt tolerance and key growth traits in the inbred quinoa lines and generated a heatmap that provides a succinct overview of the genotype–phenotype relationship between inbred quinoa lines. We also demonstrate that, in contrast to northern highland lines, most lowland and southern highland lines can germinate even under high salinity conditions. These findings provide a basis for the molecular elucidation and genetic improvement of quinoa and improve our understanding of the evolutionary process underlying quinoa domestication.
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Affiliation(s)
- Nobuyuki Mizuno
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masami Toyoshima
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686, Japan
| | - Miki Fujita
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki 305-0074, Japan
| | - Shota Fukuda
- Faculty of Agriculture, Tottori University, Tottori, Tottori 680-8550, Japan
| | - Yasufumi Kobayashi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686, Japan
| | - Mariko Ueno
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kojiro Tanaka
- Technology Development Group, Actree Corporation, Hakusan, Ishikawa 924-0053, Japan
| | - Tsutomu Tanaka
- Technology Development Group, Actree Corporation, Hakusan, Ishikawa 924-0053, Japan
| | - Eiji Nishihara
- Faculty of Agriculture, Tottori University, Tottori, Tottori 680-8550, Japan
| | - Hiroharu Mizukoshi
- Technology Development Group, Actree Corporation, Hakusan, Ishikawa 924-0053, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yasunari Fujita
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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12
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Liu M, Sun W, Li C, Yu G, Li J, Wang Y, Wang X. A multilayered cross-species analysis of GRAS transcription factors uncovered their functional networks in plant adaptation to the environment. J Adv Res 2021; 29:191-205. [PMID: 33842016 PMCID: PMC8020295 DOI: 10.1016/j.jare.2020.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/07/2020] [Accepted: 10/24/2020] [Indexed: 11/16/2022] Open
Abstract
Introduction Environmental stress is both a major force of natural selection and a prime factor affecting crop qualities and yields. The impact of the GRAS [gibberellic acid-insensitive (GAI), repressor of GA1-3 mutant (RGA), and scarecrow (SCR)] family on plant development and the potential to resist environmental stress needs much emphasis. Objectives This study aims to investigate the evolution, expansion, and adaptive mechanisms of GRASs of important representative plants during polyploidization. Methods We explored the evolutionary characteristics of GRASs in 15 representative plant species by systematic biological analysis of the genome, transcriptome, metabolite, protein complex map and phenotype. Results The GRAS family was systematically identified from 15 representative plant species of scientific and agricultural importance. The detection of gene duplication types of GRASs in all species showed that the widespread expansion of GRASs in these species was mainly contributed by polyploidization events. Evolutionary analysis reveals that most species experience independent genome-wide duplication (WGD) events and that interspecies GRAS functions may be broadly conserved. Polyploidy-related Chenopodium quinoa GRASs (CqGRASs) and Arabidopsis thaliana GRASs (AtGRASs) formed robust networks with flavonoid pathways by crosstalk with auxin and photosynthetic pathways. Furthermore, Arabidopsis thaliana population transcriptomes and the 1000 Plants (OneKP) project confirmed that GRASs are components of flavonoid biosynthesis, which enables plants to adapt to the environment by promoting flavonoid accumulation. More importantly, the GRASs of important species that may potentially improve important agronomic traits were mapped through TAIR and RARGE-II publicly available phenotypic data. Determining protein interactions and target genes contributes to determining GRAS functions. Conclusion The results of this study suggest that polyploidy-related GRASs in multiple species may be a target for improving plant growth, development, and environmental adaptation.
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Affiliation(s)
- Moyang Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China
| | - Wenjun Sun
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China
| | - Chaorui Li
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guolong Yu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiahao Li
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yudong Wang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xu Wang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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13
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Heitkam T, Weber B, Walter I, Liedtke S, Ost C, Schmidt T. Satellite DNA landscapes after allotetraploidization of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:32-52. [PMID: 31981259 DOI: 10.1111/tpj.14705] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/10/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
If two related plant species hybridize, their genomes may be combined and duplicated within a single nucleus, thereby forming an allotetraploid. How the emerging plant balances two co-evolved genomes is still a matter of ongoing research. Here, we focus on satellite DNA (satDNA), the fastest turn-over sequence class in eukaryotes, aiming to trace its emergence, amplification, and loss during plant speciation and allopolyploidization. As a model, we used Chenopodium quinoa Willd. (quinoa), an allopolyploid crop with 2n = 4x = 36 chromosomes. Quinoa originated by hybridization of an unknown female American Chenopodium diploid (AA genome) with an unknown male Old World diploid species (BB genome), dating back 3.3-6.3 million years. Applying short read clustering to quinoa (AABB), C. pallidicaule (AA), and C. suecicum (BB) whole genome shotgun sequences, we classified their repetitive fractions, and identified and characterized seven satDNA families, together with the 5S rDNA model repeat. We show unequal satDNA amplification (two families) and exclusive occurrence (four families) in the AA and BB diploids by read mapping as well as Southern, genomic, and fluorescent in situ hybridization. Whereas the satDNA distributions support C. suecicum as possible parental species, we were able to exclude C. pallidicaule as progenitor due to unique repeat profiles. Using quinoa long reads and scaffolds, we detected only limited evidence of intergenomic homogenization of satDNA after allopolyploidization, but were able to exclude dispersal of 5S rRNA genes between subgenomes. Our results exemplify the complex route of tandem repeat evolution through Chenopodium speciation and allopolyploidization, and may provide sequence targets for the identification of quinoa's progenitors.
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Affiliation(s)
- Tony Heitkam
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Beatrice Weber
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Ines Walter
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Susan Liedtke
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Charlotte Ost
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
- Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
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14
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Deciphering species relationships and evolution in Chenopodium through sequence variations in nuclear internal transcribed spacer region and amplified fragment-length polymorphism in nuclear DNA. J Genet 2019. [DOI: 10.1007/s12041-019-1079-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
The global population is on the path of an increasing trajectory with a simultaneous decline in arable land resources through salinization and desertification that have resulted mainly from climate change and other anthropogenic activities. Rising temperatures will cause changes in the entire ecosystem, resulting in significant alterations in global climate paradigms and a threat to food security. This review focuses on how the highly resilient Chenopodium quinoa Willd. can sustainably mitigate some of the detrimental impacts, such as starvation, and support or provide ecosystem services. In comparison, compared with the traditional staple food crops, quinoa has remarkable tolerance to abiotic stresses and is highly nutritious, with a unique balance and higher amounts of nutrients, and can therefore be an important crop for food security and nutritional adequacy. This crop has the potential to ameliorate global challenges with respect to increase in global population, effects of climate change, desalinization, phytoremediation, satisfying nutrient deficiency, and alleviating poverty.
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Lusinska J, Majka J, Betekhtin A, Susek K, Wolny E, Hasterok R. Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon, B. stacei and B. hybridum. ANNALS OF BOTANY 2018; 122:445-459. [PMID: 29893795 PMCID: PMC6110338 DOI: 10.1093/aob/mcy086] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/12/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS The Brachypodium genus represents a useful model system to study grass genome organization. Palaeogenomic analyses (e.g. Murat F, Armero A, Pont C, Klopp C, Salse J. 2017. Reconstructing the genome of the most recent common ancestor of flowering plants. Nature Genetics49: 490-496) have identified polyploidization and dysploidy as the prime mechanisms driving the diversity of plant karyotypes and nested chromosome fusions (NCFs) crucial for shaping grass chromosomes. This study compares the karyotype structure and evolution in B. distachyon (genome Bd), B. stacei (genome Bs) and in their putative allotetraploid B. hybridum (genomes BdBs). METHODS Brachypodium chromosomes were measured and identified using multicolour fluorescence in situ hybridization (mcFISH). For higher resolution, comparative chromosome barcoding was developed using sets of low-repeat, physically mapped B. distachyon-derived bacterial artificial chromosome (BAC) clones. KEY RESULTS All species had rather small chromosomes, and essentially all in the Bs genome were morphometrically indistinguishable. Seven BACs combined with two rDNA-based probes provided unambiguous and reproducible chromosome discrimination. Comparative chromosome barcoding revealed NCFs that contributed to the reduction in the x = 12 chromosome number that has been suggested for the intermediate ancestral grass karyotype. Chromosome Bd3 derives from two NCFs of three ancestral chromosomes (Os2, Os8, Os10). Chromosome Bs6 shows an ancient Os8/Os10 NCF, whilst Bs4 represents Os2 only. Chromosome Bd4 originated from a descending dysploidy that involves two NCFs of Os12, Os9 and Os11. The specific distribution of BACs along Bs9 and Bs5, in both B. stacei and B. hybridum, suggests a Bs genome-specific Robertsonian rearrangement. CONCLUSIONS mcFISH-based karyotyping identifies all chromosomes in Brachypodium annuals. Comparative chromosome barcoding reveals rearrangements responsible for the diverse organization of Bd and Bs genomes and provides new data regarding karyotype evolution since the split of the two diploids. The fact that no chromosome rearrangements were observed in B. hybridum compared with the karyotypes of its phylogenetic ancestors suggests prolonged genome stasis after the formation of the allotetraploid.
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Affiliation(s)
- Joanna Lusinska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Joanna Majka
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Alexander Betekhtin
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Karolina Susek
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Elzbieta Wolny
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
- For correspondence. E-mail
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Orzechowska M, Majka M, Weiss-Schneeweiss H, Kovařík A, Borowska-Zuchowska N, Kolano B. Organization and evolution of two repetitive sequences, 18-24J and 12-13P, in the genome of Chenopodium (Amaranthaceae). Genome 2018; 61:643-652. [PMID: 30067084 DOI: 10.1139/gen-2018-0044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The abundance and chromosomal organization of two repetitive sequences named 12-13P and 18-24J were analyzed in 24 diploid and nine polyploid species of Chenopodium s.l., with special attention to Chenopodium s.s. Both sequences were predominantly present in species of Chenopodium s.s.; however, differences in the amplification levels were observed among the species. The 12-13P repeat was highly amplified in all of the analyzed Eurasian species, whereas the American diploids showed a marked variation in the amplification levels. The 12-13P repeat contains a tandemly arranged 40 bp minisatellite element forming a large proportion of the genome of Chenopodium (up to 3.5%). FISH revealed its localization to the pericentromeric regions of the chromosomes. The chromosomal distribution of 12-13P delivered additional chromosomal marker for B-genome diploids. The 18-24J repeat showed a dispersed organization in all of the chromosomes of the analyzed diploid species and the Eurasian tetraploids. In the American allotetraploids (C. quinoa, C. berlandieri) and Eurasian allohexaploids (e.g., C. album) very intense hybridization signals of 18-24J were observed only on 18 chromosomes that belong to the B subgenome of these polyploids. Combined cytogenetic and molecular analyses suggests that reorganization of these two repeats accompanied the diversification and speciation of diploid (especially A genome) and polyploid species of Chenopodium s.s.
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Affiliation(s)
- Maja Orzechowska
- a Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28,40-032 Katowice, Poland
| | - Maciej Majka
- a Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28,40-032 Katowice, Poland
| | - Hanna Weiss-Schneeweiss
- b Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, Austria
| | - Ales Kovařík
- c Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265 Brno, Czech Republic
| | - Natalia Borowska-Zuchowska
- a Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28,40-032 Katowice, Poland
| | - Bozena Kolano
- a Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28,40-032 Katowice, Poland
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18
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Cheng A. Review: Shaping a sustainable food future by rediscovering long-forgotten ancient grains. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 269:136-142. [PMID: 29606211 DOI: 10.1016/j.plantsci.2018.01.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/14/2018] [Accepted: 01/31/2018] [Indexed: 06/08/2023]
Abstract
Genetic erosion of crops has been determined way back in the 1940s and accelerated some twenty years later by the inception of the Green Revolution. Claims that the revolution was a complete triumph remain specious, especially since the massive production boost in the global big three grain crops; wheat, maize, and rice that happened back then is unlikely to recur under current climate irregularities. Presently, one of the leading strategies for sustainable agriculture is by unlocking the genetic potential of underutilized crops. The primary focus has been on a suite of ancient cereals and pseudo-cereals which are riding on the gluten-free trend, including, among others, grain amaranth, buckwheat, quinoa, teff, and millets. Each of these crops has demonstrated tolerance to various stress factors such as drought and heat. Apart from being the centuries-old staple in their native homes, these crops have also been traditionally used as forage for livestock. This review summarizes what lies in the past and present for these underutilized cereals, particularly concerning their potential role and significance in a rapidly changing world, and provides compelling insights into how they could one day be on par with the current big three in feeding a booming population.
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Affiliation(s)
- Acga Cheng
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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19
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Ribeiro T, Buddenhagen CE, Thomas WW, Souza G, Pedrosa-Harand A. Are holocentrics doomed to change? Limited chromosome number variation in Rhynchospora Vahl (Cyperaceae). PROTOPLASMA 2018; 255:263-272. [PMID: 28844108 DOI: 10.1007/s00709-017-1154-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/14/2017] [Indexed: 05/23/2023]
Abstract
Karyotype evolution in species with non-localised centromeres (holocentric chromosomes) is usually very dynamic and associated with recurrent fission and fusion (also termed agmatoploidy/symploidy) events. In Rhynchospora (Cyperaceae), one of the most species-rich sedge genera, all analysed species have holocentric chromosomes and their numbers range from 2n = 4 to 2n = 84. Agmatoploidy/symploidy and polyploidy were suggested as the main processes in the reshuffling of Rhynchospora karyotypes, although testing different scenarios of chromosome number evolution in a phylogenetic framework has not been attempted until now. Here, we used maximum likelihood and model-based analyses, in combination with genome size estimation and ribosomal DNA distribution, to understand chromosome evolution in Rhynchospora. Overall, chromosome number variation showed a significant phylogenetic signal and the majority of the lineages maintained a karyotype of 2n = 10 (~48% of the species), the most likely candidate for the ancestral number of the genus. Higher and lower chromosome numbers were restricted to specific clades, whilst polyploidy and/or fusion/fission events were present in specific branches. Variation in genome size and ribosomal DNA site number showed no correlation with ploidy level or chromosome number. Although different mechanisms of karyotype evolution (polyploidy, fusion and fission) seem to be acting in distinct lineages, the degree of chromosome variation and the main mechanisms involved are comparable to those found in some monocentric genera and lower than expected for a holocentric genus.
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Affiliation(s)
- Tiago Ribeiro
- Departamento de Botânica, Centro de Biociências, Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | | | | | - Gustavo Souza
- Departamento de Botânica, Centro de Biociências, Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Andrea Pedrosa-Harand
- Departamento de Botânica, Centro de Biociências, Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Cidade Universitária, Recife, PE, 50670-901, Brazil.
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A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value. Cell Res 2017; 27:1327-1340. [PMID: 28994416 PMCID: PMC5674158 DOI: 10.1038/cr.2017.124] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/25/2017] [Accepted: 08/24/2017] [Indexed: 11/15/2022] Open
Abstract
Chenopodium quinoa is a halophytic pseudocereal crop that is being cultivated in an ever-growing number of countries. Because quinoa is highly resistant to multiple abiotic stresses and its seed has a better nutritional value than any other major cereals, it is regarded as a future crop to ensure global food security. We generated a high-quality genome draft using an inbred line of the quinoa cultivar Real. The quinoa genome experienced one recent genome duplication about 4.3 million years ago, likely reflecting the genome fusion of two Chenopodium parents, in addition to the γ paleohexaploidization reported for most eudicots. The genome is highly repetitive (64.5% repeat content) and contains 54 438 protein-coding genes and 192 microRNA genes, with more than 99.3% having orthologous genes from glycophylic species. Stress tolerance in quinoa is associated with the expansion of genes involved in ion and nutrient transport, ABA homeostasis and signaling, and enhanced basal-level ABA responses. Epidermal salt bladder cells exhibit similar characteristics as trichomes, with a significantly higher expression of genes related to energy import and ABA biosynthesis compared with the leaf lamina. The quinoa genome sequence provides insights into its exceptional nutritional value and the evolution of halophytes, enabling the identification of genes involved in salinity tolerance, and providing the basis for molecular breeding in quinoa.
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21
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Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B, Borm TJA, Ohyanagi H, Mineta K, Michell CT, Saber N, Kharbatia NM, Rupper RR, Sharp AR, Dally N, Boughton BA, Woo YH, Gao G, Schijlen EGWM, Guo X, Momin AA, Negrão S, Al-Babili S, Gehring C, Roessner U, Jung C, Murphy K, Arold ST, Gojobori T, Linden CGVD, van Loo EN, Jellen EN, Maughan PJ, Tester M. The genome of Chenopodium quinoa. Nature 2017; 542:307-312. [PMID: 28178233 DOI: 10.1038/nature21370] [Citation(s) in RCA: 353] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 01/08/2017] [Indexed: 01/11/2023]
Abstract
Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.
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Affiliation(s)
- David E Jarvis
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Yung Shwen Ho
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Damien J Lightfoot
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Sandra M Schmöckel
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Bo Li
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Theo J A Borm
- Wageningen University and Research, Wageningen UR Plant Breeding, Wageningen, The Netherlands
| | - Hajime Ohyanagi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Katsuhiko Mineta
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences &Engineering Division (CEMSE), Thuwal, 23955-6900, Saudi Arabia
| | - Craig T Michell
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Noha Saber
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Najeh M Kharbatia
- King Abdullah University of Science and Technology (KAUST), Analytical Core Lab, Thuwal, 23955-6900, Saudi Arabia
| | - Ryan R Rupper
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, Utah 84602, USA
| | - Aaron R Sharp
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, Utah 84602, USA
| | - Nadine Dally
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24118 Kiel, Germany
| | - Berin A Boughton
- Metabolomics Australia, The School of Biosciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yong H Woo
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Ge Gao
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Elio G W M Schijlen
- PRI Bioscience, Plant Research International, Wageningen UR, Wageningen, The Netherlands
| | - Xiujie Guo
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Afaque A Momin
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Sónia Negrão
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Salim Al-Babili
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Christoph Gehring
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Ute Roessner
- Metabolomics Australia, The School of Biosciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, D-24118 Kiel, Germany
| | - Kevin Murphy
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Stefan T Arold
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - C Gerard van der Linden
- Wageningen University and Research, Wageningen UR Plant Breeding, Wageningen, The Netherlands
| | - Eibertus N van Loo
- Wageningen University and Research, Wageningen UR Plant Breeding, Wageningen, The Netherlands
| | - Eric N Jellen
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, Utah 84602, USA
| | - Peter J Maughan
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, Utah 84602, USA
| | - Mark Tester
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences &Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
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22
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Stetter MG, Schmid KJ. Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop. Mol Phylogenet Evol 2017; 109:80-92. [PMID: 28057554 DOI: 10.1016/j.ympev.2016.12.029] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/22/2016] [Accepted: 12/25/2016] [Indexed: 11/19/2022]
Abstract
The genus Amaranthus consists of 50-70 species and harbors several cultivated and weedy species of great economic importance. A small number of suitable traits, phenotypic plasticity, gene flow and hybridization made it difficult to establish the taxonomy and phylogeny of the whole genus despite various studies using molecular markers. We inferred the phylogeny of the Amaranthus genus using genotyping by sequencing (GBS) of 94 genebank accessions representing 35 Amaranthus species and measured their genome sizes. SNPs were called by de novo and reference-based methods, for which we used the distant sugarbeet Beta vulgaris and the closely related Amaranthus hypochondriacus as references. SNP counts and proportions of missing data differed between methods, but the resulting phylogenetic trees were highly similar. A distance-based neighbor joining tree of individual accessions and a species tree calculated with the multispecies coalescent supported a previous taxonomic classification into three subgenera although the subgenus A. Acnida consists of two highly differentiated clades. The analysis of the Hybridus complex within the A. Amaranthus subgenus revealed insights on the history of cultivated grain amaranths. The complex includes the three cultivated grain amaranths and their wild relatives and was well separated from other species in the subgenus. Wild and cultivated amaranth accessions did not differentiate according to the species assignment but clustered by their geographic origin from South and Central America. Different geographically separated populations of Amaranthus hybridus appear to be the common ancestors of the three cultivated grain species and A. quitensis might be additionally be involved in the evolution of South American grain amaranth (A. caudatus). We also measured genome sizes of the species and observed little variation with the exception of two lineages that showed evidence for a recent polyploidization. With the exception of two lineages, genome sizes are quite similar and indicate that polyploidization did not play a major role in the history of the genus.
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Affiliation(s)
- Markus G Stetter
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany
| | - Karl J Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany.
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