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Amosova AV, Gnutikov AA, Rodionov AV, Loskutov IG, Nosov NN, Yurkevich OY, Samatadze TE, Zoshchuk SA, Muravenko OV. Genome Variability in Artificial Allopolyploid Hybrids of Avena sativa L. and Avena macrostachya Balansa ex Coss. et Durieu Based on Marker Sequences of Satellite DNA and the ITS1-5.8S rDNA Region. Int J Mol Sci 2024; 25:5534. [PMID: 38791572 PMCID: PMC11122565 DOI: 10.3390/ijms25105534] [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: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Artificial hybrids between cultivated Avena species and wild Avena macrostachya that possess genes for resistance to biotic and abiotic stresses can be important for oat breeding. For the first time, a comprehensive study of genomes of artificial fertile hybrids Avena sativa × Avena macrostachya and their parental species was carried out based on the chromosome FISH mapping of satellite DNA sequences (satDNAs) and also analysis of intragenomic polymorphism in the 18S-ITS1-5.8S rDNA region, using NGS data. Chromosome distribution patterns of marker satDNAs allowed us to identify all chromosomes in the studied karyotypes, determine their subgenomic affiliation, and detect several chromosome rearrangements. Based on the obtained cytogenomic data, we revealed differences between two A. macrostachya subgenomes and demonstrated that only one of them was inherited in the studied octoploid hybrids. Ribotype analyses showed that the second major ribotype of A. macrostachya was species-specific and was not represented in rDNA pools of the octoploids, which could be related to the allopolyploid origin of this species. Our results indicate that the use of marker satDNAs in cytogenomic studies can provide important data on genomic relationships within Avena allopolyploid species and hybrids, and also expand the potential for interspecific crosses for breeding.
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Affiliation(s)
- Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander A. Gnutikov
- Komarov Botanical Institute of Russian Academy of Sciences, 197376 St. Petersburg, Russia
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
| | - Alexander V. Rodionov
- Komarov Botanical Institute of Russian Academy of Sciences, 197376 St. Petersburg, Russia
| | - Igor G. Loskutov
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
| | - Nikolai N. Nosov
- Komarov Botanical Institute of Russian Academy of Sciences, 197376 St. Petersburg, Russia
| | - Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Svyatoslav A. Zoshchuk
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, 119991 Moscow, Russia
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Mehtab-Singh, Tripathi RK, Bekele WA, Tinker NA, Singh J. Differential expression and global analysis of miR156/SQUAMOSA promoter binding-like proteins (SPL) module in oat. Sci Rep 2024; 14:9928. [PMID: 38688976 PMCID: PMC11061197 DOI: 10.1038/s41598-024-60739-7] [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: 10/31/2023] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
SQUAMOSA promoter binding-like proteins (SPLs) are important transcription factors that influence growth phase transition and reproduction in plants. SPLs are targeted by miR156 but the SPL/miR156 module is completely unknown in oat. We identified 28 oat SPL genes (AsSPLs) distributed across all 21 oat chromosomes except for 4C and 6D. The oat- SPL gene family represented six of eight SPL phylogenetic groups, with no AsSPLs in groups 3 and 7. A novel oat miR156 (AsmiR156) family with 21 precursors divided into 7 groups was characterized. A total of 16 AsSPLs were found to be targeted by AsmiR156. Intriguingly, AsSPL3s showed high transcript abundance during early inflorescence (GS-54), as compared to the lower abundance of AsmiR156, indicating their role in reproductive development. Unravelling the SPL/miR156 regulatory hub and alterations in expression patterns of AsSPLs could provide an essential toolbox for genetic improvement in the cultivated oat.
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Affiliation(s)
- Mehtab-Singh
- Plant Science Department, McGill University, 21111 Rue Lakeshore, Montreal, QC, H9X 3V9, Canada
| | - Rajiv K Tripathi
- Plant Science Department, McGill University, 21111 Rue Lakeshore, Montreal, QC, H9X 3V9, Canada
| | - Wubishet A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Jaswinder Singh
- Plant Science Department, McGill University, 21111 Rue Lakeshore, Montreal, QC, H9X 3V9, Canada.
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Androsiuk P, Milarska SE, Dulska J, Kellmann-Sopyła W, Szablińska-Piernik J, Lahuta LB. The comparison of polymorphism among Avena species revealed by retrotransposon-based DNA markers and soluble carbohydrates in seeds. J Appl Genet 2023; 64:247-264. [PMID: 36719514 PMCID: PMC10076396 DOI: 10.1007/s13353-023-00748-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/01/2023]
Abstract
Here, we compared the polymorphism among 13 Avena species revealed by the iPBS markers and soluble carbohydrate profiles in seeds. The application of seven iPBS markers generated 83 bands, out of which 20.5% were polymorphic. No species-specific bands were scored. Shannon's information index (I) and expected heterozygosity (He) revealed low genetic diversity, with the highest values observed for A. nuda (I = 0.099; He = 0.068). UPGMA clustering of studied Avena accessions and PCoA results showed that the polyploidy level is the main grouping criterion. High-resolution gas chromatography revealed that the studied Avena accessions share the same composition of soluble carbohydrates, but significant differences in the content of total (5.30-22.38 mg g-1 of dry weight) and particular sugars among studied samples were observed. Sucrose appeared as the most abundant sugar (mean 61.52% of total soluble carbohydrates), followed by raffinose family oligosaccharides (31.23%), myo-inositol and its galactosides (6.16%), and monosaccharides (1.09%). The pattern of interspecific variation in soluble carbohydrates, showed by PCA, was convergent to that revealed by iPBS markers. Thus, both methods appeared as a source of valuable data useful in the characterization of Avena resources or in the discussion on the evolution of this genus.
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Affiliation(s)
- Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719, Olsztyn, Poland.
| | - Sylwia Eryka Milarska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Justyna Dulska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Wioleta Kellmann-Sopyła
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Joanna Szablińska-Piernik
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Lesław Bernard Lahuta
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719, Olsztyn, Poland
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Charalambous I, Ioannou N, Kyratzis AC, Kourtellarides D, Hagidimitriou M, Nikoloudakis N. Genome Size Variation across a Cypriot Fabeae Tribe Germplasm Collection. PLANTS (BASEL, SWITZERLAND) 2023; 12:1469. [PMID: 37050095 PMCID: PMC10096862 DOI: 10.3390/plants12071469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
DNA content is an important trait linked to the evolutionary routes of taxa and often connected to speciation. In the present study, we studied C-values variation across the Cypriot Fabeae gene pool. Several hundred plants (Vicia spp., Lens spp., Pisum spp.) were sampled across Cyprus. Accurate estimates were established by flow cytometry and propidium iodine staining for 155 discrete populations/accessions. A ten-fold variation was detected across lineages with 1C DNA content varying from 1.584 pg for V. cretica (ARI02420) to 13.983 pg for V. faba (ARI00187). In general, flow cytometry was precise for the characterization of species, even though there were instances of genome overlapping across taxa. Most analyses in the current work refer to species that have not been characterized before by flow cytometry (or any other DNA content estimation method). Still, a correlation to C-values previously reported in Kew Plant DNA C-values database was attempted. A high degree of correlation except for V. dalmatica was established. The evaluation of genome size trait in relation with the Fabeae phylogeny, revealed that Pisum and Lens genera were rather homogenous, but an astonishing fluctuation was shown for Vicia spp. Moreover, it was established that genome up- or down-scaling was not directly linked to speciation drivers. The genomic size measurements presented here could deliver extra quality control for the identification and characterization of taxa in germplasm collections, particularly in cases where species share morphological characters.
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Affiliation(s)
- Iliana Charalambous
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, 3036 Limassol, Cyprus; (I.C.); (N.I.)
| | - Nektaria Ioannou
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, 3036 Limassol, Cyprus; (I.C.); (N.I.)
| | - Angelos C. Kyratzis
- Vegetable Crop Sector, Agricultural Research Institute-Ministry of Agriculture, Rural Development and Environment, 1516 Nicosia, Cyprus; (A.C.K.); (D.K.)
| | - Dimitrios Kourtellarides
- Vegetable Crop Sector, Agricultural Research Institute-Ministry of Agriculture, Rural Development and Environment, 1516 Nicosia, Cyprus; (A.C.K.); (D.K.)
| | | | - Nikolaos Nikoloudakis
- Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, 3036 Limassol, Cyprus; (I.C.); (N.I.)
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Wang L, Xu J, Wang H, Chen T, You E, Bian H, Chen W, Zhang B, Shen Y. Population structure analysis and genome-wide association study of a hexaploid oat landrace and cultivar collection. FRONTIERS IN PLANT SCIENCE 2023; 14:1131751. [PMID: 37025134 PMCID: PMC10070682 DOI: 10.3389/fpls.2023.1131751] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Oat (Avena sativa L.) is an important cereal crop grown worldwide for grain and forage, owing to its high adaptability to diverse environments. However, the genetic and genomics research of oat is lagging behind that of other staple cereal crops. METHODS In this study, a collection of 288 oat lines originating worldwide was evaluated using 2,213 single nucleotide polymorphism (SNP) markers obtained from an oat iSelect 6K-beadchip array to study its genetic diversity, population structure, and linkage disequilibrium (LD) as well as the genotype-phenotype association for hullessness and lemma color. RESULTS The average gene diversity and polymorphic information content (PIC) were 0.324 and 0.262, respectively. The first three principal components (PCs) accounted for 30.33% of the genetic variation, indicating that the population structure of this panel of oat lines was stronger than that reported in most previous studies. In addition, accessions could be classified into two subpopulations using a Bayesian clustering approach, and the clustering pattern of accessions was closely associated with their region of origin. Additionally, evaluation of LD decay using 2,143 mapped markers revealed that the intrachromosomal whole-genome LD decayed rapidly to a critical r2 value of 0.156 for marker pairs separated by a genetic distance of 1.41 cM. Genome-wide association study (GWAS) detected six significant associations with the hullessness trait. Four of these six markers were located on the Mrg21 linkage group between 194.0 and 205.7 cM, while the other two significant markers mapped to Mrg05 and Mrg09. Three significant SNPs, showing strong association with lemma color, were located on linkage groups Mrg17, Mrg18, and Mrg20. DISCUSSION Our results discerned relevant patterns of genetic diversity, population structure, and LD among members of a worldwide collection of oat landraces and cultivars proposed to be 'typical' of the Qinghai-Tibetan Plateau. These results have important implications for further studies on association mapping and practical breeding in high-altitude oat.
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Affiliation(s)
- Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Jinqing Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Handong Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tongrui Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - En You
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haiyan Bian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Wenjie Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, China
| | - Bo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, China
| | - Yuhu Shen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, China
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Konieczna W, Warchoł M, Mierek-Adamska A, Skrzypek E, Waligórski P, Piernik A, Dąbrowska GB. Changes in physio-biochemical parameters and expression of metallothioneins in Avena sativa L. in response to drought. Sci Rep 2023; 13:2486. [PMID: 36775830 PMCID: PMC9922688 DOI: 10.1038/s41598-023-29394-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/03/2023] [Indexed: 02/13/2023] Open
Abstract
Drought is one of the major threats to food security. Among several mechanisms involved in plant stress tolerance, one protein family-the plant metallothioneins (MTs)-shows great promise for enhancing drought resistance. Plant metallothioneins in oat (Avena sativa L.) have not yet been deeply analysed, and the literature lacks a comprehensive study of the whole family of plant MTs in response to drought. In this study, we showed that the number and nature of cis-elements linked with stress response in promoters of AsMTs1-3 differed depending on the MT type. Drought stress in oat plants caused an increase in the expression of AsMT2 and AsMT3 and a decrease in the expression of AsMT1 compared to well-watered plants. Moreover, the low values of relative water content, water use efficiency, net photosynthesis (PN), transpiration (E), stomatal conductance (gs), chlorophyll a, and carotenoid were accompanied by high levels of electrolyte leakage, internal CO2 concentration (Ci) and abscisic acid content, and high activity of antioxidants enzymes in plants under drought stress. The present study puts forward the idea that AsMTs are crucial for oat response to drought stress not only by regulating antioxidant activity but also by changing the plant water regime and photosynthesis. Our results support the hypothesis that structural differences among types of plant MTs reflect their diversified physiological roles.
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Affiliation(s)
- Wiktoria Konieczna
- Department of Genetics, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland
| | - Marzena Warchoł
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - Agnieszka Mierek-Adamska
- Department of Genetics, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100, Toruń, Poland
| | - Edyta Skrzypek
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - Piotr Waligórski
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Kraków, Poland
| | - Agnieszka Piernik
- Department of Geobotany and Landscape Planning, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
| | - Grażyna B Dąbrowska
- Department of Genetics, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland.
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Kadluczka D, Sliwinska E, Grzebelus E. Combining genome size and pollen morphology data to study species relationships in the genus Daucus (Apiaceae). BMC PLANT BIOLOGY 2022; 22:382. [PMID: 35909100 PMCID: PMC9341078 DOI: 10.1186/s12870-022-03743-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/06/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND The genus Daucus (Apiaceae) comprises about 40 wild species and the cultivated carrot, a crop of great economic and nutritional importance. The rich genetic diversity of wild Daucus species makes them a valuable gene pool for carrot improvement breeding programs. Therefore, it is essential to have good knowledge of the genome structure and relationships among wild Daucus species. To broaden such knowledge, in this research, the nuclear DNA content for 14 Daucus accessions and four closely related species was estimated by flow cytometry and their pollen morphology was analyzed by light and scanning electron microscopy (SEM). RESULTS The flow cytometric analysis showed a 3.2-fold variation in the mean 2C values among Daucus taxa, ranging from 0.999 (D. carota subsp. sativus) to 3.228 pg (D. littoralis). Among the outgroup species, the mean 2C values were 1.775-2.882 pg. The pollen grains of Daucus were tricolporate, mainly prolate or perprolate (rarely) in shape, and mainly medium or small (rarely) in size (21.19-40.38 µm), whereas the outgroup species had tricolporate, perprolate-shaped, and medium-sized (26.01-49.86 µm) pollen grains. In the studied taxa, SEM analysis revealed that exine ornamentation was striate, rugulate, perforate, or the ornamentation pattern was mixed. At the time of shedding, all pollen grains were three-celled, as evidenced by DAPI staining. We also found high positive correlations between the length of the polar axis (P) and the length of the equatorial diameter (E) of pollen grains, as well as between P and P/E. However, when comparing cytogenetic information with palynological data, no significant correlations were observed. CONCLUSIONS This study complements the information on the nuclear DNA content in Daucus and provides comprehensive knowledge of the pollen morphology of its taxa. These findings may be important in elucidating the taxonomic relationships among Daucus species and can help in the correct identification of gene bank accessions. In a broader view, they could also be meaningful for the interpretation of evolutionary trends in the genus.
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Affiliation(s)
- Dariusz Kadluczka
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, al. Mickiewicza 21, 31-120 Krakow, Poland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Faculty of Agriculture and Biotechnology, Bydgoszcz University of Science and Technology, al. Kaliskiego 7, 85-796 Bydgoszcz, Poland
| | - Ewa Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, al. Mickiewicza 21, 31-120 Krakow, Poland
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Peng Y, Yan H, Guo L, Deng C, Wang C, Wang Y, Kang L, Zhou P, Yu K, Dong X, Liu X, Sun Z, Peng Y, Zhao J, Deng D, Xu Y, Li Y, Jiang Q, Li Y, Wei L, Wang J, Ma J, Hao M, Li W, Kang H, Peng Z, Liu D, Jia J, Zheng Y, Ma T, Wei Y, Lu F, Ren C. Reference genome assemblies reveal the origin and evolution of allohexaploid oat. Nat Genet 2022; 54:1248-1258. [PMID: 35851189 PMCID: PMC9355876 DOI: 10.1038/s41588-022-01127-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022]
Abstract
Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated a reference-quality genome assembly of hulless common oat, comprising 21 pseudomolecules with a total length of 10.76 Gb and contig N50 of 75.27 Mb. We also produced genome assemblies for diploid and tetraploid Avena ancestors, which enabled the identification of oat subgenomes and provided insights into oat chromosomal evolution. The origin of hexaploid oat is inferred from whole-genome sequencing, chloroplast genomes and transcriptome assemblies of different Avena species. These findings and the high-quality reference genomes presented here will facilitate the full use of crop genetic resources to accelerate oat improvement.
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Affiliation(s)
- Yuanying Peng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- National Oat Improvement Center, Baicheng Academy of Agricultural Sciences, Baicheng, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Honghai Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Laichun Guo
- National Oat Improvement Center, Baicheng Academy of Agricultural Sciences, Baicheng, China
- China Oat and Buckwheat Research Center, Baicheng, China
| | - Cao Deng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Departments of Bioinformatics, DNA Stories Bioinformatics Center, Chengdu, China
| | - Chunlong Wang
- National Oat Improvement Center, Baicheng Academy of Agricultural Sciences, Baicheng, China
- China Oat and Buckwheat Research Center, Baicheng, China
| | - Yubo Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Lipeng Kang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pingping Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Kaiquan Yu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaolong Dong
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaomeng Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | | | - Yun Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jun Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Di Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yinghong Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ying Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Liming Wei
- National Oat Improvement Center, Baicheng Academy of Agricultural Sciences, Baicheng, China
- China Oat and Buckwheat Research Center, Baicheng, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ming Hao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhengsong Peng
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Xichang, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jizeng Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China.
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Changzhong Ren
- National Oat Improvement Center, Baicheng Academy of Agricultural Sciences, Baicheng, China.
- China Oat and Buckwheat Research Center, Baicheng, China.
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9
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Leišová-Svobodová L, Sovová T, Dvořáček V. Analysis of oat seed transcriptome with regards to proteins involved in celiac disease. Sci Rep 2022; 12:8660. [PMID: 35606450 PMCID: PMC9127096 DOI: 10.1038/s41598-022-12711-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/09/2022] [Indexed: 12/21/2022] Open
Abstract
Oat (Avena sativa L.) is considered to be a healthy food. In contrast to other grain crops, oat is high in protein, lipids, dietary fiber, antioxidants, and uniquely in avenanthramides. The question of whether it can also be consumed by people suffering from celiac disease is still unresolved. The main aim of this study was to extract and sequence genes for potentially harmful avenins, globulins, and α-amylase/trypsin inhibitors in six oat varieties and to establish their variability using PacBio sequencing technology of enriched libraries. The results were compared with sequences of the genes already present in databases. In total, 21 avenin, 75 globulin, and 25 α-amylase/trypsin inhibitor genes were identified and mapped in the hexaploid oat chromosomes. In all of the three gene families, only marginal sequence differences were found between the oat varieties within the individual genes. Avenin epitopes were found in all four types of avenin genes occurring in all oat varieties tested within this study. However, the number of avenin genes was nearly four times lower than of globulin genes and, on the protein level, formed only 10% of storage proteins. Therefore, the question of whether oat is safe to celiac disease people is a question of boundary values.
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Affiliation(s)
| | - Tereza Sovová
- Crop Research Institute, Drnovská 507, Prague 6, Ruzyne, Czech Republic
| | - Václav Dvořáček
- Crop Research Institute, Drnovská 507, Prague 6, Ruzyne, Czech Republic
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10
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Toward the development of Ac/Ds transposon-mediated gene tagging system for functional genomics in oat (Avena sativa L.). Funct Integr Genomics 2022; 22:669-681. [PMID: 35467221 DOI: 10.1007/s10142-022-00861-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/04/2022]
Abstract
Cultivated oat (Avena sativa L.) is an important cereal grown worldwide due to its multifunctional uses for animal feed and human food. Oat has lagged behind other cereals in the genetic and genomic studies attributed to its large and complex genomes. Transposon-based genome characterization has been utilized successfully for identifying and determining gene function in large genome cereals. To develop gene tagging and gene-editing resources for oat, maize Activator (Ac) and Dissociation (Ds) transposons were introduced into the oat genome using the biolistic delivery system. A total of 2035 oat calli were bombarded and twenty-four independent, stable transgenic events were obtained. Transformation frequencies were up to 19.0%, and 1.9% for bialaphos and hygromycin selection, respectively. Re-mobilization of the non-autonomous Ds element, by introducing Ac transposase source, led to a transposition frequency up to 16.8%. The properties of ten unique flanking sequences have been characterized to reveal the Ds-tagged sites in the oat genome. Genes at Ds insertion sites showed homology to gibberellin 20-oxidase 3, (1,3;1,4)-beta-D-glucan synthase, and aspartate kinase. This Ac/Ds transposon-based gene tagging system could facilitate and expedite functional genomic studies in oat.
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11
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Gnutikov AA, Nosov NN, Loskutov IG, Blinova EV, Shneyer VS, Probatova NS, Rodionov AV. New Insights into the Genomic Structure of Avena L.: Comparison of the Divergence of A-Genome and One C-Genome Oat Species. PLANTS (BASEL, SWITZERLAND) 2022; 11:1103. [PMID: 35567104 PMCID: PMC9102028 DOI: 10.3390/plants11091103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
We used next-generation sequencing analysis of the 3′-part of 18S rDNA, ITS1, and a 5′-part of the 5.8S rDNA region to understand genetic variation among seven diploid A-genome Avena species. We used 4−49 accessions per species that represented the As genome (A. atlantica, A. hirtula, and wiestii), Ac genome (A. canariensis), Ad genome (A. damascena), Al genome (A. longiglumis), and Ap genome (A. prostrata). We also took into our analysis one C-genome species, A. clauda, which previously was found to be related to A-genome species. The sequences of 169 accessions revealed 156 haplotypes of which seven haplotypes were shared by two to five species. We found 16 ribotypes that consisted of a unique sequence with a characteristic pattern of single nucleotide polymorphisms and deletions. The number of ribotypes per species varied from one in A. longiglumis to four in A. wiestii. Although most ribotypes were species-specific, we found two ribotypes shared by three species (one for A. damascena, A. hirtula, and A. wiestii, and the second for A. longiglumis, A. atlantica, and A. wiestii), and a third ribotype shared between A. atlantica and A. wiestii. A characteristic feature of the A. clauda ribotype, a diploid C-genome species, is that two different families of ribotypes have been found in this species. Some of these ribotypes are characteristic of Cc-genome species, whereas others are closely related to As-genome ribotypes. This means that A. clauda can be a hybrid between As- and C-genome oats.
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Affiliation(s)
- Alexander A. Gnutikov
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Nikolai N. Nosov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
| | - Igor G. Loskutov
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Elena V. Blinova
- Department of Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia; (A.A.G.); (I.G.L.); (E.V.B.)
| | - Viktoria S. Shneyer
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
| | - Nina S. Probatova
- Laboratory of Botany, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia;
| | - Alexander V. Rodionov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (V.S.S.); (A.V.R.)
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12
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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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13
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Discovery and Chromosomal Location a Highly Effective Oat Crown Rust Resistance Gene Pc50-5. Int J Mol Sci 2021; 22:ijms222011183. [PMID: 34681841 PMCID: PMC8540790 DOI: 10.3390/ijms222011183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 01/15/2023] Open
Abstract
Crown rust, caused by Puccinia coronata f. sp. avenae, is one of the most destructive fungal diseases of oat worldwide. Growing disease-resistant oat cultivars is the preferred method of preventing the spread of rust and potential epidemics. The object of the study was Pc50-5, a race-specific seedling crown rust resistant gene, highly effective at all growth stages, selected from the differential line Pc50 (Avena sterilis L. CW 486-1 × Pendek). A comparison of crown rust reaction as well as an allelism test showed the distinctiveness of Pc50-5, whereas the proportions of phenotypes in segregating populations derived from a cross with two crown rust-susceptible Polish oat cultivars, Kasztan × Pc50-5 and Bingo × Pc50-5, confirmed monogenic inheritance of the gene, indicating its usefulness in oat breeding programs. Effective gene introgression depends on reliable gene identification in the early stages of plant development; thus, the aim of the study was to develop molecular markers that are tightly linked to Pc50-5. Segregating populations of Kasztan × Pc50-5 were genotyped using DArTseq technology based on next-generation Illumina short-read sequencing. Markers associated with Pc50-5 were located on chromosome 6A of the current version of the oat reference genome (Avena sativa OT3098 v2, PepsiCo) in the region between 434,234,214 and 440,149,046 bp and subsequently converted to PCR-based SCAR (sequence-characterized amplified region) markers. Furthermore, 5426978_SCAR and 24031809_SCAR co-segregated with the Pc50-5 resistance allele and were mapped to the partial linkage group at 0.6 and 4.0 cM, respectively. The co-dominant 58163643_SCAR marker was the best diagnostic and it was located closest to Pc50-5 at 0.1 cM. The newly discovered, very strong monogenic crown rust resistance may be useful for oat improvement. DArTseq sequences converted into specific PCR markers will be a valuable tool for marker-assisted selection in breeding programs.
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14
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Loskutov IG, Gnutikov AA, Blinova EV, Rodionov AV. The Origin and Resource Potential of Wild and Cultivated Species of the Genus of Oats (Avena L.). RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421060065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Li Y, Leveau A, Zhao Q, Feng Q, Lu H, Miao J, Xue Z, Martin AC, Wegel E, Wang J, Orme A, Rey MD, Karafiátová M, Vrána J, Steuernagel B, Joynson R, Owen C, Reed J, Louveau T, Stephenson MJ, Zhang L, Huang X, Huang T, Fan D, Zhou C, Tian Q, Li W, Lu Y, Chen J, Zhao Y, Lu Y, Zhu C, Liu Z, Polturak G, Casson R, Hill L, Moore G, Melton R, Hall N, Wulff BBH, Doležel J, Langdon T, Han B, Osbourn A. Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals. Nat Commun 2021; 12:2563. [PMID: 33963185 PMCID: PMC8105312 DOI: 10.1038/s41467-021-22920-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Non-random gene organization in eukaryotes plays a significant role in genome evolution. Here, we investigate the origin of a biosynthetic gene cluster for production of defence compounds in oat-the avenacin cluster. We elucidate the structure and organisation of this 12-gene cluster, characterise the last two missing pathway steps, and reconstitute the entire pathway in tobacco by transient expression. We show that the cluster has formed de novo since the divergence of oats in a subtelomeric region of the genome that lacks homology with other grasses, and that gene order is approximately colinear with the biosynthetic pathway. We speculate that the positioning of the late pathway genes furthest away from the telomere may mitigate against a 'self-poisoning' scenario in which toxic intermediates accumulate as a result of telomeric gene deletions. Our investigations reveal a striking example of adaptive evolution underpinned by remarkable genome plasticity.
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Affiliation(s)
- Yan Li
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | | | - Qiang Zhao
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Qi Feng
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Hengyun Lu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jiashun Miao
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Zheyong Xue
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Eva Wegel
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Jing Wang
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Miroslava Karafiátová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Ryan Joynson
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - James Reed
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Lei Zhang
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Xuehui Huang
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Tao Huang
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Danling Fan
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Congcong Zhou
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Qilin Tian
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Wenjun Li
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yiqi Lu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Jiaying Chen
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yan Zhao
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Ying Lu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Chuanrang Zhu
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Guy Polturak
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Lionel Hill
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Rachel Melton
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Bin Han
- National Centre for Gene Research, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Centre of Excellence for Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai, China.
| | - Anne Osbourn
- John Innes Centre, Norwich Research Park, Norwich, UK.
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16
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Wei G, Li X, Fang Y. Sympatric genome size variation and hybridization of four oak species as determined by flow cytometry genome size variation and hybridization. Ecol Evol 2021; 11:1729-1740. [PMID: 33614000 PMCID: PMC7882991 DOI: 10.1002/ece3.7163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 01/31/2023] Open
Abstract
The Quercus species serve as a powerful model for studying introgression in relation to species boundaries and adaptive processes. Coexistence of distant relatives, or lack of coexistence of closely relative oak species, introgression may play a role. In the current study, four closely related oak species were found in Zijinshan, China. We generated a comprehensive genome size (GS) database for 120 individuals of four species using flow cytometry-based approaches. We examined GS variability within and among the species and hybridization events among the four species. The mean GSs of Q. acutissima, Q. variabilis, Q. fabri, and Q. serrata var. brevipetiolata were estimated to be 1.87, 1.92, 1.97, and 1.97 pg, respectively. The intraspecific and interspecific variations of GS observed among the four oak species indicated adaptation to the environment. Hybridization occurred both within and between the sections. A hybrid offspring was produced from Q. fabri and Q. variabilis, which belonged to different sections. The GS evolutionary pattern for hybrid species was expansion. Hybridization between the sections may be affected by habitat disturbance. This study increases our understanding of the evolution of GS in Quercus and will help establish guidelines for the ecological protection of oak trees.
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Affiliation(s)
- GaoMing Wei
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCo‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
- School of Physics, and Electronics Henan UniversityKaifengChina
| | - Xuan Li
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCo‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - YanMing Fang
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCo‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
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17
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Yan H, Ren Z, Deng D, Yang K, Yang C, Zhou P, Wight CP, Ren C, Peng Y. New evidence confirming the CD genomic constitutions of the tetraploid Avena species in the section Pachycarpa Baum. PLoS One 2021; 16:e0240703. [PMID: 33417607 PMCID: PMC7793304 DOI: 10.1371/journal.pone.0240703] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/21/2020] [Indexed: 11/28/2022] Open
Abstract
The tetraploid Avena species in the section Pachycarpa Baum, including A. insularis, A. maroccana, and A. murphyi, are thought to be involved in the evolution of hexaploid oats; however, their genome designations are still being debated. Repetitive DNA sequences play an important role in genome structuring and evolution, so understanding the chromosomal organization and distribution of these sequences in Avena species could provide valuable information concerning genome evolution in this genus. In this study, the chromosomal organizations and distributions of six repetitive DNA sequences (including three SSR motifs (TTC, AAC, CAG), one 5S rRNA gene fragment, and two oat A and C genome specific repeats) were investigated using non-denaturing fluorescence in situ hybridization (ND-FISH) in the three tetraploid species mentioned above and in two hexaploid oat species. Preferential distribution of the SSRs in centromeric regions was seen in the A and D genomes, whereas few signals were detected in the C genomes. Some intergenomic translocations were observed in the tetraploids; such translocations were also detected between the C and D genomes in the hexaploids. These results provide robust evidence for the presence of the D genome in all three tetraploids, strongly suggesting that the genomic constitution of these species is DC and not AC, as had been thought previously.
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Affiliation(s)
- Honghai Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zichao Ren
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Di Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Kehan Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chuang Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pingping Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Charlene P. Wight
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Changzhong Ren
- Baicheng Academy of Agricultural Sciences, Baicheng, China
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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18
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Huang CT, Klos KE, Huang YF. Genome-Wide Association Study Reveals the Genetic Architecture of Seed Vigor in Oats. G3 (BETHESDA, MD.) 2020; 10:4489-4503. [PMID: 33028627 PMCID: PMC7718755 DOI: 10.1534/g3.120.401602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/02/2020] [Indexed: 12/29/2022]
Abstract
Seed vigor is crucial for crop early establishment in the field and is particularly important for forage crop production. Oat (Avena sativa L.) is a nutritious food crop and also a valuable forage crop. However, little is known about the genetics of seed vigor in oats. To investigate seed vigor-related traits and their genetic architecture in oats, we developed an easy-to-implement image-based phenotyping pipeline and applied it to 650 elite oat lines from the Collaborative Oat Research Enterprise (CORE). Root number, root surface area, and shoot length were measured in two replicates. Variables such as growth rate were derived. Using a genome-wide association (GWA) approach, we identified 34 and 16 unique loci associated with root traits and shoot traits, respectively, which corresponded to 41 and 16 unique SNPs at a false discovery rate < 0.1. Nine root-associated loci were organized into four sets of homeologous regions, while nine shoot-associated loci were organized into three sets of homeologous regions. The context sequences of five trait-associated markers matched to the sequences of rice, Brachypodium and maize (E-value < 10-10), including three markers matched to known gene models with potential involvement in seed vigor. These were a glucuronosyltransferase, a mitochondrial carrier protein domain containing protein, and an iron-sulfur cluster protein. This study presents the first GWA study on oat seed vigor and data of this study can provide guidelines and foundation for further investigations.
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Affiliation(s)
- Ching-Ting Huang
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
| | - Kathy Esvelt Klos
- Small Grains and Potato Germplasm Research, USDA, ARS, Aberdeen, ID 83210
| | - Yung-Fen Huang
- Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan
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Liu Q, Li X, Li M, Xu W, Schwarzacher T, Heslop-Harrison JS. Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny. BMC PLANT BIOLOGY 2020; 20:406. [PMID: 32878602 PMCID: PMC7466839 DOI: 10.1186/s12870-020-02621-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 08/25/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Oat (Avena sativa L.) is a recognized health-food, and the contributions of its different candidate A-genome progenitor species remain inconclusive. Here, we report chloroplast genome sequences of eleven Avena species, to examine the plastome evolutionary dynamics and analyze phylogenetic relationships between oat and its congeneric wild related species. RESULTS The chloroplast genomes of eleven Avena species (size range of 135,889-135,998 bp) share quadripartite structure, comprising of a large single copy (LSC; 80,014-80,132 bp), a small single copy (SSC; 12,575-12,679 bp) and a pair of inverted repeats (IRs; 21,603-21,614 bp). The plastomes contain 131 genes including 84 protein-coding genes, eight ribosomal RNAs and 39 transfer RNAs. The nucleotide sequence diversities (Pi values) range from 0.0036 (rps19) to 0.0093 (rpl32) for ten most polymorphic genes and from 0.0084 (psbH-petB) to 0.0240 (petG-trnW-CCA) for ten most polymorphic intergenic regions. Gene selective pressure analysis shows that all protein-coding genes have been under purifying selection. The adjacent position relationships between tandem repeats, insertions/deletions and single nucleotide polymorphisms support the evolutionary importance of tandem repeats in causing plastome mutations in Avena. Phylogenomic analyses, based on the complete plastome sequences and the LSC intermolecular recombination sequences, support the monophyly of Avena with two clades in the genus. CONCLUSIONS Diversification of Avena plastomes is explained by the presence of highly diverse genes and intergenic regions, LSC intermolecular recombination, and the co-occurrence of tandem repeat and indels or single nucleotide polymorphisms. The study demonstrates that the A-genome diploid-polyploid lineage maintains two subclades derived from different maternal ancestors, with A. longiglumis as the first diverging species in clade I. These genome resources will be helpful in elucidating the chloroplast genome structure, understanding the evolutionary dynamics at genus Avena and family Poaceae levels, and are potentially useful to exploit plastome variation in making hybrids for plant breeding.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Center for Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
| | - Xiaoyu Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingzhi Li
- Independent Researcher, Guangzhou, China
| | - Wenkui Xu
- Independent Researcher, Guangzhou, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
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Odintsova TI, Slezina MP, Istomina EA. Defensins of Grasses: A Systematic Review. Biomolecules 2020; 10:E1029. [PMID: 32664422 PMCID: PMC7407236 DOI: 10.3390/biom10071029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 12/20/2022] Open
Abstract
The grass family (Poaceae) is one of the largest families of flowering plants, growing in all climatic zones of all continents, which includes species of exceptional economic importance. The high adaptability of grasses to adverse environmental factors implies the existence of efficient resistance mechanisms that involve the production of antimicrobial peptides (AMPs). Of plant AMPs, defensins represent one of the largest and best-studied families. Although wheat and barley seed γ-thionins were the first defensins isolated from plants, the functional characterization of grass defensins is still in its infancy. In this review, we summarize the current knowledge of the characterized defensins from cultivated and selected wild-growing grasses. For each species, isolation of defensins or production by heterologous expression, peptide structure, biological activity, and structure-function relationship are described, along with the gene expression data. We also provide our results on in silico mining of defensin-like sequences in the genomes of all described grass species and discuss their potential functions. The data presented will form the basis for elucidation of the mode of action of grass defensins and high adaptability of grasses to environmental stress and will provide novel potent molecules for practical use in medicine and agriculture.
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Hunt SP, Jarvis DE, Larsen DJ, Mosyakin SL, Kolano BA, Jackson EW, Martin SL, Jellen EN, Maughan PJ. A Chromosome-Scale Assembly of the Garden Orach ( Atriplex hortensis L.) Genome Using Oxford Nanopore Sequencing. FRONTIERS IN PLANT SCIENCE 2020; 11:624. [PMID: 32523593 PMCID: PMC7261831 DOI: 10.3389/fpls.2020.00624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/22/2020] [Indexed: 05/16/2023]
Abstract
Atriplex hortensis (2n = 2x = 18, 1C genome size ∼1.1 gigabases), also known as garden orach and mountain-spinach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae alliance (Chenopodiaceae sensu stricto, subfam. Chenopodioideae) that has spread in cultivation from its native primary domestication area in Eurasia to other temperate and subtropical regions worldwide. Atriplex L. is a highly complex but, as understood now, a monophyletic group of mainly halophytic and/or xerophytic plants, of which A. hortensis has been a vegetable of minor importance in some areas of Eurasia (from Central Asia to the Mediterranean) at least since antiquity. Nonetheless, it is a crop with tremendous nutritional potential due primarily to its exceptional leaf and seed protein quantities (approaching 30%) and quality (high levels of lysine). Although there is some literature describing the taxonomy and production of A. hortensis, there is a general lack of genetic and genomic data that would otherwise help elucidate the genetic variation, phylogenetic positioning, and future potential of the species. Here, we report the assembly of the first high-quality, chromosome-scale reference genome for A. hortensis cv. "Golden." Long-read data from Oxford Nanopore's MinION DNA sequencer was assembled with the program Canu and polished with Illumina short reads. Contigs were scaffolded to chromosome scale using chromatin-proximity maps (Hi-C) yielding a final assembly containing 1,325 scaffolds with a N50 of 98.9 Mb - with 94.7% of the assembly represented in the nine largest, chromosome-scale scaffolds. Sixty-six percent of the genome was classified as highly repetitive DNA, with the most common repetitive elements being Gypsy-(32%) and Copia-like (11%) long-terminal repeats. The annotation was completed using MAKER which identified 37,083 gene models and 2,555 tRNA genes. Completeness of the genome, assessed using the Benchmarking Universal Single Copy Orthologs (BUSCO) metric, identified 97.5% of the conserved orthologs as complete, with only 2.2% being duplicated, reflecting the diploid nature of A. hortensis. A resequencing panel of 21 wild, unimproved and cultivated A. hortensis accessions revealed three distinct populations with little variation within subpopulations. These resources provide vital information to better understand A. hortensis and facilitate future study.
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Affiliation(s)
- Spencer P. Hunt
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - David E. Jarvis
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Dallas J. Larsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Sergei L. Mosyakin
- M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Bozena A. Kolano
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | | | - Sara L. Martin
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Eric N. Jellen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Peter J. Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
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Sowa S, Paczos-Grzęda E. Identification of molecular markers for the Pc39 gene conferring resistance to crown rust in oat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1081-1094. [PMID: 31927607 PMCID: PMC7064627 DOI: 10.1007/s00122-020-03533-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/03/2020] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE Six new PCR-based markers for the Pc39 crown rust resistance gene in Avena sativa L. were developed. Pc39 was mapped to Mrg11 of the oat consensus map using BLASTn analysis. The aim of this study was the identification of molecular markers for the Pc39 gene in cultivated oat (Avena sativa L.). Pc39 is a major race-specific crown rust resistance gene originally found in an Israeli accession of the wild hexaploid Avena sterilis. The effectiveness of this gene in Europe has decreased in recent years, but is still relatively high and breeding programs would benefit from the availability of molecular markers to aid in its mapping and deployment. The complexity of the oat genome poses a significant obstacle to genetic research. No oat rust resistance genes have yet been cloned, and even the number of relevant molecular markers is very limited. Here, genotyping of a segregating population derived from a cross 'Celer' (Pc39)/STH9210 (susceptible) was conducted using RAPD- and SRAP-PCR-based methods, as well as microarray-based DArT™ and next-generation sequencing DArTseq™ techniques. Markers associated with Pc39 were placed on the hexaploid oat consensus linkage group Mrg11 at 3.7-6.7 cM. Six new PCR-based markers were developed to allow identification of the resistant Pc39 allele. These tightly linked markers will be useful in marker-assisted selection, with the closest, SCAR_3456624, being within 0.37 cM of Pc39. The newly developed markers could find applications in the fine mapping or positional cloning of this gene. Moreover, easy-to-use PCR-based markers linked to Pc39 could facilitate the utilization of this gene in oat breeding programs, especially as a component of crown rust resistance gene pyramids.
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Affiliation(s)
- Sylwia Sowa
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Lublin, Poland
| | - Edyta Paczos-Grzęda
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Lublin, Poland.
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Mellers G, Mackay I, Cowan S, Griffiths I, Martinez‐Martin P, Poland JA, Bekele W, Tinker NA, Bentley AR, Howarth CJ. Implementing within-cross genomic prediction to reduce oat breeding costs. THE PLANT GENOME 2020; 13:e20004. [PMID: 33016630 PMCID: PMC8638661 DOI: 10.1002/tpg2.20004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/26/2019] [Indexed: 05/23/2023]
Abstract
A barrier to the adoption of genomic prediction in small breeding programs is the initial cost of genotyping material. Although decreasing, marker costs are usually higher than field trial costs. In this study we demonstrate the utility of stratifying a narrow-base biparental oat population genotyped with a modest number of markers to employ genomic prediction at early and later generations. We also show that early generation genotyping data can reduce the number of lines for later phenotyping based on selections of siblings to progress. Using sets of small families selected at an early generation could enable the use of genomic prediction for adaptation to multiple target environments at an early stage in the breeding program. In addition, we demonstrate that mixed marker data can be effectively integrated to combine cheap dominant marker data (including legacy data) with more expensive but higher density codominant marker data in order to make within generation and between lineage predictions based on genotypic information. Taken together, our results indicate that small programs can test and initiate genomic predictions using sets of stratified, narrow-base populations and incorporating low density legacy genotyping data. This can then be scaled to include higher density markers and a broadened population base.
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Affiliation(s)
- Greg Mellers
- The John Bingham LaboratoryNIABCambridgeUnited Kingdom
| | - Ian Mackay
- IMplant Consultancy Ltd.ChelmsfordUnited Kingdom
| | - Sandy Cowan
- Institute of Biological, Environmental and Rural Sciences, Plas GogerddanAberystwyth UniversityAberystwythUnited Kingdom
| | - Irene Griffiths
- Institute of Biological, Environmental and Rural Sciences, Plas GogerddanAberystwyth UniversityAberystwythUnited Kingdom
| | - Pilar Martinez‐Martin
- Institute of Biological, Environmental and Rural Sciences, Plas GogerddanAberystwyth UniversityAberystwythUnited Kingdom
| | - Jesse A. Poland
- Wheat Genetics Resource Center, Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Wubishet Bekele
- Ottawa Research and Development Centre, Agriculture and Agri‐Food CanadaOttawaCanada
| | - Nicholas A. Tinker
- Ottawa Research and Development Centre, Agriculture and Agri‐Food CanadaOttawaCanada
| | | | - Catherine J. Howarth
- Institute of Biological, Environmental and Rural Sciences, Plas GogerddanAberystwyth UniversityAberystwythUnited Kingdom
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24
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Maughan PJ, Lee R, Walstead R, Vickerstaff RJ, Fogarty MC, Brouwer CR, Reid RR, Jay JJ, Bekele WA, Jackson EW, Tinker NA, Langdon T, Schlueter JA, Jellen EN. Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species. BMC Biol 2019; 17:92. [PMID: 31757219 PMCID: PMC6874827 DOI: 10.1186/s12915-019-0712-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As- and Cp-subgenomes, Avena atlantica and Avena eriantha respectively. The diploid Avena species serve as important genetic resources for improving common oat's adaptive and food quality characteristics. RESULTS The A. atlantica and A. eriantha genome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species-including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance (Pc91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species. CONCLUSIONS The genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.
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Affiliation(s)
- Peter J Maughan
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA.
| | - Rebekah Lee
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
| | - Rachel Walstead
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | | | - Melissa C Fogarty
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
| | - Cory R Brouwer
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Robert R Reid
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jeremy J Jay
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | | | | | | | - Tim Langdon
- IBERS, Aberystwyth University, Aberystwyth, Wales, UK
| | | | - Eric N Jellen
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
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Comparative linkage mapping of diploid, tetraploid, and hexaploid Avena species suggests extensive chromosome rearrangement in ancestral diploids. Sci Rep 2019; 9:12298. [PMID: 31444367 DOI: 10.1038/s41598-019-48639-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/10/2019] [Indexed: 12/30/2022] Open
Abstract
The genus Avena (oats) contains diploid, tetraploid and hexaploid species that evolved through hybridization and polyploidization. Four genome types (named A through D) are generally recognized. We used GBS markers to construct linkage maps of A genome diploid (Avena strigosa x A. wiestii, 2n = 14), and AB genome tetraploid (A. barbata 2n = 28) oats. These maps greatly improve coverage from older marker systems. Seven linkage groups in the tetraploid showed much stronger homology and synteny with the A genome diploids than did the other seven, implying an allopolyploid hybrid origin of A. barbata from distinct A and B genome diploid ancestors. Inferred homeologies within A. barbata revealed that the A and B genomes are differentiated by several translocations between chromosomes within each subgenome. However, no translocation exchanges were observed between A and B genomes. Comparison to a consensus map of ACD hexaploid A. sativa (2n = 42) revealed that the A and D genomes of A. sativa show parallel rearrangements when compared to the A genomes of the diploids and tetraploids. While intergenomic translocations are well known in polyploid Avena, our results are most parsimoniously explained if translocations also occurred in the A, B and D genome diploid ancestors of polyploid Avena.
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Rejlová L, Chrtek J, Trávníček P, Lučanová M, Vít P, Urfus T. Polyploid evolution: The ultimate way to grasp the nettle. PLoS One 2019; 14:e0218389. [PMID: 31260474 PMCID: PMC6602185 DOI: 10.1371/journal.pone.0218389] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/01/2019] [Indexed: 11/18/2022] Open
Abstract
Polyploidy is one of the major forces of plant evolution and widespread mixed-ploidy species offer an opportunity to evaluate its significance. We therefore selected the cosmopolitan species Urtica dioica (stinging nettle), examined its cytogeography and pattern of absolute genome size, and assessed correlations with bioclimatic and ecogeographic data (latitude, longitude, elevation). We evaluated variation in ploidy level using an extensive dataset of 7012 samples from 1317 populations covering most of the species' distribution area. The widespread tetraploid cytotype (87%) was strongly prevalent over diploids (13%). A subsequent analysis of absolute genome size proved a uniform Cx-value of core U. dioica (except for U. d. subsp. cypria) whereas other closely related species, namely U. bianorii, U. kioviensis and U. simensis, differed significantly. We detected a positive correlation between relative genome size and longitude and latitude in the complete dataset of European populations and a positive correlation between relative genome size and longitude in a reduced dataset of diploid accessions (the complete dataset of diploids excluding U. d. subsp. kurdistanica). In addition, our data indicate an affinity of most diploids to natural and near-natural habitats and that the tetraploid cytotype and a small part of diploids (population from the Po river basin in northern Italy) tend to inhabit synanthropic sites. To sum up, the pattern of ploidy variation revealed by our study is in many aspects unique to the stinging nettle, being most likely first of all driven by the greater ecological plasticity and invasiveness of the tetraploid cytotype.
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Affiliation(s)
- Ludmila Rejlová
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jindřich Chrtek
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Trávníček
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
| | - Magdalena Lučanová
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
- Department of Botany, Faculty of Science University of South Bohemia, České Budějovice, Czech Republic
| | - Petr Vít
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Tomáš Urfus
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
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Dolch K, Judas M, Schwägele F, Brüggemann D. Development and validation of two triplex real-time PCR systems for the simultaneous detection of six cereal species in processed meat products. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Liu Q, Li X, Zhou X, Li M, Zhang F, Schwarzacher T, Heslop-Harrison JS. The repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads. BMC PLANT BIOLOGY 2019; 19:226. [PMID: 31146681 PMCID: PMC6543597 DOI: 10.1186/s12870-019-1769-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 04/09/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Repetitive DNA motifs - not coding genetic information and repeated millions to hundreds of times - make up the majority of many genomes. Here, we identify the nature, abundance and organization of all the repetitive DNA families in oats (Avena sativa, 2n = 6x = 42, AACCDD), a recognized health-food, and its wild relatives. RESULTS Whole-genome sequencing followed by k-mer and RepeatExplorer graph-based clustering analyses enabled assessment of repetitive DNA composition in common oat and its wild relatives' genomes. Fluorescence in situ hybridization (FISH)-based karyotypes are developed to understand chromosome and repetitive sequence evolution of common oat. We show that some 200 repeated DNA motifs make up 70% of the Avena genome, with less than 20 families making up 20% of the total. Retroelements represent the major component, with Ty3/Gypsy elements representing more than 40% of all the DNA, nearly three times more abundant than Ty1/Copia elements. DNA transposons are about 5% of the total, while tandemly repeated, satellite DNA sequences fit into 55 families and represent about 2% of the genome. The Avena species are monophyletic, but both bioinformatic comparisons of repeats in the different genomes, and in situ hybridization to metaphase chromosomes from the hexaploid species, shows that some repeat families are specific to individual genomes, or the A and D genomes together. Notably, there are terminal regions of many chromosomes showing different repeat families from the rest of the chromosome, suggesting presence of translocations between the genomes. CONCLUSIONS The relatively small number of repeat families shows there are evolutionary constraints on their nature and amplification, with mechanisms leading to homogenization, while repeat characterization is useful in providing genome markers and to assist with future assemblies of this large genome (c. 4100 Mb in the diploid). The frequency of inter-genomic translocations suggests optimum strategies to exploit genetic variation from diploid oats for improvement of the hexaploid may differ from those used widely in bread wheat.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Xiaoyu Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangying Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingzhi Li
- Genepioneer Biotechnologies Co. Ltd., Nanjing, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
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Genome Size Unaffected by Variation in Morphological Traits, Temperature, and Precipitation in Turnip. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9020253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Genome size (GS) was proposed as proxy for gross phenotypic and environmental changes in plants. GS organismal complexity is an enigma in evolutionary biology. While studies pertaining to intraspecific GS variation are abundant, literatures reporting the adaptive significance of GS are largelymissing. During food shortage, Brassica rapa var. rapa (turnip) is used as food and fodder for sustaining the livelihood of residents in the Qinghai Tibetan Plateau (QTP), which is also known as “the roof of the world”. Thus, climatic extremities make this region a natural environment to test adaptive significance of GS variation in turnip landraces. Therefore, from the QTP and its adjacent regions (the Hengduanshan and the Himalayas), we investigated adaptive evolution of GS in turnip landraces. Tuber diameter of turnip landraces was found to be significantly correlated with most of the environmental factors. GS was also shown not to be associated with morphological traits, temperature, and precipitation. Moreover, principal component analyses based on the whole dataset trisected the landraces into three distinct populations based on landrace usage—Hengduanshan, QTP, and the Himalayas. Nonetheless, our cumulative dataset showed evidence of adaptation of turnip landrace to different environments throughnonassociated genomic and phenomic plasticity.
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Peng Y, Zhou P, Zhao J, Li J, Lai S, Tinker NA, Liao S, Yan H. Phylogenetic relationships in the genus Avena based on the nuclear Pgk1 gene. PLoS One 2018; 13:e0200047. [PMID: 30408035 PMCID: PMC6224039 DOI: 10.1371/journal.pone.0200047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/29/2018] [Indexed: 11/18/2022] Open
Abstract
The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 3-phosphoglycerate kinase gene (Pgk1). A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a major structural divergence between the A and C genomes. Phylogenetic analysis indicated the Cp genome is more closely related to the polyploid species than is the Cv genome. Two haplotypes of Pgk1 gene were obtained from most of the AB genome tetraploids. Both types of the barbata group showed a close relationship with the As genome diploid species, supporting the hypothesis that both the A and B genomes are derived from an As genome. Two haplotypes were also detected in A. agadiriana, which showed close relationships with the As genome diploid and the Ac genome diploid, respectively, emphasizing the important role of the Ac genome in the evolution of A. agadiriana. Three homoeologues of the Pgk1 gene were detected in five hexaploid accessions. The homoeologues that might represent the D genome were tightly clustered with the tetraploids A. maroccana and A. murphyi, but did not show a close relationship with any extant diploid species.
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Affiliation(s)
- Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Pingping Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
- Collaborative Innovation Center of Tissue Repair Material of Sichuan Province, China West Normal University, Nanchong, People’s Republic of China
| | - Jun Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Junzhuo Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Shikui Lai
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Nicholas A. Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Shu Liao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Honghai Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
- Collaborative Innovation Center of Tissue Repair Material of Sichuan Province, China West Normal University, Nanchong, People’s Republic of China
- * E-mail:
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Bekele WA, Wight CP, Chao S, Howarth CJ, Tinker NA. Haplotype-based genotyping-by-sequencing in oat genome research. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1452-1463. [PMID: 29345800 PMCID: PMC6041447 DOI: 10.1111/pbi.12888] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/05/2018] [Accepted: 01/10/2018] [Indexed: 05/05/2023]
Abstract
In a de novo genotyping-by-sequencing (GBS) analysis of short, 64-base tag-level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag-level (TL) genetic variants containing 241224 SNPs. From this, the marker density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635-line diversity panel were used to infer chromosome-level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel. We then explored potential benefits of SNP vs. TL vs. CL GBS variants for mapping, high-resolution genome analysis and genomic selection in oats. A combined genome-wide association study (GWAS) of heading date from multiple locations using both TL haplotypes and individual SNP markers identified 184 significant associations. A comparative GWAS using TL haplotypes, CL haplotype blocks and their combinations demonstrated the superiority of using TL haplotype markers. Using a principal component-based genome-wide scan, genomic regions containing signatures of selection were identified. These regions may contain genes that are responsible for the local adaptation of oats to Northern American conditions. Genomic selection for heading date using TL haplotypes or SNP markers gave comparable and promising prediction accuracies of up to r = 0.74. Genomic selection carried out in an independent calibration and test population for heading date gave promising prediction accuracies that ranged between r = 0.42 and 0.67. In conclusion, TL haplotype GBS-derived markers facilitate genome analysis and genomic selection in oat.
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Affiliation(s)
- Wubishet A. Bekele
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
| | - Charlene P. Wight
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
| | - Shiaoman Chao
- USDA‐ARS Cereal Crops Research UnitRed River Valley Agricultural Research CenterFargoNDUSA
| | - Catherine J. Howarth
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Nicholas A. Tinker
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
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Zhao J, Tang X, Wight CP, Tinker NA, Jiang Y, Yan H, Ma J, Lan X, Wei Y, Ren C, Chen G, Peng Y. Genetic mapping and a new PCR-based marker linked to a dwarfing gene in oat (Avena sativa L.). Genome 2018; 61:497-503. [PMID: 29733232 DOI: 10.1139/gen-2017-0006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Short straw is a desired trait in cultivated hexaploid oat (Avena sativa L.) for some production environments. Marker-assisted selection, a key tool for achieving this objective, is limited by a lack of mapping data and available markers. Here, bulked-segregant analysis was used to identify PCR-based markers associated with a dwarfing gene. Genetic analysis identified a monogenic dominant inheritance of one dwarfing gene from WAOAT2132, temporarily designated DwWA. A simple sequence repeat (SSR) marker (AME117) that was already available and a new codominant PCR-based marker (bi17) developed by homologous cloning in the present study were both associated with the dwarfing gene. The two markers were located 21 and 1.2 cM from DwWA, respectively. The bi17 marker was mapped to neighboring SNP markers on chromosome 18D of the oat consensus map. Since Dw6 was previously mapped on chromosome 18, and since our new marker bi17 is also diagnostic for NILs generated for Dw6, there is strong evidence that the dwarfing gene identified in WAOAT2132 is Dw6. The newly developed markers could find applications in the identification of this gene in oat germplasm and in the fine mapping or positional cloning of the gene.
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Affiliation(s)
- Jun Zhao
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Xueqin Tang
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China.,b Agricultural Bureau of Xingwen County, Yibin 644400, Sichuan, China
| | - Charlene P Wight
- c Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Nicholas A Tinker
- c Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Yunfeng Jiang
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Honghai Yan
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China.,c Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Jian Ma
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Xiujin Lan
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Yuming Wei
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Changzhong Ren
- d Baicheng Academy of Agricultural Sciences, Baicheng 137000, Jilin, China
| | - Guoyue Chen
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Yuanying Peng
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
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Luo X, Tinker NA, Zhou Y, Wight CP, Liu J, Wan W, Chen L, Peng Y. Genomic relationships among sixteen species of Avena based on (ACT)6 trinucleotide repeat FISH. Genome 2018; 61:63-70. [DOI: 10.1139/gen-2017-0132] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Knowledge of the locations of repeat elements could be very important in the assembly of genome sequences and their assignment to physical chromosomes. Genomic and species relationships among 16 species were investigated using fluorescence in situ hybridization (FISH) with the Am1 and (ACT)6 probes. The Am1 oligonucleotide probe was particularly enriched in the C genomes, whereas the (ACT)6 trinucleotide repeat probe showed a diverse distribution of hybridization patterns in the A, AB, C, AC, and ACD genomes but might not be present in the B and D genomes. The hybridization pattern of Avena sativa was very similar to that of A. insularis, indicating that this species most likely originated from A. insularis as a tetraploid ancestor. Although the two FISH probes failed to identify relationships of more species, this proof-of-concept approach opens the way to the use of FISH probes in assigning other signature elements from genomic sequence to physical chromosomes.
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Affiliation(s)
- Xiaomei Luo
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, Sichuan Province, China
| | - Nick A. Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, KW Neatby Bldg., Central Experimental Farm, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, Sichuan Province, China
| | - Charlene P. Wight
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, KW Neatby Bldg., Central Experimental Farm, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Juncheng Liu
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, Sichuan Province, China
| | - Wenlin Wan
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, Sichuan Province, China
| | - Liang Chen
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, Sichuan Province, China
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Huimin Road 211, Wenjiang District 611130, Chengdu City, Sichuan Province, China
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Unraveling the evolutionary dynamics of ancient and recent polyploidization events in Avena (Poaceae). Sci Rep 2017; 7:41944. [PMID: 28157193 PMCID: PMC5291219 DOI: 10.1038/srep41944] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/30/2016] [Indexed: 11/08/2022] Open
Abstract
Understanding the diversification of polyploid crops in the circum-Mediterranean region is a challenging issue in evolutionary biology. Sequence data of three nuclear genes and three plastid DNA fragments from 109 accessions of Avena L. (Poaceae) and the outgroups were used for maximum likelihood and Bayesian analyses. The evolution of cultivated oat (Avena sativa L.) and its close relatives was inferred to have involved ancient allotetraploidy and subsequent recent allohexaploidy events. The crown ages of two infrageneric lineages (Avena sect. Ventricosa Baum ex Romero-Zarco and Avena sect. Avena) were estimated to be in the early to middle Miocene, and the A. sativa lineages were dated to the late Miocene to Pliocene. These periods coincided with the mild seasonal climatic contrasts and the Mediterranean climate established in the Mediterranean Basin. Our results suggest that polyploidy, lineage divergence, and complex reticulate evolution have occurred in Avena, exemplifying the long-term persistence of tetraploids and the multiple origins of hexaploids related to paleoclimatic oscillations during the Miocene-Pliocene interval in the circum-Mediterranean region. This newly-resolved infrageneric phylogenetic framework represents a major step forward in understanding the origin of the cultivated oat.
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Jia H, Yang H, Sun P, Li J, Zhang J, Guo Y, Han X, Zhang G, Lu M, Hu J. De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila. Sci Rep 2016; 6:39591. [PMID: 27995985 PMCID: PMC5171774 DOI: 10.1038/srep39591] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 11/25/2016] [Indexed: 12/27/2022] Open
Abstract
Salix psammophila, a sandy shrub known as desert willow, is regarded as a potential biomass feedstock and plays an important role in maintaining local ecosystems. However, a lack of genomic data and efficient molecular markers limit the study of its population evolution and genetic breeding. In this study, chromosome counts, flow cytometry and SSR analyses indicated that S. psammophila is tetraploid. A total of 6,346 EST-SSRs were detected based on 71,458 de novo assembled unigenes from transcriptome data. Twenty-seven EST-SSR markers were developed to evaluate the genetic diversity and population structure of S. psammophila from eight natural populations in Northern China. High levels of genetic diversity (mean 10.63 alleles per locus; mean HE 0.689) were dectected in S. psammophila. The weak population structure and little genetic differentiation (pairwise FST = 0.006-0.016) were found among Population 1-Population 7 (Pop1-Pop7; Inner Mongolia and Shaanxi), but Pop8 (Ningxia) was clearly separated from Pop1-Pop7 and moderate differentiation (pairwise FST = 0.045-0.055) was detected between them, which may be influenced by local habitat conditions. Molecular variance analyses indicated that most of the genetic variation (94.27%) existed within populations. These results provide valuable genetic informations for natural resource conservation and breeding programme optimisation of S. psammophila.
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Affiliation(s)
- Huixia Jia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Haifeng Yang
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, 010019, China
| | - Pei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jianbo Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yinghua Guo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Guosheng Zhang
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, 010019, China
| | - Mengzhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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Yan H, Bekele WA, Wight CP, Peng Y, Langdon T, Latta RG, Fu YB, Diederichsen A, Howarth CJ, Jellen EN, Boyle B, Wei Y, Tinker NA. High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2133-2149. [PMID: 27522358 PMCID: PMC5069325 DOI: 10.1007/s00122-016-2762-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/02/2016] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.
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Affiliation(s)
- Honghai Yan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wubishet A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
| | - Charlene P Wight
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Robert G Latta
- Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS, B3H 4R2, Canada
| | - Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Catherine J Howarth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Eric N Jellen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Brian Boyle
- Plateforme d'analyses génomiques, Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada.
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Chaffin AS, Huang YF, Smith S, Bekele WA, Babiker E, Gnanesh BN, Foresman BJ, Blanchard SG, Jay JJ, Reid RW, Wight CP, Chao S, Oliver R, Islamovic E, Kolb FL, McCartney C, Mitchell Fetch JW, Beattie AD, Bjørnstad Å, Bonman JM, Langdon T, Howarth CJ, Brouwer CR, Jellen EN, Klos KE, Poland JA, Hsieh TF, Brown R, Jackson E, Schlueter JA, Tinker NA. A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement. THE PLANT GENOME 2016; 9. [PMID: 27898818 DOI: 10.3835/plantgenome2015.10.0102] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Hexaploid oat ( L., 2 = 6 = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.
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