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Vintsek L, Klichowska E, Nowak A, Nobis M. Insight into the phylogeny and responses of species from the genus Sergia (Campanulaceae) to the climate changes predicted for the Mountains of Central Asia (a world biodiversity hotspot). BMC PLANT BIOLOGY 2024; 24:228. [PMID: 38561665 PMCID: PMC10986085 DOI: 10.1186/s12870-024-04938-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Together with other elevated areas, the Mountains of Central Asia are significantly threatened by ongoing climate change. The presence of refuges during the glaciations makes the region extremely rich in species, especially endemic ones. However, the limited potential for colonisation of other habitats makes rocky-related species with 'island-like' distribution, particularly vulnerable to climate change. To understand the processes underlying species response to climate warming, we assessed differences in ecological niches and phylogenetic relationship of two geographically disjunctive alpine species belonging to the genus Sergia. The taxa are considered Tertiary relicts, endemic to the Tian Shan and Pamir-Alai Mountains. To illustrate range dynamics and differences in occupied niches of Sergia species, we used Ecological Niche Modelling of current and future distribution. Whereas, to reconstruct the phylogenetic relationship within and between Sergia and other related Campanulaceae species from the region we used molecular data (ITS, cpDNA, DArTseq-derived SNPs). RESULTS The results reveal that the genus Sergia is a polyphyletic group, and its representatives differ geographically, ecologically and genetically. Both S. regelii and S. sewerzowii constitute a common clade with Asyneuma group, however, S. sewerzowii is more closely related to Campanula alberti (a species that has never previously been considered closely related to the genus Asyneuma or Sergia) than to S. regelii. Sergia sewerzowii is adapted to lower elevations with higher temperatures, while S. regelii prefers higher elevations with lower temperatures. The future distribution models demonstrate a dramatic loss of S. regelii range with a shift to suitable habitats in higher elevations, while the potential range of S. sewerzowii increases and shifts to the north. CONCLUSIONS This study shows that S. regelii and S. sewerzowii have a long and independent evolution history. Sergia regelii and S. sewerzowii significantly differ in realised niches. These differences are mirrored in the response of the studied endemics to future climate warming. As suitable habitats shrink, rapid changes in distribution can lead to species' range loss, which is also directly related to declines in genetic variability. The outcomes of this paper will help to more precisely assess the impact of climate changes on rocky-related plant species found in this world's biodiversity hotspot.
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Affiliation(s)
- Lizaveta Vintsek
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, Kraków, 30-387, Poland.
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, Kraków, 30-387, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, Warsaw, 02-973, Poland
- Botanical Garden of the Wrocław University, Sienkiewicza 23, 50-335, Wrocław, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, Kraków, 30-387, Poland.
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Farooq M, Ahmad R, Shahzad M, Rehman SU, Sajjad Y, Hassan A, Shah MM, Afroz A, Khan SA. Real-time expression and in silico characterization of pea genes involved in salt and water-deficit stress. Mol Biol Rep 2023; 51:18. [PMID: 38099977 DOI: 10.1007/s11033-023-09064-2] [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: 06/13/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND To tolerate salt and water-deficit stress, the plant adapts to the adverse environment by regulating its metabolism and expressing certain stress-induced metabolic pathways. This research analyzed the relative expression of four pea genes (P5CR, PAL1, SOD, and POX) in three pea varieties (Climax, Green grass, and Meteor) under different levels of salt and water-deficit stress. METHODS AND RESULTS The experiments on salt stress and water-deficit stress were carried out within greenhouse settings under controlled environment. The saturation percentage was employed to create artificial salinity conditions: Control without NaCl treatment, Treatment 1: 50 mM NaCl treatment, Treatment 2: 75 mM NaCl treatment, and Treatment 3: 100 mM NaCl treatment. Field capacity (FC) was used for the development of artificial water-deficit treatments in the pots, i.e., Treatment 1 (Control; water application 100% of FC), Treatment 2 (water application 75% of FC), and Treatment 3 (water application 50% of FC). Pea genes involved in biosynthetic pathways of proline, flavonoids, and enzymatic antioxidant enzymes including P5CR, PAL1, SOD, and POX were selected based on literature. Quantitative real-time PCR using cDNA as a template was used to analyze the gene expression. Pea genes were analyzed for phylogenetic analysis in closely related crops having similarity percent identity 80% and above. In silico characterization of selected proteins including the family classification was done by the NCBI CDD and INTERPRO online servers. Results from RT-qPCR analysis showed increased expression of P5CR, PAL1, and POX genes, while SOD gene expression decreased under both stresses. Climax exhibited superior stress tolerance with elevated expression of P5CR and PAL1, while Meteor showed better tolerance through increased POX expression. Phylogenetic analysis revealed common ancestry with other species like chickpea, red clover, mung bean, and barrel clover, suggesting the cross relationship among these plant species. Conserved domain analysis of respective proteins revealed that these proteins contain PLNO 2688, PLN02457, Cu-Zn Superoxide dismutase, and secretory peroxidase conserved domains. Furthermore, protein family classification indicated that the oxidation-reduction process is the most common chemical process involved in these stresses given to pea plant which validates the relationship of these proteins. CONCLUSIONS Salt and water-deficit stresses trigger distinct metabolic pathways, leading to the up-regulation of specific genes and the synthesis of corresponding proteins. These findings further emphasize the conservation of stress-tolerance-related genes and proteins across various plant species. This knowledge enhances our understanding of plant adaptation to stress and offers opportunities for developing strategies to improve stress resilience in crops, thereby addressing global food security challenges.
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Affiliation(s)
- Muhammad Farooq
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, University Road, Abbottabad, 22060, Pakistan
| | - Rafiq Ahmad
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, University Road, Abbottabad, 22060, Pakistan
| | - Muhammad Shahzad
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, University Road, Abbottabad, 22060, Pakistan
| | - Saad Ur Rehman
- Department of Bioinformatics, Government Postgraduate College, Mandian, Abbottabad, Pakistan
| | - Yasar Sajjad
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, University Road, Abbottabad, 22060, Pakistan
| | - Amjad Hassan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, University Road, Abbottabad, 22060, Pakistan
| | - Mohammad Maroof Shah
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, University Road, Abbottabad, 22060, Pakistan
| | - Amber Afroz
- Department of Biochemistry and Biotechnology, University of Gujrat, Gujrat, Punjab, Pakistan
| | - Sabaz Ali Khan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, University Road, Abbottabad, 22060, Pakistan.
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Ellis N, Hofer J, Sizer-Coverdale E, Lloyd D, Aubert G, Kreplak J, Burstin J, Cheema J, Bal M, Chen Y, Deng S, Wouters RHM, Steuernagel B, Chayut N, Domoney C. Recombinant inbred lines derived from wide crosses in Pisum. Sci Rep 2023; 13:20408. [PMID: 37990072 PMCID: PMC10663473 DOI: 10.1038/s41598-023-47329-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/12/2023] [Indexed: 11/23/2023] Open
Abstract
Genomic resources are becoming available for Pisum but to link these to phenotypic diversity requires well marked populations segregating for relevant traits. Here we describe two such resources. Two recombinant inbred populations, derived from wide crosses in Pisum are described. One high resolution mapping population involves cv Caméor, for which the first pea whole genome assembly was obtained, crossed to JI0281, a basally divergent P. sativum sativum landrace from Ethiopia. The other is an inter sub-specific cross between P. s. sativum and the independently domesticated P. s. abyssinicum. The corresponding genetic maps provide information on chromosome level sequence assemblies and identify structural differences between the genomes of these two Pisum subspecies. In order to visualise chromosomal translocations that distinguish the mapping parents, we created a simplified version of Threadmapper to optimise it for interactive 3-dimensional display of multiple linkage groups. The genetic mapping of traits affecting seed coat roughness and colour, plant height, axil ring pigmentation, leaflet number and leaflet indentation enabled the definition of their corresponding genomic regions. The consequence of structural rearrangement for trait analysis is illustrated by leaf serration. These analyses pave the way for identification of the underlying genes and illustrate the utility of these publicly available resources. Segregating inbred populations derived from wide crosses in Pisum, together with the associated marker data, are made publicly available for trait dissection. Genetic analysis of these populations is informative about chromosome scale assemblies, structural diversity in the pea genome and has been useful for the fine mapping of several discrete and quantitative traits.
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Affiliation(s)
- N Ellis
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK.
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK.
| | - J Hofer
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
| | - E Sizer-Coverdale
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
- Germinal Horizon, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
| | - D Lloyd
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
- Germinal Horizon, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
| | - G Aubert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - J Kreplak
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - J Burstin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - J Cheema
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - M Bal
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Y Chen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - S Deng
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - R H M Wouters
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - B Steuernagel
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - N Chayut
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - C Domoney
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
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New Insights into Plastid and Mitochondria Evolution in Wild Peas (Pisum L.). DIVERSITY 2023. [DOI: 10.3390/d15020216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Plastids and mitochondria are organelles of plant cells with small genomes, which may exhibit discordant microevolution as we earlier revealed in pea crop wild relatives. We sequenced 22 plastid and mitochondrial genomes of Pisum sativum subsp. elatius and Pisum fulvum using Illumina platform, so that the updated sample comprised 64 accessions. Most wild peas from continental southern Europe and a single specimen from Morocco were found to share the same organellar genome constitution; four others, presumably hybrid constitutions, were revealed in Mediterranean islands and Athos Peninsula. A mitochondrial genome closely related to that of Pisum abyssinicum, from Yemen and Ethiopia, was unexpectedly found in an accession of P. sativum subsp. elatius from Israel, their plastid genomes being unrelated. Phylogenetic reconstructions based on plastid and mitochondrial genomes revealed different sets of wild peas to be most related to cultivated P. sativum subsp. sativum, making its wild progenitor and its origin area enigmatic. An accession of P. fulvum representing ‘fulvum-b’ branch, according to a nuclear marker, appeared in the same branch as other fulvum accessions in organellar trees. The results stress the complicated evolution and structure of genetic diversity of pea crop wild relatives.
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Bajgain P, Brandvain Y, Anderson JA. Influence of Pollen Dispersal and Mating Pattern in Domestication of Intermediate Wheatgrass, a Novel Perennial Food Crop. FRONTIERS IN PLANT SCIENCE 2022; 13:871130. [PMID: 35574146 PMCID: PMC9096613 DOI: 10.3389/fpls.2022.871130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Intermediate wheatgrass (IWG) is a perennial forage grass that is currently being domesticated as a grain crop. It is a primarily wind-pollinated outcrossing species and expresses severe inbreeding depression when self-pollinated. Characterization of pollen dispersal, mating parameters, and change in genetic diversity due to pollen movement is currently lacking in IWG. In this study, we examined pollen dispersal in an IWG selection nursery by evaluating 846 progeny from 15 mother plants and traced their parentage to 374 fathers. A set of 2,500 genomic loci was used to characterize the population. We assigned paternity to 769 (91%) progeny and the average number of fathers per mother plant was 37, from an average of 56 progeny examined per mother. An extensive number (80%) of pollination events occurred within 10 m of the mother plants. Pollination success was not correlated with trait attributes of the paternal genotypes. Mating system analysis confirmed that IWG is highly outcrossing and inbreeding was virtually absent. Neither genetic diversity nor the genome-estimated trait values of progeny were significantly affected by pollinator distance. The distance of pollinator in an IWG breeding nursery therefore was not found to be a major contributor in maintaining genetic diversity. These findings reveal the pollen dispersal model in IWG for the first time and its effect on genetic diversity, which will be valuable in designing future IWG breeding populations. Information generated and discussed in this study could be applied in understanding gene flow and genetic diversity of other open-pollinated species.
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Affiliation(s)
- Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Yaniv Brandvain
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, United States
| | - James A. Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
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Hellwig T, Abbo S, Ophir R. Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:419-439. [PMID: 35061306 PMCID: PMC9303476 DOI: 10.1111/tpj.15678] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/15/2022] [Indexed: 05/25/2023]
Abstract
Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well-diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so-called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.
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Affiliation(s)
- Timo Hellwig
- The Levi Eshkol School of AgricultureThe Hebrew University of JerusalemJerusalem, RehovotIsrael
- Volcani Center, Agricultural Research OrganizationRishon LeZionIsrael
- Institute of Plant Genetics, Heinrich‐Heine‐UniversityDüsseldorfGermany
| | - Shahal Abbo
- The Levi Eshkol School of AgricultureThe Hebrew University of JerusalemJerusalem, RehovotIsrael
| | - Ron Ophir
- Volcani Center, Agricultural Research OrganizationRishon LeZionIsrael
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Fernie AR, Alseekh S, Liu J, Yan J. Using precision phenotyping to inform de novo domestication. PLANT PHYSIOLOGY 2021; 186:1397-1411. [PMID: 33848336 PMCID: PMC8260140 DOI: 10.1093/plphys/kiab160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/22/2021] [Indexed: 05/09/2023]
Abstract
An update on the use of precision phenotyping to assess the potential of lesser cultivated species as candidates for de novo domestication or similar development for future agriculture.
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Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Author for communication: (A.R.F.)
| | - Saleh Alseekh
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
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8
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Bogdanova VS, Shatskaya NV, Mglinets AV, Kosterin OE, Vasiliev GV. Discordant evolution of organellar genomes in peas (Pisum L.). Mol Phylogenet Evol 2021; 160:107136. [PMID: 33684529 DOI: 10.1016/j.ympev.2021.107136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 01/30/2023]
Abstract
Plastids and mitochondria have their own small genomes, which do not undergo meiotic recombination and may have evolutionary fates different from each other and that of the nuclear genome. For the first time, we sequenced mitochondrial genomes of pea (Pisum L.) from 42 accessions mostly representing diverse wild germplasm from throughout the wild pea geographical range. Six structural types of the pea mitochondrial genome were revealed. From the same accessions, plastid genomes were sequenced. Phylogenetic trees based on the plastid and mitochondrial genomes were compared. The topologies of these trees were highly discordant, implying not less than six events of hybridisation between diverged wild peas in the past, with plastids and mitochondria differently inherited by the descendants. Such discordant inheritance of organelles could have been driven by plastid-nuclear incompatibility, which is known to be widespread in crosses involving wild peas and affects organellar inheritance. The topology of the phylogenetic tree based on nucleotide sequences of a nuclear gene, His5, encoding a histone H1 subtype, corresponded to the current taxonomy and resembled that based on the plastid genome. Wild peas (Pisum sativum subsp. elatius s.l.) inhabiting Southern Europe were shown to be of hybrid origin, resulting from crosses of peas related to those presently inhabiting the eastern Mediterranean in a broad sense. These results highlight the roles of hybridisation and cytonuclear conflict in shaping plant microevolution.
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Affiliation(s)
- Vera S Bogdanova
- Institute of Cytology and Genetics of the Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia V Shatskaya
- Institute of Cytology and Genetics of the Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoliy V Mglinets
- Institute of Cytology and Genetics of the Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Oleg E Kosterin
- Institute of Cytology and Genetics of the Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.
| | - Gennadiy V Vasiliev
- Institute of Cytology and Genetics of the Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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Toker C, Berger J, Eker T, Sari D, Sari H, Gokturk RS, Kahraman A, Aydin B, von Wettberg EJ. Cicer turcicum: A New Cicer Species and Its Potential to Improve Chickpea. FRONTIERS IN PLANT SCIENCE 2021; 12:662891. [PMID: 33936152 PMCID: PMC8082243 DOI: 10.3389/fpls.2021.662891] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Genetic resources of the genus Cicer L. are not only limited when compared to other important food legumes and major cereal crops but also, they include several endemic species with endangered status based on the criteria of the International Union for Conservation of Nature. The chief threats to endemic and endangered Cicer species are over-grazing and habitat change in their natural environments driven by climate changes. During a collection mission in east and south-east Anatolia (Turkey), a new Cicer species was discovered, proposed here as C. turcicum Toker, Berger & Gokturk. Here, we describe the morphological characteristics, images, and ecology of the species, and present preliminary evidence of its potential utility for chickpea improvement. C. turcicum is an annual species, endemic to southeast Anatolia and to date has only been located in a single population distant from any other known annual Cicer species. It belongs to section Cicer M. Pop. of the subgenus Pseudononis M. Pop. of the genus Cicer L. (Fabaceae) and on the basis of internal transcribed spacer (ITS) sequence similarity appears to be a sister species of C. reticulatum Ladiz. and C. echinospermum P.H. Davis, both of which are inter-fertile with domestic chickpea (C. arietinum L.). With the addition of C. turcicum, the genus Cicer now comprises 10 annual and 36 perennial species. As a preliminary evaluation of its potential for chickpea improvement two accessions of C. turcicum were field screened for reproductive heat tolerance and seeds were tested for bruchid resistance alongside a representative group of wild and domestic annual Cicer species. C. turcicum expressed the highest heat tolerance and similar bruchid resistance as C. judaicum Boiss. and C. pinnatifidum Juab. & Spach, neither of which are in the primary genepool of domestic chickpea. Given that C. arietinum and C. reticulatum returned the lowest and the second lowest tolerance and resistance scores, C. turcicum may hold much potential for chickpea improvement if its close relatedness supports interspecific hybridization with the cultigen. Crossing experiments are currently underway to explore this question.
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Affiliation(s)
- Cengiz Toker
- Department of Field Crops, Akdeniz University, Antalya, Turkey
| | - Jens Berger
- CSIRO Agriculture and Food, Wembley, WA, Australia
| | - Tuba Eker
- Department of Field Crops, Akdeniz University, Antalya, Turkey
| | - Duygu Sari
- Department of Field Crops, Akdeniz University, Antalya, Turkey
| | - Hatice Sari
- Department of Field Crops, Akdeniz University, Antalya, Turkey
| | | | | | - Bilal Aydin
- Department of Field Crops, Harran University, Şanlıurfa, Turkey
| | - Eric J. von Wettberg
- Department of Plant and Soil Science and Gund Institute for Environment, University of Vermont, Burlington, VT, United States
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10
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Pandey AK, Rubiales D, Wang Y, Fang P, Sun T, Liu N, Xu P. Omics resources and omics-enabled approaches for achieving high productivity and improved quality in pea (Pisum sativum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:755-776. [PMID: 33433637 DOI: 10.1007/s00122-020-03751-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/10/2020] [Indexed: 05/09/2023]
Abstract
Pea (Pisum sativum L.), a cool-season legume crop grown in more than 85 countries, is the second most important grain legume and one of the major green vegetables in the world. While pea was historically studied as the genetic model leading to the discovery of the laws of genetics, pea research has lagged behind that of other major legumes in the genomics era, due to its large and complex genome. The evolving climate change and growing population have posed grand challenges to the objective of feeding the world, making it essential to invest research efforts to develop multi-omics resources and advanced breeding tools to support fast and continuous development of improved pea varieties. Recently, the pea researchers have achieved key milestones in omics and molecular breeding. The present review provides an overview of the recent important progress including the development of genetic resource databases, high-throughput genotyping assays, reference genome, genes/QTLs responsible for important traits, transcriptomic, proteomic, and phenomic atlases of various tissues under different conditions. These multi-faceted resources have enabled the successful implementation of various markers for monitoring early-generation populations as in marker-assisted backcrossing breeding programs. The emerging new breeding approaches such as CRISPR, speed breeding, and genomic selection are starting to change the paradigm of pea breeding. Collectively, the rich omics resources and omics-enable breeding approaches will enhance genetic gain in pea breeding and accelerate the release of novel pea varieties to meet the elevating demands on productivity and quality.
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Affiliation(s)
- Arun K Pandey
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, 14004, Córdoba, Spain
| | - Yonggang Wang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Pingping Fang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Ting Sun
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Na Liu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
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11
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Hellwig T, Abbo S, Sherman A, Coyne CJ, Saranga Y, Lev-Yadun S, Main D, Zheng P, Ophir R. Limited divergent adaptation despite a substantial environmental cline in wild pea. Mol Ecol 2020; 29:4322-4336. [PMID: 32964548 DOI: 10.1111/mec.15633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 08/09/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022]
Abstract
Isolation by environment (IBE) is a widespread phenomenon in nature. It is commonly expected that the degree of difference among environments is proportional to the level of divergence between populations in their respective environments. It is therefore assumed that a species' genetic diversity displays a pattern of IBE in the presence of a strong environmental cline if gene flow does not mitigate isolation. We tested this common assumption by analysing the genetic diversity and demographic history of Pisum fulvum, which inhabits contrasting habitats in the southern Levant and is expected to display only minor migration rates between populations, making it an ideal test case. Ecogeographical and subpopulation structure were analysed and compared. The correlation of genetic with environmental distances was calculated to test the effect of isolation by distance and IBE and detect the main drivers of these effects. Historical effective population size was estimated using stairway plot. Limited overlap of ecogeographical and genetic clustering was observed, and correlation between genetic and environmental distances was statistically significant but small. We detected a sharp decline of effective population size during the last glacial period. The low degree of IBE may be the result of genetic drift due to a past bottleneck. Our findings contradict the expectation that strong environmental clines cause IBE in the absence of extensive gene flow.
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Affiliation(s)
- Timo Hellwig
- Institute of Plant Sciences and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, Rishon LeZion, Israel
| | - Shahal Abbo
- Institute of Plant Sciences and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Amir Sherman
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, Rishon LeZion, Israel
| | | | - Yehoshua Saranga
- Institute of Plant Sciences and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Simcha Lev-Yadun
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa-Oranim, Tivon, Israel
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Ron Ophir
- Institute of Plant Sciences, Agricultural Research Organization - Volcani Center, Rishon LeZion, Israel
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12
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Kioukis A, Michalopoulou VA, Briers L, Pirintsos S, Studholme DJ, Pavlidis P, Sarris PF. Intraspecific diversification of the crop wild relative Brassica cretica Lam. using demographic model selection. BMC Genomics 2020; 21:48. [PMID: 31937246 PMCID: PMC6961386 DOI: 10.1186/s12864-019-6439-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/29/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Crop wild relatives (CWRs) contain genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops to adapt to changing conditions that they experience due to climate change. An impressive global effort for the conservation of various CWR will facilitate their use in crop breeding for food security. The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage), a species native to southern and western Europe, has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves. Brassica cretica Lam. (Bc) is a CWR in the brassica group and B. cretica subsp. nivea (Bcn) has been suggested as a separate subspecies. The species Bc has been proposed as a potential gene donor to brassica crops, including broccoli, cabbage, cauliflower, oilseed rape, etc. RESULTS: We sequenced genomes of four Bc individuals, including two Bcn and two Bc. Demographic analysis based on our whole-genome sequence data suggests that populations of Bc are not isolated. Classification of the Bc into distinct subspecies is not supported by the data. Using only the non-coding part of the data (thus, the parts of the genome that has evolved nearly neutrally), we find the gene flow between different Bc population is recent and its genomic diversity is high. CONCLUSIONS Despite predictions on the disruptive effect of gene flow in adaptation, when selection is not strong enough to prevent the loss of locally adapted alleles, studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow. Thus, in the genomic era it is important to link the selected demographic models with the underlying processes of genomic variation because, if this variation is largely selectively neutral, we cannot assume that a diverse population of crop wild relatives will necessarily exhibit the wide-ranging adaptive diversity required for further crop improvement.
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Affiliation(s)
- Antonios Kioukis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Heraklion, 70013, Crete, Greece
| | - Vassiliki A Michalopoulou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, 70013, Crete, Greece
| | - Laura Briers
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Stergios Pirintsos
- Department of Biology, University of Crete, 714 09, Heraklion, Greece
- Botanical Garden, University of Crete, Gallos Campus, 741 00, Rethymnon, Greece
| | - David J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Heraklion, 70013, Crete, Greece
| | - Panagiotis F Sarris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, 70013, Crete, Greece.
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK.
- Department of Biology, University of Crete, 714 09, Heraklion, Greece.
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13
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Bariotakis M, Georgescu L, Laina D, Oikonomou I, Ntagounakis G, Koufaki MI, Souma M, Choreftakis M, Zormpa OG, Smykal P, Sourvinos G, Lionis C, Castanas E, Karousou R, Pirintsos SA. From wild harvest towards precision agriculture: Use of Ecological Niche Modelling to direct potential cultivation of wild medicinal plants in Crete. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133681. [PMID: 31756796 DOI: 10.1016/j.scitotenv.2019.133681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Understanding the distribution of wild medicinal plants and areas that are suitable for cultivation of these plants is important for both conservation and agriculture. Here, we study ten taxa with known ethnopharmacological uses, which have been used extensively in traditional medicine and as culinary supplements. We aim to (1) predict and map the potential habitat suitability for these taxa across the study area, (2) investigate spatial patterns that could have management implications, such as niche similarities among the taxa and suitability "hotspots" with the use of novel indices, and (3) develop a platform where parts of this information can be accessed and utilized by all interested groups, from the policy-maker level to the individual practitioner level. Ecological Niche Models developed for each study taxon, based on topographic, bioclimatic, soil, and land use variables had high predictive power and were used as the basis for suitability visualization. A series of informative indices were also calculated and mapped, revealing spatial patterns not readily observable from the single-taxon predictions, and providing valuable information to managers. Finally, a web-based, easy-to-use application was also created, where the predicted suitability scores for the study area can be made accessible to anyone interested. The application can provide information both in a visual form (i.e. maps of predicted suitability) and in a numerical form (i.e. estimated suitability scores for all taxa in a given geographical location). This study provides the scientific tools to make a step towards cultivating a group of economically important wild medicinal plants in Crete, as well as the tools to disseminate this information to decision makers and practitioners, and eventually integrate the research findings in local agricultural practices.
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Affiliation(s)
- Michael Bariotakis
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece; Botanical Garden, University of Crete, Gallos University Campus, GR 741 00 Rethymnon, Greece
| | - Luciana Georgescu
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece
| | - Danae Laina
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece
| | - Ioanna Oikonomou
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece
| | - George Ntagounakis
- Botanical Garden, University of Crete, Gallos University Campus, GR 741 00 Rethymnon, Greece
| | | | - Maria Souma
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece
| | | | - Ourania Grigoriadou Zormpa
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece; Botanical Garden, University of Crete, Gallos University Campus, GR 741 00 Rethymnon, Greece
| | - Petr Smykal
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - George Sourvinos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion, Greece
| | - Christos Lionis
- Clinic of Social and Family Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Elias Castanas
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, Heraklion, Greece
| | - Regina Karousou
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stergios A Pirintsos
- Department of Biology, University of Crete, GR 714 09 Heraklion, Greece; Botanical Garden, University of Crete, Gallos University Campus, GR 741 00 Rethymnon, Greece.
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14
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Bhattacharyya D, Uddin A, Das S, Chakraborty S. Mutation pressure and natural selection on codon usage in chloroplast genes of two species in Pisum L. (Fabaceae: Faboideae). Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:664-673. [DOI: 10.1080/24701394.2019.1616701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, India
| | - Sudipa Das
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
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15
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Nováková E, Zablatzká L, Brus J, Nesrstová V, Hanáček P, Kalendar R, Cvrčková F, Majeský Ľ, Smýkal P. Allelic Diversity of Acetyl Coenzyme A Carboxylase accD/ bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea ( Pisum sp.). Int J Mol Sci 2019; 20:E1773. [PMID: 30974846 PMCID: PMC6480052 DOI: 10.3390/ijms20071773] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 01/09/2023] Open
Abstract
Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set of 195 geographically diverse samples of both cultivated (Pisum sativum, P. abyssinicum) and wild (P. fulvum and P. elatius) peas. Based on deduced protein sequences, we identified 34 accD and 31 bccp alleles that are partially geographically and genetically structured. The accD is highly variable due to insertions of tandem repeats. P. fulvum and P. abyssinicum have unique alleles and combinations of both genes. On the other hand, partial overlap was observed between P. sativum and P. elatius. Mapping of protein sequence polymorphisms to 3D structures revealed that most of the repeat and indel polymorphisms map to sequence regions that could not be modeled, consistent with this part of the protein being less constrained by requirements for precise folding than the enzymatically active domains. The results of this study are important not only from an evolutionary point of view but are also relevant for pea breeding when using more distant wild relatives.
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Affiliation(s)
- Eliška Nováková
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Lenka Zablatzká
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Jan Brus
- Department of Geoinformatics, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Viktorie Nesrstová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University, 78371 Olomouc, Czech Republic.
| | - Pavel Hanáček
- Department of Plant Biology, Faculty of Agronomy, Mendel University, 61300 Brno, Czech Republic.
| | - Ruslan Kalendar
- National Center for Biotechnology, Astana 010000, Kazakhstan.
- Department of Agricultural Sciences, Viikki Plant Science Centre and Helsinki Sustainability Centre, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Fatima Cvrčková
- Department of Experimental Plant Biology, Faculty of Sciences, Charles University, 12844 Prague, Czech Republic.
| | - Ľuboš Majeský
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
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16
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Hradilová I, Duchoslav M, Brus J, Pechanec V, Hýbl M, Kopecký P, Smržová L, Štefelová N, Vaclávek T, Bariotakis M, Machalová J, Hron K, Pirintsos S, Smýkal P. Variation in wild pea ( Pisum sativum subsp. elatius) seed dormancy and its relationship to the environment and seed coat traits. PeerJ 2019; 7:e6263. [PMID: 30656074 PMCID: PMC6336014 DOI: 10.7717/peerj.6263] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/11/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Seed germination is one of the earliest key events in the plant life cycle. The timing of transition from seed to seedling is an important developmental stage determining the survival of individuals that influences the status of populations and species. Because of wide geographical distribution and occurrence in diverse habitats, wild pea (Pisum sativum subsp. elatius) offers an excellent model to study physical type of seed dormancy in an ecological context. This study addresses the gap in knowledge of association between the seed dormancy, seed properties and environmental factors, experimentally testing oscillating temperature as dormancy release clue. METHODS Seeds of 97 pea accessions were subjected to two germination treatments (oscillating temperatures of 25/15 °C and 35/15 °C) over 28 days. Germination pattern was described using B-spline coefficients that aggregate both final germination and germination speed. Relationships between germination pattern and environmental conditions at the site of origin (soil and bioclimatic variables extracted from WorldClim 2.0 and SoilGrids databases) were studied using principal component analysis, redundancy analysis and ecological niche modelling. Seeds were analyzed for the seed coat thickness, seed morphology, weight and content of proanthocyanidins (PA). RESULTS Seed total germination ranged from 0% to 100%. Cluster analysis of germination patterns of seeds under two temperature treatments differentiated the accessions into three groups: (1) non-dormant (28 accessions, mean germination of 92%), (2) dormant at both treatments (29 acc., 15%) and (3) responsive to increasing temperature range (41 acc., with germination change from 15 to 80%). Seed coat thickness differed between groups with dormant and responsive accessions having thicker testa (median 138 and 140 µm) than non-dormant ones (median 84 mm). The total PA content showed to be higher in the seed coat of dormant (mean 2.18 mg g-1) than those of non-dormant (mean 1.77 mg g-1) and responsive accessions (mean 1.87 mg g-1). Each soil and bioclimatic variable and also germination responsivity (representing synthetic variable characterizing germination pattern of seeds) was spatially clustered. However, only one environmental variable (BIO7, i.e., annual temperature range) was significantly related to germination responsivity. Non-dormant and responsive accessions covered almost whole range of BIO7 while dormant accessions are found in the environment with higher annual temperature, smaller temperature variation, seasonality and milder winter. Ecological niche modelling showed a more localized potential distribution of dormant group. Seed dormancy in the wild pea might be part of a bet-hedging mechanism for areas of the Mediterranean basin with more unpredictable water availability in an otherwise seasonal environment. This study provides the framework for analysis of environmental aspects of physical seed dormancy.
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Affiliation(s)
- Iveta Hradilová
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - Martin Duchoslav
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jan Brus
- Department of Geoinformatics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Vilém Pechanec
- Department of Geoinformatics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Miroslav Hýbl
- The Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Prague, Olomouc, Czech Republic
| | - Pavel Kopecký
- The Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Prague, Olomouc, Czech Republic
| | - Lucie Smržová
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - Nikola Štefelová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Tadeáš Vaclávek
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Michael Bariotakis
- Department of Biology and Botanical Garden, University of Crete, Heraklion, Greece
| | - Jitka Machalová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Karel Hron
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Stergios Pirintsos
- Department of Biology and Botanical Garden, University of Crete, Heraklion, Greece
| | - Petr Smýkal
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
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17
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Hradilová I, Duchoslav M, Brus J, Pechanec V, Hýbl M, Kopecký P, Smržová L, Štefelová N, Vaclávek T, Bariotakis M, Machalová J, Hron K, Pirintsos S, Smýkal P. Variation in wild pea ( Pisum sativum subsp. elatius) seed dormancy and its relationship to the environment and seed coat traits. PeerJ 2019; 7:e6263. [PMID: 30656074 DOI: 10.7717/peerj6263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/11/2018] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND Seed germination is one of the earliest key events in the plant life cycle. The timing of transition from seed to seedling is an important developmental stage determining the survival of individuals that influences the status of populations and species. Because of wide geographical distribution and occurrence in diverse habitats, wild pea (Pisum sativum subsp. elatius) offers an excellent model to study physical type of seed dormancy in an ecological context. This study addresses the gap in knowledge of association between the seed dormancy, seed properties and environmental factors, experimentally testing oscillating temperature as dormancy release clue. METHODS Seeds of 97 pea accessions were subjected to two germination treatments (oscillating temperatures of 25/15 °C and 35/15 °C) over 28 days. Germination pattern was described using B-spline coefficients that aggregate both final germination and germination speed. Relationships between germination pattern and environmental conditions at the site of origin (soil and bioclimatic variables extracted from WorldClim 2.0 and SoilGrids databases) were studied using principal component analysis, redundancy analysis and ecological niche modelling. Seeds were analyzed for the seed coat thickness, seed morphology, weight and content of proanthocyanidins (PA). RESULTS Seed total germination ranged from 0% to 100%. Cluster analysis of germination patterns of seeds under two temperature treatments differentiated the accessions into three groups: (1) non-dormant (28 accessions, mean germination of 92%), (2) dormant at both treatments (29 acc., 15%) and (3) responsive to increasing temperature range (41 acc., with germination change from 15 to 80%). Seed coat thickness differed between groups with dormant and responsive accessions having thicker testa (median 138 and 140 µm) than non-dormant ones (median 84 mm). The total PA content showed to be higher in the seed coat of dormant (mean 2.18 mg g-1) than those of non-dormant (mean 1.77 mg g-1) and responsive accessions (mean 1.87 mg g-1). Each soil and bioclimatic variable and also germination responsivity (representing synthetic variable characterizing germination pattern of seeds) was spatially clustered. However, only one environmental variable (BIO7, i.e., annual temperature range) was significantly related to germination responsivity. Non-dormant and responsive accessions covered almost whole range of BIO7 while dormant accessions are found in the environment with higher annual temperature, smaller temperature variation, seasonality and milder winter. Ecological niche modelling showed a more localized potential distribution of dormant group. Seed dormancy in the wild pea might be part of a bet-hedging mechanism for areas of the Mediterranean basin with more unpredictable water availability in an otherwise seasonal environment. This study provides the framework for analysis of environmental aspects of physical seed dormancy.
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Affiliation(s)
- Iveta Hradilová
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - Martin Duchoslav
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jan Brus
- Department of Geoinformatics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Vilém Pechanec
- Department of Geoinformatics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Miroslav Hýbl
- The Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Prague, Olomouc, Czech Republic
| | - Pavel Kopecký
- The Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Prague, Olomouc, Czech Republic
| | - Lucie Smržová
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
| | - Nikola Štefelová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Tadeáš Vaclávek
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Michael Bariotakis
- Department of Biology and Botanical Garden, University of Crete, Heraklion, Greece
| | - Jitka Machalová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Karel Hron
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University Olomouc, Olomouc, Czech Republic
| | - Stergios Pirintsos
- Department of Biology and Botanical Garden, University of Crete, Heraklion, Greece
| | - Petr Smýkal
- Department of Botany, Palacký University Olomouc, Olomouc, Czech Republic
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18
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Bogdanova VS, Mglinets AV, Shatskaya NV, Kosterin OE, Solovyev VI, Vasiliev GV. Cryptic divergences in the genus Pisum L. (peas), as revealed by phylogenetic analysis of plastid genomes. Mol Phylogenet Evol 2018; 129:280-290. [PMID: 30195476 DOI: 10.1016/j.ympev.2018.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
Abstract
Organellar genomes may shed light on complicated patterns of plant evolution at inter- and intraspecies level. Primary structure of plastid genomes sequenced in this study and taken from public databases was characterised and compared in 22 diverse, mostly wild representatives of the genus Pisum (peas). Phylogenetic trees reconstructed via Bayesian approach on the basis of entire plastid genomes resembled those reconstructed on the basis of a nuclear gene His5 coding for a minor histone H1 subtype. They reveal Pisum fulvum as an early divergence of the genus but do not support other taxonomical subdivisions. The positions of three accessions, classified as P. sativum subsp. elatius (the wild subspecies of the common pea), appeared quite unexpected. On the entire plastid genome tree, two accessions, from the Black Sea area of Turkey and Georgia, clustered with representatives of another species, P. fulvum, while the other, from Greece, was the first divergence of the P. sativum branch. We suppose these unusual plastid genomes to be ancient lineages ascending to a 'missing link' between P. fulvum and P. sativum, represented by accession Pe 013 from Turkey. Accessions with common pea appearance but deeply diverged plastids could occur through occasional crossing of diverged pea lines in the past and biparental plastid inheritance, both events being possible in peas.
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Affiliation(s)
- Vera S Bogdanova
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoliy V Mglinets
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia V Shatskaya
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Oleg E Kosterin
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.
| | - Vladimir I Solovyev
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - Gennadiy V Vasiliev
- Institute of Cytology and Genetics of Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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19
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Trněný O, Brus J, Hradilová I, Rathore A, Das RR, Kopecký P, Coyne CJ, Reeves P, Richards C, Smýkal P. Molecular Evidence for Two Domestication Events in the Pea Crop. Genes (Basel) 2018; 9:genes9110535. [PMID: 30404223 PMCID: PMC6265838 DOI: 10.3390/genes9110535] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 12/02/2022] Open
Abstract
Pea, one of the founder crops from the Near East, has two wild species: Pisum sativum subsp. elatius, with a wide distribution centered in the Mediterranean, and P. fulvum, which is restricted to Syria, Lebanon, Israel, Palestine and Jordan. Using genome wide analysis of 11,343 polymorphic single nucleotide polymorphisms (SNPs) on a set of wild P. elatius (134) and P. fulvum (20) and 74 domesticated accessions (64 P. sativum landraces and 10 P. abyssinicum), we demonstrated that domesticated P. sativum and the Ethiopian pea (P. abyssinicum) were derived from different P. elatius genepools. Therefore, pea has at least two domestication events. The analysis does not support a hybrid origin of P. abyssinicum, which was likely introduced into Ethiopia and Yemen followed by eco-geographic adaptation. Both P. sativum and P. abyssinicum share traits that are typical of domestication, such as non-dormant seeds. Non-dormant seeds were also found in several wild P. elatius accessions which could be the result of crop to wild introgression or natural variation that may have been present during pea domestication. A sub-group of P. elatius overlaps with P. sativum landraces. This may be a consequence of bidirectional gene-flow or may suggest that this group of P. elatius is the closest extant wild relative of P. sativum.
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Affiliation(s)
- Oldřich Trněný
- Agricultural Research Ltd., 66441 Troubsko, Czech Republic.
| | - Jan Brus
- Department of Geoinformatics, Palacký University, 783 71 Olomouc, Czech Republic.
| | - Iveta Hradilová
- Department of Botany, Palacký University, 783 71 Olomouc, Czech Republic.
| | - Abhishek Rathore
- The International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana 502324, India.
| | - Roma R Das
- The International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana 502324, India.
| | - Pavel Kopecký
- Crop Research Institute, The Centre of the Region Haná for biotechnological and Agricultural Research, 783 71 Olomouc, Czech Republic.
| | - Clarice J Coyne
- United States Department of Agriculture, Washington State University, Pullman, WA 99164-6402, USA.
| | - Patrick Reeves
- United States Department of Agriculture, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA.
| | - Christopher Richards
- United States Department of Agriculture, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA.
| | - Petr Smýkal
- Department of Botany, Palacký University, 783 71 Olomouc, Czech Republic.
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Smýkal P, Trněný O, Brus J, Hanáček P, Rathore A, Roma RD, Pechanec V, Duchoslav M, Bhattacharyya D, Bariotakis M, Pirintsos S, Berger J, Toker C. Correction: Genetic structure of wild pea (Pisum sativum subsp. elatius) populations in the northern part of the Fertile Crescent reflects moderate cross-pollination and strong effect of geographic but not environmental distance. PLoS One 2018; 13:e0196376. [PMID: 29672627 PMCID: PMC5908173 DOI: 10.1371/journal.pone.0196376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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