Genomic diversity and macroecology of the crop wild relatives of domesticated pea

. 2017 Dec 12 ; 7 (1) : 17384. [epub] 20171212

Jazyk angličtina Země Anglie, Velká Británie Médium electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid29234080
Odkazy

PubMed 29234080
PubMed Central PMC5727218
DOI 10.1038/s41598-017-17623-4
PII: 10.1038/s41598-017-17623-4
Knihovny.cz E-zdroje

There is growing interest in the conservation and utilization of crop wild relatives (CWR) in international food security policy and research. Legumes play an important role in human health, sustainable food production, global food security, and the resilience of current agricultural systems. Pea belongs to the ancient set of cultivated plants of the Near East domestication center and remains an important crop today. Based on genome-wide analysis, P. fulvum was identified as a well-supported species, while the diversity of wild P. sativum subsp. elatius was structured into 5 partly geographically positioned clusters. We explored the spatial and environmental patterns of two progenitor species of domesticated pea in the Mediterranean Basin and in the Fertile Crescent in relation to the past and current climate. This study revealed that isolation by distance does not explain the genetic structure of P. sativum subsp. elatius in its westward expansion from its center of origin. The genetic diversity of wild pea may be driven by Miocene-Pliocene events, while the phylogenetic diversity centers may reflect Pleisto-Holocene climatic changes. These findings help set research and discussion priorities and provide geographical and ecological information for germplasm-collecting missions, as well as for the preservation of extant diversity in ex-situ collections.

Erratum v

PubMed

Zobrazit více v PubMed

Smýkal P, Coyne C, Ambrose MJ, et al. Legume crops phylogeny and genetic diversity for science and breeding. Crit. Rev. Plant Sci. 2015;34:43–104. doi: 10.1080/07352689.2014.897904. DOI

Foyer CH, Lam HM, Nguyen HT, et al. Neglecting legumes has compromised human health and sustainable food production. Nature Plants. 2016;2:1–10. doi: 10.1038/nplants.2016.112. PubMed DOI

Godfray HC, et al. Food security: the challenge of feeding 9 billion people. Science. 2010;327:812–818. doi: 10.1126/science.1185383. PubMed DOI

International Treaty on Plant Genetic Resources for Food and Agriculture, FAO, Roma, Italy (2009)

Vincent H, et al. A prioritized crop wild relative inventory to help underpin global food security. Biol. Conserv. 2013;167:265–275. doi: 10.1016/j.biocon.2013.08.011. DOI

McCouch S, Baute GJ, Bradeen J, et al. Agriculture: feeding the future. Nature. 2013;499:23–24. doi: 10.1038/499023a. PubMed DOI

Dempewolf H, et al. agriculture to climate change: a global initiative to collect, conserve, and use crop wild relatives. Agroecol.Sust.Food Systems. 2014;38:369–377. doi: 10.1080/21683565.2013.870629. DOI

Ellis, T. H. N. Wild Crop Relatives, Genomic and Breeding Resources(ed. Kole C.), 237–248 (Berlin-Heidelberg, Springer-Verlag 2011).

Castañeda-Álvarez NP, Khoury CK, Achicanoy HA, et al. Global conservation priorities for crop wild relatives. Nature Plants. 2016;2:16022. doi: 10.1038/nplants.2016.22. PubMed DOI

Ford-Lloyd BV, Schmidt M, Armstrong SJ, et al. Crop wild relatives - undervalued, underutilized and under threat? BioScience. 2001;61:559–565. doi: 10.1525/bio.2011.61.7.10. DOI

Hajjar R, Hodgkin T. The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica. 2007;156:1–13. doi: 10.1007/s10681-007-9363-0. DOI

Smýkal PPea. Pisum sativum L.) in biology prior and after Mendel’s discovery. Czech J: Genet. Plant Breed. 2014;50:52–64.

Abbo S, Lev-Yadun S, &Gopher A. Agricultural origins, centers and noncenters; a Near Eastern reappraisal. Crit. Rev. Plant Sci. 2010;29:317–328. doi: 10.1080/07352689.2010.502823. DOI

Smýkal P, Kenicer G, Flavell A, et al. Phylogeny, phylogeography and genetic diversity of the Pisum genus. Plant Genet.Res. 2011;9:4–18. doi: 10.1017/S147926211000033X. DOI

De Candolle, A. Origin of cultivated plants. (1884) Whitefish, Kessinger Publishing (2006).

Vavilov NI. The origin, variation, immunity and breeding of cultivated plants.Translated from the Russian by K. Starchester. Chronica Botanica1. 1951;3:1–364.

Kislev ME, Bar-Yosef O. The Legumes, The Earliest Domesticated Plants in the Near East? Curr.Anthrol. 1988;29:175–179. doi: 10.1086/203623. DOI

Smartt, J. Grain Legumes, Evolution and Genetic Resources. Cambridge, Cambridge University Press (1990).

Zohary, D. & Hopf, M. Domestication of Plants in the Old World. Oxford University Press, Oxford.(2000).

Schaefer H, Hechenleitner P, Santos-Guerra A, et al. Systematics, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages. BMC Evol.Biol. 2012;12:250. doi: 10.1186/1471-2148-12-250. PubMed DOI PMC

Maxted, N. & Ambrose, M. Peas (Pisum L.). In, Maxted N., & Bennett, S.J., eds Plant Genetic Resources of Legumes in the Mediterranean.Dordrecht, Kluwer Academic Publishers, 181–190 (2001).

Smýkal, P., Coyne, C., Redden R. & Maxted, N. Peas. In, Singh, M., Upadhyaya,H.D., Bisht, I.S., eds. Genetic and Genomic Resources of Grain Legume Improvement. Amsterdam, Elsevier (2013).

Jing R, Johnson R, Seres A, et al. Gene-based sequence diversity analysis of field pea (Pisum) Genetics. 2007;177:2263–2275. doi: 10.1534/genetics.107.081323. PubMed DOI PMC

Jing R, Vershinin A, Grzebyta J, et al. The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evol.Biol. 2010;10:44. doi: 10.1186/1471-2148-10-44. PubMed DOI PMC

Holdsworth WL, Gazave E, Cheng P, et al. A community resource for exploring and utilizing genetic diversity in the USDA pea single plant plus collection. Hort. Res. 2017;4:17017. doi: 10.1038/hortres.2017.17. PubMed DOI PMC

Earl DA, von Holdt BM. STRUCTURE HARVESTER, a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv.Genet.Resources. 2012;4:359–361. doi: 10.1007/s12686-011-9548-7. DOI

Warschefsky E, Penmetsa RV, Cook DR, von Wettberg EJ. Back to the wilds, Tapping evolutionary adaptations for resilient crops through systematic hybridization with crop wild relatives. Am. J. Bot. 2014;101:1791–1800. doi: 10.3732/ajb.1400116. PubMed DOI

Palmer JD, Jorgensen RA, Thompson WF. Chloroplast DNA variation and evolution in Pisum, Patterns of change and phylogenetic analysis. Genetics. 1985;109:195–213. PubMed PMC

Polans NO, Moreno RR. Microsatellite and ITS sequence variation in wild species and cultivars of pea. Pisum Genet. 2009;41:3–6.

Kosterin OE, Bogdanova VS. Relationship of wild and cultivated forms of Pisum L. as inferred from an analysis of three markers, of the plastid, mitochondrial and nuclear genomes. Genet.Resour. Crop Evol. 2008;55:735–755. doi: 10.1007/s10722-007-9281-y. DOI

Kujur A, Bajaj D, Upadhyaya HD, et al. Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea. Front. Plant Sci. 2015;6:162. doi: 10.3389/fpls.2015.00162. PubMed DOI PMC

van Oss R, et al. Genetic relationship in Cicer sp. expose evidence for geneflow between the cultigen and its wild progenitor. PLoS ONE. 2015;10:e0139789. doi: 10.1371/journal.pone.0139789. PubMed DOI PMC

Saxena RK, von Wettberg E, Upadhyaya HD, et al. Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs. PLoS ONE. 2014;9:e88568. doi: 10.1371/journal.pone.0088568. PubMed DOI PMC

Rodriguez M, et al. Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris. New Phytol. 2015;209:1781–1794. doi: 10.1111/nph.13713. PubMed DOI

Zhou Z, Yu Jiang Y, Wang Z, Gou Z, et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nature Biotech. 2015;33:408–416. doi: 10.1038/nbt.3096. PubMed DOI

Wang J, et al. Development and application of a novel genome-wide SNP array reveals domestication history in soybean. Sci. Rep. 2016;6:20728. doi: 10.1038/srep20728. PubMed DOI PMC

Ladizinsky, G., Abbo, S. The search for wild relatives of cool season legumes.The Pisum genus.pp. 55-71 (Springer 2015).

Desiderio F, et al. Chloroplast microsatellite diversity in Phaseolus vulgaris. Front. Plant Sci. 2013;3:312. doi: 10.3389/fpls.2012.00312. PubMed DOI PMC

Kim, K., Lee, S. C., Lee, J., Yu, Y. et al. Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. Sci Rep5, 15655, 10.1038/srep15655. PubMed PMC

Vershinin AV, Allnutt TR, Knox MR, Ambrose MJ, Ellis THN. Transposable elements reveal the impact of introgression, rather than transposition, in Pisum diversity, evolution, and domestication. Mol. Biol. Evol. 2003;20:2067–2075. doi: 10.1093/molbev/msg220. PubMed DOI

Bogdanova VS, Kosterin OE. Hybridization barrier between Pisum fulvum Sibth.et Smith and P. sativum L. is partly due to nuclear-chloroplast incompatibility. Pisum. Genetics. 2007;39:8–9. PubMed

Raven, P. H. & Polhill, R. M. Biogeography of the Leguminosae. In: Polhill, R. M. & Raven P. H., eds Advances in Legume Systematics Kew, RBG, 27–34 (1981).

Schrire BD, Lavin M, Lewis GP. Global distribution patterns of the Leguminosae: insights from recent phylogenies. BiologiskeSkrifter. 2005;55:375–422.

Axelrod DI. Evolution and biogeography of Madrean-Tethyansclerophyll vegetation. Ann. Missouri Bot. Garden. 1975;62:280–334. doi: 10.2307/2395199. DOI

Fernández-Palacios JM, et al. A reconstruction of Palaeo-Macaronesia, with particular reference to the long-term biogeography of the Atlantic island laurel forests. J. Biogeog. 2011;38:226–246. doi: 10.1111/j.1365-2699.2010.02427.x. DOI

Toussaint-Samat, M. A History of Food. John Wiley & Sons (2009).

Nieto Feliner G. Patterns and processes in plant phylogeography in the Mediterranean Basin. A review. Persp. Plant Ecol. Evol. Syst. 2014;16:265–278. doi: 10.1016/j.ppees.2014.07.002. DOI

Kropf M, Kadereit JW, Comes HP. Late Quaternary distributional stasis in the submediterranean mountain plant Anthyllismontana L. (Fabaceae) inferred from ITS sequences and amplified fragment length polymorphism markers. Mol. Ecol. 2002;11:447–463. doi: 10.1046/j.1365-294X.2002.01446.x. PubMed DOI

Russell J, et al. Genetic Diversity and Ecological Niche Modelling of Wild Barley: Refugia, Large-Scale Post-LGM Range Expansion and Limited Mid-Future Climate Threats? PLoS ONE. 2014;9:e86021. doi: 10.1371/journal.pone.0086021. PubMed DOI PMC

Fady B, Conord C. Macroecological patterns of species and genetic diversity in vascular plants of the Mediterranean basin. Diver.Distr. 2010;16:53–64. doi: 10.1111/j.1472-4642.2009.00621.x. DOI

Casimiro-Soriguer R, et al. Phylogeny and genetic structure of Erophaca (Leguminosae), a East–West Mediterranean disjunct genus from the Tertiary. Mol. Phyl. Evol. 2010;56:441–450. doi: 10.1016/j.ympev.2010.02.025. PubMed DOI

Manafzadeh, S., Staedler, Y. M. & Conti, E. Visions of the past and dreams of the future in the Orient: the Irano‐Turanian region from classical botany to evolutionary studies. Biol. Rev, 10.1111/brv.12287 (2016). PubMed

Coyne C. J. et al. Chapter 8. Genetic Adjustment to Changing Climates: Pea In: S. S. Yadav, B. Redden, J. L. Hatfield, H. Lotze-Campen, Editors. Crop Adaptation to Climate Change.Wiley-Blackwell, Ames, IA. pp. 238–249 (2011).

Bena G, Lyet A, Huguet T, Olivier I. Medicago–Sinorhizobium symbiotic specificity evolution and the geographic expansion of Medicago. J. Evol. Biol. 2005;18:1547–1558. doi: 10.1111/j.1420-9101.2005.00952.x. PubMed DOI

Guisan A, et al. Using niche‐based models to improve the sampling of rare species. Conserv.Biol. 2006;20:501–511. doi: 10.1111/j.1523-1739.2006.00354.x. PubMed DOI

Ramirez-Villegas J, Khoury C, Jarvis A, Debouck DG, Guarino L. A gap analysis methodology for collecting crop gene pools: A case study with Phaseolus beans. PLoS ONE. 2010;5:e13497. doi: 10.1371/journal.pone.0013497. PubMed DOI PMC

Pavelková A, Moravec J, Hájek D, Baren I, Sehnalová J. Descriptor list genus Pisum L. RICP Prague. GenovéZdroje. 1986;32:46.

Smýkal P, et al. Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis. Theor. Appl. Genet. 2008;117:413–424. doi: 10.1007/s00122-008-0785-4. PubMed DOI

Bandelt H, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 1999;16:37–48. doi: 10.1093/oxfordjournals.molbev.a026036. PubMed DOI

Kilian A, Wenzl P, Huttner E, et al. Diversity Arrays Technology, a generic genome profiling technology on open platforms. Methods Mol. Biol. 2012;888:67–89. doi: 10.1007/978-1-61779-870-2_5. PubMed DOI

Pritchard JK, Stephens M, Donnelly PJ. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945–959. PubMed PMC

Patterson N, Price AL, Reich D. Population Structure and Eigenanalysis. PLoS Genetic. 2006;2:e190. doi: 10.1371/journal.pgen.0020190. PubMed DOI PMC

Hardy OJ, Vekemans X. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes. 2002;2:618–620. doi: 10.1046/j.1471-8286.2002.00305.x. DOI

Ritland K. Estimators for pairwise relatedness and individual inbreeding coefficients. Genet Res. 1996;67:175–185. doi: 10.1017/S0016672300033620. DOI

Huson DH, Bryant D. Application of Phylogenetic Networks in Evolutionary Studies. Mol. Biol. Evol. 2006;23:254–267. doi: 10.1093/molbev/msj030. PubMed DOI

Phillips SJ, Anderson RP, Schapire RE. Maximum entropy modeling of species geographic distributions. Ecol. Model. 2006;190:231–259. doi: 10.1016/j.ecolmodel.2005.03.026. DOI

Alsos IG, Alm T, Normand S, Brochmann C. Past and future range shifts and loss of diversity in dwarf willow (Salix herbacea L.) inferred from genetics, fossils and modelling. Glob.Ecol. Biog. 2009;18:223e239.

Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. Very high resolution interpolated climate surfaces for global land areas. Inter. J. Climatol. 2005;25:1965–1978. doi: 10.1002/joc.1276. DOI

Warren DL, Glor RE, Turelli M. Environmental niche equivalency versus conservatism, quantitative approaches to niche evolution. Evolution. 2008;62:2868–2883. doi: 10.1111/j.1558-5646.2008.00482.x. PubMed DOI

Allouche O, Steinitz O, Rotem D, Rosenfeld A, Kadmon R. Incorporating distance constraints into species distribution models. J. Appl. Ecol. 2008;45:599–609. doi: 10.1111/j.1365-2664.2007.01445.x. DOI

Warren DL, Glor RE, Turelli M. ENMTools, a toolbox for comparative studies of environmental niche models. Ecography. 2010;33:607–611. doi: 10.1111/j.1600-0587.2009.06041.x. DOI

Vorsino AE, et al. Modeling Hawaiian ecosystem degradation due to invasive plants under current and future climates. PLoS One. 2014;9:e95427. doi: 10.1371/journal.pone.0095427. PubMed DOI PMC

Pebesma EJ, Bivand RS. Classes and methods for spatial data in R. R News. 2005;5:9–13.

Van Der Wal, J., Falconi, L., Januchowski, S., Shoo, L. & Storlie, C. SDMTools, Species Distribution Modelling Tools, Tools for processing data associated with species distribution modelling exercises. http,//CRAN.R-project.org/package=SDMTools. (2014).

Lemon J, Plotrix a. package in the red light district of R. R News. 2006;6:8–12.

Nejnovějších 20 citací...

Zobrazit více v
Medvik | PubMed

Climate Change Dependence in Ex Situ Conservation of Wild Medicinal Plants in Crete, Greece

. 2023 Oct 11 ; 12 (10) : . [epub] 20231011

The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies

. 2022 Nov 22 ; 63 (11) : 1554-1572.

How Could the Use of Crop Wild Relatives in Breeding Increase the Adaptation of Crops to Marginal Environments?

. 2022 ; 13 () : 886162. [epub] 20220616

A reference genome for pea provides insight into legume genome evolution

. 2019 Sep ; 51 (9) : 1411-1422. [epub] 20190902

Allelic Diversity of Acetyl Coenzyme A Carboxylase accD/bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea (Pisum sp.)

. 2019 Apr 10 ; 20 (7) : . [epub] 20190410

Variation in wild pea (Pisum sativum subsp. elatius) seed dormancy and its relationship to the environment and seed coat traits

. 2019 ; 7 () : e6263. [epub] 20190114

Molecular Evidence for Two Domestication Events in the Pea Crop

. 2018 Nov 06 ; 9 (11) : . [epub] 20181106

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...