Genetic variability in landraces populations and the risk to lose genetic variation. The example of landrace ‘Kyperounda’ and its implications for ex situ conservation
Autoři:
Angelos C. Kyratzis aff001; Nikolaos Nikoloudakis aff002; Andreas Katsiotis aff002
Působiště autorů:
Department of Vegetable Crops, Agricultural Research Institute, Nicosia, Cyprus
aff001; Department of Agricultural Science, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
aff002
Vyšlo v časopise:
PLoS ONE 14(10)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0224255
Souhrn
Genetic characterization enhances the development of rational conservation strategies and the utilization of germplasm to plant breeding programs. In the present study, 19 microsatellite markers were employed to evaluate the genetic diversity and the genetic affiliations across 20 Cypriot durum wheat (Triticum turgidum L. subsp. durum) landraces, 13 landraces from the broader Mediterranean basin and 22 modern varieties. Cluster analysis depicted a clear separation among modern varieties and landraces, regardless of their origin. Landraces presented the highest genetic variation (average discriminating power of 0.89) and a high number of private alleles (131) was detected; underlying the unique genetic mark-up of this genepool. AMOVA revealed that the highest variability was detected within the landraces originating from Cyprus and landraces from the broader Mediterranean basin. The Cypriot landrace ‘Kyperounda’ was selected for further evaluation of its’ intra-genetic variation and it was determined that genetic diversity was higher in accessions conserved as sublines (He 0.643–0.731) than bulks (He 0.384–0.469). Bayesian analysis revealed substantial admixture within ‘Kyperounda’ accessions, depicted also by Principal Coordinate Analysis. The findings of the current manuscript emphasize that high intra-genetic diversity is retained when landraces are conserved as sublines in ex situ collections, while landraces that are conserved as bulks have a higher risk of bottleneck. Hence, a more exhausting diversity evaluation is needed in order to fully utilize landraces in breeding schemes and to prevent the loss of genetic variation.
Klíčová slova:
Alleles – Conservation genetics – Ears – Genetic polymorphism – Plant breeding – Population genetics – Wheat – Cyprus
Zdroje
1. Mackey JM. Wheat: its concept, evolution and taxonomy. In: Royo C, Nachit MM, Di Fonzo N, Araus JL, Pfeiffer WH, Slafer GA, editors. Durum wheat breeding: current approaches and future strategies. New York: Food Products Press; 2005. pp. 3–61.
2. Vigne J-D, Briois F, Zazzo A, Willcox G, Cucchi T, Thiébault S, et al. First wave of cultivators spread to Cyprus at least 10,600 years ago. PNAS. 2012;109(22):8445–8449. https://doi/10.1073/pnas.1201693109 22566638
3. Medini M, Hamza S, Rebai A, Baum M. Analysis of genetic structure in Tunisian durum wheat cultivars and related wild species by SSR and AFLP markers. Genet Resour Crop Evol. 2005;52:21–31. https://doi.org/10.1007/s10722-005-0225-0
4. Moragues M, Moralejo M, Sorrells ME, Royo C. Dispersal of durum wheat [Tritigum turgidum L. ssp. turgidum convar. durum (Desf.) MacKey] landraces across the Mediterranean basin assessed by AFLPs and microsatellites. Genet Resour Crop Evol. 2007;54(5):1133–1144.
5. Ruiz M, Giraldo P, Royo C, Villegas D, Aranzana MJ, Carrillo JM. Diversity and genetic structure of a collection of Spanish durum wheat landraces. Crop Sci. 2012;52(5):2262–2275. doi: 10.2135/cropsci2012.02.0081
6. Soriano JM, Villegas D, Aranzana MJ, García del Moral LF, Royo C. Genetic structure of modern durum wheat cultivars and Mediterranean landraces matches with their agronomic performance. PLoS ONE. 2016;11(8):e0160983. doi: 10.1371/journal.pone.0160983 27513751
7. Bennett E. Wheats of the Mediterranean basin. In: Frankel OH, editor. Survey of crop genetic resources in their centers of diversity. Rome: FAO; 1973. pp. 1–8.
8. Hadjichristodoulou A, Della A. Genetic diversity in Cyprus. Plant Genet Resour Newsl. 1976;32:8–15.
9. Villa TCC, Maxted N, Scholten M, Ford-Loyd B. Defining and identifying landraces. Plant Genet Resour. 2005;3(3):373–384. https://doi.org/10.1079/PGR200591
10. Royo C, Nazco R, Villegas D. The climate of the zone of origin of Mediterranean durum wheat (Triticum durum Desf.) landraces affects their agronomic performance. Genet Resour Crop Evol. 2014;61(7):1345–1358.
11. Skovmand B, Warburton ML, Sullivan SN, Lage J. Managing the collecting genetic resources. In: Royo C, Nachit MM, Di Fonzo N, Araus JL, Pfeiffer WH, Slafer GA, editors. Durum wheat breeding: current approaches and future strategies. New York: Food Products Press; 2005. pp.143–163.
12. Lopes MS, El-Basyoni I, Baenziger PS, Singh S, Royo C, Ozbek K, et al. Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change. J Exp Bot. 2015;66(12):3477–3486. doi: 10.1093/jxb/erv122 25821073
13. Dwivedi SL, Ceccarelli S, Blair MW, Upadhyaya HD, Are AK, Ortiz R. Landrace germplasm for improving yield and abiotic stress adaptation. Trends Plant Sci. 2016;21(1):31–42. https://dx.doi.org/10.1016/j.tplants.2015.10.012 26559599
14. Alsaleh A, Baloch FS, Nachit M, Özkan H. Phenotypic and genotypic intra-diversity among Anatolian durum wheat “Kunduru” landraces. Biochem Syst Ecol. 2016;65:9–16. https://dx.doi.org/10.1016/j.bse.2016.01.008
15. Ganeva G, Korzun V, Landjeva S, Popova Z, Christov NK. Genetic diversity assessment of Bulgarian durum wheat (Triticum durum Desf.) landraces and modern cultivars using microsatellite markers. Genet Resour Crop Evol. 2010;57(2):273–285.
16. Maccaferri M, Sanguineti MC, Donini P, Tuberosa R. Microsatellite analysis reveals a progressive widening of the genetic basis in the elite durum wheat germplasm. Theor Appl Genet. 2003;107(5):783–797. 12845433
17. Martos V, Royo C, Rharrabti Y, Garcia del Moral LF. Using AFLPs to determine phylogenetic relationships and genetic erosion in durum wheat cultivars released in Italy and Spain throughout the 20th century. Field Crops Res. 2005;91:107–116.
18. Maccaferri M, Sanguineti C, Noli E, Tuberosa R. Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Molecular Breed. 2005;15(3):271–289.
19. Royo C, Maccaferri M, Álvaro F, Moragues M, Sanguineti MC, Tuberosa R, et al. Understanding the relationships between genetic and phenotypic structures of a collection of elite durum wheat accessions. Field Crops Res. 2010;119(1):91–105.
20. Kabbaj H, Sall AT, Al-Abdallat A, Geleta M, Amri A, Filali-Maltouf A, et al. Genetic diversity within a global panel of durum wheat (Trticum durum) landraces and modern germplasm reveals the history of alleles exchange. Front Plant Sci. 2017;8:1277. doi: 10.3389/fpls.2017.01277 28769970
21. Riaz A, Hathorn A, Dinglasan E, Ziems L, Richard C, Singh D, et al. Into the vault of the Vavilov wheats: old diversity for new alleles. Genet Resour Crop Evol. 2017;64(3):531–544.
22. Laidὸ G, Mangini G, Taranto F, Gadaleta A, Blanco A, Cattivelli L, et al. Genetic diversity and population structure of tetraploid wheats (Trticum turgidum L.) estimated by SSR, DArT and pedigree data. PLoS ONE. 2013;8:e67280. doi: 10.1371/journal.pone.0067280 23826256
23. Vikram P, Franco J, Burgueño-Ferreira J, Li H, Sehgal D, Pierre CS, et al. Unlocking the genetic diversity of creole wheats. Sci Rep. 2016;6:23092. doi: 10.1038/srep23092 26976656
24. Röder MS, Plaschke J, König SU, Börner A, Sorrells ME, Tanksley SD, et al. Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet. 1995;246(3):327–333. https://doi.org/10.1007/BF00288605 7854317
25. Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier M-H, Leroy P, et al. A microsatellite map of wheat. Genetics. 1998;149(4):2007–2023. 9691054
26. Gupta PK, Balyan HS, Edwards KJ, Isaac P, Korzun V, Röder M, et al. Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat. Theor Appl Genet. 2002;105:413–422. 12582546
27. Song QJ, Shi JR, Singh S, Fickus EW, Costa JM, Lewis J, et al. Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet. 2005;110(3):550–560. 15655666
28. Maccaferri M, Stefanelli S, Rotondo F, Tuberosa R, Sanguineti MC. Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data. Genome. 2007;50(4):373–384. https://doi.org/10.1139/G06-151 17546096
29. Mantovani P, Maccaferri M, Sanguineti MC, Tuberosa R, Catizone I, Wenzl P, et al. An integrated DArT-SSR linkage map of durum wheat. Mol Breed. 2008;22(4):629–648. doi: 10.1007/s11032-008-9205-3
30. Dreisigacker S, Zhang P, Warburton B, Skovmand D, Hoisington D, Melchinger AE. Genetic diversity among and within CIMMYT wheat landrace accessions investigated with SSRs and implications for plant genetic resources management. Crop Sci. 2005;45(2):653–661. doi: 10.2135/cropsci2005.0653
31. Ren J, Sun D, Chen L, You FM, Wang J, Peng Y, et al. Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat. Int J Mol Sci. 2013;14(4):7061–7088. doi: 10.3390/ijms14047061 23538839
32. Baloch FS, Alsaleh A, Shahid MQ, Ҫiftҫi V, Sáenz de Miera LE, Aasim M, et al. A whole genome DArTseq and SNP analysis for genetic diversity assessment in durum wheat from the central fertile crescent. PLoS ONE. 2017;12:e0167821. doi: 10.1371/journal.pone.0167821 28099442
33. Zhang P, Dreisigacker S, Buerkert A, Alkhanjari S, Melchinger AE, Warburton ML. Genetic diversity and relationships of wheat landraces from Oman investigated with SSR markers. Genet Resour Crop Evol. 2006;53(7):1351–1360.
34. Hagenblad J, Zie J, Leino MW. Exploring the population genetics of genebank and historical landrace varieties. Genet Resour Crop Evol. 2012;59(6):1185–1199.
35. Oliveira HR, Campana MG, Jones H, Hunt HV, Leigh F, Redhouse DI, et al. Tetraploid wheat landraces in the Mediterranean basin: Taxonomy, evolution and genetic diversity. PLoS ONE. 2012;7:e37063. doi: 10.1371/journal.pone.0037063 22615891
36. Pagnotta MA, Impiglia A, Tanzarella OA, Nachit MM, Porceddu E. Genetic variation of the durum wheat landrace Haurani from different agro-ecological regions. Genet Resour Crop Evol. 2004;51(8):863–869. https://doi.org/10.1007/s10722-005-0775-1
37. Ribeiro-Carvalho C, Guedes-Pinto H, Igrejas G, Stephenson P, Schwarzacher T, Heslop-Harrison S. High levels of genetic diversity throughout the range of the Portuguese wheat landrace “Barbel”. Ann Bot. 2004;94(5):699–705. doi: 10.1093/aob/mch194 15355867
38. Colomba MS, Gregorini A. Genetic diversity analysis of the durum wheat Graziella Ra, Trticum turgidum L. subsp. durum (Desf.) Husn. (Poales, Poaceae). Biodivers J. 2011;2(2):73–84.
39. Mangini G, Margiotta B, Marcotuli I, Signorile MA, Gadaleta A, Blanco A. Genetic diversity and phenetic analysis in wheat (Trticum turgidum subsp. durum and Triticum aestivum subsp. aestivum) landraces based on SNP markers. Genet Resour Crop Evol. 2017;64(6):1269–1280.
40. Della A, Farias RM, Josephides C. Barley and durum wheat in Cyprus. Plant Genet Resour Newsl. 1980;43:2–6.
41. Zeven AC, Waninge J. The presence of three groups of Scalavatis and other hexaploid bread wheat plants contaminating durum wheat fields in Cyprus. Euphytica. 1989;43:117–124. https://doi.org/10.1007/BF00037904
42. Figliuolo G, Mazzeo M, Greco I. Temporal variation of diversity in Italian durum wheat germplasm. Genet Resour Crop Evol. 2007;54(3):615–626.
43. Tessier C, David J, This P, Boursiquot JM, Charrier A. Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theor Appl Genet. 1999;98(1):171–177. https://doi.org/10.1007/s001220051054
44. Prevost A, Wilkinson MJ. A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet. 1999;98(1):107–112. https://doi.org/10.1007/s001220051046
45. Peakall R, Smouse PE. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes. 2006;6(1):288–295. doi: 10.1111/j.1471-8286.2005.01155.x
46. Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ. W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 2016; 44.
47. Cornuet JM, Luikart G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics. 1996;144(4):2001–2014. 8978083
48. Piry S, Luikart G, Cornuet JM. BOTTLENECK—a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered. 1999;90(4):502–503. https://doi.org/10.1093/jhered/90.4.502
49. Pritchard JK, Stephens M, Donnelly P. Inference of population structure from multilocus genotype data. Genetics. 2000;155(2):945–959. 10835412
50. Salem KFM, Röder MS, Börner A. Assessing genetic diversity of Egyptian hexaploid wheat (Triticum aestivum L.) using microsatellite markers. Genet Resour Crop Evol. 2015;62(3):77–385. doi: 10.1007/s10722-014-0159-5
51. Leigh F, Lea V, Law J, Wolters P, Powell W, Donini P. Assessment of EST- and genomic microsatellite markers for variety discrimination and genetic diversity studies in wheat. Euphytica. 2003;133(3):359–366. https://doi.org/10.1023/A:1025778227751
52. Khanjari SA, Hammer K, Buerkert A, Röder M. Molecular diversity of Omani wheat revealed by microsatellites: I. Tetraploid landraces. Genet Resour Crop Evol. 2007;54(6):1291–1300.
53. Landjeva S, Ganeva G, Korzun V, Palejev D, Chebotar S, Kudrjavstev A. Genetic diversity of old bread wheat germplasm from Black Sea region evaluated by microsatellites and agronomic traits. Plant Genet Resour. 2015;13(2):119–130. https://doi.org/10.1017/S1479262114000781
54. Alamerew S, Chebotar S, Huang X, Röder M, Börner A. Genetic diversity in Ethiopian hexaploid and tetraploid wheat germplasm assessed by microsatellite markers. Genet Resour Crop Evol. 2004;51(5):559–567. https://doi.org/10.1023/B:GRES.0000024164.80444.f0
55. Pereira GS, Cazé ALR, Silva MG, Almeida VC, Magalhães FOC, Filho JLS, et al. Optimal use of SSR markers for varietal identification of upland cotton. Pesqui Agropecu Bras. 2015;50:571–581. https://doi.org/10.1590/S0100-204X2015000700007
56. Teklu Y, Hammer K, Huang XQ, Röder MS. Analysis of microsatellite diversity in Ethiopian tetraploid wheat landraces. Genet Resour Crop Evol. 2006;53(6):1115–1126.
57. Achtar S, Moualla MY, Kalhout A, Röder MS, MirAli N. Assessment of genetic diversity among Syrian durum (Triticum ssp. durum) and bread wheat (Triticum aestivum L.) using SSR markers. Russ J Genet. 2010;46(11):1320–1326. doi: 10.1134/S1022795410110074
58. Vavilov NI. Geographical regularities in the distribution of the genes of cultivated plants. Comp Cytogenet. 2009;3(1):71–78. doi: 10.3897/compcytogen.v3i1.10
59. Flaksberger C. Report on the liguleless durum wheats of the island of Cyprus. The Cyprus Agricultural Journal. 1927;22:71–74.
60. Parisinos J. Breeding cereal varieties in Cyprus. Talk given during a seminar at the Agricultural Research Institute. Nicosia: Archives of the Agricultural Research Institute. 1965.
61. Dobrovolskaya O, Saleh U, Malysheva-Otto L, Röder MS, Börner A. Rationalizing germplasm collections: a case study for wheat. Theor Appl Genet. 2005;111(7):1322–1329. 16133307
62. Börner A, Chebotar S, Korzun V. Molecular characterization of the genetic integrity of wheat (Trticum aestivum L.) germplasm after long-term maintenance. Theor Appl Genet. 2000;100:494–497. https://doi.org/10.1007/s001220050064
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