Molecular characterization of the cucumber (Cucumis sativus L.) accessions held at the COMAV’s genebank
Abstract
The cucumber (Cucumis sativus L.) is an important crop worldwide. In the present study, the molecular genetic diversity of 131 Spanish accessions was analyzed using 23 simple sequence repeat (SSRs). Eighteen of these SSRs were polymorphic; the mean number of alleles, mean observed heterozygosity and mean polymorphic information content were 3.2, 0.065 and 0.229, respectively. Seven SSRs showed a polymorphic information content (PIC) ranging from 0.31 to 0.44, therefore they were reasonably informative. Around 60% of the alleles showed a frequency higher than 0.05, and only one allele in the SSR31399 showed a frequency lower than 0.01. In addition, three accession-specific alleles were found. A high proportion of variation among accessions was obtained. In no case all plants of any accession showed the same genotype and only 18 of 131 Spanish accessions had at least two plants with the same genotype. A cluster analysis did not show any relation with morphological types or geographical area. Therefore, these results demonstrated that molecular diversity of the cucumber did not reflect its phenotypic variability. Finally, this study provided information for the rationalization of the cucumber collection of the COMAV. Morphological traits, origin and molecular data were taken into account to select 47 accessions, six belonging to ‘French’ type, 15 to ‘Long’ type, and 24 to ‘Short’ type. Phenotypic and molecular variability contained in the complete collection was conserved in the selected accessions.
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References
Areshchenkova T, Ganal MW, 1999. Long tomato microsatellites are predominantly associated with centromeric regions. Genome 42: 536-544. https://doi.org/10.1139/g98-155
Baker RH, Yu XB, DeSalle R, 1998. Assessing the relative contribution of molecular and morphological characters in simultaneous analysis trees. Mol Phylogenet Evol 9: 427-436. https://doi.org/10.1006/mpev.1998.0519
Botstein D, White RL, Skolnick M, Davis RW, 1980. Construction of genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32: 314-331.
Cavagnaro PF, Senalik DA, Yang L, Simon PW, Harkins TT, Kodira CD, Huang S, Weng Y, 2010. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics 11: 569. https://doi.org/10.1186/1471-2164-11-569
Chen SX, Chen WF, Shen XQ, Yang YT, Qi F, Liu Y, Meng H, 2014. Analysis of the genetic diversity of garlic (Allium sativum L.) by simple sequence repeat and inter simple sequence repeat analysis and agro-morphological traits. Biochem Syst Ecol 55: 260-267. https://doi.org/10.1016/j.bse.2014.03.021
Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK, 2005. An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 142: 169-196. https://doi.org/10.1007/s10681-005-1681-5
Dijkhuizen A, Kennard WC, Havey MJ, Staub JE, 1996. RFLP variation and genetic relationships in cultivated cucumber. Euphytica 90: 79-87.
Doyle JJ, Doyle JL, 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15.
Elameen A, Larsen A, Klemsdal SS, Fjellheim S, Sundheim L, Msolla S, Masumba E, Rognli OA, 2011. Phenotypic diversity of plant morphological and root descriptor traits within a sweet potato, Ipomoea batatas (L.) Lam., germplasm collection from Tanzania. Genet Resour Crop Evol 58: 397-407. https://doi.org/10.1007/s10722-010-9585-1
FAOSTAT, 2017. Food and agriculture data. Cucumber production. http://faostat3.fao.org
Fehet T, 1992. Watermelon. In: Genetic improvement of vegetable crops; Kaloo G, Bergh BO (eds.). pp: 295-314. Pergamon Press, NY.
Geleta N, Labuschagne MT, Viljoen CD, 2006. Genetic diversity analysis in sorghum germplasm as estimated by AFLP, SSR and morpho-agronomical markers. Biodivers Conserv 15: 3251-3265. https://doi.org/10.1007/s10531-005-0313-7
Horejsi T, Staub JE, 1999. Genetic variation in cucumber (Cucumis sativus L.) as assessed by random amplified polymorphic DNA. Genet Res Crop Evol 46: 337-350. https://doi.org/10.1023/A:1008650509966
Hu J, Zho X, Lia J, 2010a. Development of novel EST-SSR markers for cucumber (Cucumis sativus) and their transferability to related species. Sci Hortic 125: 534-538. https://doi.org/10.1016/j.scienta.2010.03.021
Hu J, Liang F, Liu L, Si S, 2010b. Genetic relationship of a cucumber germplasm collection revealed by newly developed EST-SSR markers. J Genet 89: 28-32.
Hu J, Wang L, Li J, 2011. Comparison of genomic SSR and EST-SSR markers for estimating genetic diversity in cucumber. Biol Plant 55: 577-580. https://doi.org/10.1007/s10535-011-0129-0
Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, et al., 2009. The genome of the cucumber, Cucumis sativus L. Nat Genet 41: 1275-1281. https://doi.org/10.1038/ng.475
Knerr LD, Staub JE, Holder DJ, May BP, 1989. Genetic diversity in Cucumis sativus L. assessed by variation at 18 allozyme coding loci. Theor Appl Genet 78: 119-128. https://doi.org/10.1007/BF00299764
Kong Q, Xiang C, Yu Z, 2006. Development of EST-SSRs in Cucumis sativus from sequence database. Mol Ecol Notes 6: 1234-1236. https://doi.org/10.1111/j.1471-8286.2006.01500.x
Li X, Zhu D, Du Y, Shen D, Kong Q, Song J, 2004. Studies on genetic diversity and phylogenetic relationship of cucumber (Cucumis sativus L.) germplasm by AFLP technique. Acta Hortic Sin 34: 309-314.
Liu J, Qu J, Hu K, Zhang L, Li J, Wu B, Luo C, Wei A, Han Y, Cui X, 2015. Development of genomewide simple sequence repeat fingerprints and highly polymorphic markers in cucumbers based on next-generation sequence data. Plant Breed 134: 605-611. https://doi.org/10.1111/pbr.12304
Liu K, Muse SV, 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 1: 2128-2129. https://doi.org/10.1093/bioinformatics/bti282
Lv J, Qi J, Shi Q, Shen D, Zhang S, Shao G, Li H, Sun Z, Weng Y, Shang Y, et al., 2012. Genetic diversity and population structure of cucumber (Cucumis sativus L.). PLoS One 7: 1-9. https://doi.org/10.1371/journal.pone.0046919
MAPAMA, 2017. Statistical Yearbook 2015. Ministerio de Agricultura y Pesca, Alimentación y Medio Ambiente, Gobierno de España. http://www.mapama.gob.es
McCreight JD, Nerson H, Grumet R, 1992. Melon. In: Genetic improvement of vegetable crops; Kaloo G, Bergh BO (eds.). pp. 267-294. Pergamon Press, NY.
Meglic V, Serquen F, Staub JE, 1996. Genetic diversity in cucumber (Cucumis sativus L.): I. A reevaluation of the U.S. germplasm collection. Genet Resour Crop Evol 43: 533-546. https://doi.org/10.1007/BF00138830
Mliki A, Staub JE, Zhangyong S, Ghorbel A, 2003. Genetic diversity in African cucumber (Cucumis sativus L.) provides potential for germplasm enhancement. Genet Resour Crop Evol 50: 461-468. https://doi.org/10.1023/A:1023957813397
Mu S, Gu X, Zhang S, Wang X, Wang Y, 2008. Genetic diversity of cucumber (Cucumis sativus L.) germplasm by SSR. Acta Hortic Sin 35: 1323-1330.
Nei M, 1978. Estimation of average heterozygosity and genetic distance from small number of individuals. Genetics 89: 583-590.
Odong TL, Jansen J, van Eeuwijk FA, van Hintum TJL, 2013. Quality of core collections for effective utilization of genetic resources review, discussion and interpretation. Theor Appl Genet 126: 289-305. https://doi.org/10.1007/s00122-012-1971-y
Page RDM, 1996. Treeview: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358.
Panaud O, Chen SR, McCouch R, 1996. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252: 597-607. https://doi.org/10.1007/BF02172406
Pandey S, Ansari WA, Mishra VK, Singh AK, Singh M, 2013. Genetic diversity in Indian cucumber based on microsatellite and morphological markers. Biochem Syst Ecol 51: 19-27. https://doi.org/10.1016/j.bse.2013.08.002
Parra-Quijano M, Iriondo JM, Torres E, De la Rosa L, 2011. Evaluation and validation of ecogeographical core collection using phenotypic data. Crop Sci 51: 694-703. https://doi.org/10.2135/cropsci2010.05.0273
Peakall R, Smouse P, 2012. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28: 2537-2539. https://doi.org/10.1093/bioinformatics/bts460
Powell W, Machray GC, Provan J, 1996. Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1: 215-222. https://doi.org/10.1016/S1360-1385(96)86898-0
Qi J, Liu X, Shen D, Miao H, Xie B, Li X, Zeng P, Wang S, Shang Y, Gu X, et al., 2013. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet 45: 1510-1515. https://doi.org/10.1038/ng.2801
Raghami M, López-Sesé AI, Hasandokht MR, Zamani Z, Moghadam MR, Kashi A, 2014. Genetic diversity among melon accessions from Iran and their relationships with melon germplasm of diverse origins using microsatellite markers. Plant Syst Evol 300: 139-151. https://doi.org/10.1007/s00606-013-0866-y
Reche J, 2011. Cultivo del pepino en invernadero. Ministerio de Medio Ambiente, Medio Rural y Marino, Gobierno de España.
Ren Y, Zhang Z, Liu J, Staub JE, Han Y, Cheng Z, Li X, Lu J, Miao H, Kang H, et al., 2009. An integrated genetic and cytogenetic map of the cucumber genome. PLoS One 4 (6): e5795. https://doi.org/10.1371/journal.pone.0005795
Roldán-Ruiz I, van Euwijk FA, Gilliland TJ, Dubreuil P, Dillmann C, Lallemand J, De Loose M, Baril CP, 2001. A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties. Theor Appl Genet 103: 1138-1150. https://doi.org/10.1007/s001220100571
Rubinstein M, Katzenellenbogen M, Eshed R, Rozen A, Katzir N, Colle M, Yang L, Grumet R, Weng Y, Sherman A, Ophir R, 2015. Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array. PLoS One 10 (4): e0124101. https://doi.org/10.1371/journal.pone.0124101
Staub JE, Serquen F, McCreight JD, 1997a. Genetic diversity in cucumber (Cucumis sativus L): III. An evaluation of Indian germplasm. Genet Resour Crop Evol 44: 315-326. https://doi.org/10.1023/A:1008639103328
Staub JE, Box J, Meglic V, Horejsi TF, McCreight JD, 1997b. Comparison of isozyme and random amplified polymorphic DNA data for determining intraspecific variation in Cucumis. Genet Resour Crop Evol 44: 257-269. https://doi.org/10.1023/A:1008639616331
Staub JE, Serquen FC, Horejsi T, Chen J, 1999. Genetic diversity in cucumber (Cucumis sativus L.): IV. An evaluation of Chinese germplasm. Genet Res Crop Evol 46: 297-310. https://doi.org/10.1023/A:1008663225896
Struss D, Plieske J, 1998. The use of microsatellite markers for detection of genetic diversity in barley populations. Theor Appl Genet 97: 308-315. https://doi.org/10.1007/s001220050900
Sun X, Xie Y, Bi Y, Liu J, Amombo E, Hu T, Fu J, 2015. Comparative study of diversity based on heat tolerant-related morpho-physiological traits and molecular markers in tall fescue accessions. Sci Rep 5: 18213. https://doi.org/10.1038/srep18213
Szewc-McFadden AK, Kresovich SK, Bliek SM, Mitchell SE, McFerson JR, 1996. Identification of polymorphic, conserved simple sequence repeats (SSRs) in cutlivated Brassica species. Theor Appl Genet 93: 534-538. https://doi.org/10.1007/BF00417944
Tatlioglu TP, 1992. Cucumber. In: Genetic improvement of vegetable crops; Kaloo G, Bergh BO (eds.). pp: 197-234. Pergamon Press, NY.
Thomas MR, Scott NS, 1993. Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theor Appl Genet 86: 985-990. https://doi.org/10.1007/BF00211051
Valcárcel JV, Peiró R, Pérez-de-Castro A, Díez MJ, 2018. Morphological characterization of the cucumber (Cucumis sativus L.) collection of the COMAV's genebank. Genet Res Crop Evol 65 (4): 1293-1306. https://doi.org/10.1007/s10722-018-0614-9
van Hintum TJL, Brown AH, Spillane C, Hodgkin T, 2000. Core collections of plant genetic resources, IPGRI technical bulletin no. 3. IPGRI, Rome, Italy. 51 pp.
van Treuren R, de Groot EC, Boukema IW, van de Wiel CCM, van Hintum TJL, 2010. Marker-assisted reduction of redundancy in a genebank collection of cultivated lettuce. Plant Genet Resour 8: 95-105. https://doi.org/10.1017/S1479262109990220
Watcharawongpaiboon N, Chunwongse J, 2008. Development and characterization of microsatellite markers from an enriched genomic library of cucumber (Cucumis sativus). Plant Breed 127: 74-81.
Wóycicki R, Witkowicz J, Gawroński P, Dabrowska J, Lomsadze A, Pawełkowicz M, Siedlecka E, Yagi K, Plader W, Seroczyńska A, et al., 2011. The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS One 6 (7): e22728. https://doi.org/10.1371/journal.pone.0022728
Yang L, Koo D, Li Y, Zhang X, Luan F, Havey M, Jiang J, Weng Y, 2012. Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly. Plant J 71: 895-906. https://doi.org/10.1111/j.1365-313X.2012.05017.x
Yang YT, Liu Y, Qi F, Xu LL, Li XZ, Cong LJ, Guo X, Chen SX, Fang YL, 2015. Assessment of genetic diversity of cucumber cultivars in China based on simple sequence repeats and fruit traits. Genet Mol Res 14: 19028-19039. https://doi.org/10.4238/2015.December.29.10
Zhou Q, Miao H, Li S, Zhang S, Wang Y, Weng Y, Zhang Z, Huang S, Gu X, 2015. A sequencing-based linkage map of cucumber. Mol Plant 8: 961-963. https://doi.org/10.1016/j.molp.2015.03.008
Zhu H, Song P, Koo DH, Guo L, Li Y, Sun S, Weng Y, Yang L, 2016. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis. BMC Genomics 17: 557. https://doi.org/10.1186/s12864-016-2870-4
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