Phenotypic variability evaluation and genetic variation in F2 intraspecific hybrids of cucumber (Cucumis sativus L.) using retrotransposon-based markers

##plugins.themes.bootstrap3.article.main##

AGUS BUDI SETIAWAN
QONITA AULIA ZAHIDAH
DIAS NABILA KALTSUM
AZIZ PURWANTORO

Abstract


Abstract. Setiawan AB, Zahidah QA, Kaltsum DN, Purwantoro A. 2023. Phenotypic variability evaluation and genetic variation in F2 intraspecific hybrids of cucumber (Cucumis sativus L.) using retrotransposon-based markersBiodiversitas 24: 2596-2604Cucumber (Cucumis sativus L.) has a narrow genetic base compared to other Cucumis species. The genetic base of the cucumber can be improved by crossing two distantly related cultivars from different geographical locations. This study aimed to evaluate phenotypic variability and investigate genetic variation of F2 cucumber population using two retrotransposon-based markers, namely Inter Retrotransposon Amplified Polymorphism (IRAP)andInter-SINE Amplified Polymorphism(ISAP). Two parental lines and the selected 59 genotypes from F2 population were subjected to PCR analysis for DNA profiling. The phenotypic variation of F2 genotypes revealed significant diversity in fruit weight, fruit diameter, fruit radian, pedicel length, fruit length, and fruit ratio (length-diameter). The genetic variation of the F2 hybrids was successfully detected and discriminated by IRAP and ISAP markers. Both IRAP and ISAP markers showed high heterozygosity ranged from 0.4021 to 0.4997, with an average of 0.4649 and moderate polymorphic information content ranged from 0.3489 to 0.3929 with an average of 0.3648. Cluster analysis showed that the F2 population and parental lines were grouped into two major clusters with a similarity coefficient ranged from 0.67 to 0.96. These findings imply that the F2 population is highly segregated and can be utilized to create new cultivars of cucumber.


##plugins.themes.bootstrap3.article.details##

References
Alikhani L, Rahmani M-S, Shabanian N, Badakhshan H, Khadivi-Khub A. 2014. Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers. Gene. 552:176–183. DOI:10.1016/j.gene.2014.09.034.
Amanullah S, Osae BA, Yang T, Abbas F, Liu S, Liu H, Wang X, Gao P, Luan F. 2022. Mapping of genetic loci controlling fruit linked morphological traits of melon using developed CAPS markers. Mol Biol Rep. 49:5459–5472. DOI:10.1007/s11033-022-07263-x.
Amiryousefi A, Hyvönen J, Poczai P. 2018. iMEC: Online Marker Efficiency Calculator. Appl Plant Sci. 6:4–7. DOI:10.1002/aps3.1159.
Aziz RR, Tahir NAR. 2022. Genetic diversity and structure analysis of melon (Cucumis melo L.) genotypes using URP, SRAP, and CDDP markers. Genet Resour Crop Evol. DOI:10.1007/s10722-022-01462-y.
Botstein D, White RL, Skolnick M, Davis RW. 1980. Construction of a Genetic Linkage Map in Man Using Restriction Fragment Length Polymorphisms. Am J Hum Genet. 32:314–331.
Cazzola F, Bermejo CJ, Cointry E. 2020. Transgressive segregations in two pea F2 populations and their respective F2:3 families. Pesqui Agropecu Bras. 55. DOI:10.1590/S1678-3921.PAB2020.V55.01623.
Chandrasekaran J, Brumin M, Wolf D, Leibman D, Klap C, Pearlsman M, Sherman A, Arazi T, Gal-On A. 2016. Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology. Mol Plant Pathol. 17:1140–1153. DOI:10.1111/mpp.12375.
Chen J, Staub J, Qian C, Jiang J, Luo X, Zhuang F. 2003. Reproduction and cytogenetic characterization of interspecific hybrids derived from Cucumis hystrix Chakr. x Cucumis sativus L. Theoretical and Applied Genetics. 106:688–695. DOI:10.1007/s00122-002-1118-7.
Chen JF, Staub J, Adelberg J, Lewis S, Kunkle B. 2002. Synthesis and preliminary characterization of a new species (amphidiploid) in Cucumis. Euphytica. 123:315–322. DOI:10.1023/A:1015095430624.
Chen JF, Staub JE, Tashiro Y, Isshiki S, Miyazaki S. 1997. Successful interspecific hybridization between Cucumis sativus L. and C. hystrix Chakr. Euphytica. 96:413–419. DOI:10.1023/A:1003017702385.
Cheraghi A, Rahmani F, Hassanzadeh-Ghorttapeh A. 2018. IRAP and REMAP based genetic diversity among varieties of Lallemantia iberica. Mol Biol Res Commun. 7:125–132. DOI:10.22099/mbrc.2018.29924.1327.
Chesnokov Y v, Artemyeva AM. 2015. Evaluation of the measure of polymorphism information of genetic diversity. Agric Biol. 50:571–578. DOI:10.15389/agrobiology.2015.5.571rus.
Choi S, Lee JH, Kang WH, Kim J, Huy HN, Park SW, Son EH, Kwon JK, Kang BC. 2018. Identification of cucumber mosaic resistance 2 (cmr2) that confers resistance to a new cucumber mosaic virus isolate p1 (cmv-p1) in pepper (capsicum spp.). Front Plant Sci. 9. DOI:10.3389/fpls.2018.01106.
Diekmann K, Seibt KM, Muders K, Wenke T, Junghans H, Schmidt T, Dehmer KJ. 2017. Diversity studies in genetic resources of Solanum spp. (section Petota) by comparative application of ISAP markers. Genet Resour Crop Evol. 64:1937–1953. DOI:10.1007/s10722-016-0484-y.
Elbarbary RA, Lucas BA, Maquat LE. 2016. Retrotransposons as regulators of gene expression. Science. 351:1–18. DOI:10.1126/science.aac7247.
Eltaher S, Sallam A, Belamkar V, Emara HA, Nower AA, Salem KFM, Poland J, Baenziger PS. 2018. Genetic diversity and population structure of F3:6 Nebraska Winter wheat genotypes using genotyping-by-sequencing. Front Genet. 9:1–9. DOI:10.3389/fgene.2018.00076.
Fatmawati Y, Setiawan AB, Purwantoro A, Respatie DW, Teo CH. 2021. Analysis of genetic variability in f2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system. Biodiversitas. 22:4880–4889. DOI:10.13057/biodiv/d221121.
Huang Q, Ju C, Cheng Y, Cui D, Han B, Zhao Z, Ma X, Han L. 2022. QTL Mapping of Mesocotyl Elongation and Confirmation of a QTL in Dongxiang Common Wild Rice in China. Agronomy. 12(8). DOI:10.3390/agronomy12081800.
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. DOI:10.1038/ng.475.
Kalendar R, Schulman AH. 2006. IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nat Protoc. 1:2478–2484. DOI:10.1038/nprot.2006.377.
Koide Y, Sakaguchi S, Uchiyama T, Ota Y, Tezuka A, Nagano AJ, Ishiguro S, Takamure I, Kishima Y. 2019. Genetic properties responsible for the transgressive segregation of days to heading in rice. G3: Genes, Genomes, Genetics. 9:1655–1662. DOI:10.1534/g3.119.201011.
Kozik EU, Klosinska U, Call AD, Wehner TC. 2013. Heritability and genetic variance estimates for resistance to downy mildew in cucumber accession ames 2354. Crop Sci. 53:177–182. DOI:10.2135/cropsci2012.05.0297.
Kuligowska K, Lütken H, Christensen B, Skovgaard I, Linde M, Winkelmann T, Müller R. 2015. Evaluation of reproductive barriers contributes to the development of novel interspecific hybrids in the Kalanchoë genus. BMC Plant Biol. 15. DOI:10.1186/s12870-014-0394-0.
Li H, Wang S, Chai S, Yang Z, Zhang Q, Xin H, Xu Y, Lin S, Chen X, Yao Z, et al. 2022. Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. Nat Commun. 13. DOI:10.1038/s41467-022-28362-0.
Li S, Ramakrishnan M, Vinod KK, Kalendar R, Yrjälä K, Zhou M. 2020. Development and deployment of high-throughput retrotransposon-based markers reveal genetic diversity and population structure of asian bamboo. Forests. 11:1–25. DOI:10.3390/f11010031.
Li SF, She HB, Yang LL, Lan LN, Zhang XY, Wang LY, Zhang YL, Li N, Deng CL, Qian W, et al. 2022. Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species. Int J Mol Sci. 23. DOI:10.3390/ijms231710158.
Liu Chunqing, Yao X, Li G, Huang L, Liu Chenghong, Xie Z. 2022. Development of Novel Markers and Creation of Non-Anthocyanin and Anthocyanin-Rich Broccoli (Brassica oleracea var. italica) Cultivars. Applied Sciences (Switzerland). 12. DOI:10.3390/app12126267.
Lv Y, Gao P, Liu S, Fang X, Zhang T, Liu T, Amanullah S, Wang X, Luan F. 2022. Genetic Mapping and QTL Analysis of Stigma Color in Melon (Cucumis melo L.). Front Plant Sci. 13. DOI:10.3389/fpls.2022.865082.
Mirani AA, Teo CH, Markhand GS, Abul-Soad AA, Harikrishna JA. 2020. Detection of somaclonal variations in tissue cultured date palm (Phoenix dactylifera L.) using transposable element-based markers. Plant Cell Tissue Organ Cult. 141:119–130. DOI:10.1007/s11240-020-01772-y.
Moghaddam SM, Song Q, Mamidi S, Schmutz J, Lee R, Cregan P, Osorno JM, McClean PE. 2014. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L. Front Plant Sci. 5:1–13. DOI:10.3389/fpls.2014.00185.
Nei M, Li W-H. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci. 76:5269–5273.
Nie J, Wang Y, He H, Guo C, Zhu W, Pan Jian, Li D, Lian H, Pan Junsong, Cai R. 2015. Loss-of-function mutations in CsMLO1 confer durable powdery mildew resistance in cucumber (Cucumis sativus L.). Front Plant Sci. 6. DOI:10.3389/fpls.2015.01155.
Orozco-Arias S, Isaza G, Guyot R. 2019. Retrotransposons in plant genomes: Structure, identification, and classification through bioinformatics and machine learning. Int J Mol Sci. 20:3837. DOI:10.3390/ijms20153837.
Peakall R, Smouse PE. 2012. GenALEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics. 28:2537–2539. DOI:10.1093/bioinformatics/bts460.
Rohlf FJ. 2009. NTSYSpc. Numerical taxonomy and multivariate analysis: version 2.2. New York: Exeter Software Setauket.
Sáez C, Ambrosio LGM, Miguel SM, Valcárcel JV, Díez MJ, Picó B, López C. 2021. Resistant sources and genetic control of resistance to tolcndv in cucumber. Microorganisms. 9. DOI:10.3390/microorganisms9050913.
Schulman AH, Flavell AJ, Paux E, Ellis THN. 2012. The Application of LTR Retrotransposons as Molecular Markers in Plants. In: Bigot Y, editor. Mobile Genetics Element: Protocols and Genomic Applications, Method in Molecular Biology. Vol. 21. Humana Press. p. 115–153. DOI:10.1007/978-1-61779-603-6_7.
Seibt KM, Wenke T, Muders K, Truberg B, Schmidt T. 2016. Short interspersed nuclear elements (SINEs) are abundant in Solanaceae and have a family-specific impact on gene structure and genome organization. Plant J. 86:268–285. DOI:10.1111/tpj.13170.
Seibt KM, Wenke T, Wollrab C, Junghans H, Muders K, Dehmer KJ, Diekmann K, Schmidt T. 2012. Development and application of SINE-based markers for genotyping of potato varieties. Theoretical and Applied Genetics. 125:185–196. DOI:10.1007/s00122-012-1825-7.
Setiawan Agus Budi, Purwantoro A, Wibowo A. 2020a. Cytological Distinctions Between Timun Suri and Cucumber Discovered by Fluorescence In Situ Hybridization (FISH) Using 45S Ribosomal DNA Gene. AGRIVITA Journal of Agricultural Science. 42:584–592. DOI:10.17503/agrivita.v42i3.2142.
Setiawan Agus Budi, Teo CH, Kikuchi S, Sassa H, Kato K, Koba T. 2020b. Centromeres of Cucumis melo L. comprise Cmcent and two novel repeats, CmSat162 and CmSat189. Dalal Y, editor. PLoS One. 15:e0227578. DOI:10.1371/journal.pone.0227578.
Setiawan Agus B., Teo CH, Kikuchi S, Sassa H, Kato K, Koba T. 2020c. Chromosomal Locations of a Non-LTR Retrotransposon, Menolird18, in Cucumis melo and Cucumis sativus, and Its Implication on Genome Evolution of Cucumis Species. Cytogenet Genome Res. 160:554–564. DOI:10.1159/000511119.
Sharma V, Sharma L, Sandhu KS. 2020. Cucumber (Cucumis sativus L.). In: Antioxidants in Vegetables and Nuts - Properties and Health Benefits. Singapore: Springer Singapore. p. 333–340. http://link.springer.com/10.1007/978-981-15-7470-2_17.
Sormin SYM, Purwantoro A, Setiawan AB, Teo CH. 2021. Application of inter-SINE amplified polymorphism (ISAP) markers for genotyping of Cucumis melo accessions and its transferability in Coleus spp. Biodiversitas. 22:2918–2929. DOI:10.13057/biodiv/d220557
Staub JE, Chung S-M, Fazio G. 2005. Conformity and genetic relatedness estimation in crop species having a narrow genetic base: the case of cucumber (Cucumis sativus L.). Plant Breeding. 124:44–53. DOI:10.1111/j.1439-0523.2004.01061.x.
Teo CH, Tan SH, Ho CL, Faridah QZ, Othman YR, Heslop-harrison JS, Kalendar R, Schulman AH. 2005. Genome Constitution and Classification Using Retrotransposon- Based Markers in the Orphan Crop Banana. Journal of Plant Biology. 48:96–105.
Verma H, Borah JL, Sarma RN. 2019. Variability Assessment for Root and Drought Tolerance Traits and Genetic Diversity Analysis of Rice Germplasm using SSR Markers. Sci Rep. 9. DOI:10.1038/s41598-019-52884-1.
Wang Y, Zhao Q, Qin X, Yang S, Li Z, Li J, Lou Q, Chen J. 2017. Identification of all homoeologous chromosomes of newly synthetic allotetraploid Cucumis × hytivus and its wild parent reveals stable subgenome structure. Chromosoma. 126:713–728. DOI:10.1007/s00412-017-0635-8.
Wenke T, Seibt KM, Döbel T, Muders K, Schmidt T. 2015. Inter-SINE Amplified Polymorphism (ISAP) for Rapid and Robust Plant Genotyping. Batley J, editor. New York, NY: Springer New York. DOI:10.1007/978-1-4939-1966-6.
Wibowo A, Setiawan AB, Purwantoro A, Kikuchi S, Koba T. 2018. Cytological Variation of rRNA Genes and Subtelomeric Repeat Sequences in Indonesian and Japanese Cucumber Accessions. Chromosome Science. 21:81–87. DOI: 10.11352/scr.21.81.
Xin T, Tian H, Ma Y, Wang S, Yang L, Li X, Zhang M, Chen C, Wang H, Li H, et al. 2022. Targeted creation of new mutants with compact plant architecture using CRISPR/Cas9 genome editing by an optimized genetic transformation procedure in cucurbit plants. Hortic Res. 9. DOI:10.1093/hr/uhab086.
Zein I, Jawhar M, Arabi MIE. 2010. Efficiency of IRAP and ITS-RFLP marker systems in accessing genetic variation of Pyrenophora graminea. Genet Mol Biol. 33:328–332. DOI:10.1590/S1415-47572010005000041.
Zhu P, Meng Y, Zhang K, Wang X, Liang K, Wang T, Xu J, Qin X, Wu Z, Cheng C, et al. 2022. Mapping of fruit apex shape related QTLs across multi-genetic backgrounds in cucumber (Cucumis sativus L.). Hortic Plant J. 8:328–340. DOI:10.1016/j.hpj.2021.12.001.

Most read articles by the same author(s)

1 2 > >>