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The analogy of simple and inter simple sequence repeat markers in the assessment of genetic diversity of pumpkin accessions in Kenya

By: James Kiramana Kiramana, Dorcas Khasungu Isutsa, Aggrey Bernard Nyende

Key Words: Alleles, Genetic variation, Polymorphism, Pumpkin accessions.

Int. J. Biosci. 17(3), 148-163, September 2020.

DOI: http://dx.doi.org/10.12692/ijb/17.3.148-163

Certification: ijb 2020 0042 [Generate Certificate]

Abstract

Pumpkin is found growing in many parts of Kenya although its genetic variation has not been determined using available molecular markers. This study compared SSR and ISSR efficacy in assessing diversity of 139 pumpkin accessions using the multiplex ratio (MR), polymorphic information content (PIC), effective multiplex ratio (EMR), marker index (MI), different (Na) and effective (Ne) alleles, Shannon index (I), expected (He) and unbiased expected heterozygosity (UHe), analysis of molecular variance (AMOVA), clusters and mantel correspondence. DNA ranged from 27-2992ng/µl and 0.45-2.1 of 260/280nm. SSR detected 23 total alleles and 4.6 average alleles of 100-700bp. ISSR detected 152 total alleles and 21.7 average alleles of 200-2000bp. Amplified and polymorphic DNA bands were 437 and 117 for SSR, 512 and 391 for ISSR, respectively. Total and polymorphic bands MR was 87.4 and 29.4 for SSR, 73.1 and 55.9 for ISSR, respectively. PIC, EMR and MI for ISSR were higher than for SSR. Markers with high polymorphism portrayed high EMR and MI. SSR PKCT-122 and ISSR 17899A had the highest polymorphism, PIC, EMR and MI. Ne, I, He and UHe was high for SSR, while Na was high for ISSR. AMOVA revealed significant (P=0.01; P=0.02) differentiation. Genetic diversity was 14% and 7% among, 86% and 93% within accessions for SSR and ISSR, respectively. Three clusters independent of geographic origin were revealed. SSR and ISSR Euclidean matrices showed positive significant (r=0.272, P=0.0001) correlation, which implied they reflected the same genetic diversity. Hence, the genetic diversity of pumpkins can be assessed effectively using either SSR or ISSR markers.

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The analogy of simple and inter simple sequence repeat markers in the assessment of genetic diversity of pumpkin accessions in Kenya

AbdelLatif A, Osman G. 2017. Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods 13(1), 1-9.

https://doi.org/10.1186/s13007-016-0152-4

Aboul-Maaty NA, Oraby HA. 2019. Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method. Bulletin of the National Research Centre 43(25), 1-10.

Adawy SS, Hussein E, Samer E, Ismail S, El-Itriby HA. 2005. Genomic diversity in date palm (Phoenix dactylifera L) as revealed by AFLPs in comparison to RAPDs and ISSRs. Arab Journal of Biotechnology 8(1), 99-114.

Ansari S, Narayanan C, Wali S, Kumar R, Shukla N, Rahangdale S. 2012. ISSR markers for analysis of molecular diversity and genetic structure of Tectona grandis L.f. populations. Annals of Forest Research 55(1), 11-23.

https://doi.org/10.15287/afr.2012.71.

Barzegar R, Peyvast G, Ahadi A, Rabiei B, Ebadi A, Babagolzadeh A. 2013. Biochemical systematic, population structure and genetic variability studies in Iranian Cucurbita pepo L accessions using genomic SSRs and implications for their breeding potential. Biochemical Systematics and Ecology 50, 187-198.

https://doi.org/10.1016/j.bse.2013.03.048

Behera TK, Singh AK, Staub JE. 2008. Comparative analysis of genetic diversity in Indian bitter gourd (Momordica charantia L) using RAPD and ISSR markers for developing crop improvement strategies. Scientia Horticulturae 115, 209–217.

https://doi.org/10.1016/j.scienta.2007.08.013.

Bilska K, Szczecinska M. 2016. Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics of Pulsatilla patens populations. Peer Journal 4, 1-25.

https://doi.org/10.7717/peerj.2504.

Datta J, Lal N, Kaashyap M, Gupta P. 2010. Efficiency of PCR based marker systems for detecting DNA polymorphism in Cicer arietinum L and Cajanus cajan L Millspaugh. Genetic Engineering and Biotechnology Journal 5, 1-15.

Domyati FM, Younis S, Edris RAA, Mansour A, Sabir G, Bahieldin A. 2011. Molecular markers associated with genetic diversity of some medicinal plants in Sinai. Journal of Medicinal Plants Research 5(2), 200-210.

Doyle JJ, Doyle JL. 1987. A Rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19, 11-15.

El-Assal SE, Gaber A. 2012. Discrimination capacity of RAPD, ISSR and SSR markers and of their effectiveness in establishing genetic relationship and diversity among Egyptian and Saudi wheat cultivars. American Journal of Applied Science 9(5), 724-735. https://doi.org/10.3844/ajassp.2012.724.735

Esmailnia E, Arefrad M, Shabani S, Karimi M, Vafadar F, Dehestani A. 2015. Genetic diversity and phylogenetic relationship of Iranian indigenous cucurbits investigated by inter simple sequence repeat (ISSR) markers. Biharean Biologist 9(1), 47-54.

http://biozoojournals.ro/bihbiol/index.html

Esteras C, Nuez F, Pico B. 2012. Genetic diversity studies in cucurbits using molecular tools. In: Wang Y, Behera TK, Kole C. (Eds.). Cucurbits: Genetics, Genomics and Breeding of Cucurbits. Science Publishers Inc., New Hampshire, p 140-198.

https://doi.org/10.1201/b11436-6

Gong L, Stift G, Kofler R, Pachner M, Lelley T. 2008. Microsatellites for Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L. Theoretical and Applied Genetics 117, 37-48.

https://doi.org/10.1007/s00122-008-0750-2

Greenbaum G, Templeton A, Zarmi Y, Bar-David S. 2015. Allelic richness following population founding events: A stochastic modeling framework incorporating gene flow and genetic drift. PLoS ONE 10(3), e0119663.

https://doi.org/10.1371/journal.pone.0119663

Grisales SO, García DB, Cabrera FAV. 2009. Effect of inbreeding on the quality traits of squash fruit. Acta Agronómica 58(3), 1-7.

Guichoux E, Lagache L, Wagner S, Chaumeil P, Leger P, Lepais O, Lepoittevin C, Malausa T, Revardel E, Salin F, Petit RJ. 2011. Current trends in microsatellite genotyping. Molecular Ecology Resources 11, 591-611.

https://doi.org/10.1111/j.1755-0998.2011.03014.x

Gyorgy Z, Szabo M, Bacharov D, Pedryc A. 2012. Genetic diversity within and among populations of roseroot (Rhodiola rosea L) based on molecular markers. Notulae Botanicae Horti Agrobotanici Cluj-Napoca 40(2), 266-273.

https://doi.org/10.15835/nbha4028212

Hardy OJ, Charbonnel N, Freville H, Heuertz M. 2003. Microsatellite allele sizes: A simple test to assess their significance on genetic differentiation. Genetics 163, 1467–1482.

Harris AM, Degiorgio M. 2017. An unbiased estimator of gene diversity with improved variance for samples containing related and inbred individuals of any ploidy. Genes, Genome and Genetics 7, 671-691.

https://doi.org/10.1534/g3.116.037168

Hazra P, Mandal AK, Datta AK, Ram HH. 2007. Breeding pumpkin (Cucurbita moschata Duch) for fruit yield and other characters. International Journal of Plant Breeding 1(1), 51-64.

https://doi.org/10.17660/ActaHortic.2007.752.78

Heikal AH, Abdel-Razzak HS, Hafez EE. 2008. Assessment of genetic relationships among and within Cucurbita species using RAPD and ISSR markers. Journal of Applied Science Research 4, 515-525.

Hemalatha T, Shanmugasundaram P. 2010. Efficiency of DNA marker systems in discriminating Cajanus cajan L Millsp and its wild relatives. Indian Journal of Plant Genetic Resources 23(1), 93-99.

Hintze J. 2001. NCSS 2001 Statistical System for Windows. Number Cruncher Statistical Systems. Kaysville, Utah.

Holland SM. 2006. Cluster Analysis. University of Georgia, Athens, GA 30602-2501.

Inan N, Yildiz M, Sensoy S, Kafkas S, Abak K. 2012. Efficacy of ISSR and SRAP techniques for molecular characterization of some Cucurbita genotypes including naked (hull-less) seed pumpkin. Journal of Animal and Plant Sciences 22(1), 126-136.

Khanam S, Sham A, Bennetzen J, Mohammed A. 2012. Analysis of molecular marker-based characterization and genetic variation in date palm (Phoenix dactylifera L). Australian Journal of Crop Science 6(8), 1236-1244.

Kiramana JK, Isutsa DK. 2019. Determination of factors influencing cultivation and utilisation of pumpkins among smallholders in Kakamega and Nyeri Counties, Kenya. East African Agricultural and Forestry Journal 83(1), 34-48,

https://doi.org/10.1080/00128325.2018.1516419.

Kiramana JK, Isutsa DK, Nyende A. 2017. Fluorescent SSR and capillary electrophoresis reveal significant genetic diversity in naturalized pumpkin accessions in Kenya. Global Journal of Biosciences and Biotechnology 6(1), 34-45.

Li M, Zhao Z, Miao X, Zhou J. 2014. Genetic diversity and population structure of Siberian apricot (Prunus sibirica L) in China. International Journal of Molecular Sciences 15, 377-400.

https://doi.org/10.3390/ijms15010377

Liu K, Muse SV. 2005. PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics 21(9), 2128-2129.

https://doi.org/10.1093/bioinformatics/bti282

Luo Z, Jordan BJ, Dyer JM, Kutchan T, Schachtman D, Augustin M, Ge Y, Fahlgren N, Abdel-Haleem H. 2019. Genetic Diversity and population structure of a Camelina sativa Spring Panel. Frontiers in Plant Science 10(184), 1-12. https://doi.org/10.3389/fpls.2019.00184

Mantel N. 1967. The detection of disease clustering and generalized regression approach. Cancer Research 27, 209-220.

Marilene HD, Rosana R, Leandro SA, Cláudia P, Messias G. 2012. Agrobiodiversity in Cucurbita spp. landraces collected in Rio de Janeiro assessed by molecular markers. Crop Breeding and Applied Biotechnology 12, 96-103.

https://doi.org/10.1590/S198470332012000200001.

Mladenovic E, Berenji J, Ognjanov V, Ljubojevic M, Cukanovic J, Salamun T. 2014. Genetic diversity in a collection of ornamental squash (Cucurbita pepo L.). Genetika 46(1), 199-207.

https://doi.org/10.2298/GENSR1401199M

Mondini L, Noorani A, Pagnotta MA. 2009. Assessing plant genetic diversity by molecular tools. Diversity 1, 19-35.

https://doi.org/10.3390/d1010019.

Myskow B, Milczarski P, Masojc P. 2010. Comparison of RAPD, ISSR and SSR markers in assessing genetic diversity among rye. Plant Breeding and Seed Science 60, 107-115.

https://doi.org/10.2478/v10129-011-0009-y.

Najaphy A, Parchin RA, Farshadfar E. 2011. Evaluation of genetic diversity in wheat cultivars and breeding lines using inter simple sequence repeat markers. Biotechnology and Biotechnological Equipment 25(4), 2634-2638.

https://doi.org/10.5504/BBEQ.2011.0093.

Ng WL, Tan SG. 2015. Inter simple sequence repeat (ISSR) markers: Are we doing it right? ASM Science Journal 9(1), 30-39.

Noormohammadi Z, Sheidai M, Dehghani A, Parvini F, Hosseini-Mazinani SM. 2012. Inter-population genetic diversity in Olea cuspidata revealed by SSR and ISSRs. Acta Biologica Szegediensis 56(2), 155-163.

Ntuli NR, Zobolo AM, Tongoona PB, Kunene NW. 2013. Genetic diversity in Cucurbita pepo landraces from northern KwaZulu-Natal, South Africa, revealed by random amplified polymorphic DNA (RAPD) markers. African Journal of Biotechnology 12(44), 6253-6261.

https://doi.org/10.5897/AJB12.2940.

Paris HS. 2000. First two publications by Duchesne of Cucurbita moschata (Cucurbitaceae). Taxon 49, 305-319.

https://doi.org/10.2307/1223852

Peakall R, Smouse PE. 2012. Genetic analysis in excel. Population genetic software for teaching and research. Bioinformatics 28, 2537-2539.

https://doi.org/10.1093/bioinformatics/bts460

Rostami F, Moghaddam FK, Sabbagh SK, Saeidi S. 2015. Comparison of PCR-RFLP based on ribosomal regions and SSR markers in genetic diversity of pistachio die-back caused by Paecilomyces variotii. Gene Cell and Tissue 2(1),  e24340.

https://doi.org/10.17795/GCT-24340

Rousseeuw PJ, Kaufman L. 1990. Finding groups in data: An introduction to cluster analysis. A Wiley-Interscience Publication, New York.

https://doi.org/10.1002/9780470316801.

Semagn K, Bjornstad A, Ndjiondjop MN. 2006. An overview of molecular marker methods for plants. African Journal of Biotechnology 5(25), 2540-2568. Available online at:

http://www.academicjournals.org/AJB

Serra I, Procaccini G, Intrieri M, Migliaccio M, Mazzuca S, Innocenti M. 2007. Comparison of ISSR and SSR markers analysis of genetic diversity in seagrass, Posidonia oceanic. Marine Ecology Progress Series 338, 71-79.

https://doi.org/10.3354/meps338071

Sethi K, Siwach P, Verma SK. 2016. Simple sequence repeats (SSR) and interspersed sequence repeats (ISSR) markers for genetic diversity analysis among selected genotypes of Gossypium arboreum race ‘bengalense’. African Journal of Biotechnology 15(1), 7-19.

https://doi.org/10.5897/AJB2015.14878.

Sheidai M, Noormohammadi Z, Shojaei-Jeshvaghani F, Ghsemzadeh-Baraki S, Farahani F, Alishah O. 2012. Simple sequence repeats (SSR) and inter simple sequence repeat (ISSR) analyses of genetic diversity in tissue culture regenerated plants of cotton. African Journal of Biotechnology 11(56), 11894-11900.

https://doi.org/10.5897/AJB12.079

Singh D, Kumar A, Sirohi A, Kumar P, Singh J, Kumar V, Jindal A, Kumar S, Kumar N, Sharma N, Gupta S, Chand S. 2011. Improvement of basmati rice (Oryza sativa L) using traditional breeding supplemented with molecular markers. African Journal of Biotechnology 10(4), 499-506.

https://doi.org/10.5897/AJB10.413.

Stift G, Zraidi A. Lelley T. 2004. Development and characterization of microsatellite markers (SSR) in Cucurbita species. Cucurbit Genetics Cooperative Report 27, 61-65.

Tonk FA, Tosun M, Ilker E, Istipliler D, Tatar O. 2014. Evaluation and comparison of ISSR and RAPD markers for assessment of genetic diversity in triticale genotypes. Bulgarian Journal of Agricultural Science 20(6), 1413-1420.

Valgimigli MC. 2005. Genetic variability in Italian populations of Cupressus sempervirens L assessed by SSR and RAPD markers. In: Dottorato DR. Biotecnologie Molecolari Industriali E Ambientali XVIII Ciclo. Facoltá Di Scienze MM.FF.NN. Universitá Degli Studi Di Verona. Anno Accademico 2004-2005, p 1-76.

Verma KS, Haq SU, Kachhwaha S, Kothari SL. 2017. RAPD and ISSR marker assessment of genetic diversity in Citrullus colocynthis L Schrad: A unique source of germplasm highly adapted to drought and high-temperature stress. 3 Biotech 7(288), 1-24.

https://doi.org/10.1007/s13205-017-0918-z.

Wang F, JiuRan Z, JingRui D, HongMei Y, Meng K, YanMei S, XinYan Y, JingLun G, Lu W. 2007. Selection and development of representative simple sequence repeat primers and multiplex SSR sets for high throughput automated genotyping in maize. Chinese Science Bulletin 52(2), 215-223.

https://doi.org/10.1007/s11434-007-0038-y.

Watcharawongpaiboon N, Chunwongse J. 2007. Development of microsatellite markers from an enriched genomic library of pumpkin (Cucurbita moschata L). Songklanakarin Journal of Science and Technology 29(5), 1217-1223.

Xanthopoulou A, Ganopoulos I, Kalivas A, Nianiou-Obeidat I, Ralli P, Moysiadis T, Tsaftaris A, Madesis P. 2015. Comparative analysis of genetic diversity in Greek gene bank collection of summer squash (Cucurbita pepo) landraces using start codon targeted (SCoT) polymorphism and ISSR markers. Australian Journal of Crop Science 9(1), 14-21.

Yousefi V, Najaphy A, Zebarjadi A, Safari H. 2015. Molecular characterization of Thymus species using ISSR markers. Journal of Animal and Plant Sciences 25(4), 1087-1094.

Zhang Y, Zhang X, Chen X, Sun W, LiF J. 2018. Genetic diversity and structure of tea plant in Qinba area in China by three types of molecular markers. Hereditas 155(22), 1-12.

https://doi.org/10.1186/s41065-018-0058-4

James Kiramana Kiramana, Dorcas Khasungu Isutsa, Aggrey Bernard Nyende.
The analogy of simple and inter simple sequence repeat markers in the assessment of genetic diversity of pumpkin accessions in Kenya.
Int. J. Biosci. 17(3), 148-163, September 2020.
https://innspub.net/ijb/analogy-simple-inter-simple-sequence-repeat-markers-assessment-genetic-diversity-pumpkin-accessions-kenya/
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