Abstract
Gene encoding enzyme based EST–SSR markers are more potent or functional marker system to evaluate astounding genetic and structural differentiation in plants. It is very useful in shaping divergences in metabolic fingerprinting, ecological interactions, conservation and adaptation among plants. Therefore, gene encoding enzyme mediated EST–SSR markers system were used presently to evaluate genetic and population structure among 48 Capsicum accessions. Total of 35 gene encoding enzyme based EST–SSR markers was used and generated 184 alleles at 35 loci with an average of 5.25 alleles per locus. The average value of polymorphic information content, marker index and discriminating power was 0.40, 0.232, and 0.216 respectively which revealed noteworthy degree of marker efficacy and their competency was further supported by primer polymorphism (93.57%) and cross transferability (44.52%). A significant genetic variability (Na = 1.249, Ne = 1.269, I = 0.247, He = 0.163, and uHe = 0.183) was identified among the Capsicum accession using EST–SSR markers. The mean value for Nei gene diversity, total species diversity (Ht), and diversity within population (Hs) were 0.277, 0.240 and 0.170 respectively. The coefficient of gene differentiation (Gst) was 0.296 indicating significant genetic differentiation within the population and Gene flow (Nm) was 1.189, which reflect a constant gene flow among populations. AMOVA revealed more genetic differentiation within the population which is similarly supported by principal coordinate analysis among the different Capsicum population. Thus, gene encoding enzyme based EST–SSR markers represent a potent system for estimation of genetic and structural relationship and is helpful for estimation of relationships or variations studies in plants.
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References
Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27(4):617–631. https://doi.org/10.1007/s00299-008-0507-z
Agarwal A, Gupta V, Haq SU, Jatav PK, Kothari S, Kachhwaha S (2018) Assessment of genetic diversity in 29 rose germplasms using SCoT marker. J King Saud Univ Sci 31(4):780–788. https://doi.org/10.1016/j.jksus.2018.04.022
Albrecht E, Zhang D, Saftner RA, Stommel JR (2012) Genetic diversity and population structure of Capsicum baccatum genetic resources. Genet Resour Crop Evol 59(4):517–538. https://doi.org/10.1007/s10722-011-9700-y
Aljumaili JS, Rafii M, Latif M, Sakimin SZ, Arolu IW, Miah G (2018) Genetic diversity of aromatic rice germplasm revealed by SSR markers. BioMed Res Int 2018:11. https://doi.org/10.1155/2018/7658032
Amiryousefi A, Hyvönen J, Poczai P (2018) iMEC: online marker efficiency calculator. Appl Plant Sci 6(6):e01159. https://doi.org/10.1002/aps3.1159
Bouck A, Vision T (2007) The molecular ecologist’s guide to expressed sequence tags. Mol Ecol 16(5):907–924. https://doi.org/10.1111/j.1365-294X.2006.03195.x
Bunnik EM, Le Roch KG (2013) An introduction to functional genomics and systems biology. Adv Wound Care 2(9):490–498. https://doi.org/10.1089/wound.2012.0379
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R (2020) TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant 13(8):1194–1202. https://doi.org/10.1016/j.molp.2020.06.009
Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15
Earl DA, VonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361. https://doi.org/10.1007/s12686-011-9548-7
Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5(6):435. https://doi.org/10.1038/nrg1348
Ellis J, Burke J (2007) EST–SSRs as a resource for population genetic analyses. Heredity 99(2):125–132
Eujayl I, Sledge M, Wang L, May G, Chekhovskiy K, Zwonitzer J, Mian M (2004) Medicago truncatula EST–SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108(3):414–422. https://doi.org/10.1007/s00122-003-1450-6
Gupta V, Jatav PK, Haq SU, Verma KS, Kaul VK, Kothari S, Kachhwaha S (2019) Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity. J Genet 98(2):1–12. https://doi.org/10.1007/s12041-019-1095-0
Haq S, Jain R, Sharma M, Kachhwaha S, Kothari S (2014) Identification and characterization of microsatellites in expressed sequence tags and their cross transferability in different plants. Int J Genom 2014:12. https://doi.org/10.1155/2014/863948
Haq SU, Kumar P, Singh R, Verma KS, Bhatt R, Sharma M, Kachhwaha S, Kothari S (2016) Assessment of functional EST–SSR markers (Sugarcane) in cross-species transferability, genetic diversity among poaceae plants, and bulk segregation analysis. Genet Res Int 2016:16. https://doi.org/10.1155/2016/7052323
Haq SU, Dhingra P, Sharma M, Kothari SL, Kachhwaha S (2021) Plasticity of tandem repeats in expressed sequence tags of angiospermic and non-angiospermic species: insight into cladistic, phenetic, and elementary explorations. J Appl Biol 9(2):36–59. https://doi.org/10.7324/JABB.2021.9204
Haq S, Dubey S, Dhingra P, Verma KS, Kumari D, Kothari SL, Kachhwaha S (2022) Exploring the genetic makeup and population structure among Capsicum accessions for crop improvement and breeding curriculum insights. J Genet Eng Biotechnol 20:116. https://doi.org/10.1186/s43141-022-00398-1
Hernández-Verdugo S, Luna-Reyes R, Oyama K (2001) Genetic structure and differentiation of wild and domesticated populations of Capsicum annuum (Solanaceae) from Mexico. Plant Syst Evol 226(3):129–142. https://doi.org/10.1007/s006060170061
Huang H-H, Zhang Z-H, Zhang Z-H, Mao S-L, Wang L-H, Zhang B-X (2011) Analysis of SSRs information in Capsicum spp. from EST database. Agric Sci China 10(10):1532–1536. https://doi.org/10.1016/S1671-2927(11)60148-X
Husnudin U, Daryono B, Purnomo P (2019) Genetic variability of Indonesian eggplant (Solanum melongena) based on ISSR markers. Biodivers J Biol Divers 20(10):3049–3055. https://doi.org/10.13057/biodiv/d201038
Ince AG, Karaca M, Onus AN (2010) Polymorphic microsatellite markers transferable across Capsicum species. Plant Mol Biol Rep 28(2):285–291. https://doi.org/10.1007/s11105-009-0151-y
Jaiswal V, Rawoof A, Dubey M, Chhapekar SS, Sharma V, Ramchiary N (2020) Development and characterization of non-coding RNA based simple sequence repeat markers in Capsicum species. Genomics 112(2):1554–1564. https://doi.org/10.1016/j.ygeno.2019.09.005
Kantety RV, La Rota M, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48(5–6):501–510. https://doi.org/10.1023/A:1014875206165
Kong Q, Zhang G, Chen W, Zhang Z, Zou X (2012) Identification and development of polymorphic EST–SSR markers by sequence alignment in pepper, Capsicum annuum (Solanaceae). Am J Bot 99(2):e59–e61. https://doi.org/10.3732/ajb.1100347
Li S, Gan X, Han H, Zhang X, Tian Z (2018) Low within-population genetic diversity and high genetic differentiation among populations of the endangered plant Tetracentron sinense Oliver revealed by inter-simple sequence repeat analysis. Ann For Sci 75(3):1–11. https://doi.org/10.1007/s13595-018-0752-4
Nagaraj SH, Gasser RB, Ranganathan S (2007) A hitchhiker’s guide to expressed sequence tag (EST) analysis. Brief Bioinform 8(1):6–21. https://doi.org/10.1093/bib/bbl015
Nagy I, Stágel A, Sasvári Z, Röder M, Ganal M (2007) Development, characterization, and transferability to other Solanaceae of microsatellite markers in pepper (Capsicum annuum L.). Genome 50(7):668–688. https://doi.org/10.1139/G07-04
Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89(3): 583–590
Page R (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358. https://doi.org/10.1093/bioinformatics/12.4.357
Parida S, Pandit A, Gaikwad K, Sharma T, Srivastava P, Singh N, Mohapatra T (2010) Functionally relevant microsatellites in sugarcane unigenes. BMC Plant Biol 10(1):251. https://doi.org/10.1186/1471-2229-10-251
Parkinson J, Blaxter M (2009) Expressed sequence tags: an overview. Expressed sequence tags (ESTs). Springer, pp 1–12. https://doi.org/10.1007/978-1-60327-136-3_1
Pashley CH, Ellis JR, McCauley DE, Burke JM (2006) EST databases as a source for molecular markers: lessons from Helianthus. J Hered 97(4):381–388. https://doi.org/10.1093/jhered/esl013
Pavlicek A, Hrda S, Flegr J (1999) Free-tree—freeware program for construction of phylogenetic trees on the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application in the RAPD analysis of genus Frenkelia. Folia Biol 45(3):97
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28(19):2537–2539. https://doi.org/10.1093/bioinformatics/bts460
Portis E, Nagy I, Sasvari Z, Stagel A, Barchi L, Lanteri S (2007) The design of Capsicum spp. SSR assays via analysis of in silico DNA sequence, and their potential utility for genetic mapping. Plant Sci 172(3):640–648. https://doi.org/10.1016/j.plantsci.2006.11.016
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959. https://doi.org/10.1093/genetics/155.2.945
Rai VP, Kumar R, Kumar S, Rai A, Kumar S, Singh M, Singh SP, Rai AB, Paliwal R (2013) Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers. Physiol Mol Biol Plants 19(4):575–586. https://doi.org/10.1007/s12298-013-0185-3
Rudd S (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci 8(7):321–329. https://doi.org/10.1016/S1360-1385(03)00131-6
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. 2001. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
Schläpfer P, Zhang P, Wang C, Kim T, Banf M, Chae L, Dreher K, Chavali AK, Nilo-Poyanco R, Bernard T (2017) Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants. Plant Physiol 173(4):2041–2059. https://doi.org/10.1104/pp.16.01942
Schnabel A, Hamrick J (1995) Understanding the population genetic structure of Gleditsia triacanthos L.: the scale and pattern of pollen gene flow. Evolution 49(5):921–931. https://doi.org/10.2307/2410414
Shirasawa K, Ishii K, Kim C, Ban T, Suzuki M, Ito T, Muranaka T, Kobayashi M, Nagata N, Isobe S (2013) Development of Capsicum EST–SSR markers for species identification and in silico mapping onto the tomato genome sequence. Mol Breed 31(1):101–110. https://doi.org/10.1007/s11032-012-9774-z
Singh RB, Singh B, Singh RK (2019) Development of potential dbEST-derived microsatellite markers for genetic evaluation of sugarcane and related cereal grasses. Ind Crops Prod 128:38–47. https://doi.org/10.1016/j.indcrop.2018.10.071
Singh RB, Mahenderakar MD, Jugran AK, Singh RK, Srivastava RK (2020) Assessing genetic diversity and population structure of sugarcane cultivars, progenitor species and genera using microsatellite (SSR) markers. Gene 753:144800. https://doi.org/10.1016/j.gene.2020.144800
Slatkin M (1985) Rare alleles as indicators of gene flow. Evolution 39(1):53–65. https://doi.org/10.2307/2408516
Souframanien J, Gopalakrishna T (2004) A comparative analysis of genetic diversity in blackgram genotypes using RAPD and ISSR markers. Theor Appl Genet 109(8):1687–2169. https://doi.org/10.1007/s00122-004-1797-3
Tsaballa A, Ganopoulos I, Timplalexi A, Aliki X, Bosmali I, Irini N-O, Athanasios T, Madesis P (2015) Molecular characterization of Greek pepper (Capsicum annuum L) landraces with neutral (ISSR) and gene-based (SCoT and EST–SSR) molecular markers. Biochem Syst Ecol 59:256–263. https://doi.org/10.1016/j.bse.2015.02.005
Ukoskit K, Posudsavang G, Pongsiripat N, Chatwachirawong P, Klomsa-ard P, Poomipant P, Tragoonrung S (2018) Detection and validation of EST–SSR markers associated with sugar-related traits in sugarcane using linkage and association mapping. Genomics 111(1):1–9. https://doi.org/10.1016/j.ygeno.2018.03.019
van der Knaap JA, Peter Verrijzer C (2016) Undercover: gene control by metabolites and metabolic enzymes. Genes Dev 30(21):2345–2369. https://doi.org/10.1101/gad.289140.116
Varshney RK, Chabane K, Hendre PS, Aggarwal RK, Graner A (2007a) Comparative assessment of EST–SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci 173(6):638–649. https://doi.org/10.1016/j.plantsci.2007.08.010
Varshney RK, Mahendar T, Aggarwal RK, Börner A (2007) Genic molecular markers in plants: development and applications. Genomics-assisted crop improvement. Springer, pp 13–29. https://doi.org/10.1007/978-1-4020-6295-7_2
Wang J (2005) Estimation of effective population sizes from data on genetic markers. Philos Trans R Soc Lond B Biol Sci 360(1459):1395–1409. https://doi.org/10.1098/rstb.2005.1682
Yan W, Li J, Zheng D, Friedman C, Wang H (2019) Analysis of genetic population structure and diversity in Mallotus oblongifolius using ISSR and SRAP markers. PeerJ 7:e7173. https://doi.org/10.7717/peerj.7173
Yang Q, Fu Y, Wang Y-q, Wang Y, Zhang W-h, Li X-y, Reng Y-Q, Zhang J (2014) Genetic diversity and differentiation in the critically endangered orchid (Amitostigma hemipilioides): implications for conservation. Plant Syst Evol 300(5):871–879. https://doi.org/10.1007/s00606-013-0926-3
Yeh F, Yang R, Boyle T (1999) Microsoft Window-based freeware for population genetic analysis (POPGENE), ver. 1.31. University of Alberta, Canada
Yi G, Lee JM, Lee S, Choi D, Kim B-D (2006) Exploitation of pepper EST–SSRs and an SSR-based linkage map. Theor Appl Genet 114(1):113–130. https://doi.org/10.1007/s00122-006-0415-y
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Authors are thankful to Council of Scientific and Industrial Research (CSIR) for the fellowship (CSIR-RA), DST-PURSE, DBT-BIF, RUSA 2.0 (P3) and Department of Botany, University of Rajasthan for providing necessary facilities.
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Haq, S., Singh, R.B., Gupta, V. et al. Metabolic pathway responsive gene encoding enzyme anchored EST–SSR markers based genetic and population assessment among Capsicum accessions. Genet Resour Crop Evol 70, 1767–1783 (2023). https://doi.org/10.1007/s10722-022-01534-z
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DOI: https://doi.org/10.1007/s10722-022-01534-z