Genetic diversity and relationship of husk tomato (Physalis spp.) from East Java Province revealed by SSR markers
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Abstract. Sadiyah H, Ashari S, Waluyo B, Soegianto A. 2021. Genetic diversity and relationship of husk tomato (Physalis spp.) from East Java Province revealed by SSR markers. Biodiversitas 22: 184-192. This study aimed to investigate the genetic diversity and relationship of Physalis spp. from East Java province, Indonesia. A total of the 33 Physalis accessions was analyzed employing 16 SSR markers. AMOVA, UPGMA clustering, and non-parametric ANOVA analyses were applied. The results showed Genetic diversity in this sample showed lower levels (He =0.171), as compared to other studies of Physalis that used different molecular markers. The dendrogram revealed the presence of five groups, the different species belong to different small groups. The two major groups consist of accessions originated from eastern Java and Madura Island, indicating that there is no significant difference between accessions from both areas although there is geographic isolation in the form of the strait. It is consistent with the low population differentiation and high genetic drift. The AMOVA revealed that 96% of the total variation came from the within-population (among accession), reflect that the accessions used in this study have high variation and valuable for plant improvement through breeding programs. It is recommended that future evaluation studies include more accession from minor accessions detected in the sample of this study to better represent the genetic diversity available in this crop.
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References
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Aljumaili SJ, Rafii MY, Latif MA, et al. 2018. Genetic diversity of aromatic rice germplasm revealed by SSR markers. Biomed Res. Int. 2018: 1–11.
Bohra A, Jha R, Pandey G, et al. 2017 New hypervariable SSR markers for diversity analysis, hybrid purity testing and trait mapping in pigeonpea [Cajanus cajan (L.) Millspaugh]. Front. Plant Sci. 8: 1–15.
Carvalho YGS, Vitorino LC, de Souza UJB, Bessa LA. 2019. Recent trends in research on the genetic diversity of plants: Implications for conservation. Diversity 11: 1–21.
Chacón MI, Sánchez Y del P, Barrero LS. 2016. Genetic structure of a Colombian cape gooseberry (Physalis peruviana L.) collection by means of microsatellite markers. Agron. Colomb. 34: 5–16.
Cobaleda-Velasco M, Alanis-Bañuelos RE, Almaraz-Abarca N, et al. 2017. Phenolic profiles and antioxidant properties of Physalis angulata L. as quality indicators. J. Pharm. Pharmacogn. Res. 5(2): 114–128.
Crossa J, Franco J. 2004. Statistical methods for classifying genotypes. Euphytica 137(1): 19–37.
de Vicente MC, Lopez C, Fulton T, Molina L. 2003. Genetic diversity analysis with molecular marker data: learning module. In: [online] Int. Plant Genet. Resour. Inst. Cornell Univ.
Djakbé JD, Ngakou A, Christian W, et al. 2017. Pollination and yield components of Physalis minima (Solanaceae) as affected by the foraging activity of Apis mellifera (Hymenoptera: Apidae) and compost at Dang (Ngaoundéré, Cameroon). Int. J. Agron. Agric. Res. 11(3): 43–60.
Feng S, Jiang M, Shi Y, et al. 2016. Application of the ribosomal DNA ITS2 region of Physalis (Solanaceae): DNA barcoding and phylogenetic study. Front. Plant Sci. 7: 1–11.
Figueiredo MCC, Passos AR, Hughes FM, et al. 2020. Reproductive biology of Physalis angulata L. (Solanaceae). Sci. Hortic. 267: 1–10.
Garzón-Martínez GA, Osorio-Guarín JA, Delgadillo-Durán P, et al. 2015. Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers. Plant Gene 4: 29–37.
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Govindaraj M, Vetriventhan M, Srinivasan M. 2015. Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet. Res. Int. 2015: 1–14.
Kumar V, Sahay S, Singh RS, et al. 2018. Molecular marker based genetic diversity analysis in cape gooseberry (Physalis peruviana L.). Curr. J. Appl. Sci. Technol. 31(3): 1–6.
Lagos TCB, Cabrera FAV, Escobar HC, Flórez JEM. 2008. Sexual reproduction of the cape gooseberry. Acta Agron. 57: 81–87
Liu K, Muse S V. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9): 2128–2129.
Mason AS. 2015. SSR genotyping. In: Batley J (ed) Plant Genotyping: Methods and Protocols. Springer, New York.
Morales-Saavedra J del C, Zaragoza FAR, Toledo DC, et al. 2019. Agromorphological characterization of wild and weedy populations of Physalis angulata in Mexico. Sci. Hortic. 246: 86–94
Pagare S, Mishra RP, Tripathi N, et al. 2016. Assessment of genetic diversity among different biotypes of Physalis minima. Indian J. Weed Sci. 48(4): 417–420.
Peakall R, Smouse PE. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics 28(19): 2537–9.
Rao VR, Hodgkin T. 2002. Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue Organ Cult. 68: 1–19.
Sadiyah H, Soegianto A, Waluyo B, Ashari S. 2020. Short communication: Preliminary characterization of groundcherry (Physalis angulata) from east Java Province, Indonesia based on morpho-agronomic traits. Biodiversitas 21(2): 759–769.
Simbaqueba J, Sánchez P, Sanchez E, et al. 2011. Development and characterization of microsatellite markers for the cape gooseberry (Physalis peruviana). PLoS One 6:e26719.
Usaizan N, Ashikin N, Abdullah P, Saleh G. 2014. Assessment of genetic diversity of Physalis minima L . (Solanaceae) based on ISSR marker. J. Appl. Sci. Agric. 9: 18–25.
Wei J, Hu X, Yang J, Yang W. 2012. Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers. PLoS One 7:e50164.
Wright, S. 1965. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19: 395–420.
Zamora-Tavares P, Vargas-Ponce O, Sánchez-Martínez J, Cabrera-Toledo D. 2014. Diversity and genetic structure of the husk tomato (Physalis philadelphica Lam.) in Western Mexico. Genet. Resour. Crop. Evol. 62: 141–153.
Aljumaili SJ, Rafii MY, Latif MA, et al. 2018. Genetic diversity of aromatic rice germplasm revealed by SSR markers. Biomed Res. Int. 2018: 1–11.
Bohra A, Jha R, Pandey G, et al. 2017 New hypervariable SSR markers for diversity analysis, hybrid purity testing and trait mapping in pigeonpea [Cajanus cajan (L.) Millspaugh]. Front. Plant Sci. 8: 1–15.
Carvalho YGS, Vitorino LC, de Souza UJB, Bessa LA. 2019. Recent trends in research on the genetic diversity of plants: Implications for conservation. Diversity 11: 1–21.
Chacón MI, Sánchez Y del P, Barrero LS. 2016. Genetic structure of a Colombian cape gooseberry (Physalis peruviana L.) collection by means of microsatellite markers. Agron. Colomb. 34: 5–16.
Cobaleda-Velasco M, Alanis-Bañuelos RE, Almaraz-Abarca N, et al. 2017. Phenolic profiles and antioxidant properties of Physalis angulata L. as quality indicators. J. Pharm. Pharmacogn. Res. 5(2): 114–128.
Crossa J, Franco J. 2004. Statistical methods for classifying genotypes. Euphytica 137(1): 19–37.
de Vicente MC, Lopez C, Fulton T, Molina L. 2003. Genetic diversity analysis with molecular marker data: learning module. In: [online] Int. Plant Genet. Resour. Inst. Cornell Univ.
Djakbé JD, Ngakou A, Christian W, et al. 2017. Pollination and yield components of Physalis minima (Solanaceae) as affected by the foraging activity of Apis mellifera (Hymenoptera: Apidae) and compost at Dang (Ngaoundéré, Cameroon). Int. J. Agron. Agric. Res. 11(3): 43–60.
Feng S, Jiang M, Shi Y, et al. 2016. Application of the ribosomal DNA ITS2 region of Physalis (Solanaceae): DNA barcoding and phylogenetic study. Front. Plant Sci. 7: 1–11.
Figueiredo MCC, Passos AR, Hughes FM, et al. 2020. Reproductive biology of Physalis angulata L. (Solanaceae). Sci. Hortic. 267: 1–10.
Garzón-Martínez GA, Osorio-Guarín JA, Delgadillo-Durán P, et al. 2015. Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers. Plant Gene 4: 29–37.
Gede M, Barancsuk A. 2015. Determining the projection of small scale maps based on graticule line shapes. In: Digital Approaches to Cartographic Heritage; Proceeding of 10th Jubilee Conference + Workshop Digital Approaches to Cartographic Heritage; Corfu, 27-29 May 2015.
Govindaraj M, Vetriventhan M, Srinivasan M. 2015. Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet. Res. Int. 2015: 1–14.
Kumar V, Sahay S, Singh RS, et al. 2018. Molecular marker based genetic diversity analysis in cape gooseberry (Physalis peruviana L.). Curr. J. Appl. Sci. Technol. 31(3): 1–6.
Lagos TCB, Cabrera FAV, Escobar HC, Flórez JEM. 2008. Sexual reproduction of the cape gooseberry. Acta Agron. 57: 81–87
Liu K, Muse S V. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9): 2128–2129.
Mason AS. 2015. SSR genotyping. In: Batley J (ed) Plant Genotyping: Methods and Protocols. Springer, New York.
Morales-Saavedra J del C, Zaragoza FAR, Toledo DC, et al. 2019. Agromorphological characterization of wild and weedy populations of Physalis angulata in Mexico. Sci. Hortic. 246: 86–94
Pagare S, Mishra RP, Tripathi N, et al. 2016. Assessment of genetic diversity among different biotypes of Physalis minima. Indian J. Weed Sci. 48(4): 417–420.
Peakall R, Smouse PE. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics 28(19): 2537–9.
Rao VR, Hodgkin T. 2002. Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue Organ Cult. 68: 1–19.
Sadiyah H, Soegianto A, Waluyo B, Ashari S. 2020. Short communication: Preliminary characterization of groundcherry (Physalis angulata) from east Java Province, Indonesia based on morpho-agronomic traits. Biodiversitas 21(2): 759–769.
Simbaqueba J, Sánchez P, Sanchez E, et al. 2011. Development and characterization of microsatellite markers for the cape gooseberry (Physalis peruviana). PLoS One 6:e26719.
Usaizan N, Ashikin N, Abdullah P, Saleh G. 2014. Assessment of genetic diversity of Physalis minima L . (Solanaceae) based on ISSR marker. J. Appl. Sci. Agric. 9: 18–25.
Wei J, Hu X, Yang J, Yang W. 2012. Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers. PLoS One 7:e50164.
Wright, S. 1965. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19: 395–420.
Zamora-Tavares P, Vargas-Ponce O, Sánchez-Martínez J, Cabrera-Toledo D. 2014. Diversity and genetic structure of the husk tomato (Physalis philadelphica Lam.) in Western Mexico. Genet. Resour. Crop. Evol. 62: 141–153.
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