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Assessment of the genetic diversity and population structure of apricot (Prunus armeniaca L.) germplasm of the Northwestern Himalaya using SSR markers

Published online by Cambridge University Press:  17 September 2021

Aijaz A. Wani Open the ORCID record for Aijaz A. Wani [Opens in a new window] ,
Khalid Hussain ,
Showkat A. Zargar Open the ORCID record for Showkat A. Zargar [Opens in a new window] ,
Faizan Ahmad ,
Reetika Mahajan ,
Sajad Majeed Zargar Open the ORCID record for Sajad Majeed Zargar [Opens in a new window]  and
Anzar A. Khuroo
Aijaz A. Wani*
Affiliation:
Cytogenetics and Reproductive Biology Laboratory, Department of Botany, University of Kashmir, Srinagar 190006, J & K, India
Khalid Hussain
Affiliation:
Department of Botany, Centre for Biodiversity & Taxonomy, University of Kashmir, Srinagar190006, J & K, India
Showkat A. Zargar
Affiliation:
Cytogenetics and Reproductive Biology Laboratory, Department of Botany, University of Kashmir, Srinagar 190006, J & K, India Department of Botany, Punjabi University, Patiala, Punjab 147002, India
Faizan Ahmad
Affiliation:
Krishi Vigyan Kendra, SKUAST-K, Kargil, Ladakh 194103, J & K, India
Reetika Mahajan
Affiliation:
Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology, Shalimar, Srinagar, J & K, India
Sajad Majeed Zargar
Affiliation:
Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology, Shalimar, Srinagar, J & K, India
Anzar A. Khuroo
Affiliation:
Department of Botany, Centre for Biodiversity & Taxonomy, University of Kashmir, Srinagar190006, J & K, India
*
Author for correspondence: Aijaz A. Wani, E-mail: aijazbotku@gmail.com, aawani@kashmiruniversity.ac.in
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Abstract

Apricot is considered an ecologically and economically important tree species of the stone-fruit crops that is widely grown in temperate regions of the world. Very few studies on apricot genetic diversity assessment have been carried out from the regions of Kashmir and Ladakh. In this backdrop, the present study was carried out to analyse the genetic diversity and population structure of 120 apricot genotypes collected from both the regions using 21 SSR markers. A total of 52 alleles were amplified with average values of marker index (MI) = 0.7084, resolving power (RP) = 2.8690, polymorphism information content (PIC) = 0.3132, Na = 2.317, Ne = 1.720, I = 0.572, Ho = 0.284, He = 0.360 and an average polymorphism of 91.2% per assay indicating high level of genetic diversity. The neighbour-joining (NJ) dendrogram generated three main clusters among selected apricot genotypes independent of their geographical locations. Interestingly, the result of the dendrogram coincides with the results of structure analysis which showed that the 120 apricot genotypes could be assigned to three (K = 3) sub-populations and the grouping of genotypes did not follow their geographical location suggesting that they share the same genetic pool. Moreover, analysis of molecular variance showed that 73% of the variation was attributed to differences within the individuals, 25% among individuals while only 2% of the variation was observed among the populations. The present study represents the most comprehensive analysis of the genetic diversity and population structure of apricot genotypes in Kashmir and Ladakh regions of India.

Keywords

AMOVAapricotgenetic diversityheterozygositySSRstructure analysis
Type
Research Article
Information
Plant Genetic Resources , Volume 19 , Issue 5 , October 2021 , pp. 384 - 393
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of NIAB

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References

Abdul, K, Ram, RB, Dwivedi, SK, Dwivedi, DH and Meena, ML (2016) Genetic variability, heritability and genetic advance studies for physico-chemical characters of apricot germplasm under Ladakh region. Progressive Horticulture 48, 22–27.Google Scholar
Ai, PF, Zhen, ZJ and Jin, ZZ (2011) Genetic diversity and relationships within sweet kernel apricot and related Armeniaca species based on sequence-related amplified polymorphism markers. Biochemical Systematics and Ecology 39, 694–699.10.1016/j.bse.2011.05.026CrossRefGoogle Scholar
Angmo, P, Angmo, S, Upadhyay, SS, Targais, K, Kumar, B and Stobdan, T (2017) Apricots (Prunus armeniaca L.) of trans-Himalayan Ladakh: potential candidate for fruit quality breeding programs. Scientia Horticulturae 218, 187–192.10.1016/j.scienta.2017.02.032CrossRefGoogle Scholar
Bakır, M, Dumanoğlu, H, Erdoğan, V, Ernim, C and Macit, T (2019) Characterization of wild apricot (Prunus armeniaca L.) genotypes selected from Cappadocia region (Nevşehir-Turkey) by SSR markers. Journal of Agricultural Sciences 25, 498–507.Google Scholar
Bhat, MY, Padder, BA, Wani, IA, Banday, FA, Ahsan, H, Dar, MA and Lone, A (2013) Evaluation of apricot cultivars based on physicochemical characteristics observed under temperate conditions. International Journal of Agricultural Science 3, 535–537.Google Scholar
Bourguiba, H, Krichen, L, Audergon, JM, Khadari, B and Trifi-Farah, N (2010 a) Impact of mapped SSR markers on the genetic diversity of apricot (Prunus armeniaca L.) in Tunisia. Plant Molecular Biology Reporter 28, 578–587.10.1007/s11105-010-0189-xCrossRefGoogle Scholar
Bourguiba, H, Khadari, B, Krichen, L, Trifi-Farah, N, Santoni, S and Audergon, JM (2010 b) Grafting versus seed propagated apricot populations: two main gene pools in Tunisia evidenced by SSR markers and model-based Bayesian clustering. Genetica 138, 1023–1032.10.1007/s10709-010-9488-2CrossRefGoogle ScholarPubMed
Bourguiba, H, Audergon, JM, Krichen, L, Trifi-Farah, N, Mamouni, A, Trabelsi, S and Khadari, B (2012) Genetic diversity and differentiation of grafted and seed propagated apricot (Prunus armeniaca L.) in the Maghreb region. Scientia Horticulturae 142, 7–13.10.1016/j.scienta.2012.04.024CrossRefGoogle Scholar
Bourguiba, H, Batnini, MA, Krichen, L, Trifi-Farah, N and Audergon, JM (2017) Population structure and core collection construction of apricot (Prunus armeniaca L.) in North Africa based on microsatellite markers. Plant Genetic Resources 15, 21.10.1017/S1479262115000313CrossRefGoogle Scholar
Bourguiba, H, Scotti, I, Sauvage, C, Zhebentyayeva, T, Ledbetter, C, Krška, B, Remay, A, D'Onofrio, C, Iketani, H, Christen, D, Krichen, L, Trifi-Farah, N, Liu, W, Roch, G and Audergon, J-M (2020) Genetic structure of a worldwide germplasm collection of Prunus armeniaca L. Reveals three major diffusion routes for varieties coming from the Species’ Center of Origin. Frontiers in Plant Science 11, 638.10.3389/fpls.2020.00638CrossRefGoogle ScholarPubMed
Chen, J, Dong, S, Zhang, X, Wu, Y, Zhang, H, Sun, Y and Zhang, J (2021) Genetic diversity of Prunus sibirica L. superior accessions based on the SSR markers developed using restriction-site associated DNA sequencing. Genetic Resources and Crop Evolution 68, 615–628.10.1007/s10722-020-01011-5CrossRefGoogle Scholar
Dar, AA and Mahajan, R, Lay, P and Sharma, S (2017) Genetic diversity and population structure of Cucumis sativus L. by using SSR markers. 3 Biotech 7, 307.10.1007/s13205-017-0944-xCrossRefGoogle ScholarPubMed
Dauthy, ME (1995) Fruit and Vegetables Processing, FAO agriculture services bulletins 119. Rome: FAO.Google Scholar
Dettori, MT, Micali, S, Giovinazzi, J, Scalabrin, S, Verde, I and Cipriani, G (2015) Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species. SpringerPlus 4, 337.10.1186/s40064-015-1098-0CrossRefGoogle ScholarPubMed
Dida, MM, Wanyera, N, Dunn, MLH, Bennetzen, JL and Devos, KM (2008) Population structure and diversity in finger millet (Eleusine coracana) germplasm. Tropical Plant Biology 1, 131–141.10.1007/s12042-008-9012-3CrossRefGoogle Scholar
Dokupilová, I, Sturdik, E and Mihálik, D (2013) Characterization of vine varieties by SSR markers. Acta Chimica Slovaca 6, 227–234.10.2478/acs-2013-0035CrossRefGoogle Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14, 2611–2620.CrossRefGoogle ScholarPubMed
Faust, M, Suranyi, D and Nyujto, F (1998) Origin and dissemination of apricot. Horticultural Reviews-Westport Then New York 22, 225–260.Google Scholar
Fernandez, A, Marti, J, Alonso, M, Espiau, M, Rubio, M and Socias, R (2009) Genetic diversity in Spanish and foreign almond germplasm assessed by molecular characterization with simple sequence repeats. Journal of American Society for Horticultural Science 134, 535–542.10.21273/JASHS.134.5.535CrossRefGoogle Scholar
Girish, K, Tsering, S, Dwivedi, SK, Ashish, Y and Srivastava, RB (2012) Pomological and fruit quality characteristics of Halman and Raktsey-Karpo apricot cultivars of trans-Himalayan Ladakh region, India. Progressive Horticulture 44, 211–214.Google Scholar
Goldstein, DB and Pollock, DD (1997) Launching microsatellites: a review of mutation processes and methods of phylogenetic inference. Journal of Heredity 88, 335–342.10.1093/oxfordjournals.jhered.a023114CrossRefGoogle Scholar
Gupta, PK and Varshney, RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113, 163–185.CrossRefGoogle Scholar
Gürcan, K, Öcal, N, Yılmaz, KU, Ullah, S, Erdoğan, A and Zengin, Y (2015) Evaluation of Turkish apricot germplasm using SSR markers: genetic diversity assessment and search for plum pox virus resistance alleles. Scientia Horticulturae 193, 155–164.CrossRefGoogle Scholar
Hormaza, JI (2002) Molecular characterization and similarity relationships among apricot (Prunus armeniaca L.) genotypes using simple sequence repeats. Theoretical and Applied Genetics 104, 321–328.10.1007/s001220100684CrossRefGoogle ScholarPubMed
Hu, X, Zheng, P, Ni, B, Miao, X, Zhao, Z and Li, M (2018) Population genetic diversity and structure analysis of wild apricot (Prunus armeniaca L.) revealed by SSR markers in the Tien-Shan mountains of China. Pakistan Journal of Botany 50, 609–615.Google Scholar
Hurtado, MA, Westman, A, Beck, E, Abbott, GA, Llácer, G and Badenes, ML (2002) Genetic diversity in apricot cultivars based on AFLP markers. Euphytica 127, 297–301.10.1023/A:1020206601328CrossRefGoogle Scholar
Khadivi-Khub, A, Yarahmadi, M, Jannatizadeh, A and Ebrahimi, A (2015) Genetic relationships and diversity of common apricot (Prunus armeniaca L.) based on simple sequence repeat (SSR) markers. Biochemical Systematics and Ecology 61, 366–371.10.1016/j.bse.2015.07.006CrossRefGoogle Scholar
Kostina, KF (1964) Application the phytogeographical method to apricot classification (in Russian). In: Proceedings (Trudi) of the Nikita Botanical Gardens, Moscow, p. 24.Google Scholar
Krichen, L, Audergon, JM and Trifi-Farah, N (2014) Assessing the genetic diversity and population structure of Tunisian apricot germplasm. Scientia Horticulturae 172, 86–100.10.1016/j.scienta.2014.03.038CrossRefGoogle Scholar
Kumar, M, Mishra, GP, Singh, R, Kumar, J, Naik, PK and Singh, SB (2009 a) Correspondence of ISSR and RAPD markers for comparative analysis of genetic diversity among different apricot genotypes from cold arid deserts of trans-Himalayas. Physiology and Molecular Biology of Plants 15, 225.10.1007/s12298-009-0026-6CrossRefGoogle ScholarPubMed
Kumar, M, Mishra, GP, Singh, R, Naik, PK, Dwivedi, S, Ahmad, Z and Singh, SB (2009 b) Genetic variability studies among apricot populations from cold arid desert of Ladakh using DNA markers. Indian Journal of Horticulture 66, 147–153.Google Scholar
Kumar, D, Lal, S and Ahmed, N (2015) Morphological and pomological diversity among apricot (Prunus armeniaca L.) genotypes grown in India. Indian Journal of Agricultural Science 85, 1349–1355.Google Scholar
Lamia, K, Hedia, B, Jean-Marc, A and Neila, TF (2010) Comparative analysis of genetic diversity in Tunisian apricot germplasm using AFLP and SSR markers. Scientia Horticulturae 127, 54–63.10.1016/j.scienta.2010.09.012CrossRefGoogle Scholar
Layne, REC, Bailey, CH and Hough, LF (1996) Apricot. In Janick, J and Moore, JN (eds), Fruit Breeding, vol. 1. Tree and Tropical Fruits. New York, USA: John Wiley and Sons, pp. 79–111.Google Scholar
Li, M, Zhao, Z, Miao, X and Zhou, J (2014) Genetic diversity and population structure of Siberian apricot (Prunus sibirica L.) in China. International Journal of Molecular Sciences 15, 377–400.CrossRefGoogle Scholar
Li, W, Liu, L, Wang, Y, Zhang, Q, Fan, G, Zhang, S, Wang, Y and Liao, K (2020) Genetic diversity, population structure, and relationships of apricot (Prunus) based on restriction site-associated DNA sequencing. Horticulture Research 7, 1–13.10.1038/s41438-020-0284-6CrossRefGoogle ScholarPubMed
Liu, K and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics (Oxford, England) 21, 2128–2129.10.1093/bioinformatics/bti282CrossRefGoogle ScholarPubMed
Malik, SK, Chaudhury, R, Dhariwal, OP and Mir, S (2010) Genetic diversity and traditional uses of wild apricot (Prunus armeniaca L.) in high-altitude north-western Himalayas of India. Plant Genetic Resources 8, 249–257.10.1017/S1479262110000304CrossRefGoogle Scholar
Martínez-Mora, C, Rodríguez, J, Cenis, JL and Ruiz García, L (2009) Genetic variability among local apricots (Prunus armeniaca L.) from the Southeast of Spain. Spanish Journal of Agricultural Research 7, 855–868.CrossRefGoogle Scholar
Messina, R, Lain, O, Marrazzo, MT, Cipriani, G and Testolin, R (2004) New set of microsatellite loci isolated in apricot. Molecular Ecology Notes 4, 432–434.10.1111/j.1471-8286.2004.00674.xCrossRefGoogle Scholar
Mir, JI, Ahmed, N, Rashid, R, Wani, SH, Sheikh, MA, Mir, H, Parveen, I and Shah, S (2012) Genetic diversity analysis in apricot (Prunus armeniaca L.) germplasms using RAPD markers. Indian Journal of Biotechnology 11, 187–190.Google Scholar
Mishra, GP (2009) Correspondence of DNA markers for genetic diversity studies among different apricot genotypes from cold arid deserts of Ladakh. DRDO Science Spectrum 151–156.Google Scholar
Peakall, R and Smouse, PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and researchdan update. Bioinformatics (Oxford, England) 28, 2537–2539.10.1093/bioinformatics/bts460CrossRefGoogle ScholarPubMed
Perrier, X and Jacquemoud-Collet, JP (2006) DARwin software. Available at http://darwin.cirad.fr/darwin (Accessed 20 June 2019).Google Scholar
Powell, W, Morgante, M, Andre, C, Hanafey, M, Vogel, J, Tingey, S and Rafalski, A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding 2, 225–238.10.1007/BF00564200CrossRefGoogle Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945–959.10.1093/genetics/155.2.945CrossRefGoogle ScholarPubMed
Raji, R, Jannatizadeh, A, Fattahi, R and Esfahlani, MA (2014) Investigation of variability of apricot (Prunus armeniaca L.) using morphological traits and microsatellite markers. Scientia Horticulturae 176, 225–231.10.1016/j.scienta.2014.06.033CrossRefGoogle Scholar
Ramakrishnan, M, Ceasar, SA, Duraipandiyan, V, Al-Dhabi, NA and Ignacimuthu, S (2016) Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers. SpringerPlus 5, 120.10.1186/s40064-015-1626-yCrossRefGoogle ScholarPubMed
Sharma, JK (2000) Morphological studies on apricot and its wild relatives. Journal of Hill Research 13, 5–10.Google Scholar
Sofi, AA, Zaffar, G and Mir, MS (2001) Genetic variability and association of component characters for fruit weight in apricot (Prunus armeniaca L.) cultivars of Kargil (Ladakh). Indian Journal of Horticulture 58, 239–243.Google Scholar
Tian-Ming, H, Xue-Sen, C, Zheng, X, Jiang-Sheng, G, Pei-Jun, L, Wen, L, Qing, L and Yan, W (2007) Using SSR markers to determine the population genetic structure of wild apricot (Prunus armeniaca L.) in the Ily Valley of West China. Genetic Resource and Crop Evolution 54, 563–572.10.1007/s10722-006-0013-5CrossRefGoogle Scholar
Vavilov, NI (1951) The origin, variation, immunity and breeding of cultivated plants; selected writings. Chronica botanica 13, 1–6.Google Scholar
Vilanova, S, Soriano, JM, Lalli, DA, Romero, C, Abbott, AG, Llácer, G and Badenes, ML (2006) Development of SSR markers located in the G1 linkage group of apricot (Prunus armeniaca L.) using a bacterial artificial chromosome library. Molecular Ecology Notes 6, 789–791.CrossRefGoogle Scholar
Wang, Z, Kang, M, Liu, H, Gao, J, Zhang, Z, Li, Y, Wu, R and Pang, X (2014) High-level genetic diversity and complex population structure of Siberian apricot (Prunus sibirica L.) in China as revealed by nuclear SSR markers. PLoS One 9, e87381.10.1371/journal.pone.0087381CrossRefGoogle ScholarPubMed
Wani, AA, Zargar, SA, Malik, AH, Kashtwari, M, Nazir, M, Khuroo, AA, Ahmad, F and Dar, TA (2017) Assessment of variability in morphological characters of apricot germplasm of Kashmir, India. Scientia Horticulturae 225, 630–637.10.1016/j.scienta.2017.07.029CrossRefGoogle Scholar
Wright, S (1951) The genetic structure of populations. Annals of Eugenics 15, 323–354.10.1111/j.1469-1809.1949.tb02451.xCrossRefGoogle Scholar
Wünsch, A (2009) Cross-transferable polymorphic SSR loci in Prunus species. Scientia Horticulturae 120, 348–352.CrossRefGoogle Scholar
Yilmaz, KU, Paydas-Kargi, S, Dogan, Y and Kafkas, S (2012) Genetic diversity analysis based on ISSR, RAPD and SSR among Turkish Apricot Germplasms in Iran Caucasian eco-geographical group. Scientia Horticulturae 138, 138–143.10.1016/j.scienta.2012.02.017CrossRefGoogle Scholar
Zaffar, G, Mir, MS and Sofi, AA (2004) Genetic divergence among apricot (Prunus armeniaca L.) genotypes of Kargil, Ladakh. Indian Journal of Horticulture 61, 6–9.Google Scholar
Zhou, Q, Mu, K, Ni, Z, Liu, X, Li, Y and Xu, LA (2020) Analysis of genetic diversity of ancient Ginkgo populations using SSR markers. Industrial Crops and Products 145, 111942.10.1016/j.indcrop.2019.111942CrossRefGoogle Scholar
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