1 3 Mol Genet Genomics DOI 10.1007/s00438-015-1003-0 ORIGINAL PAPER Genetic diversity and association mapping of bacterial blight and other horticulturally important traits with microsatellite markers in pomegranate from India Nripendra Vikram Singh · Venkata Lakshmi Abburi · D. Ramajayam · Ravinder Kumar · Ram Chandra · Kuldeep Kumar Sharma · Jyotsana Sharma · K. Dhinesh Babu · Ram Krishna Pal · Dhananjay M. Mundewadikar · Thangasamy Saminathan · Robert Cantrell · Padma Nimmakayala · Umesh K. Reddy Received: 6 January 2015 / Accepted: 27 January 2015 © Springer-Verlag Berlin Heidelberg 2015 cultivated pomegranate collections from India. Our study placed all 88 germplasm into four clusters. We identified a cultivated clade of pomegranates in close proximity to Daru types of wild-type pomegranates that grow naturally near the foothills of the Himalayas. Admixture analysis sorted various lineages of cultivated pomegranates to their respec- tive ancestral forms. We identified four linked markers for fruit weight, titratable acidity and bacterial blight sever- ity. PGCT001 was found associated with both fruit weight and bacterial blight, and the association with fruit weight during both seasons analyzed was significant after Bonfer- roni correction. This research demonstrates effectiveness of microsatellites to resolve population structure among the wild and cultivar collection of pomegranates and future use for association mapping studies. Keywords Heterozygosity · Population structure · Association mapping · Fruit quality · Bacterial blight · Pomegranate Introduction Pomegranate (Punica granatum L.) of the Lythraceae family is one of the oldest edible fruit known to humans and grows naturally in India, Afghanistan and Syria; it is a native of Iran. The fruit was domesticated around 2000 BC (Rana et al. 2007). Although pomegranate is widely adapted across the world, the five major produc- ers of pomegranate are India, Iran, China, the USA and Turkey (Holland and Bar-Ya’akov 2014; Teixeira da Silva et al. 2013). India gained importance in cultivation of pomegranate after 1986; thereafter, it steadily increased to become first in cultivation at the global level, with approximately 113 thousand ha under cultivation and Abstract This genetic diversity study aimed to estimate the population structure and explore the use of association mapping strategies to identify linked markers for bacterial resistance, growth and fruit quality in pomegranate col- lections from India. In total, 88 accessions including 37 cultivated types were investigated. A total of 112 alleles were amplified by use of 44 publicly available microsatel- lites for estimating molecular genetic diversity and popu- lation structure. Neighbor-joining analysis, model-based population structure and principal component analysis cor- roborated the genetic relationships among wild-type and Communicated by S. Hohmann. Electronic supplementary material The online version of this article (doi:10.1007/s00438-015-1003-0) contains supplementary material, which is available to authorized users. N. V. Singh · R. Chandra · K. K. Sharma · J. Sharma · K. D. Babu · R. K. Pal ICAR-National Research Center on Pomegranate, Kegaon, Solapur, Maharashtra 413255, India V. L. Abburi · T. Saminathan · R. Cantrell · P. Nimmakayala · U. K. Reddy Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USA D. Ramajayam ICAR-Indian Institute of Oil Palm Research, Pedavegi, West Godavari, Andhra Pradesh 534450, India R. Kumar ICAR-Sugarcane Breeding Institute’s Regional Centre, Karnal, Haryana 132 001, India D. M. Mundewadikar · U. K. Reddy (*) MGM’s Institute of Biosciences and Technology, Aurangabad, Maharashtra 431 003, India e-mail: ureddy@wvstateu.edu