title: Genetic diversity and association mapping of bacterial blight and other horticulturally important traits with microsatellite markers in pomegranate from India.
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 collections 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 microsatellites for estimating molecular genetic diversity and population structure. Neighbor-joining analysis, model-based population structure and principal component analysis corroborated the genetic relationships among wild-type and 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 respective ancestral forms. We identified four linked markers for fruit weight, titratable acidity and bacterial blight severity. PGCT001 was found associated with both fruit weight and bacterial blight, and the association with fruit weight during both seasons analyzed was significant after Bonferroni 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.
authors: ICAR-National Research Center on Pomegranate, Kegaon, Solapur, Maharashtra, 413255, India.
authors: Nripendra Vikram
authors: NV
authors: Singh
authors: Venkata Lakshmi
authors: VL
authors: Abburi
authors: D
authors: D
authors: Ramajayam
authors: Ravinder
authors: R
authors: Kumar
authors: Ram
authors: R
authors: Chandra
authors: Kuldeep Kumar
authors: KK
authors: Sharma
authors: Jyotsana
authors: J
authors: Sharma
authors: K Dhinesh
authors: KD
authors: Babu
authors: Ram Krishna
authors: RK
authors: Pal
authors: Dhananjay M
authors: DM
authors: Mundewadikar
authors: Thangasamy
authors: T
authors: Saminathan
authors: Robert
authors: R
authors: Cantrell
authors: Padma
authors: P
authors: Nimmakayala
authors: Umesh K
authors: UK
authors: Reddy
mesh_terms: D000704:Analysis of Variance; D002874:Chromosome Mapping; D016000:Cluster Analysis; D060467:Disease Resistance / Q000235:genetics; D051456:Gene Flow; D014644:Genetic Variation; D005828:Genetics, Population; D054884:Host-Pathogen Interactions; D007194:India; D029561:Lythraceae / Q000145:classification / Q000235:genetics* / Q000382:microbiology; D018895:Microsatellite Repeats / Q000235:genetics*; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D025341:Principal Component Analysis; D012621:Seasons; D013045:Species Specificity; D053532:Xanthomonas axonopodis / Q000502:physiology