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Published on: February 20, 2012
Developing single nucleotide polymorphism markers for the identification of pineapple (Ananas comosus) germplasm
Lin Zhou1, Tracie Matsumoto2, Hua-Wei Tan3
1Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center , Beltsville, MD 20705, USA ; College of Horticulture, Nanjing Agricultural University , Nanjing 210095, Jiangsu, China.
Single nucleotide polymorphism (SNP) markers revealed extensive genetic redundancy in pineapple collections, with somatic mutations driving variation. This highlights the need for improved genebank management in pineapple and other clonally propagated crops.
Area of Science:
- * Agricultural Science
- * Genetics
- * Plant Breeding
Background:
- * Pineapple (Ananas comosus) is a globally significant tropical fruit, ranking third after bananas and mangoes.
- * Vegetative propagation in pineapple presents challenges for genebank management and breeding due to genetic redundancy.
Purpose of the Study:
- * To develop and validate single nucleotide polymorphism (SNP) markers for pineapple genetic analysis.
- * To assess the genetic diversity and identify duplicates within a pineapple germplasm collection.
- * To investigate the origins and evolutionary relationships of pineapple cultivars.
Main Methods:
- * Development of 213 SNP markers using expressed sequence tag and nucleotide sequences from public databases.
- * Validation of 96 SNPs by genotyping the USDA-ARS pineapple germplasm collection.
- * Application of multivariate clustering and population stratification analyses.
Main Results:
- * A set of 57 polymorphic SNP markers was identified.
- * A high rate of duplicates (130 out of 170 accessions) was detected, organized into 24 groups.
- * Somatic mutation was identified as the primary source of intra-cultivar variation.
- * Evidence suggests modern cultivars originate from different wild Ananas varieties, with A. comosus var. bracteatus and A. comosus var. ananassoides as likely progenitors.
- * Traditional horticultural classifications were not strongly supported by the genetic data.
Conclusions:
- * Developed SNP markers are effective tools for pineapple DNA fingerprinting, germplasm management, and cultivar protection.
- * The high genetic redundancy underscores the need for advanced genotyping technologies in managing clonally propagated crops.
- * Genetic analysis provides new insights into pineapple cultivar origins, challenging traditional classifications.
