Developing Single Nucleotide Polymorphism (SNP) markers for the identification of pineapple (Ananas comosus) germplasm

Authors: ZHOU, LIN - Nanjing Agricultural University; Matsumoto Brower, Tracie; TAN, HUAWEI - Nanjing Agricultural University; Meinhardt, Lyndel; Mischke, Barbara; WANG, BOYI - Yunan Academy Of Agricultural Sciences; Zhang, Dapeng

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/19/2015
Publication Date: 12/19/2015
Citation: Zhou, L., Matsumoto Brower, T.K., Tan, H., Meinhardt, L.W., Mischke, B.S., Wang, B., Zhang, D. 2015. Developing Single Nucleotide Polymorphism (SNP) markers for the identification of pineapple (Ananas comosus) germplasm. Horticulture Research. 2:15056.

Interpretive Summary: Pineapple is the third most important tropical fruit in the world after banana and mango and a major agricultural commodity in Hawaii. Like many tropical perennial crops, most of the pineapple germplasm is maintained in field genebanks. But records and labels of the cultivars have not always been properly maintained and accessions often arrive bearing limited information about their correct identity. In the present study, we developed a set of single nucleotide polymorphism (SNP) markers and used them to genotype the USDA ARS pineapple germplasm collection, maintained in Hilo, Hawaii. The validation led to the designation of 57 SNP markers that unambiguously identified all tested pineapple cultivars. Multiple trees belonging to the same clone were verified and duplicated clones were identified. Our results revealed insight into the relationship among and origin of modern pineapple cultivars. These SNP markers offer good potential for manage pineapple genetic resources, with accurate and efficient cultivar identification. This information will be used by researchers, pineapple producers and pineapple industry to improve the accuracy in germplasm management, breeding, and plant material propagation.

Technical Abstract: Pineapple (Ananas comosus [L.] Merr.) is the third most important tropical fruit in the world after banana and mango and a major agricultural commodity in Hawaii. As a crop with vegetative propagation, genetic redundancy is a major challenge for efficient genebank management and in breeding. Using EST and nucleotide sequences from public databases, we developed 213potential nucleotide polymorphism (SNP) markers. The USDA ARS pineapple germplasm collection, maintained in Hilo, Hawaii, was used to validate 96 of these markers for cultivar identification, resulting in designation of a set of 57SNP markers that identified all tested pineapple cultivars. The SNP fingerprints revealed a high rate of duplicates in this pineapple collection. Twenty-four groups of duplicate accessions were detected, encompassing 133 of the total 174 Ananas cosmosaccessions in the collection. The results suggest that somatic mutation has been the main source of intra-cultivar variations in pineapple. Sixty-three per percent of the collection (109 accessions) are either somatic mutation groups or are duplicates, thus could be further reduced for the purpose of long term conservation. Multivariate clustering and a model-based population stratification revealed genetic relationships among the analyzed accessions, indicating that the modern pineapple cultivars are comprised of progenies derived from different wild Ananasbotanical accessions. Parentage analysis further revealed that both A. comosus var. bracteatus and A. comosus var. ananassoides are likely progenitors of pineapple cultivars. However, the traditional classification of cultivated pineapple into horticultural groups (e.g. “Cayenne”, “Spanish”, “Queen”) was not well-supported by the present study. These SNP markers offer good potential for manage pineapple genetic resources, with accurate and efficient genotype identification. The high rate of genetic redundancy detected in this collection, suggests the potential impact of applying this technology on other tropical perennial crops.