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Developing single nucleotide polymorphism markers for the identification of pineapple (Ananas comosus) germplasm.

Zhou L, Matsumoto T, Tan HW, Meinhardt LW, Mischke S, Wang B, Zhang D - Hortic Res (2015)

Bottom Line: The validation resulted in designation of a set of 57 polymorphic SNP markers that revealed a high rate of duplicates in this pineapple collection.The results show that somatic mutation has been the main source of intra-cultivar variations in pineapple.These SNP markers provide robust and universally comparable DNA fingerprints; thus, they can serve as an efficient genotyping tool to assist pineapple germplasm management, propagation of planting material, and pineapple cultivar protection.

View Article: PubMed Central - PubMed

Affiliation: Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center , Beltsville, MD 20705, USA ; College of Horticulture, Nanjing Agricultural University , Nanjing 210095, Jiangsu, China.

ABSTRACT
Pineapple (Ananas comosus [L.] Merr.) is the third most important tropical fruit in the world after banana and mango. As a crop with vegetative propagation, genetic redundancy is a major challenge for efficient genebank management and in breeding. Using expressed sequence tag and nucleotide sequences from public databases, we developed 213 single nucleotide polymorphism (SNP) markers and validated 96 SNPs by genotyping the United States Department of Agriculture - Agricultural Research Service pineapple germplasm collection, maintained in Hilo, Hawaii. The validation resulted in designation of a set of 57 polymorphic SNP markers that revealed a high rate of duplicates in this pineapple collection. Twenty-four groups of duplicates were detected, encompassing 130 of the total 170 A cosmos accessions. The results show that somatic mutation has been the main source of intra-cultivar variations in pineapple. Multivariate clustering and a model-based population stratification suggest that the modern pineapple cultivars are comprised of progenies that are derived from different wild Ananas botanical varieties. 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 provide robust and universally comparable DNA fingerprints; thus, they can serve as an efficient genotyping tool to assist pineapple germplasm management, propagation of planting material, and pineapple cultivar protection. The high rate of genetic redundancy detected in this pineapple collection suggests the potential impact of applying this technology on other clonally propagated perennial crops.

No MeSH data available.


Inferred clusters in the pineapple accessions varieties using STRUCTURE in the overall analyzed pineapple accessions. Each vertical line represents one individual multilocus genotype. Individuals with multiple colors have admixed genotypes from multiple clusters. Each color represents the most likely ancestry of the cluster from which the genotype or partial genotype was derived. Clusters of individuals are represented by colors.
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fig4: Inferred clusters in the pineapple accessions varieties using STRUCTURE in the overall analyzed pineapple accessions. Each vertical line represents one individual multilocus genotype. Individuals with multiple colors have admixed genotypes from multiple clusters. Each color represents the most likely ancestry of the cluster from which the genotype or partial genotype was derived. Clusters of individuals are represented by colors.

Mentions: Population stratification of the 64 accessions, based on ΔK value computed by STRUCTURE HARVESTER, revealed two clusters as the most probable number of K (Figures 3 and 4) and this partitioning was largely compatible with the cluster analysis (Figure 2). All the accessions related to var. ananassoides were assigned to one Bayesian cluster, whereas the cultivated germplasm, as well as vars. bracteatus and erectifolius, were grouped in a different cluster. The F1 hybrid of Wild Brazil × Plot 520 was confirmed by analysis with STRUCTURE. In addition, several accessions were classified as hybrids of the two clusters, such as N94-92, F1 Ananassoides × Plot 435, Wild Brazil × Cayenne Lot 520, and Cb 32 (Figures 3 and 4). The result of assignment by STRUCTURE is largely compatible with the result of clustering analysis (Figure 4). All the accessions assigned by STRUCTURE in the cluster of var. ananassoides or its hybrids were in the first cluster of the NJ tree.


Developing single nucleotide polymorphism markers for the identification of pineapple (Ananas comosus) germplasm.

Zhou L, Matsumoto T, Tan HW, Meinhardt LW, Mischke S, Wang B, Zhang D - Hortic Res (2015)

Inferred clusters in the pineapple accessions varieties using STRUCTURE in the overall analyzed pineapple accessions. Each vertical line represents one individual multilocus genotype. Individuals with multiple colors have admixed genotypes from multiple clusters. Each color represents the most likely ancestry of the cluster from which the genotype or partial genotype was derived. Clusters of individuals are represented by colors.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4660223&req=5

fig4: Inferred clusters in the pineapple accessions varieties using STRUCTURE in the overall analyzed pineapple accessions. Each vertical line represents one individual multilocus genotype. Individuals with multiple colors have admixed genotypes from multiple clusters. Each color represents the most likely ancestry of the cluster from which the genotype or partial genotype was derived. Clusters of individuals are represented by colors.
Mentions: Population stratification of the 64 accessions, based on ΔK value computed by STRUCTURE HARVESTER, revealed two clusters as the most probable number of K (Figures 3 and 4) and this partitioning was largely compatible with the cluster analysis (Figure 2). All the accessions related to var. ananassoides were assigned to one Bayesian cluster, whereas the cultivated germplasm, as well as vars. bracteatus and erectifolius, were grouped in a different cluster. The F1 hybrid of Wild Brazil × Plot 520 was confirmed by analysis with STRUCTURE. In addition, several accessions were classified as hybrids of the two clusters, such as N94-92, F1 Ananassoides × Plot 435, Wild Brazil × Cayenne Lot 520, and Cb 32 (Figures 3 and 4). The result of assignment by STRUCTURE is largely compatible with the result of clustering analysis (Figure 4). All the accessions assigned by STRUCTURE in the cluster of var. ananassoides or its hybrids were in the first cluster of the NJ tree.

Bottom Line: The validation resulted in designation of a set of 57 polymorphic SNP markers that revealed a high rate of duplicates in this pineapple collection.The results show that somatic mutation has been the main source of intra-cultivar variations in pineapple.These SNP markers provide robust and universally comparable DNA fingerprints; thus, they can serve as an efficient genotyping tool to assist pineapple germplasm management, propagation of planting material, and pineapple cultivar protection.

View Article: PubMed Central - PubMed

Affiliation: Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center , Beltsville, MD 20705, USA ; College of Horticulture, Nanjing Agricultural University , Nanjing 210095, Jiangsu, China.

ABSTRACT
Pineapple (Ananas comosus [L.] Merr.) is the third most important tropical fruit in the world after banana and mango. As a crop with vegetative propagation, genetic redundancy is a major challenge for efficient genebank management and in breeding. Using expressed sequence tag and nucleotide sequences from public databases, we developed 213 single nucleotide polymorphism (SNP) markers and validated 96 SNPs by genotyping the United States Department of Agriculture - Agricultural Research Service pineapple germplasm collection, maintained in Hilo, Hawaii. The validation resulted in designation of a set of 57 polymorphic SNP markers that revealed a high rate of duplicates in this pineapple collection. Twenty-four groups of duplicates were detected, encompassing 130 of the total 170 A cosmos accessions. The results show that somatic mutation has been the main source of intra-cultivar variations in pineapple. Multivariate clustering and a model-based population stratification suggest that the modern pineapple cultivars are comprised of progenies that are derived from different wild Ananas botanical varieties. 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 provide robust and universally comparable DNA fingerprints; thus, they can serve as an efficient genotyping tool to assist pineapple germplasm management, propagation of planting material, and pineapple cultivar protection. The high rate of genetic redundancy detected in this pineapple collection suggests the potential impact of applying this technology on other clonally propagated perennial crops.

No MeSH data available.