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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.


Somaclonal mutation of clone ‘Cayenne 7898’ showing the difference in dark yellow (Cayenne 7898 4N, HANA 97) and white (Cayenne 7898, HANA96) flesh colors.
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fig1: Somaclonal mutation of clone ‘Cayenne 7898’ showing the difference in dark yellow (Cayenne 7898 4N, HANA 97) and white (Cayenne 7898, HANA96) flesh colors.

Mentions: SNP profiles of the multiple accessions from the same pineapple cultivar showed that genotyping results were highly consistent (Table 3). Multilocus matching of SNP fingerprints revealed a high rate of duplicates in this pineapple collection. A total of 130 accessions could be classified into 24 synonymous groups (Table 4). The largest synonymous group, which includes 36 accessions, was found in cultivar Cayenne. It is also noticeable that some accessions within the same synonymous group have apparent morphological differences, despite matching SNP profiles, indicting somaclonal mutation within the synonymous group. For example, Cayenne 7898 QC has atypical yellow flesh color, whereas Cayenne 7898 4N has a white color, but their SNP profiles are the same (Figure 1).


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)

Somaclonal mutation of clone ‘Cayenne 7898’ showing the difference in dark yellow (Cayenne 7898 4N, HANA 97) and white (Cayenne 7898, HANA96) flesh colors.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig1: Somaclonal mutation of clone ‘Cayenne 7898’ showing the difference in dark yellow (Cayenne 7898 4N, HANA 97) and white (Cayenne 7898, HANA96) flesh colors.
Mentions: SNP profiles of the multiple accessions from the same pineapple cultivar showed that genotyping results were highly consistent (Table 3). Multilocus matching of SNP fingerprints revealed a high rate of duplicates in this pineapple collection. A total of 130 accessions could be classified into 24 synonymous groups (Table 4). The largest synonymous group, which includes 36 accessions, was found in cultivar Cayenne. It is also noticeable that some accessions within the same synonymous group have apparent morphological differences, despite matching SNP profiles, indicting somaclonal mutation within the synonymous group. For example, Cayenne 7898 QC has atypical yellow flesh color, whereas Cayenne 7898 4N has a white color, but their SNP profiles are the same (Figure 1).

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.