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Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm.

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

Bottom Line: Cultivated varieties differed significantly from wild populations (F st=0.300; P<0.001), demonstrating untapped genetic diversity for germplasm conservation and utilization.Within cultivated varieties, apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation.These SNP markers provide a powerful tool to manage longan genetic resources and breeding, with accurate and efficient genotype identification.

View Article: PubMed Central - PubMed

Affiliation: Yunnan Forestry Technological College , Kunming 650224, Yunnan, China ; Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center , Beltsville, MD 20705, USA.

ABSTRACT
Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in 50 longan germplasm accessions, including cultivated varieties and wild germplasm; and designated 25 SNP markers that unambiguously identified all tested longan varieties with high statistical rigor (P<0.0001). Multiple trees from the same clone were verified and off-type trees were identified. Diversity analysis revealed genetic relationships among analyzed accessions. Cultivated varieties differed significantly from wild populations (F st=0.300; P<0.001), demonstrating untapped genetic diversity for germplasm conservation and utilization. Within cultivated varieties, apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation. These SNP markers provide a powerful tool to manage longan genetic resources and breeding, with accurate and efficient genotype identification.

No MeSH data available.


Related in: MedlinePlus

PCoA plot of 50 longan accessions including 25 cultivated varieties from USDA longan collection in Hilo, Hawaii and 24 wild trees collected from Mangshi, Yunnan Province, China. The plane of the first three main PCO axes accounted for 61.0% of total variation. First axis=41.1% of total information, the second=11.9% and the third=8.0%.
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fig1: PCoA plot of 50 longan accessions including 25 cultivated varieties from USDA longan collection in Hilo, Hawaii and 24 wild trees collected from Mangshi, Yunnan Province, China. The plane of the first three main PCO axes accounted for 61.0% of total variation. First axis=41.1% of total information, the second=11.9% and the third=8.0%.

Mentions: After excluding the duplicated samples, the genetic relationships among the 50 longan germplasm accessions (25 wild accessions and 25 cultivated genotypes) are presented in the principal coordinates analysis plot (Figure 1). Each of the accessions has a unique SNP profile. The 50 accessions fall into two clearly different clusters without overlapping. The first cluster includes all the cultivated germplasm and the second one includes all wild germplasm from Yunnan, China. Within the cultivated germplasm, there is significant difference in two subclusters according to the PCoA. The first subcluster was comprised mainly of the varieties from Southern China, including ‘Chu Leon’, ‘Tai Wu Yuen’, ‘Sak Ip’, ‘Fuk Yan’, as well as the Hawaii cultivar ‘Ikeda’ (HDIM 16). The second subcluster included all Thai varieties, as well as the other varieties from Hawaii. The only exception is the Chinese cultivar ‘Chaer Jum’ (HDIM 22), which falls into the Thailand/Hawaii subcluster.


Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm.

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

PCoA plot of 50 longan accessions including 25 cultivated varieties from USDA longan collection in Hilo, Hawaii and 24 wild trees collected from Mangshi, Yunnan Province, China. The plane of the first three main PCO axes accounted for 61.0% of total variation. First axis=41.1% of total information, the second=11.9% and the third=8.0%.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595986&req=5

fig1: PCoA plot of 50 longan accessions including 25 cultivated varieties from USDA longan collection in Hilo, Hawaii and 24 wild trees collected from Mangshi, Yunnan Province, China. The plane of the first three main PCO axes accounted for 61.0% of total variation. First axis=41.1% of total information, the second=11.9% and the third=8.0%.
Mentions: After excluding the duplicated samples, the genetic relationships among the 50 longan germplasm accessions (25 wild accessions and 25 cultivated genotypes) are presented in the principal coordinates analysis plot (Figure 1). Each of the accessions has a unique SNP profile. The 50 accessions fall into two clearly different clusters without overlapping. The first cluster includes all the cultivated germplasm and the second one includes all wild germplasm from Yunnan, China. Within the cultivated germplasm, there is significant difference in two subclusters according to the PCoA. The first subcluster was comprised mainly of the varieties from Southern China, including ‘Chu Leon’, ‘Tai Wu Yuen’, ‘Sak Ip’, ‘Fuk Yan’, as well as the Hawaii cultivar ‘Ikeda’ (HDIM 16). The second subcluster included all Thai varieties, as well as the other varieties from Hawaii. The only exception is the Chinese cultivar ‘Chaer Jum’ (HDIM 22), which falls into the Thailand/Hawaii subcluster.

Bottom Line: Cultivated varieties differed significantly from wild populations (F st=0.300; P<0.001), demonstrating untapped genetic diversity for germplasm conservation and utilization.Within cultivated varieties, apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation.These SNP markers provide a powerful tool to manage longan genetic resources and breeding, with accurate and efficient genotype identification.

View Article: PubMed Central - PubMed

Affiliation: Yunnan Forestry Technological College , Kunming 650224, Yunnan, China ; Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center , Beltsville, MD 20705, USA.

ABSTRACT
Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in 50 longan germplasm accessions, including cultivated varieties and wild germplasm; and designated 25 SNP markers that unambiguously identified all tested longan varieties with high statistical rigor (P<0.0001). Multiple trees from the same clone were verified and off-type trees were identified. Diversity analysis revealed genetic relationships among analyzed accessions. Cultivated varieties differed significantly from wild populations (F st=0.300; P<0.001), demonstrating untapped genetic diversity for germplasm conservation and utilization. Within cultivated varieties, apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation. These SNP markers provide a powerful tool to manage longan genetic resources and breeding, with accurate and efficient genotype identification.

No MeSH data available.


Related in: MedlinePlus