Limits...
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

Plot of ΔK (filled circles, solid line) calculated as the mean of the second-order rate of change in likelihood of K divided by the standard deviation of the likelihood of K, m/L ″(K)//s[L(K)].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4595986&req=5

fig2: Plot of ΔK (filled circles, solid line) calculated as the mean of the second-order rate of change in likelihood of K divided by the standard deviation of the likelihood of K, m/L ″(K)//s[L(K)].

Mentions: Population stratification of the 50 varieties, based on ΔK value computed by STRUCTURE HARVESTER,48 revealed two clusters as the most probable number of K (Figures 2 and 3) and this partitioning was fully compatible with the principle coordinate analysis (Figure 1). All the wild germplasm were assigned to one Bayesian cluster, whereas the cultivated germplasm were grouped in another single Bayesian cluster. The only exception is accession ‘No 2-13 (taller)’, which appeared as a hybrid genotype between the cultivated and wild longan groups. To further illuminate the diversity within the cultivated germplasm, the clustering result at K=3 is also presented in Figure 3. The wild germplasm remained as a single cluster at K=3, but the cultivated longan were split into two subclusters, revealing the difference between the Chinese and Thailand/Hawaii accessions. In addition, several hybrid-like accessions that combined both Chinese and Thailand parentage were observed at K=3. These include ‘Ponyai’, ‘Diamond River’ and the aforementioned ‘No 2–13 taller’, which showed significant contribution from Yunnan wild germplasm (Figures 3 and 4).


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)

Plot of ΔK (filled circles, solid line) calculated as the mean of the second-order rate of change in likelihood of K divided by the standard deviation of the likelihood of K, m/L ″(K)//s[L(K)].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Plot of ΔK (filled circles, solid line) calculated as the mean of the second-order rate of change in likelihood of K divided by the standard deviation of the likelihood of K, m/L ″(K)//s[L(K)].
Mentions: Population stratification of the 50 varieties, based on ΔK value computed by STRUCTURE HARVESTER,48 revealed two clusters as the most probable number of K (Figures 2 and 3) and this partitioning was fully compatible with the principle coordinate analysis (Figure 1). All the wild germplasm were assigned to one Bayesian cluster, whereas the cultivated germplasm were grouped in another single Bayesian cluster. The only exception is accession ‘No 2-13 (taller)’, which appeared as a hybrid genotype between the cultivated and wild longan groups. To further illuminate the diversity within the cultivated germplasm, the clustering result at K=3 is also presented in Figure 3. The wild germplasm remained as a single cluster at K=3, but the cultivated longan were split into two subclusters, revealing the difference between the Chinese and Thailand/Hawaii accessions. In addition, several hybrid-like accessions that combined both Chinese and Thailand parentage were observed at K=3. These include ‘Ponyai’, ‘Diamond River’ and the aforementioned ‘No 2–13 taller’, which showed significant contribution from Yunnan wild germplasm (Figures 3 and 4).

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