Computational protocol: Development of SSR markers for the tropical alpine tree species Leptospermum recurvum (Myrtaceae) on Mount Kinabalu in Borneo1

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Protocol publication

[…] Prior to development of the markers, we collected seeds of L. recurvum from a population located at an elevation of 3300 m on Mount Kinabalu (6.05824°N, 116.56566°E) and cultivated the seedlings in our laboratory. Fresh leaves were sampled from one of the seedlings for DNA extraction to construct an SSR library. The voucher specimen of this seedling was deposited in the Sabah Parks Herbarium at Kinabalu Park headquarters (KIN accession no. SNP28526). We developed SSR markers using an improved technique for compound SSR markers (; ). An adapter-ligated DNA library was constructed as described previously (). The fragments were amplified from an EcoRV (TaKaRa Biotechnology Co., Otsu, Japan) DNA library using an adapter primer, AP2 (5′-CTATAGGGCACGCGTGGT-3′), and a compound SSR primer, (AC)6(AG)7 or (AC)6(TC)7. The amplified fragments of 400–1000 bp were purified using a QIAquick Gel Extraction Kit (QIAGEN, Valencia, California, USA) and cloned using a QIAGEN PCR Cloningplus Kit (QIAGEN) in accordance with the manufacturer’s instructions. A total of 224 insert-positive clones were sequenced. We identified 33 distinct sequences containing an (AC)6(AG)n or (AC)6(TC)n compound SSR sequence at one end using ClustalX version 2.1 (). Based on these 33 sequences, specific primers were designed using Primer3 version 0.4.0 ().PCR amplifications were performed in a final volume of 5 μL using a QIAGEN Multiplex PCR Kit (QIAGEN) according to the standard protocol with a GeneAmp PCR System 2700 thermal cycler (Applied Biosystems, Carlsbad, California, USA). The combination of multiplex reactions is shown in . Compound SSR primers were labeled with fluorochromes, as shown in . PCR amplifications were performed under different cycling conditions based on the compound SSR primers: for the primers labeled with VIC or 6-FAM, initial denaturation was performed at 95°C for 15 min followed by 25 cycles of denaturation at 94°C for 30 s, annealing at 57°C for 1 min 30 s, extension at 72°C for 1 min, and a final extension at 60°C for 30 min; for the primers labeled with PET, the number of cycles was increased to 33, but the other conditions were unchanged. Size of the PCR products was determined using an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems) and Genotyper software (Applied Biosystems) with GeneScan 500 LIZ (Applied Biosystems) as an internal size standard. Although the reliability and repeatability of compound SSR primers are controversial, we conducted repeated amplification of eight identical samples and obtained consistent results using the markers described here.Eight individuals from the population located at 3300 m (GPS coordinates are shown in ) were used in initial screening of the 33 primer pairs designed here. Of these 33 primer pairs, 11 exhibited clearly identifiable bands (). We tested the characteristics of each locus with these 11 primer pairs using samples from four populations: three L. recurvum populations with various phenotypes from different habitats ranging from the lowest altitude (2700 m, forest), middle altitudes (3300 m, shrub), to the highest altitude (3900 m, alpine cushion community) on Mount Kinabalu, and one L. polygalifolium population found at 1900 m on Mount Kinabalu. Because the locus Lrec401 was monomorphic in all populations, this locus was excluded from the subsequent analyses. We found that all loci had more than one allele except for the locus Lrec139 in the L. recurvum population at the lowest altitude. Using GenAlEx version 6.3 (), the observed heterozygosity, expected heterozygosity, and inbreeding coefficient values of L. recurvum were found to range from 0.04 to 0.94, from 0.04 to 0.83, and from −0.48 to 0.42 (except for the monomorphic locus Lrec139), respectively, and those for L. polygalifolium ranged from 0.07 to 0.67, from 0.29 to 0.84, and from −0.18 to 0.84, respectively. We also tested for departure from Hardy–Weinberg equilibrium (HWE) for all populations and loci as well as for linkage disequilibrium (LD) between all pairs of polymorphic loci using FSTAT version 2.3.9.2 (, ). We found that no population demonstrated significant departure from HWE, and that no pair of loci exhibited significant LD (P < 0.05 after Bonferroni correction). […]

Pipeline specifications

Software tools Clustal W, Primer3, GenAlEx
Applications Population genetic analysis, qPCR