Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

• DOI: 10.12657/denbio.076.007
• Publication Date: 2016-10-06T07:01:46Z
• Authors: Yan Su; Dehuo Hu; Huiquan Zheng
• Keywords: Cunninghamia; Tag SNP; Linkage Disequilibrium

Compared to angiosperms, conifers represent more complex genomes with larger giga-genome size.To detect large-scale single nucleotide polymorphisms (SNPs), whole genome sequencing of a conifer population is still unaffordable.In this work, we report the use DNA specific-locus amplified fragment (SLAF-seq) for SNP detection in Chinese fir (Cunninghamia lanceolata (Lamb.)Hook), an ecological and economic important China.SLAF libraries 18 parent clones 2.5 generation seed orchard were sequenced total 117,924 SLAFs developed.We detected 147,376 SNPs from these SLAFs; 146,231 them represented simple change A/G, C/T, A/C, A/T, C/G or G/T.The most frequent occurred C/T (34.3%), while majority (68.2%) belonged transition events (A/G C/T).Notably, all samples had high portion (78.2-80.9%) common indicating that tended its nucleotides at loci.48,406 informative then successfully utilized genotype tested (n = 18) followed by phylogenetic tree clarify their genetic relationship.Furthermore, set very linkage disequilibrium (0.51-1.00) identified SNPs.In brief, our work demonstrated SLAF-seq alternative cost-effectively high-throughput approach exploitation fir.While obtained offer useful marker resource further genomic studies will be helpful breeding programs.