- Tytuł:
- Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)
- Autorzy:
-
Su, Y.
Hu, D.
Zheng, H. - Powiązania:
- https://bibliotekanauki.pl/articles/41243.pdf
- Data publikacji:
- 2016
- Wydawca:
- Polska Akademia Nauk. Instytut Dendrologii PAN
- Tematy:
-
detection
single nucleotide polymorphism
DNA specific-locus amplified fragment sequencing
fir
Chinese fir
Cunninghamia lanceolata
genotyping - Opis:
- 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 of DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook), an ecological and economic important conifer in China. SLAF libraries of 18 parent clones of a Chinese fir 2.5 generation seed orchard were sequenced and a total of 117,924 SLAFs were developed. We detected 147,376 SNPs from these SLAFs; 146,231 of them represented simple nucleotide change in A/G, C/T, A/C, A/T, C/G or G/T. The most frequent SNPs occurred in C/T (34.3%), while the majority of SNPs (68.2%) belonged to transition events (A/G and C/T). Notably, all the sequenced samples had high portion (78.2–80.9%) of common SNPs indicating that the Chinese fir genomes tended to change its nucleotides at common loci. 48,406 informative SNPs were then successfully utilized to genotype the tested samples (n = 18) followed by a phylogenetic tree to clarify their genetic relationship. Furthermore, a set of very high linkage disequilibrium (0.51–1.00) were identified from these informative SNPs. In brief, our work demonstrated that SLAF-seq is an alternative and cost-effectively high-throughput approach for large-scale SNP exploitation in Chinese fir. While the obtained SNPs offer useful marker resource for further genetic and genomic studies and will be helpful for Chinese fir breeding programs.
- Źródło:
-
Dendrobiology; 2016, 76
1641-1307 - Pojawia się w:
- Dendrobiology
- Dostawca treści:
- Biblioteka Nauki
Artykuł