SNP Detection And Linkage Disequilibrium Analysis Of The Extension Gene Family In Populus Deltoids

Extensins are important structural proteins in cellwall of higher plant and riched in hydroxyproline. They account for 1~15% of the dry weight of primary cellwall in eudicots. A typical extensin possess repeating pentapeptide sequence Ser-(Hyp)4, which belongs to a superfamily of cell wall structural proteins. Recent studies on the rsh mutant of Arabidopsis show that extensins play a critical role, not only in the cell shaping and cell walls strengthening, but also in positioning the cell plate during cytokinesis and formulating normal embryo development. Therefore, studying the function and structure of extensins in Populus deltoids is important in variety breeding of Populus deltoids.In this study, 92 unrelated individuals of Populus deltoids were selected,and 9 extensin genes were amplified by PCR. These genes were sequenced with the Roche 454 FLX sequencer, and SNP and LD were analyzed respectively. The main results were as follows:1) 454 sequencing: 41 fragments from 9 genes were amplified by mixing equal amount of each sample. 394 Mb oligonucleotides were obtained, including more than 947000 high quality reads, of which the average length were 416 bp. These sequences were about 160 times sequencing depth, and high sequencing depth ensure the accuracy of the SNP analysis.2) Statistical analysis of SNPs in 9 PdEXT genes showed that the numbers of SNPs identified in PdEXT6, PdEXT18, PdEXT22, PdEXT25, PdEXT29, PdEXT32, PdEXT34, PdEXT40, and PdEXT41 were 35, 12, 61, 36, 177, 123, 26, 65, and 49, respectively. Transition bias(Ts/Tv?0.64) occurred in 8 PdEXT genes except for PdEXT18(Ts/Tv=0.5). The lowest SNP frequency was 1/86bp(PdEXT34), whereas the highest was 1/7bp(PdEXT29).3) Statistical analysis of the InDel of 9 PdEXT genes showed that 5, 5, 32, 50, 127, 18, 24, 79 and 15 InDels identified in PdEXT6, PdEXT6, PdEXT18, PdEXT22, PdEXT25, PdEXT29, PdEXT32, PdEXT34, PdEXT40 and PdEXT41 respectively. More deletions were detected than insertions in 7 PdEXT genes, except for PdEXT32 and PdEXT22. Among all Indels, the number of mononucleotides were the most, which account for 58.77% of the total InDels, and 86.35% of the Indels shorter than 10 bp. In general, the frequency of detected InDels decreased with its length increased.4) LD analysis of PdEXT6, PdEXT34, and PdEXT41 revealed that PdEXT6 gene has 1 distinct haplotype block and 5 pairwise SNP sites(r2>0.75); PdEXT34 gene has 3 distinct haplotype blocks; PdEXT41 gene has 7 distinct haplotype blocks and 26 pairwise SNP sites.