| 【Objectice】The present research aimed to collect potato variety（strain）resources, study the
population structure and genetic diversity of potato germplasm and develop SNP molecular markers, with a view to
providing theoretical foundation for potato variety identification and molecular marker-assisted selection breeding.
【Method】Genome DNA of potato tender shoots was extracted and digested with restriction enzymes MseI and SacI.
After quality verification, Paired-end sequencing was carried out on Illumina HiSeq platform, sequencing data was aligned to potato reference genome with BWA software, SNP and InDel variation sites were detected and annotated with
GATK and ANNOVAR respectively, and population structure analysis, principal component analysis and genetic diversity
analysis were conducted based on the SNPs.【Result】By simplifying genome sequencing, 7.50×108
sequencing reads
and 2.04×1011 bases were obtained. A total of 39038 variation sites were detected, of which 36 267 were SNP sites and
the other 2 771 sites were InDel. Based on the Structure analysis and PCA analysis, the 185 samples were divided into 2
subgroups. Population phylogenetic analysis showed that the individuals in G2 subgroup were clustered together with close
genetic relationship, but the branches in G2 subgroup were far from the center and accumulated more variations than other
individuals. PIC, He, Ho and Fis were 0.3107, 0.3932, 0.1852 and 0.553 respectively, which indicated that the genetic
diversity of potato varieties（strains）was poor, SNP-Panel with 120 SNPs distributing on all the 12 potato chromosomes
was developed and 60 SNPs of 46 samples were verified. 【Conclusion】The research results laid a foundation for the
study of potato genetic diversity, molecular marker-assisted selection breeding, development of molecular identity card and
construction of genetic map. |
