| Potato (Solanum tuberosum L.) is an important staple food and economic crop in many countries.China, possessing the largest potato growing acreage and highest yield production among other countries, plays a leading role in the potato industry in the world. The objectives of this study are to understand the genetic diversity and population structure of the current potato germplasm collections;develop the new single nucleotide polymorphism (SNP) markers for potato genetic study; and identify SNPs and candidate genes related to the important traits of potato tuber and the disease resistance genes against potato major disease, late blight disease (Phytophthora infestans). The results in this study will be used to enrich potato gene pool and develop new potato germplasms and cultivars. In this project,using a panel of potato germplasms collection consisting of 288 accessions from eight countries and the International Potato Center (CIP), I studied their genetic diversity and population structure, conducted the genome-wide association analysis among the SNPs and four traits (bud-eye color, bud-eye depth,fresh color and skin color ) of potato tubers, and performed the selective sweep analysis for the SNPs markers in the region harboring resistance genes to late blight disease. The main results are summarized as follows:1. The genetic diversity and population structure of potato germplasms were studied using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) techniques. A total of 190 polymorphic alleles were produced on 20 SSR loci and 983 polymorphic fragments produced by 10 AFLP primer pair combinations when these two marker techniques were applied on 288 potato accessions. These potato accessions were discriminated into seven subgroups (SG) and one admix group by Bayesian analysis. The results from cluster analysis, principal component analysis (PCA) and Bayesian analysis were consistent with each other. The genetic relationship between different geographical areas of potato accessions was revealed by Nei’s genetic distance through cluster analysis.The Nei’s genetic distance between the South China group and the other four groups was farther than that among other groups. The farthest distance was between the South China group and Northeast Keshan group. The genetic distance between CIP group and other three groups (North, Northeast Keshan and Foreign group) was also farther than that among the other three groups. The closest genetic distance was found between North China group and Northeast Keshan group. These results indicated that there is the lack of geographical differentiation among country-wide collections of potato germplasm and the introduction and exchange of potato germplasms was common for the countries other than the potato origin center.2. A total of 280,124 SNPs, first based on SLAF-seq technique, were developed and evenly distributed on the entire genome of potato. The genetic diversity and population structure of the natural potato population were evaluated by SNPs. Phylogenetic tree was constructed with these SNPs. Most of potato germplasms were clustered into four subgroups, except the clades consisting of 1 - 4 potato accessions. The majority accessions in subgroup 4 was from CIP. Each of the other three subgroups consisted of accessions from different areas. Based on the population structure analysis, the best subgroup number was determined as 17 by △K value,however,the most subgroups consisted of small number accessions (less than 20). Most accessions were clustered into subgroups 4, 10, 11, 14 and 17.The results obtained with PCA were consistent with those from population structure analysis. Both the phylogenetic analysis and population structure analysis were found that there was no obvious geographical differentiation among potato germplasms collections.3. Comparing the results of three molecular markers applied in genetic diversity, the assessing efficiency was SNP > AFLP > SSR.4. Using 280,124 SNPs and 142 potato accessions from our laboratory, the genome-wide association between these SNPs and four tuber traits (bud-eye color, bud-eye depth, fresh color and skin color) were studied based on the general linear model (GLM) and mixture linear model (MLM). The candidate genes for each trait were selected in a 10k flanking regions of their related SNPs. The gene annotations were performed using Clusters of Orthologous Groups (COG) database, Gene Ontology(GO) database, Encyclopedia of Genes and Genomes (KEGG) database, Swiss-Prot database and NR database. Based on GLM at 0.01 significant level, eight SNPs, located on chromosomes 1, 2, 6 and 10,were detected to be associated with bud-eye color, and six functional genes were found nearby three of eight SNPs. Fifteen SNPs, located on chromosomes 2, 3, 9, 11 and 12, were found to be related to bud-eye depth. Furthermore, the bud-eye color related SNPs were also detected on chromosome 2 by MLM analysis. The locations of the related SNPs were consistent with the results from GLM. Nine candidate genes with known functions were identified nearby six SNPs. Eleven SNPs, located on chromosomes 1, 2, 3, 5, and 7, were detected to be related to potato fresh color, and 10 functional genes were nearby six of 11 SNPs. A SNP on chromosome 1 was detected to be associated with potato skin color, and two candidate genes were found nearby this SNP. The information of candidate genes related to the four potato tube traits can be used for studying the functions of these genes.5. Using data of 280,124 SNPs, the selective weep analysis was performed in 142 potato germplasms consisting of resistant group (40 accessions) and susceptible group (75 accessions) against late blight. The candidate genes on potato late blight resistant population selective sweep sites were analyzed using GO database, COG database, Kyoto KEGG database, and plant R gene database,respectively. By GO annotation, 602 genes were found out in selective sweep sites of resistant population. The gene distribution, number and proportion in cellular component, molecular function and biological process were analyzed. The top three candidate gene numbers in cellular component catalogue were 506, 500 and 419. The top four percentages of the differentiate genes were 3.5%, 3.8%,4.1% and 10%. The highest gene numbers in molecular function catalogue were 317 and 297. The five top proportions of the differentiate genes were 3.5%, 3.1%, 3.3%, 3.6%, and 7.1%. In biological process,the highest gene numbers were 478, 451, and 435. The highest proportions of the differentiate genes 6.0% and 4.5%. Based on COG database annotation, 196 genes were found out. These genes were mainly assigned into catalogues of general function prediction only, transcription, signal transduction mechanisms and replication, recombination and repair. From KEGG database, the most genes were catalogued into seven pathways, including plant hormone signal transduction, ribosome, protein processing in endoplasmic reticulum, spliceosome, ubiquitin mediated proteolysis, RNA degradation,and RNA transport. Of which the two most significantly enriched pathways were flavone and flavonol biosynthesis and RNA degradation. By plant R gene database annotation, 19 identified genes were belonged to R genes in potato (Solanum tuberosum), including 1 of type CNL, 2 of type RLP, and 16 of type L, of which 11 candidate R genes in potato should be attached importance in the further study. |
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