| Tomato(Solanum lycopersicum)is one of the most important vegetable crops over the world and it belongs to self-pollinated plant.However,its genetic background is becoming increasingly narrowed due to the long-term domestication selected by the human beings and finally led to the bottlenecks with the lack of genetic diversity.In contrast,wild species possesses rich variation and are the gene pool for the future genetic improvement of tomato.Solanum pimpinellifolium is the closest wild species with the cultivated tomato and can be directly crossed with the cultivar.It has been used as the most important germplasm for the genetic improvement.Although many excellent horticultural traits have been explored in this wild species,there is still a big gap for understanding the genetic diversity of population.Hence,to further explore the elite traits from this wild species is one of the most approaches for tomato breeding program.In this study,a globle collection containing 433 S.pimpinellifolium accessions was conducted.After phenotyping and genetic diversity analysis of molecular markers,192 accessions without segregation were identified.Low coverage re-sequencing approach was used to explore huge SNP through the whole genome.These SNP markers were then used to analyze the population structure.Meanwhile,these accessions were phenotyped respectively in two seasons.Combing the genome and phenotype data,GWAS was conducted.The main results were listed as follows:(1)The results of phenotyping indicated that about 14% of these accessions are Solanum lycopersicum var.cerasiforme.Among 370 accessions of typical S.pimpinellifolium,about 22% of them are segregated on certain degree.Population variation analysis showed that variation coefficient varied among different traits.The maximum variation existed in stigma and is about 56.716% while the minimum one is petals number with about 2.082%.Correlation analysis of different traits showed that there is significant correlation between different traits.Based on the data of phenotyping and genotyping,S.pimpinellifolium population was divided into two groups.Principal component analysis further showed that fruiting rate,fruit weight and soluble solids content makes great contribution to the variation.(2)In total,62 Gb data was generated through the whole genome low coverage sequencing(0.5×).The average sequencing depth is about 0.3×.995300 SNPs were identified and the average distribution frequency is 1.24 SNPs/kb over the chromosomes.Among them,728269 SNPs are located in intergenic region and is about 73.17% of the total SNPs.26703 SNPs are located within genes and is 26.83%.(3)The population structure of 192 accessions was further studied through the whole genome SNP and results showed that two main groups and several intermediate accessions were divided through the phylogenetic tree analysis,principal component analysis and population structure analysis.Group I consisted of 3 accessions,group II consists of 176 accessions and 13 accessions between in the two groups.(4)192 accessions were phenotyped respectively in two seasons including premature aging,fruit weight,soluble solids content,lateral branch length,leaf number below first inflorescence,flowering days,inflorescence length,seedling plant height and stem diameter.The results indicated that leaf number below first inflorescence,flowering days,stem diameter were greatly influenced by the environment;however,premature aging,inflorescence length,fruit weight,soluble solids content etc.were less affected by the environment.Meanwhile,two accessions were identified with high soluble solids content up to 11.0%,LA1256,LA0112 accessions with typical long inflorescence and typical premature aging trait respectively.Then GWAS was conducted with fruit weight,premature aging and soluble solids content and did not detected significant SNPs.We analysis genetic diversity and GWAS of S.pimpinellifolium,it will lay a foundation for the study of excellent traits. |
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