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The heterozygosity, population structure and genetic diversity of Moringa oleifera and its progeny were analyzed using the SNP markers. The characteristics of genetic variation of M. oleifera and its progeny were studied. Simplified genome sequencing of 96 M. oleifera materials was performed by AFSM technology. The obtained sequencing filtering data were compared to the reference genome. SNP and Indel loci were detected and counted by using VCFtools and BCFtools. In order to analyze the reproduction types of M. oleifera, AWK language was used to analyze heterozygous loci, and compare the different loci of the progeny with the parents. The mutation sites were filtered by Plink software, and the high-quality mutation sites were reserved. The population structure was analyzed by ADMIXTURE software, and the optimal K value was determined according to the cross validation error rate. At the same time, GCTA software was used for principal component analysis, and the phylogenetic tree was constructed to analyze the population structure of the materials. VCFtools was used to calculate the genetic diversity index and population differentiation index for analyzing the genetic polymorphism of the population. LDBlockShow software was used for linkage imbalance analysis, and the linkage imbalance degree between loci was obtained. The result showed that a total of 1 187 831 SNP sites and 150 861 Indel sites were detected in this paper. We compared M. oleifera progeny genes with parents, which found that among the heterozygous genes in Moringa progeny, about 4.89% of the genes are self-heterozygous genes, and 19.96% of the heterozygous genes caused by foreign genetic materia. It indicates that M. oleifera produce offspring by the ways of self-pollination and cross-flowering. M. oleifera samples were divided into 3 subgroups by population structure and principal component analysis. The cluster analysis is roughly consistent with the above results. The subgroups can be clustered together, and there is a little crossover between the samples. The low genetic differentiation index (0.0049-0.0110) and genetic diversity index (0.001) among different populations of M. oleifera indicated that the level of genetic diversity was low and genetic differentiation was weak. The SNPS of 136 scaffolds which detected were counted and linkage imbalance analysis was performed, we found that scaffold 1 had the most SNPS (62 225), there was strong linkage imbalance between 6 748 044 and 6 748 185 loci. This study analyzed the genetic diversity of M. oleifera and its progeny. It would provide genetic basis for the cross breeding of M. oleifera.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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