| Brassica rapa is an important vegetable crop and it has a very rich variety of types.China is the center of origin and diversity of cabbage,and a large number of landrace and improved varieties have been collected and preserved.However,the understanding of the genetic diversity and genetic related information of these germplasm resources is limited.In addition,there are cases of "synonyms" or "different objects with the same name",which greatly hinders the preservation and application of Chinese cabbage variety resources.Although single marker detection technologies such as SSR and KASP can be used to evaluate the genetic diversity of germplasm resources and analyze the genetic relationship of varieties,these marker technologies have the shortcomings including high cost and low throughput.In this study,two sets of Chinese cabbage SNP Panels based on multiplex PCR amplicon sequencing were developed.A total of 405 asscessions of non-heading Chinese cabbage from the Institute of Vegetable Crops,Guangdong Academy of Agricultural Sciences were analyzed for genetic diversity and genetic relationship.The main results are as follows:1.Design multiple PCR primers according to the sequence information of 568 KASP markers reported in the literature,and convert these KASP markers into a high-throughput marker SNP-Panel-1 based on multiplex PCR amplicon sequencing,named Brapa＿568SNP.Using Brapa＿568SNP to test 30 Chinese cabbage cultivars and 20 mustard cultivars,538(94.72%)markers were successfully sequenced,and 390(68.67%)markers were polymorphic.According to the genotypes of SNP loci of each variety,the 50 materials can be divided into three categories:Caixin,Caitai and mustard.The result of genotype classification is the same as that of morphological classification.2.Analyze the published resequencing data of 199 Chinese cabbage varieties to obtain 2.22 million SNP loci.According to factors such as allele frequency and location information,650high-quality SNP loci that are evenly distributed in the chromosomes were screened,and were designed as For primers,all primers were mixed to construct SNP-Panel-2,named Brapa＿650SNP.The Brapa＿650SNP was used to evaluate the genetic diversity,genetic relationship and population structure of 405 non-heading cabbage varieties mainly from Guangdong,my country.Only 6(0.92%)markers were not detected in the detection results of 650 amplicon markers.By sequence,587(90.31%)markers were polymorphic.3.The average polymorphism information content(PIC)and expected heterozygosity(GD)values of non-heading Chinese cabbage were 0.30 and 0.38,respectively,indicating that the genetic diversity level of non-heading Chinese cabbage materials in Guangdong Province was low to medium and the genetic base is narrower.In addition,the collected 103 landraces have high genetic diversity and can be added to future cabbage breeding programs.Phylogenetic analysis,principal component analysis and population structure analysis showed that the 405 materials could be divided into two main subgroups.Subgroup I contained 312 materials,mainly Xiaocaixin,Chicaixin,PAK-CHOI and Naibaicai.Part of the collected landraces belonged to this group;subgroup II contained 93 materials,most of which were improved varieties of Qinggengcai.Molecular analysis of variance(AMOVA)found a variance of 16% between the two subpopulations and 84% within the subpopulations,indicating a very low degree of population differentiation and frequent gene flow between the two subpopulations.The Chinese cabbage genome-wide SNP-Panel shows high accuracy,flexibility,and economic benefits in the study of genetic diversity.In addition,it can also be applied to molecular marker-assisted breeding,variety identification and DNA fingerprinting analysis of Chinese cabbage,gene/QTL initial mapping or construction of genetic map,GWAS analysis,and division of heterotic groups. |
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