Association Analysis Of Bolting And Flowering Time With SSR And InDel Markers In Chinese Cabbage

Chinese cabbage (Brassica campestris ssp. pekinensis) is native to China, which belongs to Brassica campestiris species of Brassica genus in Brassicaceae family. Bolting and flowering time are important agronomic characters in Chinese cabbage. It is necessary to investigate the variation and genetic basis in bolting and flowering time at molecular level, which will help to explore the interesting alleles. The genetic information obtained is limited to indentify the germplasm diversity by only one kind of molecular marker. Thirty SSR and 27 InDel markers distributed equally over the genomes were used to amply 190 Chinese cabbage accessions for population structure analysis in the present study, and the association analysis of bolting flowering time with markers was performed systematically. The population structure analysis will help to exploit distantly related germplasm resources used as appropriate parents to make crosses. The population structure analysis will also provide the theoretical basis for breeding excellent Chinese cabbage varieties, improving breeding efficiency and performing association analysis. By association analysis, it can be clarified the contribution of alleles carried by different genotypes in the population to target traits, and it can be explained the genetic basis of rich phenotypic variations. The results are as follows:1. Twenty-four primers with high polymorphism were screened from 199 random SSR primers. Six primers with high polymorphism were screened from 36 gene-specific SSR primers. Twenty-seven primers with high polymorphism were screened from 100 InDel primers. Seventy-six alleles were detected from 24 random SSR primers, and 3.2 alleles were detected from average each primer ranging from 2 to 6 alleles. Fifteen alleles were detected from 6 gene-specific SSR primers, and 2.5 alleles were detected from average each primer ranging from 2 to 4 alleles. Seventy-six alleles were detected from 27 InDel primers, and 2.8 alleles were detected from average each primer ranging from 2 to 7 alleles.2. One hundred and sixty seven alleles from 30 SSR primers and 27 InDel primers were imported in the program Structure to identify subpopulations. Population genetic structure analysis showed that 190 Chinese cabbage accessions are composed of 3 subpopulations (S1, S2 and S3). Subpopulation S1 includs 66 accessions, which are all inbred lines; subpopulation S2 includs 72 accessions, 10 of them are inbred lines and 62 of them are F1; subpopulation S3 includs 52 accessions, 4 of them are inbred lines and 48 are F1.3. The bolting time of accessions in S1 is mostly 72~99d, and the flowering time of them is 83~109d; the bolting time of accessions in S2 is mostly 80~99d, and the flowering time of them is 90~109d; the bolting time of accessions in S3 is mostly 72~89d, and the flowering time of them is mostly 83~99d.4. Association analysis showed that forty two alleles from 31 markers were identified associations with bolting and flowering time (P < 0.05). Thirty two alleles from 24 markers were associated with bolting time, the allele S59(b) is the most significantly associated with bolting time. Thirty one alleles from 25 markers were associated with flowering time, the allele S155(b) is the most signicantly associated with flowering time. We found that 21 alleles from 18 markers were associated with bolting and flowering time simultaneously.