Genome-wide Association Analysis Of Main Agronomic Traits Of Flowering Chinese Cabbage

Flowering Chinese Cabbage,is a common leafy vegetable in South China.With the increasing market demand for flowering Chinese cabbage,improving the yield and quality of flowering Chinese cabbage become a research hotspot.Finding the functional genes associated with agronomic traits of flowering Chinese cabbage is of great significance for breeding high-quality cultivars and improving yield.Genomewide association analysis,which applies high-density SNP markers for research,can effectively predict important genes of breeding value.In this paper,210 flowering Chinese cabbage accessions were used as a natural population to develop genome-wide association analysis of six agronomic traits to detect variant loci that significantly affect main agronomic traits,and to predict associated candidate genes.Six agronomic traits is including plant height,plant weight,maximum leaf length,maximum leaf width,maximum petiole length,and leaf chlorophyll content.The main findings are as follows:(1)Diversity analysis of major agronomic traits in a natural population of flowering Chinese cabbage.Six agronomic traits including plant height,plant weight,maximum leaf length,maximum leaf width,maximum petiole length,and leaf chlorophyll content were investigated in 210 flowering Chinese cabbage accessions for 2 years.The results showed normal distributions for the six traits,with large variation among accessions.The greatest variation in Plant weight,with coefficients of variation of 67.93%and 68.69%,and the least variation in leaf chlorophyll content,with coefficients of variation of 11.65%and 13.17%.In addition to leaf chlorophyll content,five other traits showed stable positive correlations across both years,whereas chlorophyll content showed negative correlations with maximum petiole length and maximum leaf width.The clustering results based on agronomic traits showed that the 210 accessions could be divided into three subgroups at a genetic distance of 6.8.Subgroup III possessed most accessions with a small genetic distance among accessions.Principal component analysis revealed that the six agronomic traits could be represented by two principal components,and the variance contributions of the two principal components were 53.596%,18.943%,respectively,and their cumulative contributions reached 72.899%.(2)SNP detection and genetic diversity analysis in a natural population of flowering Chinese cabbage.A total of 210 flowering Chinese cabbage accessions were sequenced using restriction site-associated DNA sequencing.The sequencing depth greater than 6 ×,and the alignment rates ranged from 82.24%to 98.83%.A total of 219846 high-quality SNP markers were obtained after stringent quality control filtering,which coverage 10 chromosomes in flowering Chinese cabbage.Population structure analysis revealed that the natural population constituted by the 210 accessions could be divided into four subgroups,among which subgroup Q1 and Q3 contained more flowering Chinese cabbage accessions with 76 and 77 accessions,respectively.Subgroup Q4 contained the fewest accessions with 16 accessions.181 accessions with Q-values>0.60 in 210 flowering Chinese cabbage accessions,accounting for 86.19%of the natural population.Most of the inbreeding coefficients ranged from 0.5 to 1.5,and most of the flowering Chinese cabbage accessions contained some inbreeding relationships.When the threshold of R2 was 0.1,the decay distance of the flowering Chinese cabbage population was about 50 kb.(3)Association analysis of SNPs with major agronomic traits in flowering Chinese cabbage.Using three association models(MLM,CMLM,and FarmCPU),genome-wide association analysis and candidate gene prediction were conducted for six agronomic traits including plant height,plant weight,maximum leaf length,maximum leaf width,maximum petiole length,and leaf chlorophyll content.At the result,the total of 51 significant associated loci and 5 multi-effective associated loci were detected.Among the 51 significant associated loci,there are 10,11,6,7,17 significant associated loci respectively were detected in the association results with plant height,plant weight,maximum leaf length,maximum leaf width,and maximum petiole length and 51 significant associated loci were distributed among the 10 chromosomes in flowering Chinese cabbage,but there is no association locus detected with leaf chlorophyll content.Five multi-effective associated loci were distributed on chromosomes 1,9,10.(4)Prediction of candidate genes associated with major agronomic traits in flowering Chinese cabbage.Within 50 kb up and downstream of the SNP loci associated with major agronomic traits in flowering Chinese cabbage,the total of 621 genes were searched.Combined with study of orthologous genes in Arabidopsis,52 candidate genes were finally predicted.For plant height,plant weight,maximum leaf length,maximum leaf width,and maximum petiole length,the number of gene predicted respectively is 9,13,6,10,and 14 candidate genes.Most of candidate genes majorly involved in cell division and phytohormone regulation.