Construction Of A Physical Map And Analysis Of Structural Variations For Chromosome A9 In Brassica Juncea

The Brassica juncea,one of the three allotetraploids of Brassica,has a long history of planting in the world.Brassica juncea is a hybrid of Brassica.rapa and black mustard.It,s not known whether the chromosomes have been mutated during a long period of evolution and what type of structural variation has occurred.The researchers first used the various tags developed to perform mutation analysis.With the continuous improvement of sequencing technology,people began to explore the whole genome sequencing of Brassica juncea,expecting to solve the structural variation that occurred during the evolution from the sequence level.As the longest chromosome in the Brassica juncea A genome,there are many genes controlling the plant traits on chromosome A9.Therefore,Construction of genetic map and physical map of chromosome A9 in Brassica juncea is of significance for the research and production of Brassica juncea.Using markers not based on the genotype analysis of reference sequences,a high-density genetic map of Brassica juncea was eventually obtained.At the same time,BAC double-end sequencing was performed based on marker-localized BACs,BAC library was used to screen for constructing A9 chromosome physical maps of Brassica juncea using primers designed from BAC end sequences,Brassica rapa genome,and the GSS sequences of Brassica juncea.A total of 172 RIL individuals and two parents were used to RIL(Recombinant inbred lines)from Sichuan yellow seed inbred lines and purple leaf mustard.The genotyping technique was used to identify a large number of SNP loci and develop high-density GBS markers.The 15,549 markers finally developed were mapped on 18 chromosomes.The total length of the genetic map was 1,526.8 cM,and there were an average of 888 markers per chromosome with an average marker density of 0.751 cM.The markers with the same genetic position were divided into a bin and finally 2,085 bins were obtained.The GBS marker on the chromosome A9 was anchored on the reference genome of the Brassica rapa and Brassica napus A9 chromosome and analyzed by collinearity.It was found that there were structural variations in the chromosomes of A9 in Brassica rapa and Brassica napus.The contigs were constructed by tagging anchored BACs,and BACs were anchored by BES on the basis of reference genomes.Finally,the A9 chromosome map of Brassica juncea consisting of 16 contigs totaling 538 BACs was constructed.The BAC end sequence was mapped to a Brassica juncea reference genome and the physical map length was estimated to be 46.26 Mb.Compared with the published A9 chromosomes of Brassica rapa,Brassica napus and Brassica juncea reference genomes,structural mutations such as inversion and deletion of Arabidopsis thaliana chromosome A9 were found.