Development Of A SNP Capture Sequencing Kit And Its Application In The Construction Of Genetic Maps Of Large Yellow Croaker

A SNP capture sequencing kit of Larimichthys crocea was developed to base on a large number of candidate SNPs loci which were detected by resequencing data would map to the reference genome of female large yellow croaker.The high-density genetic map of two pairs of parents were constructed to use datas of capture sequencing.The results as follows:1.We designed a personalized SNP capture sequencing kit for large yellow croaker to make use of high-throughput resequencing datas of 100 individuals which physical quality were better.Using the kit could capture 50,000 genome sequences: including 25,000 the sequences of coding regions and almost 25,000 non-gene-coding regions and a total miRNA datas which came from resequencing of large yellow croaker.Adopted individualization capture technology in this research.There were 108 individuals came from LG and RY family which build in the fall of 2011 were used high-throughput sequencing and sequenced a total of 88.67 Gb data,each of their sequencing size was from 325.68 Mb to 2076.51 Mb.We searched for SNP variation locuses using the GATK,a total of 52542 polymorphic markers were genotyped,containing 50132 SNPs and 2410 indels which were assigned to 702 scaffolds of the large yellow croaker assembled sequence.Finally there were 34873 polymorphic markers in the LG family and in the RY family there were 39582 polymorphic markers,21913 molecular markers were the same between of them.2.Construction a SNP genetic linkage map,a male and female map for Larimichthys crocea of each family.In the LG family,the total length of sex-average linkage map was 3193.289 cM and contained 2814 markers which were assigned to 502 scaffolds in 24 linkage groups with an average interval of 1.145 cM.for the male map,1509 SNPs and indel markers were assigned,and spanning 1915.676 cM.On the female map,there were 1830 markers,and the total length of map had 2508.006 cM.In the RY family,the total length of sex-average linkage map was 2733.945 cM and contained 2056 markers which were assigned to 427 scaffolds in 24 linkage groups with an average interval of 1.345 cM.for the male map,1212 SNPs and indel markers were assigned,and spanning 1748.458 cM.On the female map,there were 1222 markers,and the total length of map had 1703.706 cM.3.A integrated high density genetic linkage map of large yellow croaker(Larimichthys crocea)was constructed,while the map contained 24 linkage groups,and had 3869 polymorphic markers and consisted of 106 to 225 markers.All markers were assigned to 571 scaffolds which the rate of total assembly genom was 65.86%.The total linkage distance spanned by these markers was 3870.894 cM with an average of 1.007 cM for the whole map.The results showed that the map contained 2383 marker came from sequencing data of LG family and 1791 markers were from the other family,and 305 markers were assigned 140 scaffolds were anchor markers between of them.