| We constructed a genomic library of silkworm, with average insertion of 7kb. In total,244,000 clones were picked up, which covered 3.9× silkwom genome. 13,600 positive cloneswith SSR site were obtained by screening the library with labeled (CA)15 and (CT)15 probes.The positive clones were sequenced for flanking sequences of these SSR loci. Finally, 2700robustic SSR loci were achieved by amplifying the Dazao DNA for confirmation. Thepolymorphic screening of the SSR markers in a panel of 6 silkworm strains: including Dazao,C108, jingsong, Lan10, and F50B, shows the polymorphic ratio of SSR markers in silkwormin the range of 16.9-24%. This rate is lower than those in other species, such as mouse andhuman, indicating the high homozygousity among silkworm strains. These strains wereselected to represent the silkworm system, molting and voltism. 555 pairs of polymorphismmarkers between the Dazao and C108 were selected to make genotyping.555 polymorphic markers were genotyped in the BC1M population derived from a C108female and an F1 (Dazao ×C108). Segregation data in the 189 individuals was analysed usingMapmaker 3.0 with LOD=5.0, Max distance=0.25, and a linkage map with 29 group turn out.Markers from every group were genotyped in BC1F population to test the linkage relationshipof the markers, and a fine map with 28 groups formed after the integration the Group 10 and14. The 28 groups were assigned to 28 chromosomes by genotyping in the 39 BC1Fxpopulation constructed base on 39 visible mutations have been mapped. With the aid of 12mapped CAPS makers, the assignment was confirmed. By integrating a visible mutation p(plain, larval marking) and 29 well conserved genes of insects onto this SSR-based linkagemap, a second generation consensus silkworm genetic map have a range of 7-40 makers pergroup and a total length of 3431.9cM with was constructed.Three green cocoon genes have been reported. Using our SSR map, complementarygenes Ga, Gb and dominant gene Gc was mapped base on the SSR linkage map. Takingadvantage of a lack of crossing over in females, reciprocal backcrossed progeny were used forlinkage analysis and recombination mapping of the Ga-Gb using w07 and C108, and Gc geneusing silkworm strains Dazao and i04. The phenotype segregation ratio in Ga-Gb system is1:1:2, and give hint to a passive penetrate function. Ga, Gb and Gc were mapped tochromosome 20, 28 and 28 respectively using the reciprocal BC1M (heterozygous male) cross,and the distance of the nearest markers are 0, 2.2 and 4.1 cM.The SSR linkage map in silkworm was also used for mapping of the mln gene usingsilkworm strains Dazao and i04. The genotyping in the non-recombining BC1F (heterozygousfemale) cross shows that mln was co-segregated with the SSR markers on chromosome 18.Based on the genotyping in BC1M (heterozygous male) population, we mapped the mln geneat the position of 45 cM in a linkage group consist of 20 SSR markers covering 142.3cM, andidentified two closely linked SSR markers, S1807 and S1808, which have no crossing over tothe mln gene in 171 individuals. Based on the sequence of these two markers, we made acontig of three BACs fill in the space between them. The contig will help to positionalcloning of the mln gene.
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