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Genetic Linkage

A combination method of SLAF (specific length amplified fragment) sequencing and experiment markers analysis was used to construct genetic map. We firstly detected 2,719 single nucleotide polymorphisms (SNPs) by SLAF-seq and constructed a new genetic map consisting of 257 markers (SNPs). However, it only anchored about 45% of estimated genome. We then compared the re–sequencing data of ZZM2289 to Zhongzhi No.13, and developed 97 insertion & deletion (InDel) markers to update the genetic map. Meanwhile, we screened the 200 top scaffolds that have less than 2 SNP or InDel markers for simple sequence repeat (SSR) loci, and designed 2,282 markers with each scaffold had more than 10. All the 2,282 SSR and 97 InDel markers were used to screen against the population. After filtering those markers with low PCR quality, those having no polymorphism and those showing significantly distorted segregation in the population, the retained 45 InDel and 124 SSR markers together with the 259 SNP makers were used to construct the genetic map using Joinmap3 software (http://www.kyazma.nl/index.php/mc.JoinMap). Finally, we successfully constructed a genetic map that spans 1,790.08 cM and has 406 markers including 39 InDel, 251 SNP and 116 SSR markers.

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