梯棱羊肚菌全基因组SNP/Indel分析及基于Indel标记的遗传连锁图谱构建

基于梯棱羊肚菌Morchella importuna两个子囊孢子培养物的全基因组测序数据,对全基因组范围内的变异位点进行分析。共鉴定到18 438个变异位点,平均每Mbp的变异位点数量为361个;变异位点以单核苷酸多态性SNP为主,共计17 104个,基因组中SNP的频率为335SNPs/Mbp;Indel多态性位点1 334个,以2-10bp的插入缺失为主;73.4% SNP/Indel位于基因间隔区域,外显子区域共检测到3 042个变异位点,占总数的16.50%;对基因功能产生确定影响的移码突变有1 088个,占5.90%,错义突变916个,占比4.97%;不同Scaffold上的SNP/Indel出现频率不同,SNP频率最大的为Scaffold80,平均每Mbp包含2 856个SNP,频率最低为Scaffold60和Scaffold75,分别为16SNPs/Mbp和30SNPs/Mbp;对≥11bp的Indel变异位点进行标记开发和多态性群体分析,成功开发出75对Indel标记。采用原生质体单细胞分离技术,获得了梯棱羊肚菌M04的两个可亲和的同核体菌株M04P01和M04P40,同时采用来自M04子囊果的58个单孢菌株作为作图群体,初步构建了包含75个Indel标记和1个交配型基因的梯棱羊肚菌遗传连锁图谱,共获得12个连锁群,连锁群总长度273.7cM。

Genome-wide SNP/Indel analysis and the construction of genetic linkage maps based on Indel markers of Morchella importuna

Based on two monosporic genome sequencing data, the genome-wide SNP/Indel variants’ calling was carried out of Morchella importuna. A total of 18 438 variant loci was identified, with an average of 361 variant loci per M base. The main variant loci were single nucleotide polymorphic (SNPs) with a total of 17 104 and variation rate of 335SNPs/Mbp. 1 334 insertion-deletion polymorphic loci (Indel) were identified, of which 2-10bp were dominant. 73.4% of SNP/Indels were located in the intergenic region, and 3 042 variant loci were detected in the exon region accounting for 16.50%. There were 1 088 frame-shift mutations (5.90%) and 916 missense mutations (4.97%) that have a definite effect on gene function. The SNP/Indel mutation rates on different Scaffolds were different, and Scaffold80 with the largest variation rate contained an average of 2 856 SNPs per M base, and Scaffold60 and Scaffold75 with the lowest mutation rates 16 and 30SNPs/Mbp, respectively. 75 polymorphic indel markers with the mutation loci ≥11bp were successfully developed by exploiting and polymorphic population analysis. Based on protoplast homokaryotic technology, two compatible strains M04P01 and M04P40 of parent strain M04 of Morchella importuna were obtained, together with 58 monospore populations from M04 ascocarp as mapping populations, twelve linkage groups with the total length of 273.7cM were preliminarily constructed containing 75 indel markers and a mating type gene of M. importuna.