First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome
First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome
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DOI：
10.1046/j.1467-7652.2003.00036.x
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发表时间：
2003-11-01
影响因子：
13.8
通讯作者：
Gebhardt, C
中科院分区：
文献类型：
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作者：
Rickert, AM;Kim, JH;Gebhardt, C
在马铃薯基因组中已定位了对不同病原菌的定性和/或定量抗性基因的区域，采用聚合酶链反应（PCR）产物的单核苷酸多态性（snp）和插入缺失多态性（InDels）比较序列分析，筛选了17个四倍体和11个二倍体马铃薯基因型。大多数SNP和InDel标记来源于细菌人工染色体（BAC）插入物，其序列与具有核苷酸结合位点和亮氨酸丰富重复结构域（nbs - lrr型基因）的植物抗病基因家族相似。将44个含有bac插入的nbs - lrr型基因定位到14个位点，这些位点标记了马铃薯已知的抗性数量性状位点（QTL）。未与已知抗性基因样（RGL）序列连锁的抗性QTL用其他标记进行标记。共对28个基因型的78个基因组DNA片段进行了比较测序，总长度为31 kb。共鉴定出1498个SNP和127个InDel，平均每21个碱基对对应一个SNP，每243个碱基对对应一个InDel。四倍体基因型（pi = 0.72 × 10(-3)）的核苷酸多样性低于二倍体基因型（pi = 2.31 × 10(-3)）。与其他序列相比，RGL序列显示出更高的核苷酸多样性，表明进化是通过发散选择进行的。序列、序列相似度、snp和InDels的信息在数据库中提供，可通过互联网查询。
A panel of 17 tetraploid and 11 diploid potato genotypes was screened by comparative sequence analysis of polymerase chain reaction (PCR) products for single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), in regions of the potato genome where genes for qualitative and/or quantitative resistance to different pathogens have been localized. Most SNP and InDel markers were derived from bacterial artificial chromosome (BAC) insertions that contain sequences similar to the family of plant genes for pathogen resistance having nucleotide-binding-site and leucine-rich-repeat domains (NBS-LRR-type genes). Forty-four such NBS-LRR-type genes containing BAC-insertions were mapped to 14 loci, which tag most known resistance quantitative trait loci (QTL) in potato. Resistance QTL not linked to known resistance-gene-like (RGL) sequences were tagged with other markers. In total, 78 genomic DNA fragments with an overall length of 31 kb were comparatively sequenced in the panel of 28 genotypes. 1498 SNPs and 127 InDels were identified, which corresponded, on average, to one SNP every 21 base pairs and one InDel every 243 base pairs. The nucleotide diversity of the tetraploid genotypes (pi = 0.72 x 10(-3)) was lower when compared with diploid genotypes (pi = 2.31 x 10(-3)). RGL sequences showed higher nucleotide diversity when compared with other sequences, suggesting evolution by divergent selection. Information on sequences, sequence similarities, SNPs and InDels is provided in a database that can be queried via the Internet.