High-throughput genotyping in citrus accessions using an SNP genotyping array
High-throughput genotyping in citrus accessions using an SNP genotyping array
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DOI：
10.1007/s11295-012-0542-3
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发表时间：
2013-02-01
影响因子：
2.4
通讯作者：
Omura, Mitsuo
中科院分区：
文献类型：
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作者：
Fujii, Hiroshi;Shimada, Takehiko;Omura, Mitsuo
我们开发了一个384多重SNP阵列，命名为CitSGA-1，柑橘品种的基因分型，并评估了基因分型的性能和可靠性。SNPs调查的直接序列比较的序列标记位点（STS）片段扩增的基因组DNA的品种代表在日本柑橘育种的遗传多样性。在1497个SNP候选者中，基于Illumina的珠阵列标准的物理参数选择用于高通量基因分型阵列的384个SNP。将使用CitSGA-1的测定应用于日本育种的88个后代和103个柑橘种质的杂交群体，其产生73，726个SNP调用。总共351个SNP（91%）可以在DNA样品中识别不同的基因型，导致该测定的成功率与先前报道的其他植物物种的成功率相当。为了验证SNP基因型调用的可靠性，采用亲子关系分析，结果表明，可靠的SNP和相应的STS的数量分别为276和213。本文报道的多重SNP基因分型阵列将有助于有效构建连锁图谱，用于标记辅助育种的标记检测，以及用于品种鉴定。
We developed a 384 multiplexed SNP array, named CitSGA-1, for the genotyping of Citrus cultivars, and evaluated the performance and reliability of the genotyping. SNPs were surveyed by direct sequence comparison of the sequence tagged site (STS) fragment amplified from genomic DNA of cultivars representing the genetic diversity of citrus breeding in Japan. Among 1497 SNPs candidates, 384 SNPs for a high-throughput genotyping array were selected based on physical parameters of Illumina's bead array criteria. The assay using CitSGA-1 was applied to a hybrid population of 88 progeny and 103 citrus accessions for breeding in Japan, which resulted in 73,726 SNP calls. A total of 351 SNPs (91 %) could call different genotypes among the DNA samples, resulting in a success rate for the assay comparable to previously reported rates for other plant species. To confirm the reliability of SNP genotype calls, parentage analysis was applied, and it indicated that the number of reliable SNPs and corresponding STSs were 276 and 213, respectively. The multiplexed SNP genotyping array reported here will be useful for the efficient construction of linkage map, for the detection of markers for marker-assisted breeding, and for the identification of cultivars.