White bulb colors of onion (Allium cepa L.) are determined by the C and I loci which control the so-called recessive and dominant white bulb colors, respectively. To identify the causal gene responsible for the I locus, a combined approach of bulked segregant analysis and RNA-Seq was used in the present study. A total of 68 contigs containing homozygous single nucleotide polymorphisms (SNPs) between red and dominant white bulked RNAs were identified. The position of I locus was found to be located at chromosome 3 by performing comparative analysis of these contigs and using a previously constructed linkage map. After verification of homozygous SNPs by sequencing of PCR products, 12 high resolution melting, one cleaved amplified polymorphic sequence, and one InDel markers were developed. A linkage map flanking the I locus was constructed using these markers. Two tightly linked markers (DW51596 and DW35019) flanking the I locus were identified by analyzing 1457 F4 individuals. A total of 104 and 39 contigs showing more than tenfold increase of expression in red and dominant white bulks, respectively, were identified. Transcriptions of all structural genes encoding enzymes in flavonoid biosynthesis pathway were significantly reduced in the dominant white bulk. Transcription levels of most contigs showing more than tenfold reduced expression in dominant white were also significantly reduced in the recessive white bulbs controlled by the C locus. Genomic DNA sequences of 12 genes encoding transcription factors assumed to regulate flavonoid biosynthesis were analyzed. However, the causal gene for the I locus could not be identified.

中文翻译：

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构建控制显性白球茎颜色的 I 基因座侧翼的连锁图谱，以及分析洋葱​​ (Allium cepa L.) 中显性白球和红色球茎之间差异表达的基因

洋葱 (Allium cepa L.) 的白色球茎颜色由 C 和 I 基因座决定，它们分别控制所谓的隐性和显性白色球茎颜色。为了鉴定负责 I 基因座的因果基因，本研究使用了批量分离分析和 RNA-Seq 的组合方法。共鉴定了 68 个包含红色和显性白色散装 RNA 之间纯合单核苷酸多态性 (SNP) 的重叠群。通过对这些重叠群进行比较分析并使用先前构建的连锁图，发现 I 基因座的位置位于 3 号染色体。通过 PCR 产物测序验证纯合 SNP 后，开发了 12 个高分辨率熔解、1 个切割的扩增多态性序列和 1 个 InDel 标记。使用这些标记构建了位于 I 基因座侧翼的连锁图。通过分析 1457 个 F4 个体，鉴定了位于 I 基因座侧翼的两个紧密连锁的标记（DW51596 和 DW35019）。总共鉴定了 104 个和 39 个重叠群，分别在红色和显性白色块中的表达增加了 10 倍以上。在主要的白色块体中，编码类黄酮生物合成途径中酶的所有结构基因的转录显着减少。大多数重叠群的转录水平在显性白色中的表达降低了十倍以上，在 C 基因座控制的隐性白色球茎中也显着降低。分析了 12 个基因的基因组 DNA 序列，这些基因编码假定调节类黄酮生物合成的转录因子。然而，无法鉴定 I 基因座的因果基因。