Via bulked segregant analysis sequencing combined with linkage mapping, the ist gene responsible for the irregularly striped rind mutation was delimited to a 144-kb region in cucumber. Sequencing and expression analysis identified Csa1G005490 as the candidate gene. The rind appearance of cucumber is one of the most important commercial quality traits. Usually, an immature cucumber fruit has a uniform rind that varies from green to yellow to white among different cultivated varieties. In the present paper, we isolated a novel fruit appearance cucumber mutant, ist, that has an irregularly striped rind pattern. The mutant displayed green irregular stripes on a yellow-green background at the immature fruit stage. Genetic analysis revealed that a single recessive gene, ist, is responsible for this mutation. A BSA (bulked segregant analysis) sequencing approach combined with genetic mapping delimited the ist locus to an interval with a length of 144 kb, and 21 predicted genes were annotated in the region. Based on mutation site screening and expression analysis, two single-nucleotide polymorphisms within the candidate gene, Csa1G005490, were identified as constituting the mutation. Csa1G005490 encodes a polygalacturonase-1 noncatalytic subunit beta protein (PG1β) known to be involved in fruit softening. The expression of Csa1G005490 was significantly lower in the ist mutant than in the wild type. Transcriptome analysis identified 1796 differentially expressed genes (DEGs) between the ist mutant and wild type. Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were enriched mostly in photosynthesis and chlorophyll metabolism pathways. Decreased expression patterns of several chlorophyll synthesis genes in the mutant suggest that ist plays a key role in chlorophyll biosynthesis. These results will provide new insight into the molecular mechanism underlying rind appearance polymorphisms in cucumber.

中文翻译：

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一个不规则条纹的果皮突变体揭示了对黄瓜 (Cucumis sativus L.) 中 PG1β 功能的新认识。

通过批量分离分析测序结合连锁作图，导致不规则条纹果皮突变的 ist 基因被定界到黄瓜中的 144-kb 区域。测序和表达分析确定 Csa1G005490 为候选基因。黄瓜的外皮外观是最重要的商业品质特征之一。通常，未成熟的黄瓜果实具有均匀的果皮，在不同栽培品种之间从绿色到黄色到白色不等。在本文中，我们分离了一种具有不规则条纹果皮图案的新型果实外观黄瓜突变体 ist。该突变体在未成熟果实阶段在黄绿色背景上显示出绿色不规则条纹。遗传分析表明，一个隐性基因 ist 是造成这种突变的原因。BSA（bulked segregant analysis）测序方法与遗传作图相结合，将 ist 基因座划分为一个长度为 144 kb 的区间，并在该区域注释了 21 个预测基因。基于突变位点筛选和表达分析，候选基因Csa1G005490内的两个单核苷酸多态性被鉴定为构成突变。Csa1G005490 编码一种多聚半乳糖醛酸酶-1 非催化亚基 β 蛋白 (PG1β)，该蛋白已知与水果软化有关。Ist突变体中Csa1G005490的表达明显低于野生型。转录组分析确定了 ist 突变体和野生型之间的 1796 个差异表达基因 (DEG)。基因本体（GO）注释和京都基因和基因组百科全书（KEGG）富集分析表明，这些DEG主要富集在光合作用和叶绿素代谢途径中。突变体中几个叶绿素合成基因的表达模式降低表明 ist 在叶绿素生物合成中起关键作用。这些结果将为黄瓜外皮外观多态性的分子机制提供新的见解。