To determine the causative variations associated with two chicken comb phenotypes, pendulous comb (PC) or upright comb (UC), two pooled genomic DNA samples from PC and UC chickens were re-sequenced by Next-Generation Sequencer, and genome-wide Single nucleotide polymorphisms (SNPs) were detected. Using three selective sweep approaches, FST , θπ, and Tajima's D, with top 5% window values serving as the threshold, a total of 84 positively selective genes (PSGs) were identified. There were no SNPs in exons of the PSGs with significant differences in allele frequencies between the two comb phenotype groups. Then, 515 differentially expressed genes (DEGs) between the PC and UC were identified by RNA-seq. Three genes including CD36 (CD36 molecule), ADAMTSL3 (ADAMTS-like 3), and AOX1 (aldehyde oxidases 1) are overlapped between PSGs and DEGs. After genotyping seven candidate SNPs in the regulatory regions of the three overlapping genes in 120 chickens from two other breeds, two variants (rs14607046 and rs731818051) in the regulatory regions of AOX1 and ADAMTSL3 were found to have significant differences in allele frequency between the PC and UC, suggesting that the two variants may be causative mutations for PC. Overall, our study shed light on the genetic basis underlying the PC phenotype in chickens.

中文翻译：

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全基因组重测序和转录组分析揭示了与家鸡下垂梳状表型相关的候选基因。

为了确定与两种鸡冠表型、下垂鸡冠 (PC) 或直立鸡冠 (UC) 相关的致病变异，来自 PC 和 UC 鸡的两个汇集的基因组 DNA 样本由下一代测序仪和全基因组单核苷酸重新测序检测到多态性 (SNP)。使用三种选择性扫描方法 FST、θπ 和 Tajima's D，以前 5% 的窗口值作为阈值，总共识别出 84 个正选择性基因 (PSG)。PSG 的外显子中没有 SNP，两个梳状表型组之间的等位基因频率存在显着差异。然后，通过 RNA-seq 鉴定了 PC 和 UC 之间的 515 个差异表达基因 (DEG)。包括 CD36（CD36 分子）、ADAMTSL3（ADAMTS 样 3）和 AOX1（醛氧化酶 1）在内的三个基因在 PSG 和 DEG 之间重叠。在对来自其他两个品种的 120 只鸡的三个重叠基因的调控区中的七个候选 SNP 进行基因分型后，发现 AOX1 和 ADAMTSL3 调控区的两个变体（rs14607046 和 rs731818051）在 PC 和 ADAMTSL3 的等位基因频率上存在显着差异UC，表明这两个变体可能是 PC 的致病突变。总的来说，我们的研究揭示了鸡 PC 表型的遗传基础。