鸭产蛋量相关遗传变异和功能基因筛选及鉴定

【目的】通过高通量混池重测序和选择清除分析比较鸭不同产蛋量组间基因组显著差异区域内的SNP和基因差异，以筛选和鉴定出鸭产蛋量相关的遗传变异位点和功能基因，为通过分子遗传育种手段提高鸭产蛋性能提供依据。【方法】根据金定鸭群体开产后150 d内个体产蛋量情况，选择2种极端表型，分为高产蛋组(CH)和低产蛋组(CL)。基于混池全基因组重测序和选择清除分析技术筛选不同鸭产蛋量组间基因组显著差异区域内的SNP及相关功能基因，通过单个样本PCR扩增子测序对筛选的产蛋量相关SNP进行验证，对筛选的候选基因进行GO功能和KEGG通路富集分析，确定候选基因参与的最主要生化代谢途径和信号转导途径，并分析不同基因型间产蛋量高低差异。【结果】在低产蛋量组和高产蛋量组分别获得192 071 438和229 836 820条的clean reads,共定位到的SNP差异极显著区间为1 368个，受选择候选基因为214个，而且这些区间和基因主要位于Z号染色体，主要包括KDM4C、LURAP1L、PTCH1、PRUNE2、TRPM3和VPS13AD等基因。验证结果表明重测序结果准确。GO功能分析表明，受选择基因在分子...

Screening and Identification of Genetic Variation and Functional Genes Related to Egg Production in Ducks

【Objective】 The aim of this study was to compare single nucleotide polymorphism (SNP) and gene differences in regions with significant genomic differences between groups of ducks with different egg production using mixed pool whole-genome re-sequencing and selective clearance analysis technology, and screen and identify genetic variation sites and functional genes related to egg production, so as to provide a molecular basis for improving egg-laying performance.【Method】 In this study, two extreme phenotypes of Jinding ducks were selected according to individual egg production within 150 days after the opening:A high-egg-production group (CH) and a low-egg-production group (CL). SNP and related functional genes that located in regions with significant genomic differences between two groups were screened based on mixed pool whole-genome re-sequencing and selective clearance analysis technology.The screened SNP related to egg production were verified by PCR sequencing of each sample.GO function and KEGG pathway enrichment analysis were performed on the selected candidate genes to determine the most important biochemical metabolic pathway and signal transduction pathway involved by the candidate genes.And differences in egg production among different genotype of each SNP were analyzed.【Result】 192 071 438 and 229 836 820 clean reads were obtained in CL and CH groups, respectively.There were 1 368 significantly different SNP fragment regions, and 214 candidate genes were selected.These intervals and genes were mainly located on chromosome Z, mainly including KDM4C, LURAP1L, PTCH1, PRUNE2, TRPM3 and VPS13AD genes.The verification results showed that the re-sequencing results were accurate.GO function analysis showed that these selected genes were involved in three ontologies:Molecular function, cellular component and biological process.KEGG pathway enrichment analysis showed that these genes were mainly enriched in metabolic pathway, regulation of actin cytoskeleton, ribosome biogenesis in eukaryotes and other signal pathways.Multiple mutations, Z-28286537, Z-28286879, Z-28288421, Z-28434122, Z-28436368 in the candidate gene KDM4C, Z-30802227 in LURAP1L gene, Z-36500134, Z-36503668, Z-36534782, Z-36684262, Z-36710928, Z-36732487 in TRPM3 gene, Z-37498270, Z-37513004 in VPS13A gene, and Z-41510597 in PTCH1 gene were affected the ducks egg production.【Conclusion】 There were multiple SNPs and genes significantly related to egg production on chromosome Z in ducks. These results provided a molecular basis for improving egg-laying performance and accelerating the breeding process in ducks.