Three indel variants in chicken <i>Lpin1</i> exon 6/flanking region and the association with performance traits

1. LPIN1 is a Mg²⁺-dependent phosphatidic acid phosphatase. Variation in chicken <i>Lpin1</i> exon 6 and its flanking regions were identified and three indel variants in 6 breeds and their associations with performance traits were studied.2. Seven variants were detected from 6 breeds, which contained a synonymous tri-allelic variant (c.924A/T/C) and three indels. The exon 6 variants detected from chicken breeds were conservative among bird species. The indel variation frequency presented clear differences among breeds.3. Two coding indels (c.1014-1018del3 and c.1125-1138del12) were multiples of 3 nucleotides and maintained the open reading frames of LPIN1 proteins. However, they were predicted to result in the clear change of the RNA secondary structure of chicken <i>Lpin1</i> exon 6 and LPIN1 protein conformation.4. The association analysis showed that c.871-15-22del6 variation had a significant effect on body weight at hatch (BW0) and 2 weeks (BW2); c. 1014-1018del3 variation had a significant effect on BW4, BW6, caecum length and gizzard weight (GW) traits; c.1125-1138del12 variation had a significant effect on BW12, shank length at 4 weeks (SL4), carcass weight, lactate dehydrogenase traits (LDH), glucose (GLU) and albumin (ALB) traits. The genotype combination for c.1014-1018del3 and c.1125-1138del12 also presented significant effects on SL4, SL8, GW, leg muscle weight, ALB, GLU and LDH.5. The study demonstrated that chicken <i>Lpin1</i> has an important effect on chicken hatch weight, serum GLU and ALB level.1. LPIN1为Mg²+依赖性磷脂酸磷酸酶（phosphatidic acid phosphatase）。本研究鉴定了鸡Lpin1基因第6外显子（exon）及其侧翼区域的遗传变异，并针对6个鸡品种中发现的3个插入缺失变异（indel），开展了其与生产性能性状的关联分析。 2. 从6个鸡品种中共检测到7个变异位点，其中包含1个同义三等位基因变异（c.924A/T/C）与3个插入缺失变异。鸡品种中鉴定的第6外显子变异在鸟类物种间具有保守性，且各品种间的插入缺失变异频率存在显著差异。 3. 两个编码区插入缺失变异（c.1014-1018del3与c.1125-1138del12）的核苷酸长度均为3的倍数，可维持LPIN1蛋白的开放阅读框（open reading frame, ORF）。但生物信息学预测显示，此类变异会显著改变鸡Lpin1基因第6外显子的RNA二级结构以及LPIN1蛋白的空间构象。 4. 关联分析结果表明：c.871-15-22del6变异对鸡出雏重（BW0）与2周龄体重（BW2）具有显著影响；c.1014-1018del3变异对4周龄体重（BW4）、6周龄体重（BW6）、盲肠长度与肌胃重量（GW）性状存在显著调控效应；c.1125-1138del12变异则显著影响12周龄体重（BW12）、4周龄胫长（SL4）、屠体重、乳酸脱氢酶活性（LDH）、葡萄糖（GLU）与白蛋白（ALB）相关性状。此外，c.1014-1018del3与c.1125-1138del12的基因型组合对4周龄胫长（SL4）、8周龄胫长（SL8）、肌胃重量、腿肌重量、白蛋白（ALB）、葡萄糖（GLU）与乳酸脱氢酶活性（LDH）均呈现显著关联效应。 5. 本研究证实，鸡Lpin1基因对鸡出雏重、血清葡萄糖（GLU）与白蛋白（ALB）水平具有重要调控作用。