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.