Genome-wide association studies for small intestine length in an F2 population of chickens

Abstract

Small intestine length is an important physiological index that is effected by nutrient intake and thus plays roles in growth and egg-laying in chickens. Although there are some studies about small intestine length, little information is available regarding the genetic architecture of small intestine. The current study was conducted to investigate the genetic architecture of small intestine length. A total of 1435 F2 hens from a White Leghorn and Dongxiang reciprocal cross were phenotyped for the duodenum lengths (DL), jejunum length (JL) and ileum length (IL), and genotyped using a chicken 600 K single nucleotide polymorphism (SNP) genotyping array. SNP-based heritability estimation was performed by SAS algorithm and univariate genome-wide association studies (GWAS) were performed by GEMMA, a genome-wide efficient mixed-model association algorithm. The JL and IL exhibited high SNP-based heritability estimation (0.43 and 0.49, respectively), while the heritability estimation was moderate for the DL (0.36). Three independent univariate genome-wide screens for these small intestine lengths identified 202, 298 and 119 SNPs that were significantly associated with the DL, JL and IL, respectively. The significant genomic regions indicated that ∼170 Mb on GGA1 is an important region for these small intestine lengths. In this region, 78 SNPs were associated with them, of which 4 were involved in cell proliferation and development, corresponding to RB1 (rs313207223), CKAP2 (rs312737959) and SIAH3 (rs312771221, rs15494052) genes. Small intestine length exhibited good SNP-based heritability estimation and the GWAS results indicated that an important genomic region was located on GGA1.