Genome-wide association studies for small intestine length in an F₂population 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 F 2 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.ARTICLE HISTORY

Genome-wide association scan for QTL and their positional candidate genes associated with internal organ traits in chickens

“…These QTL detected herein may exhibit pleotropic effects with abdominal fat and carcass fat content traits, thus, selection based on genotype for these internal organ traits might affect fat deposition. Moreover, changes in the gizzard weights can influence nutrient availability in the small intestine; intestine lengths are associated with feed efficiency and growth in chickens [18, 19].…”

“…This gene is expressed in human intestinal epithelial cells and changes in its expression pattern can lead to intestinal disorders [62]. In chickens, intestinal disorders can affect feed efficiency, and consequently, animal performance [18, 19], and this is consistent with the observation that feed intake exhibited a positive genetic correlation with intestine weight (0.92) in a meat-type chicken population [8]. Thus, the SLC6A4 gene should be thoroughly investigated as a candidate for regulation of intestine length in chickens.…”

“…This increases the occurrence of ascites, a metabolic disorder characterized by accumulation of fluid in the abdominal cavity of birds [10, 11], hypertension syndrome (PHS) [12, 13] or even heart failure and sudden death syndrome (SDS) [14–17]. Moreover, changes in the weight of the gizzard can influence nutrient availability in the small intestine, and intestine length is associated with feed efficiency and growth in chickens [18, 19]. Long-term intense selection for carcass traits can also increase the occurrence of fatty liver syndrome [20].…”

Genome-wide association study for carcase traits in spent hens at 72 weeks old

“…Genome-wide association study (GWAS) strategies are a method that has been used successfully to examine molecular mechanisms underlying some quantitative traits (Li et al 2017). Our study aimed to detect the candidate region or genes that are responsible for carcase traits in spent layer hens.…”

Effects of early weaning on intestinal morphology, digestive enzyme activity, antioxidant status, and cytokine status in domestic pigeon squabs (Columba livia)

“…Hence, it requires a strong and healthy digestive system ( Dong et al., 2012 ). The small intestine is a vital digestive and absorptive organ and innate barrier that maintains the balance of the inner environment ( Li et al, 2017 ). Similar to piglets, the squab stage is an essential intestinal development period that affects growth performance, such as BW, ADG and rate of survival, later in adult pigeons.…”