In this study, we speculate that RIN2 61-bp indel may have a positive effect on the growth traits of chickens and a negative effect on the abdominal fat weight of chickens. This Indel may be a potential molecular marker for auxiliary selection of good quality broilers.
In animal breeding, the discovery of key genes and molecular mechanisms that affect growth traits is an important step to improve breeding efficiency and speed up the breeding process [20, 21]. In order to improve the selection effect of main traits, traditional selection methods can be complemented by gene-assisted selection or molecular marker-assisted selection (MAS). MAS is an effective way to improve short-term traits [22, 23]. In this study, a new 61-bp deletion mutation was identified on the RIN2 gene through whole genome resequencing and PCR product sequencing. In the genetic analysis of 550 individuals of 7 varieties, it was found that there was a deletion mutation of RIN2 61-bp in all varieties. No functional studies on RIN2 gene in animal production have been reported.
Hatching weight is the main indicator of chick quality evaluation [24]. Previous studies have shown that there is a positive correlation between the hatching weight of broilers and the weight of slaughter. For every 1 g increase in hatching weight, the slaughter weight increases by 8–13 g [25, 26]. The economic value of high-hatching weight broilers is also generally higher than that of low- hatching weight broilers [27].
The abdomen is an important part of the fat deposition in chickens. Abdominal fat weight is highly related to the total body fat deposition in chickens and can be used as an index for selecting chicken fat deposition. Previous studies have found that excessive fat deposits in modern commercial broiler breeds can waste a lot of feed, while reducing slaughter rates and economic benefits [28, 29]. For consumers, eating broilers that accumulate too much fat may also cause human obesity or cause other diseases [30]. Therefore, the excessive deposition of abdominal fat in chickens has become one of the problems to be solved in the current broiler production.
In this study, we found that RIN2 gene was expressed in different tissues (Fig. 4), which is consistent with previous reports of widespread RIN2 expression [31]. In addition, RIN2 gene is highly expressed in abdominal fat, kidney, and heart, suggesting that it may be related to fat deposition and growth. The RIN2 61-bp deletion mutation site was significantly negatively correlated with chicken hatching weight (P < 0.05, Table 4). The hatching weight of type II individuals was greater than that of ID type and DD type. During the pre-growth period (1–7 weeks), the weight of the genotype II has always been the highest, while the weight of the DD genotype has generally been the lowest. Analysis of the gene frequency of 7 different chicken breeds revealed that the 61-bp deletion mutation has been highly selected in WRR (Table 1). We speculate that in terms of growth performance, RIN2 61-bp indel type II is the dominant genotype, and DD type is the inferior genotype. The 61-bp deletion of RIN2 may have a positive effect on chicken growth traits.
It is worth noting that the expression of RIN2 gene is highest in abdominal fat tissue. Quantitative analysis of RIN2 mRNA expression in abdominal fat tissue of different genotypes showed that the expression level of II was significantly higher than ID and DD (P < 0.05; Fig. 5a). Correlation analysis found that abdominal fat weight of type II individuals was significantly lower than that of ID and DD individuals (P < 0.05, Table 3). Based on the above results, it can be speculated that RIN2 61-bp indel is involved in the deposition of fat in the abdomen, which may have a negative effect on the fat traits of chickens, but the specific reason is unknown.