Research Note: Association of LEPR gene polymorphism with growth and carcass traits in Savimalt and French Giant meat-type quails

Abstract

The leptin receptor (LEPR) gene is a member of the class I cytokine receptor family, which plays an important role in weight regulation, fat accumulation and neuroendocrine function in animals. This study aimed to explore the association of single nucleotide polymorphisms (SNPs) of the LEPR gene with growth and carcass traits in meat-type quail by PCR amplification and DNA direct sequencing. In this study, genomic DNA was extracted from blood samples of 36 female Savimalt (SV) quails and 49 female French Giant (FG) quails. Growth traits (measured at 3 or 5 wk) and carcass traits (measured at 5 wk) were used for LEPR gene association analysis. The results showed the existence of 9 SNPs (T81C, G90T, C187A, A191G, A219G, G258A, C286T, G346A, and G373A) of the LEPR gene in the 2 quail strains. The statistical analyses indicated that these SNPs of LEPR gene was significantly associated with shank circumference (SC), shank length (SL), breastbone length (BBL), heart rate (HR), and whole net carcass rate (WNCR) of FG (P < 0.05); chest width (CW), body length (BL), leg muscle rate (LMR), whole net carcass rate (WNCR), and heart rate (HR) of SV (P < 0.05). While haplotypes showed significant effect on SL, BBL, heart weight (HW), WNCR, and HR of FG (P < 0.05). Therefore, the LEPR gene may serve as a molecular genetic marker for improving growth and carcass traits in quails.

INTRODUCTION

The leptin receptor (LEPR) gene is a member of the class I cytokine receptor family, which binds mainly to leptin protein. Studies had found that it is widely distributed in multiple tissues of the body, which plays an important role in weight regulation, fat accumulation and neuroendocrine function in animals (Considine et al., 1996; Matsuoka et al., 1997). The distinct mutation sites and genotypes of this gene have been found to have varying impacts on animal growth, carcass quality, and reproductive traits. De Matteis et al. (2015) have demonstrated that 8 SNPs of the LEPR gene had a significant impact on growth traits of buffalo. Ma et al. (2022) purported that the polymorphism of the LEPR gene was significantly associated with litter size in Mongolia and Ujimqin sheep. Kim et al. (2017) found 10 SNPs of the LEPR gene was significantly associated with meat quality traits in Berkshire pigs. Raza et al. (2020) found the SNP (g.24256T>A) of the LEPR gene was significantly associated with backfat thickness of Qinchuan cattle and Nanyang cattle, whereas the SNP (g.24267G>C) of the LEPR gene was significantly associated with backfat thickness of Qinchuan cattle. Thus, the LEPR gene has been widely used to evaluate genetic diversity in many regions with different breeds.

Quails are economic poultry extensively reared in China, which has characteristics such as high egg production performance, high nutritional value of both eggs and meat, significant medicinal properties, short growth cycle, and substantial economic benefits (Bai et al., 2023; Wang et al., 2023). Quails are widely welcomed by consumers worldwide for its rich minerals, high protein, beneficial fatty acids and other nutrients compared with the other poultry species such as chickens and ducks (Bai et al., 2023). With the improvement of living standards, people have gradually developed a healthy dietary habit of high protein and low cholesterol. As a result, the demand for quail products has been increasing. Furthermore, with a better understanding of the nutritional value of quail meat and eggs, the consumption of quail meat has started to gain a significant share in the poultry meat market. Products such as crispy quail, quail jerky, smoked quail, spiced quail, and cordyceps quail, which are processed from meat quails and discarded egg-laying quails, have gradually entered the consumer market. This has greatly promoted the breeding of meat quails. However, less attention has been paid to meat-type quail breeding at home and abroad, especially at the molecular level, which is still in its infancy (Priti and Satish, 2014). With the continuous development and improvement of molecular biology and genetics, the use of molecular genetic markers for assisted breeding has become a convenient, fast, and efficient method in animal breeding (Zhang et al., 2014). Multiple studies have demonstrated that the LEPR gene has a significant influence on the economic traits of animals (El Moujahid et al., 2014; Ma et al., 2022; Zhao et al., 2022). But there is little published work on association studies of LEPR gene with growth and carcass traits in quails (El-Tarabany et al., 2022). The objective of this study is to identify the LEPR gene polymorphism with the growth and carcass traits in Savimalt (SV) quail and French Giant (FG) quail strains to provide reference values for the future research of quail breeding.

MATERIALS AND METHODS

Ethics Statement

All experimental procedures conducted in this study were approved by the Animal Care and Use Committee of Henan University of Science and Technology (Luoyang, China; Latitude: 34°72′ N; Longitude: 112°45′ E). The animal experimentation was carried out in strict accordance with the Guidelines for Experimental Animals established by the Ministry of Science and Technology (Beijing, China).

Experimental Animals, Housing Condition, and Phenotypic Measurements

A total of 36 female SV strain, and 49 female FG strain were randomly selected from a commercial hatchery (Henan University of Science and Technology Quail Breeding Co. Ltd., Luoyang, China). Eighty five quails were healthy and fed in single cages at the experimental farm of Henan University of Science and Technology under the same conditions (dry, clean, and good ventilation system). The temperature was kept at 37°C from 1 to 3 d of age, at 35 °C from 4 to 7 d of age, at 30°C from 8 to 14 d of age, and then it was reduced gradually to room temperature (25°C). The humidity was 20% from 1 to 3 d and then gradually increased to 65% in room. During the whole investigation, all quails were allowed to feed and drink ad libitum. Supplemental heaters were provided first 2 wk of growth. All of the quails were exposed to a 14L:10D photoperiod, with white lights on at 5:00 AM until 35 d. All 2 strains were fed a diet with 2,900 kcal/Kg of ME and 24% CP from d 1 to 35 (NRC, 1994). The growth traits included chest depth (CD), chest width (CW), breastbone length (BBL), body length (BL), shank length (SL), and shank circumference (SC) were measured at 3 and 5 wk of age in 2 quail strains. The carcass traits included body weight (BW), dressed carcass weight (DCW), whole net carcass weight (WNCW), heart weight (HW), liver weight (LW), breast muscle weight (BMW), leg muscle weight (LMW), dressing percentage (DP), whole net carcass rate (WNCR), heart rate (HR), liver rate (LR), breast muscle rate (BMR) and leg muscle rate (LMR) were measured at 5 wk of age in 2 quail strains.

DNA Samples, Primer Designing, PCR Amplification, and DNA Sequencing

Blood samples (5 mL) were taken from the wings of 85 quails (36 SV and 49 FG) into a syringe containing 2% EDTA used as an anticoagulant and stored at -80°C for further experiment. Genomic DNA was isolated from venous blood samples using a poultry whole DNA extraction kit (Dingguo Changsheng Biotechnology Company, Beijing, China). Based on the potential SNPs of LEPR gene published in the NCBI database (https://www.ncbi.nlm.nih.gov/), the primer pairs were designed using Primer Premier 5.0 software (Premier Biosoft International, Palo Alto, CA), which were F-ATGCTGCTTGATTCTTC and R-CCCTAGGCAAATGGTA. The primer specificity was verified by BLAST at NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi). The expected amplified segment size was 492 bp. PCR was performed in a total volume of 10 μL, which included 5 μL of the 2 × Taq PCR Master Mix, 1 μL of each primer, 1 μL genomic DNA, and 3 μL double-distilled water. The reaction conditions were as follows: initial denaturation at 95°C for 4 min, followed by 35 cycles of 95°C for 40 s, annealing for 58°C for 1 min, extension at 72°C for 1 min 20 s, and a final extension at 72°C for 5 min. The reaction system was stored under 4°C (El-Tarabany et al., 2022). Then, the amplified samples of the LEPR gene were sent to Xi'an Tsingke biological Co., Ltd. for sequencing.

Statistical Analysis

All SNPs were analyzed using Chromas software (version 2.6.6; Technelysium, Queensland, Australia). The genotyping results of the LEPR gene were recorded using Excel software (version 2016; Microsoft, Redmond, Washington, DC). The population genetic information was analyzed using MSRcall software (http://www.msrcall.com/). The linkage disequilibrium (LD) and haplotype analysis were conducted using SHEsis software. Association analysis of LEPR polymorphisms with growth and carcass traits was performed using Duncan’ s multiple range test in SPSS (version 27.0; IBM Corp., Armonk, NY). The results were expressed as means ± standard error (SE). Differences were considered highly significant or significant at P ≤ 0.01 or P ≤ 0.05, respectively. The association analysis model of growth and carcass traits was as follows:

$$Y_{ij}=\mu +G_i+e_{ij}$$ (1)

Y_ij is the phenotype value, μ is the total mean value, G_i is the effect of genotype, and e_ij is the random error.

RESULTS AND DISCUSSION

Polymorphisms of LEPR Gene in Meat-type Quail

The LEPR gene is well known to play an important role in economic traits of animals. Researchers have discovered the polymorphism of the LEPR gene in multiple species. In this study, we have detected polymorphisms of the LEPR gene in quails through PCR amplification and DNA sequencing analysis. Nine SNPs (T81C, G90T, C187A, A191G, A219G, G258A, C286T, G346A and G373A) identified in 2 quail strains of LEPR gene were genotyped by sequencing technology (Figure 1). It can be seen from Table 1 that 3 genotypes were identified in the LEPR gene of the 2 quail strains except for the C187A site in SV. In SV, the dominant genotypes at the T81C, G90T, C187A, A191G, A219G, G258A, C286T, G346A, and G373A sites were TT, GT, CC, GG, AG, AG, CT, AA, and AG, respectively, with frequencies of 0.889, 0.556, 0.972, 0.528, 0.472, 0.444, 0.556, 0.500, and 0.472. In FG, the dominant genotypes at the T81C, G90T, C187A, A191G, A219G, G258A, C286T, G346A, and G373A sites were TT, GG, CC, AG, AA, GG, CT, GG, and GG, respectively, with frequencies of 0.783, 0.457, 0.804, 0.457, 0.457, 0.587, 0.478, 0.587, and 0.587. The genetic diversity at the C187A site in the studied population of SV exhibited a minimum heterozygosity level of 0.054. Conversely, the A219G and G373A sites in SV, along with the A191G and C286T sites in FG, manifested a maximum heterozygosity level of 0.500, indicating elevated genetic variation at these sites. The polymorphic information content (PIC) analysis results showed that the T81C and C187A in both quail populations exhibited low levels of polymorphism (0 < PIC < 0.25), indicating that these population genetics were subject to large artificial and directional selection. While the remaining sites showed moderate levels of polymorphism (0.25 < PIC < 0.50), indicating their genetic potential. The chi-square test revealed that only the T81C and C187A deviated from Hardy-Weinberg equilibrium (HWE) in SV (P < 0.05). The remaining mutation sites were in accordance with HWE (P > 0.05), indicating their suitability for subsequent association analysis (Table 1).

Figure 1.

Sequencing results of LEPR gene.

Table 1.

Genotype frequency, allele frequency, and Hardy-Weinberg's law data of SNPs of LEPR gene in quail.

					Allelic frequency		HWE3		Ho4	He5	PIC6	Ne7
SNP1	S2	Genotypic frequency			Major	Minor	χ2	P
T81C	SV(36)	0.889(TT)	0.083(CT)	0.028(CC)	0.931	0.069	4.543	0.033	0.871	0.129	0.121	1.148
	FG(49)	0.783(TT)	0.174(CT)	0.043(CC)	0.870	0.130	2.504	0.114	0.773	0.227	0.201	1.293
G90T	SV(36)	0.139(GG)	0.556(GT)	0.306(TT)	0.583	0.417	0.735	0.391	0.514	0.486	0.368	1.946
	FG(49)	0.457(GG)	0.348(GT)	0.196(TT)	0.630	0.370	2.957	0.085	0.534	0.466	0.357	1.873
C187A	SV(36)	0.972(CC)	0.000(AC)	0.028(AA)	0.972	0.028	36.000	0.000	0.946	0.054	0.053	1.057
	FG(49)	0.804(CC)	0.152(AC)	0.043(AA)	0.880	0.120	3.535	0.060	0.789	0.211	0.188	1.267
A191G	SV(36)	0.139(AA)	0.333(AG)	0.528(GG)	0.694	0.306	1.657	0.198	0.576	0.424	0.334	1.737
	FG(49)	0.261(AA)	0.457(AG)	0.283(GG)	0.511	0.489	0.344	0.557	0.500	0.500	0.375	1.999
A219G	SV(36)	0.250(AA)	0.472(AG)	0.278(GG)	0.514	0.486	0.108	0.742	0.500	0.500	0.375	1.998
	FG(49)	0.457(AA)	0.348(AG)	0.196(GG)	0.630	0.370	2.957	0.085	0.534	0.466	0.357	1.873
G258A	SV(36)	0.306(GG)	0.444(AG)	0.250(AA)	0.528	0.472	0.423	0.516	0.502	0.498	0.374	1.994
	FG(49)	0.587(GG)	0.304(AG)	0.109(AA)	0.739	0.261	2.044	0.153	0.614	0.386	0.311	1.628
C286T	SV(36)	0.139(CC)	0.556(CT)	0.306(TT)	0.583	0.417	0.735	0.391	0.514	0.486	0.368	1.946
	FG(49)	0.261(CC)	0.478(CT)	0.261(TT)	0.500	0.500	0.087	0.768	0.500	0.500	0.375	2.000
G346A	SV(36)	0.167(GG)	0.333(AG)	0.500(AA)	0.667	0.333	2.250	0.134	0.556	0.444	0.346	1.800
	FG(49)	0.587(GG)	0.326(AG)	0.087(AA)	0.750	0.250	0.783	0.376	0.625	0.375	0.305	1.600
G373A	SV(36)	0.278(GG)	0.472(AG)	0.250(AA)	0.514	0.486	0.108	0.742	0.500	0.500	0.375	1.998
	FG(49)	0.587(GG)	0.304(AG)	0.109(AA)	0.739	0.261	2.044	0.153	0.614	0.386	0.311	1.628

Abbreviations: FG, French Giant meat quail; He⁵, heterozygosity; Ho⁴, homozygosity; HWE³, Hardy-Weinberg equilibrium test; Ne⁷, effective allele numbers; PIC⁶, polymorphism information content; S², strain; SNP¹, single nucleotide polymorphism; SV, Savimalt meat quail.

Association Analysis of LEPR Gene With Growth and Carcass Traits

To meet the demands of animal breeding, methods such as genome sequencing or gene chip analysis are employed to analyze polymorphisms in different individuals. This involved conducting linkage disequilibrium analysis and haplotype analysis on the detected SNPs, which helped explore the correlation and genetic characteristics between genes. Consequently, more accurate genetic foundations can be provided for breeding selection. Furthermore, conducting association analysis with production performance can help identify genotype variants that significantly impact production performance. This provides a scientific basis for achieving breeding goals. El Moujahid et al. (2014) purported that the polymorphisms of the LEPR gene was significantly associated with growth and feed efficiency in meat-type chickens. Ma et al. (2022) purported that the polymorphism of the LEPR gene was significantly associated with litter size in Mongolia and Ujimqin sheep. Additionally, Raza et al. (2020) discovered that the SNP (g.24256T>A) of the LEPR gene was significantly associated with backfat thickness of Qinchuan cattle and Nanyang cattle, whereas the SNP (g.24267G>C) of the LEPR gene was significantly associated with backfat thickness of Qinchuan cattle. These results suggest that the LEPR gene may play an important role in regulating animal growth and reproduction. Our results were conducted to correlate the growth traits at 3 or 5 wk of age of meat quail (Table S1). The results showed that the C187A site was significantly associated with the SC at 3 wk of age in the FG strain, and individuals with the AC genotype had significantly higher SC (P < 0.05, Table 2). The A191G, C286T, G346A, and G373A sites were significantly associated with the SL at 3 wk of age in the FG strain, and individuals with the mutation genotypes (GG/TT/AA/AA) had significantly higher SL (P < 0.05). Additionally, the results showed that the G90T, A219G, G346A, G373A sites were significantly associated with the SL at 5 wk of age in the FG strain, and individuals with the mutation genotypes (TT/GG/AA/AA) had significantly higher SL (P < 0.05). The G258A, G346A, and G373A sites were significantly associated with the BBL at 5 wk of age in FG, and individuals with the wild genotypes (GG/GG/GG) had significantly higher BBL (P < 0.05). The G90T and C286T sites were significantly associated with the CW at 5 wk of age in the SV strain, and individuals with the mutation genotypes (TT/TT) had significantly higher CW (P < 0.05). The A191G and G346A sites were significantly associated with the BL at 5 wk of age in the FG strain, and individuals with the wild genotypes (AA/GG) had significantly higher BL (P < 0.05). Our results were conducted to correlate the carcass traits of quail at 5 wk of age (Table S2). The result showed that the C187A site was significantly associated with the HR in the FG strain, and individuals with the AC genotype had significantly higher HR (P < 0.05, Table 3). The G258A, G346A, and G373A sites were significantly associated with the WNCR in the FG strain, and individuals with the homozygous (AG/AG/AG) genotype had significantly higher WNCR (P < 0.05). The A191G and G346A sites were significantly associated with the LMR in the SV strain, and individuals with the mutation (GG/AA) genotype had significantly higher LMR (P < 0.05). The G346A sites were significantly associated with the WNCR and HR in the SV strain. Individuals with the GG genotype had significantly higher WNCR, whereas individuals with the AA genotype had significantly higher HR (P < 0.05). Similarly to our results, El-Tarabany et al. (2022) observed and compared the egg production rate, body weight, and feed conversion rate of female Japanese quails with different LEPR genotypes, and found only 2 SNPs (A277G and A304G) of LEPR gene had a significant correlation to these traits (P < 0.05). While 7 SNPs (G90T, A191G, A219G, G258A, C286T, G346A, G373A) of LEPR gene which were significantly correlated to growth and carcass traits in our results. These new findings indicates that the LEPR gene could be used as a molecular marker in SV and FG quail strains.

Table 2.

Association analysis of SNP in LEPR gene with growth traits of quail.

W	S	SNP	GT	Traits (Mean ± SE)
3	FG	C187A	SC	1.495 ± 0.014ab CC	1.543 ± 0.030a AC	1.400 ± 0.100b AA
		A191G	SL	3.479 ± 0.061b AA	3.597 ± 0.032ab AG	3.635 ± 0.064a GG
		C286T	SL	3.479 ± 0.061b CC	3.593 ± 0.031ab CT	3.646 ± 0.069a TT
		G346A	SL	3.540 ± 0.038b GG	3.594 ± 0.043ab AG	3.767 ± 0.115a AA
		G373A	SL	3.540 ± 0.038b GG	3.570 ± 0.037b AG	3.801 ± 0.095a AA
5	FG	G90T/A219G	SL	3.804 ± 0.033ab GG/AA	3.772 ± 0.027b GT/AG	3.883 ± 0.041a TT/GG
		G258A	BBL	4.356 ± 0.048a GG	4.300 ± 0.058a AG	4.012 ± 0.269b AA
		G346A	SL	3.798 ± 0.027b GG	3.784 ± 0.028b AG	3.972 ± 0.055a AA
			BBL	4.356 ± 0.048a GG	4.313 ± 0.056a AG	3.890 ± 0.310b AA
		G373A	SL	3.798 ± 0.027b GG	3.787 ± 0.030b AG	3.928 ± 0.062a AA
			BBL	4.356 ± 0.048a GG	4.321 ± 0.059a AG	3.952 ± 0.248b AA
5	SV	G90T/C286T	CW	3.275 ± 0.062ab GG/CC	3.117 ± 0.056b GT/CT	3.305 ± 0.087a TT/TT
		A191G	BL	9.540 ± 0.279a AA	9.508 ± 0.156ab AG	8.868 ± 0.226b GG
		G346A	BL	9.583 ± 0.232a GG	9.508 ± 0.156ab AG	8.817 ± 0.232b AA

^abThe difference between genotypes with different lowercase letters were significant (P < 0.05).

Abbreviations: BBL, breastbone length; BL, body length; CW, chest width; FG, French Giant meat quail; GT, growth traits; S, strain; SC, shank circumference; SL, shank length; SNP, single nucleotide polymorphism; SV, Savimalt meat quail; W, week.

Table 3.

Association analysis of SNP in LEPR gene with carcass traits of quail.

W	S	SNP	CT	Traits (Mean ± SE)
5	FG	C187A	HR	1.129 ± 0.047ab CC	1.318 ± 0.095a AC	0.902 ± 0.238b AA
		G258A	WNCR	68.754 ± 0.376ab GG	69.918 ± 0.769a AG	67.028 ± 1.023b AA
		G346A	WNCR	68.754 ± 0.376ab GG	69.696 ± 0.750a AG	67.140 ± 1.312b AA
		G373A	WNCR	68.754 ± 0.376a GG	70.026 ± 0.723a AG	66.725 ± 1.098b AA
5	SV	A191G	LMR	12.735 ± 0.581b AA	13.000 ± 0.277b AG	14.420 ± 0.347a GG
		G346A	WNCR	70.535 ± 0.762a GG	69.244 ± 0.493ab AG	67.349 ± 0.959b AA
			HR	0.840 ± 0.058b GG	1.136 ± 0.044ab AG	1.174 ± 0.101a AA
			LMR	12.761 ± 0.475b GG	13.000 ± 0.277b AG	14.505 ± 0.356a AA

^abThe difference between genotypes with different lowercase letters were significant (P < 0.05).

Abbreviations: CT, carcass traits; FG, French Giant meat quail; HR, heart rate; LMR, leg muscle rate; S, strain; SNP, single nucleotide polymorphism; SV, Savimalt meat quail; W, week; WNCR, whole net carcass rate.

Linkage Disequilibrium Analysis and Haplotype Analysis of SNPs of LEPR Gene in Meat-Type Quail

The linkage disequilibrium (LD) analysis of 7 SNPs genotyped of the HWE law was conducted in 2 meat-type quail strains. The LD analysis result showed that the G90T and C286T sites were completely linked (D' = 1) in SV. There was no significant LD (D' > 0.8 and r² > 0.33) observed between the A191G and G258A sites, as well as between the A219G and G346A sites, indicating that they tend to be genetically independent of each other (Figures 2A and 2B). However, strong linkage disequilibrium (D' > 0.8 and r² > 0.33) is observed among the remaining SNPs. The G90T and A219G, A191G and C286T, as well as G346A and G373A sites were completely linked (D’ = 1) in FG. There was no significant LD (D’ > 0.8 and r² > 0.33) observed between the A191G, G258A, and G346A, as well as between the G258A and C286T sites, indicating that they tend to be genetically independent of each other (Figures 2C and 2D). However, strong linkage disequilibrium (D' > 0.8 and r² > 0.33) is observed among the remaining SNPs. Haplotypes based on the 7 SNPs showed that a total of 4 (W1, W2, W3, W4) and 4 (J1, J2, J3, F4) haplotypes (frequencies greater than 3%) were identified in SV and FG strains (Table 4).

Figure 2.

Linkage disequilibrium coefficient between SNPs (D’ and r²) in quail of the Savimalt strain and French Giant strain, the numbers are the D'and r² value (%).

Table 4.

Haplotype analysis of SNPs of LEPR gene.

Strain	Haplotype	Polymorphic sites of LEPR gene							Frequency
		G90T	A191G	A219G	G258A	C286T	G346A	G373A
Savimalt meat quail	W1	G	A	A	G	C	G	G	0.291
	W2	G	G	A	G	C	A	G	0.111
	W3	T	G	A	G	T	A	G	0.069
	W4	T	G	G	A	T	A	A	0.458
French Giant meat quail	J1	G	A	A	G	C	G	G	0.478
	J2	G	G	A	G	T	G	G	0.130
	J3	T	G	G	A	T	A	A	0.250
	J4	T	G	G	G	T	G	G	0.109

Association Analysis of Haplotype Combinations With Growth and Carcass Traits

In the linkage between 7 SNPs, there were 5 (W1W1, W1W4, W2W3, W2W4, W4W4) and 6 (J1J1, J1J2, J1J3, J1J4, J3J3, J3J4) haplotype combinations (combinations with the number of individuals higher than or equal to 3) in SV and FG quail strains, respectively (Figure 3 and Table S3). The result showed that haplotype combination W1W1 had a significantly higher CD and BBL than W2W3 at 3 wk of age in SV strain (P < 0.05). W1W1 combination had significantly higher CW, BBL and BL at 5 wk of age in SV strain (P < 0.05). J3J3 combination had significantly higher SL at 3 or 5 wk of age in FG strain (P < 0.05). J3J4 combination had significantly higher BBL at 5 wk of age in FG strain (P < 0.05). Haplotypes based on the 7 SNPs showed that a total of 5 and 6 haplotype combinations (frequencies greater than 3%) were identified in SV and FG strains (Figure 4 and Table S4). The result showed that haplotype combination W1W1 had significantly higher WNCW and BMW than of W2W3 combination in the SV strain (P < 0.05). Combination W1W4 had significantly higher DP than of W2W3 combination in the SV strain (P < 0.05). Combination W1W1, W1W4, and W4W4 had significantly higher WNCR than of W2W3 combination in the SV strain (P < 0.05). Combination W2W4 had significantly higher HR than of W1W1 combination in the SV strain (P < 0.05). Combination W2W3 had significantly higher LR than of W1W1, W1W4, and W2W4 combination in the SV strain (P < 0.05). Combination W2W4 had significantly higher LMR than of W1W1 and W1W4 combinations in the SV strain (P < 0.05). Combination J1J1 had significantly higher HW and HR than of J3J4 combination in the FG strain (P < 0.05). Combination J3J4 had significantly higher WNCR than of J1J1, J1J4, and J3J3 combinations in the FG strain (P < 0.05). Combination J1J2 had significantly higher WNCR than of J3J3 combination in the FG strain (P < 0.05). Similar to this study, a previous study in Berkshire pigs showed that 10 SNPs of the LEPR gene was significantly associated with meat quality traits, and only haplotypes (ACDCGCTGTT) of the LEPR gene showed significant effects meat quality traits including BFT, cooking loss and pH_24h in Berkshire pigs (Kim et al., 2017). El-Tarabany et al. (2022) showed that based 3 haplotype combinations comprising of 2-SNP (A277G and A304G) of LEPR gene was significantly associated with egg weight, hen-day egg production, and egg mass (P < 0.05), which similar to this study. Similar to this study, a previous study in Rasa Aragonesa sheep showed that a SNP of the LEPR gene was significantly associated with estrous cycling months, haplotype analyses also indicated the another nonsynonymous SNP (rs405459906) showed significant correlation with reproductive seasonality traits (Lakhssassi et al., 2020). Several of the results of the studies mentioned above show a significant correlation between LEPR gene and economic traits of animals. The construction of linkage disequilibrium analysis and haplotype analysis based on the identified SNPs can help breeders in gaining a better understanding of the genetic characteristics of animals. These methods enable the determination of the combined effects of SNPs on a particular trait, overcoming the limitations of individual SNP associations. As a result, they are better suited for identifying superior genotypes and facilitating breeding and reproduction. Additionally, these analyses serve as a validation of the known SNP. The associations results of SNPs or haplotypes of LEPR gene with economic traits were reliable, and LEPR gene can be used as the major gene affecting quail growth and carcass traits in our study.

Figure 3.

Association analysis of the LEPR gene haplotype combinations with growth traits in quail.

^abThe difference between genotypes with different lowercase letters was significant (P<0.05).

Figure 4.

Association analysis of the LEPR gene haplotype combinations with carcass traits in quail.

^abThe difference between genotypes with different lowercase letters was significant (P<0.05).

In conclusion, 7 SNPs (G90T, A191G, A219G, G258A, C286T, G346A, G373A) or haplotype combination of LEPR gene which were significantly correlated to growth and carcass traits in SV and FG quail strains. The statistical analyses indicated that these SNPs of LEPR gene was significantly associated with SC, SL, BBL, HR, and WNCR of FG (P < 0.05); CW, BL, LMR, WNCR, and HR of SV (P < 0.05). While haplotypes showed significant effect on SL, BBL, HW, WNCR, and HR of FG (P < 0.05). Therefore, LEPR gene could be a molecular genetic marker to improve economic traits with quail breeding. However, due to the limitation of the number of quail population, further studies in large populations with different quail strains are required to further assess associations of the LEPR gene polymorphisms with egg quality, meat quality and other economic traits.