Genetic Varitions Of PPARs Family And PLIN Genes In Beef Cattle And Their Associations With Carcass, Meat Quality Traits In Qinchuan Cattle

Genetic variations of lipid metabolism related genes (PPARα, PPARδ, PPARγ, and PLIN) were detected by PCR-SSCP, DNA sequencing and DNA sequence analysis in 717 individuals of six populations (Nanyang, Qinchuan, Jiaxian Red cattle, Luxi, Angus, and Xianan), and association analysis were carried out to evaluate the effects of genotypes of candidate genes on carcass and meat quality traits of 108 Qinchuan cattle. Molecular markers function was analyzed by bioinformation in missense mutation loci. The object of this study were to discover the hereditary characteristics and to explore molecular markers with significant effects on economic important traits for efficient selection and improvement of Chinese cattle, and to provide genetic information for foundation of molecular marker database, protection and usage of breed resource of Chinese cattle. The results were as follows:1. Relationship between genetic variation of PPARαgene and carcass, meat quality traits in Qinchuan cattleThe variations of eight loci in PPARαgene, including seven exons and intron2, were detected in six populations using PCR-SSCP and DNA sequencing. Six SNPs were detected for the first time.Three SNPs (2666 C>G, 2678 T>C, 2706 T>C) were detected, which located at the intron2 of PPARαgene. Allele gene D was predominant in the locus. The allele frequencies of D in Qinchuan, Nanyang, Jiaxian Red cattle, Luxi, Xianan and Augus populations were 0.571, 0.404, 0.419, 0.417, 0.422 and 0.386. And in the six populations, the SNP was moderate polymorphic, the PIC values were 0.421, 0.416, 0.434, 0.447, 0.438 and 0.413, respectively. The 2666 C>G locus was high significantly with loin muscle area (P<0.01), individuals with genotype CC had higher loin muscle area than those with genotype CD (P<0.01).T>C mutation was detected in the exon5 of PPARαgene by PCR-SSCP, which located at the juncture of exon5 and intron5, and the locus was synonymous mutation. The Chi-Square tests showed Nanyang, Jiaxian Red cattle, Augus, and Luxi cattle populations were at Hardy-Weinberg equilibrium (P>0.05), but Qinchuan cattle and Xianan cattle populations were at Hardy-Weinberg disequilibrium (P<0.05). The locus was moderate polymorphic in six populations, therefore the genetic polymorphisms from higher to lower were Qinchuan cattle, Jiaxian Red cattle, Augus, Luxi, Xianan and nanyang cattle. The 138T>C SNP had significant effects on loci muscle area, back fat thickness and hold water capability in Qinchuan cattle population.184 C>T mutation located at the seventh exon of PPARαgene. In this locus, Nanyang, Jiaxian Red cattle, Xianan, and Luxi cattle populations were at Hardy-Weinberg equilibrium (P>0.05), but Qinchuan cattle and Augus cattle populations were at Hardy-Weinberg disequilibrium (P<0.05). The index of genetics showed that Qinchuan cattle, Jiaxian Red cattle, Augus, Luxi and Xianan cattle populations belonged to low polymorphic and Nanyang cattle population was moderate polymorphic. The 184 C>T SNP was significantly associated with back fat thickness and carcass length (P<0.05).260 C>T mutation was detected in the eighth exon of PPARαgene. The allele frequencies of G/H were 0.925/0.075, 0.864/0.136, 0.791/0.209, 0.828/0.172, 0.835/0.165 and 0.853/0.147 in Qinchuan, Nanyang, Jiaxian Red cattle, Luxi, Xianan and Augus populations. Genotype II was no detected in Nanyang cattle population. And genotype GG was predominant, the frequencies of allele G was the highest in this locus. Nanyang cattle population was at Hardy-Weinberg equilibrium (P>0.05), but Qinchuan cattle, Jiaxian Red cattle, Augus, Luxi and Xianan cattle populations were at Hardy-Weinberg disequilibrium (P<0.05). Except for Jiaxian Red cattle (0.25T SNP was significantly associated with hold water capability (P<0.05). Individuals with genotype GG had higher hold water capability than those with genotype GH (P<0.05).2. Relationship between genetic variation of PPARδgene and carcass, meat quality traits in Qinchuan cattleThe seventh exons were detected, and only one SNP (61 C>T) was found in the intron2 in the PPARδgene. Genotype KK and allele K were predominant in the six populations. Nanyang and Xianan cattle populations were at Hardy-Weinberg equilibrium (P>0.05), but Qinchuan cattle, Jiaxian Red cattle, Augus and Luxi cattle populations were at Hardy-Weinberg disequilibrium (P<0.05). The 61 C>T SNP was moderate polymorphic in Xianan population, was low polymorphic in Qinchuan, Nanyang, Jiaxian Red cattle, Luxi and Augus populations. The 61 C>T SNP was significantly associated with Slaughter weight and Carcass weight (P<0.05) in Qinchuan cattle. Animals with genotype KK had higher Slaughter weight than those with genotypes KL and LL (P<0.05), individuals with genotype KK had higher carcass weight than those with genotype KL (P<0.05).3. Relationship between genetic variation of PPARγgene and carcass, meat quality traits in Qinchuan cattleFour SNPs (200 A>G (exon1), 59 C>G (intron2), 62 C>T (exon5) and 74 G>T (exon7)) of PPARγgene were detected in 8 loci, which located coding region and the part of 5'control region by PCR-SSCP and DNA sequencing.A>G SNP was detected, which located at 200 bp in the first exon of PPARγgene and resulted in D7G change. The allele frequencies of A/B were 0.81/0.19, 0.86/0.14, 0.80/0.20, 0.76/0.24, 0.72/0.28 and 0.87/0.13 in Qinchuan, Nanyang, Jiaxian Red cattle, Luxi, Xianan and Augus populations. In the six populations, Augus population was at Hardy-Weinberg disequilibrium (P<0.05). In Qinchuan cattle and Xianan cattle populations, the SNP was low polymorphic, but in Nanyang, Jiaxian Red cattle, Augus and Luxi cattle populaions, the SNP was moderate polymorphic. The 200 A>G SNP was significantly associated with back fat thickness and back subcutaneous fat thickness. Individuals with genotype AA had high back fat thickness and back subcutaneous fat thickness than those with genotype AB (P<0.05). Bioinformatics analysis showed that the mutation led Asp change into Gly, which had theα-helix lost, the coil wax, the hydrophobicity increase and loose degree decrease. This change may be related to the change of gene function.The 59 C>G SNP produced at intron2 of PPARγgene, which was found when detected the SNP of exon2. Allele Y was dominant in the six populations, all populations were at Hardy-Weinberg disequilibrium (P<0.05). In Nanyang, Jiaxian Red cattle, Augus, Luxi and Xianan cattle populations, the SNP was moderate polymorphic, but in Qinchuan cattle population, the SNP was low polymorphic. The 59 C>G SNP was had significant effects on back subcutaneous fat thickness.62 C>T mutation located at exon5 of PPARγgene, six populations all displayed the lost of genotype II. The allele frequencies of J/I were 0.94/0.06, 0.87/0.13, 0.90/0.10, 0.90/0.10, 0.91/0.09 and 0.94/0.04 in Qinchuan, Nanyang, Jiaxian Red cattle, Luxi, Xianan and Augus populations. Only Qinchuan cattle was at Hardy-Weinberg disequilibrium (P<0.05). All populations were at low polymorphic. Correlation analysis showed individuals with genotype JJ had higher back subcutaneous fat thickness than those with genotype JI (P<0.05).The 74 G>T mutation resulted Glu change into His. Bioinformatics analysis revealed there had theβ-sheet lost and coil decreased in 2D structure, and the hydrophobicity increased and loose degree decreased in the locus. Qinchuan cattle, Jiaxian Red cattle, Augus, Luxi and Nanyang cattle populations were at Hardy-Weinberg equilibrium (P>0.05), but Angus and Xianan cattle populations were at Hardy-Weinberg disequilibrium (P<0.05). In Nanyang cattle and Xianan cattle populations, the SNP was low polymorphic, in other populations, the SNP was moderate polymorphic. Animal with genotype OP was higher carcass length than those with genotypes OO and PP (P<0.05), individuals with genotype OO was higher mean values than these with genotypes OP (P<0.05) and PP (P<0.01) for back fat thickness, and animals with genotype OO was lower mean values than these with genotypes OP and PP (P<0.05) for hold water capability.4. Relationship between genetic variation of PLIN gene and carcass, meat quality traits in Qinchuan cattleA total of two SNPs (156 T>C (exon3), 14 C>T (exon4)) of PLIN gene were detected in 4 loci in Qinchuan cattle population. The two SNPs were belonging to moderate polymorphic. In the 156 T>C locus, animal with genotype AB was higher slaughter weight, carcass weight, back fat thickness and loin muscle area than those with genotypes AA and BB, and compared to individual with AA genotype was very significantly different(P<0.01). In the 14 C>T locus, this analysis also showed that the carcass length, carcass chest depth and back fat thickness of individual with DE genotype was significant higher than those with EE and DD genotypes (P<0.05), and compared to individual with EE and DE genotypes, the tenderness of individual with DD genotype was very significantly different(P<0.01).