Association Between Single Nucleotide Polymorphisms In Insulin-Like Growth Factor 1 And Insulin-Like Growth Factor 2 Genes And Growth Traits, And Survivability In Three Local Chicken Ecotypes Of Ghana
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Date
2022-07
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University Of Ghana
Abstract
Local chickens have comparatively smaller body sizes and slower growth rates. As a result, many smallholder farmers often tend to cross them with heavier breeds of chicken with the aim of improving their growth traits, a process that can lead to the dilution of their genetic composition and subsequent loss of important adaptive traits. Insulin-like growth factor 1 (cIGF1) and Insulin-like growth factor 2 (cIGF2) hormones have been widely reported to be associated with embryonic and post-hatch growth and development of chicken and the genes that code them have also been reported as candidate genes for growth and carcass traits of chicken.
This research was conducted with the aim of assessing the growth, carcass, and survivability traits of three chicken ecotypes of Ghana, to analyze the diversity of the cIGF1 and cIGF2 genes in these chicken ecotypes and assess the extent to which polymorphisms in these genes influence the growth and carcass traits of the three chicken ecotypes of Ghana.
Eggs of the Forest (FO), Interior Savannah (IS) and Coastal Savannah (CS) chicken ecotypes of Ghana were obtained from breeder stocks at the Livestock and Poultry Research Center (LIPREC) of the University of Ghana. These eggs were hatched and reared by ecotype up till 22 weeks of age. During this period, the body weights were taken fortnightly up till the end of the experiment after which the chickens were all euthanized, and some carcass traits measured. The quantity of feed consumed per bird during this period and the number of deaths were recorded daily. From these measurements, growth rates, survivability, Feed Conversion Ratios, and carcass traits were computed. DNA was also extracted from the chicken, and Polymerase Chain Reaction used to amplify targeted regulatory and exonic regions of the two genes. Thereafter, Restriction Fragment Length Polymorphism was used to detect single nucleotide polymorphisms (SNPs) in the PCR amplicons. These polymorphisms were confirmed with the aid of sanger sequencing and sequence alignments.
The results of this research showed that the IS and FO chicken ecotypes were heavier and grew at a faster rate than the CS ecotype. However, the FO ecotype had significantly (p<0.05) higher breast weight and breast yield than the IS and CS chicken ecotypes. The results also showed that the CS ecotype had the highest survival rate under intensive management conditions while the IS ecotype had the lowest survival rate. The three chicken ecotypes could therefore be used together in a breed improvement programmes that seek to enhance the growth and carcass traits of local chickens of Ghana by leveraging the higher growth rates of the Interior savannah chicken ecotype, the higher breast yield of the Forest chicken ecotype and the higher survival rate of the Coastal savannah chicken ecotype.
The RFLP digestion of cIGF1 and subsequent sequencing revealed a HinfI C>A single nucleotide polymorphism (SNP) in the 5’ UTR, a PstI T>C SNP in the promoter of the 5’ flanking region, and a BstBI T>C SNP in the 3’UTR, while a NlaIII C>T SNP was identified in exon 3 of cIGF2.
At the HinfI C>A locus, the AC heterozygote was the predominant genotype amongst the FO and CS ecotypes, while the CC genotype was predominant in the IS ecotype. The C allele had the highest frequency amongst all the three chicken ecotypes. The observed heterozygosity values were higher than the expected heterozygosity values in the FO and CS ecotype populations. There was no significant association of the HinfI C>A SNP with body weights, weight gain and the carcass traits. This SNP locus may therefore not be an ideal molecular marker for selection to improve body weight and carcass traits in Ghanaian local chickens.
At the PstI T>C locus, the CT heterozygote was the most predominant genotype among the three Ghanaian chicken ecotypes, with the T allele having the highest frequency. The observed heterozygosity amongst the FO and CS chicken ecotypes was higher than the expected heterozygosity. PstI T>C was associated with body weights at hatch and at 16 and 22 weeks of age (p<0.05) but it did not influence the carcass traits that were investigated. PstI T>C could therefore be a potential molecular marker for use in marker-assisted selection for the improvement of body weight in the local chicken ecotypes of Ghana.
At the BstBI T>C locus, CT heterozygote was the common genotype among the three chicken ecotypes while the C allele had the highest frequency. The observed heterozygosity of this polymorphism was higher in the FO and CS ecotypes than in the IS ecotype. BstBI T>C was significantly (p<0.05), associated with body weights at hatch, 2, and 10 weeks of age, but it was not associated with any of the carcass traits studied. This SNP locus could be useful in future marker-assisted selection for the improvement of body weight traits in the local chicken ecotypes of Ghana.
An analysis of the diversity of the NlaIII C>T SNP showed that the AB heterozygote was the predominant genotype amongst the FO and CS ecotypes while the BB genotype was predominant in the IS ecotype. The A allele had the highest frequency in the FO ecotype, while the B allele was the predominant allele in the CS and IS ecotypes.
The FO and IS ecotypes had lower observed heterozygosity values than the expected heterozygosity values. However, in the CS ecotype, the observed heterozygosity was higher than the expected heterozygosity. NlaIII C>T had no significant effect on body weights and any of the carcass traits studied. NlaIII C>T would therefore not be a good molecular marker for use in selection to improve body weight of chicken ecotypes in Ghana.
The results of this research suggest that PstI T>C and BstBI T>C could be useful molecular markers for the improvement of body weight in future marker-assisted breeding programmes of local chicken ecotypes in Ghana. However, HinfI C>A, PstI T>C, BstBI T>C and NlaIII T>C SNPs may not be the ideal molecular makers for carcass traits improvement among the three chicken ecotypes of Ghana.
These studies conclude that genetic improvements in the economic traits of importance of the local chicken ecotypes of Ghana such as body weight could be carried out by taking advantage of the higher growth rates of the IS chicken ecotype, the higher breast yield of the FO chicken ecotype and the higher survival rate of the CS chicken ecotype. Furthermore, the PstI T>C and BstBI T>C SNPs could be considered as molecular markers for the improvement of body weight in future marker-assisted breeding programmes of local chicken ecotypes in Ghana
Description
PhD. Animal Science
Keywords
Ecotypes, Ghana, Nucleotide, Polymorphisms, Insulin