What is it about?
Indigenous and commercial chickens have developed unique adaptations to their environments, which may include nutrition, pathogens, and thermal stress. Besides, environmental pressures and artificial selection have generated significant genome-wide divergence in chickens, as those selection pressures contribute a considerable evolutionary force to phenotypic and genotypic differentiation. Herein, we determined genomic diversity of indigenous chickens from semi-deciduous rainforest (SDR), coastal savannah (CS) and Guinea savannah (GS) agro-ecological zones (AEZs) in Ghana and commercial crossbreds (CC) reared at the Kwame Nkrumah University of Science and Technology (KNUST). We generated SNP markers from 82 chickens (62 indigenous chicken ecotypes and 26 commercial crossbred ecotype) using DArT-Seq technology. A total of 85,396 SNP markers were generated and after filtering the data, 58,353 markers were used to study genetic diversity and population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 to 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 to 0.15) while 13,511 (21%) were in the highest PIC value range (0.45 to 0.50). The CC were more genetically diverse than the indigenous birds, with the highest expected heterozygosity value of 0.220. Between the commercial crossbred population and the indigenous ecotypes, pairwise FST values were estimated to be 0.105 between CS, 0.096 between SDF, and 0.133 between GS. Furthermore, PCA analysis showed that the CC, SDF, and GS chickens clustered together and are genetically distant from the commercial crossbred. We herein show that chickens from the AEZs studied can be considered as one population. However, due the abundance of agro-byproducts in the SDR compared to the CS and GS, chickens from the SDR AEZ had better growth compared to their counterparts. It is suggested that the genetic diversity within the local ecotypes could form the basis for genetic improvement.
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Why is it important?
A cascade of genes drives the traits of economic importance across the chicken genome. Consequently, breeding programs and conservation techniques require genomic profiling of varied genetic animal resources and the identification of potential parents for future generations. The use of whole genome genetic markers to explore genetic diversity and uncover the genetic basis for specific traits in many chicken breeds has been studied quite extensively. Assessment of genetic diversity based on whole genome genetic markers generated from high-throughput sequencing data has high accuracy than those based on platforms with few markers. However, the previous genomic study on the indigenous chicken population in Ghana was limited, and employed sequencing platforms with few markers such as simple sequence repeat markers (SSR markers). This study is envisaged to apply DArT markers to the genomic sequencing of chickens; and this is a novel approach not only in Ghana but globally. The present study aimed to employ DArTseq SNPs to identify the genomic diversity of chickens within three AEZs and commercial crossbreds; and also characterize the phenotypic diversity between chickens from the three different AEZs and commercial crossbred chickens. A comprehensive and deep understanding of the genome underpinnings of the indigenous and commercial crossbreds could reveal the genetic diversity and population structure of these chickens in different AEZs. They can serve as the basis for genetic conservation and/or genetic improvement.
Perspectives
Raising indigenous chickens on a small scale at the household level is common in Ghana and many parts of Africa. Some of these keepers normally buy male chicks from hatcheries and raise them for mating to improve meat production among the indigenous chickens. Scientists in this part of the globe believe indigenous chickens are no longer distinct due to indiscriminate crossbreeding. This whole genome sequencing study among indigenous chickens in Ghana and commercial ones answered two important questions: 1. Are indigenous chickens in Ghana genetically distinct and different from commercial ones? 2. Are indigenous chickens from different agroecological zones in Ghana genetically diverse? 1. The study has proven that indigenous chickens in Ghana are genetically distinct and different from commercial chickens raised in Ghana. The crossbreeding between indigenous chickens and commercial chickens practiced by some indigenous chicken keepers has not significantly influenced indigenous chickens' genetics in Ghana. 2. Indigenous chickens from different agroecological zones in Ghana are genetically distinct. This is an indication that these chickens have common ancestry. It is believed that chickens first came to Ghana through the coastal areas by sailors and spread to other zones in the country through resettlements and trade. Some differences were noticed between the chickens from the Guinea Savannah and Rainforest zones. This was due to differences in the availability of resources such as food and water. The adaptability of birds to their environment in time becomes genetic through epigenetics. However, enough genetic diversity exists among indigenous chickens in Ghana which is very important for future genetic improvement programs in meat or egg production.
Kwaku Adomako
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This page is a summary of: Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology, PLoS ONE, May 2024, PLOS,
DOI: 10.1371/journal.pone.0297643.
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