Molecular Characterization of Sudanese and Southern Sudanese Chicken Breeds Using mtDNA D-Loop.

Charles E Wani,Ibrahim A Yousif,Hassan H Musa,Muntasir E Ibrahim

doi:10.1155/2014/928420

Abstract

The objective of this study was to assess the genetic relationships and diversity and to estimate the amount of gene flow among the five chicken populations from Sudan and South Sudan and commercial strain of egg line White Leghorn chickens. The chicken populations were genotyped using mtDNA D-loop as a molecular marker. PCR product of the mtDNA D-loop segment was 600 bp and 14 haplotypes were identified. The neighbor-joining phylogenetic tree indicated that the indigenous Sudanese chickens can be grouped into two clades, IV and IIIa only. Median joining networks analysis showed that haplotype LBB49 has the highest frequency. The hierarchal analysis of molecular variance (AMOVA) showed that genetic variation within the population was 88.6% and the differentiation among the population was 11.4%. When the populations was redefined into two geographical zones, rich and poor Savanna, the results were fractioned into three genetic variations: between individuals within population 95.5%, between populations within the group 0.75%, and genetic variation between groups 3.75%. The pair wise F st showed high genetic difference between Betwil populations and the rest with F st ranging from 0.1492 to 0.2447. We found that there is large number of gene exchanges within the Sudanese indigenous chicken (Nm = 4.622).

Highlights

Chicken genetic resources comprise a wide range of breeds and populations including red jungle fowl, native and fancy breeds, middle level food producers, industrial stocks, and specialized lines
Fourteen haplotypes were identified in the Sudanese and Southern Sudan indigenous chicken populations with variation at 19 sites, and 23.5% of them are polymorphic (Figure 1)
Multiple sequence alignment was performed for the fourteen haplotypes identified in the Sudanese and Southern Sudan indigenous chicken

Summary

Introduction

Chicken genetic resources comprise a wide range of breeds and populations including red jungle fowl, native and fancy breeds, middle level food producers, industrial stocks, and specialized lines. Sudan possesses potential genetic resources of local poultry, even though most of them have not been genetically and phenotypically characterized. Genetic diversity measures using the highly polymorphic variable number of tandem repeat loci have yielded reliable and accurate information for the study of genetic relationships between chicken populations. Sequencing a specific fragment of mtDNA (e.g., D-loop) gives more accurate information on evolution and genetic diversity [3]. There is evidence from mtDNA D-loop variations in European, African, and Indian cattle breeds that indicate independent domestications of Bos taurus and Bos indicus cattle in two separate locations [5]. D-loop sequences have been used in unraveling domestication and diversity of dogs [6], horses [7], and goats [8] and in Australian red kangaroo and Macropus rufus [9].

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Conclusion