Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls

Abstract

Genetic diversity and phylogenetic relationships among 568 individuals of two red jungle fowl subspecies (Gallus gallus spadiceus in China and Gallus gallus gallus in Thailand) and 14 Chinese domestic chicken breeds were evaluated with 29 microstaellite loci, the genetic variability within population and genetic differentiation among population were estimated, and then genetic diversity and phylogenetic relationships were analyzed among red jungle fowls and Chinese domestic fowls. A total of 286 alleles were detected in 16 population with 29 microsatellite markers and the average number of the alleles observed in 29 microsatellite loci was 9.86+/-6.36. The overall expected heterozygosity of all population was 0.6708+/-0.0251, and the number of population deviated from Hardy-Weinberg equilibrium per locus ranged from 0 to 7. In the whole population, the average of genetic differentiation among population, measured as FST value, was 16.7% (P<0.001), and all loci contributed significantly (P<0.001) to this differentiation. It can also be seen that the deficit of heterozygotes was very high (0.015) (P<0.01). Reynolds' distance values varied between 0.036 (Xiaoshan chicken-Luyuan chicken pair) and 0.330 (G. gallus gallus-Gushi chicken pair). The Nm value ranged from 0.533 (between G. gallus gallus and Gushi chicken) to 5.833 (between Xiaoshan chicken and Luyuan chicken). An unrooted consensus tree was constructed using the neighbour-joining method and the Reynolds' genetic distance. The heavy-body sized chicken breeds, Luyuan chicken, Xiaoshan chicken, Beijing Fatty chicken, Henan Game chicken, Huainan Partridge and Langshan chicken formed one branch, and it had a close genetic relationship between Xiaoshan chicken-Luyuan chicken pair and Chahua chicken-Tibetan chicken pair. Chahua chicken and Tibetan chicken had closer genetic relationship with these two subspecies of red jungle fowl than other domestic chicken breeds. G. gallus spadiceus showed closer phylogenetic relationship with Chinese domestic chicken breeds than G. gallus gallus. All 29 microstaellite loci in this study showed high levels of polymorphism and significant genetic differentiation was observed among two subspecies of red jungle fowl and 14 Chinese domestic chicken breeds. The evolutional dendrogram is as follows: evolutional breeds-->primitive breeds (Chahua chicken and Tibetan)-->red jungle fowl in China (G. gallus spadiceus)-->red jungle fowl in Thailand (G. gallus gallus). The results supported the theory that the domestic fowls might originate from different subspecies of red jungle fowl and Chinese domestic fowls had independent origin.

Genetic variability determination in a long-term selected Rhode Island Red chicken strain using microsatellite markers

“…The present observation of nine polymorphic microsatellite loci out of ten, with an average allele number per locus of 3.000 ± 1.4142 was more than in the report by ARYA (2012), who observed nine polymorphic loci out of 47 microsatellite loci using 3.4% MetaPhor Agarose in a high and low egg production sub-population of White leghorn chicken, but comparable to that of DESHMUKH et al, (2015), who reported 17 polymorphic loci out of 25 microsatellite loci in different chicken breeds using 3.4% MetaPhor Agarose. The allele number and average number of alleles per locus in the present study were lower than earlier reports in various native and exotic chicken breeds (PANDEY et al, 2002;VIJH and TANTIA, 2004;PANDEY et al, 2005;BAO et al, 2008;CHATTERJEE et al, 2010b). The wide variation in numbers and sizes of alleles in the pure selected strain of RIR chicken studied could be attributed to the differences in the genetic architecture of the genomes analyzed, and also may be due to loss or fixation of alleles during its long-term selection.…”

“…In the present study, the heterozygosity at all nine polymorphic microsatellite loci varied from 0.0997 to 0.7421; the mean heterozygosity was 0.4119 ± 0.2475. The heterozygosity and PIC values observed in the present study were lower for most of the microsatellite loci as compared to the results reported earlier in different chicken populations (PANDEY et al, 2002;VIJH and TANTIA, 2004;PANDEY et al, 2005;BAO et al, 2008;CHATTERJEE et al, 2010b), which might be due to the small size of the RIR population analyzed, and it was in an extensive breeding programme, leading to either loss or fixation of some of the alleles in the course of long-term selection. The present findings are in accordance with the report by WIMMERS et al (2000), who reported lower heterozygosity (0.45) in Aseel native chicken, where the samples were taken from an organized flock and the birds were subjected to selection pressure and subsequent inbreeding.…”

The Differential Evolutionary Dynamics of Avian Cytokine and TLR Gene Classes

“…This study presents clear evidence that red JF and chickens have not been genetically isolated since domestication, as suggested elsewhere (35,74,115,116). Previous studies have found evidence for introgression of gray JF, which would have further altered the genetic variation present in the domestic chicken.…”

“…Wild population genetic variation at chicken immune genes that was originally captured by multiple origins and admixture (73,74) appears to have caused a trend of high diversity throughout the genes resequenced in this study. However, it does not sufficiently account for the distinctive patterns of variation observed between the cytokines and TLRs, and implies selective processes at one or both of these functional categories.…”

Genetic diversity of local Yunnan chicken breeds and their relationships with Red Junglefowl

“…Therefore, determining the genetic background of Yunnan domestic chicken varieties and their relationship with local Red Junglefowl could provide an improved understanding of chicken evolution and dispersal during its domestication and enable the evaluation of chicken genetic diversity and strategies for conserving its ancestral varieties. Although some local Yunnan chicken breeds have been included in genetic studies of chicken breeds using microsatellite DNA, only a few studies have discussed the diversity of Yunnan local populations in the context of their ancestral state and relationship with Red Junglefowl in remaining habitats of wild chicken populations (Qu et al, 2006;Bao et al, 2008;Li et al, 2009).…”