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

Genetic diversity and phylogenetic relationships among 568 individuals of two red jungle fowl subspe- cies (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.     

A variant in the restriction endonuclease cleavage pattern of mitochondrial DNA in the domestic fowl, Gallus gallus domesticus

Summary. The cleavage patterns of mitochondrial DNAs (mtDNAs) were investigated from 15 lines of domestic fowls, Gallus gallus domesticus . using 11 restriction endonucleases. The cleavage patterns with 10 restriction endonucleases were identical in all the lines. A variant was found in a line of White Leghorn in the pattern with Mspl digestions. Cleavage patterns of the red jungle fowl, Gallus gallus gallus , were identical to the common patterns shown by the 14 lines of domestic fowls.     

A variant in the restriction endonuclease cleavage pattern of mitochondrial DNA in the domestic fowl, Gallus gallus domesticus

The cleavage patterns of mitochondrial DNAs (mtDNAs) were investigated from 15 lines of domestic fowls, Gallus gallus domesticus, using 11 restriction endonucleases. The cleavage patterns with 10 restriction endonucleases were identical in all the lines. A variant was found in a line of White Leghorn in the pattern with MspI digestions. Cleavage patterns of the red jungle fowl, Gallus gallus gallus, were identical to the common patterns shown by the 14 lines of domestic fowls.     

中国红原鸡和泰国红原鸡遗传多样性分析

利用29个微卫星DNA标记对来自中国的红原鸡Gallus gallus spadiceus亚种和来自泰国的红原鸡Gallus gallus gallus亚种进行遗传多样性分析, 评估亚种内的遗传变异和亚种间的遗传分化, 结果表明: 共检测到168个等位基因, 每个位点的等位基因数从2到13不等, 所有位点平均的期望杂合度和PIC值分别为0.5780和0.53。中国和泰国红原鸡29个微卫星位点平均有效等位基因数分别为3.79和4.79, 平均基因杂合度为0.5379和0.6385, 两个红原鸡亚种均表现出较高的群体杂合度和丰富的遗传多样性。群体分化系数为19.4%(P<0.01), 两个红原鸡亚种间的Reynolds’遗传距离和Nm值分别为0.157和1.040。由此可见, Gallus gallus spadiceus亚种和Gallus gallus gallus亚种群体具有不同的群体遗传结构, 群体之间存在明显的遗传分化, 并不能将其认定为是同一亚种, 这也为中国家鸡具有独立的起源提供了一定的佐证。     

Phylogenetic distribution of the novel avian endogenous provirus family EAV-0

A new family of related endogenous proviruses, existing at 50 to 100 copies per haploid genome and distinguishable by remarkably short long terminal repeats, has been described for domestic chickens (Gallus gallus subsp domesticus). In this communication, by using Southern blot analysis and probes derived from both internal viral sequences and locus-specific, cellular flanking sequences, we studied the genetic distribution of this family of moderately repetitive avian endogenous retroviruses within the genomes of four Gallus species. Eight inbred lines of domestic chickens, the evolutionary progenitor to the domestic chicken (red jungle fowl), and two more distantly related species (grey and green jungle fowl) were studied. All Gallus species harbored this class of elements, although the different lines of domestic chickens and different species of jungle fowl bore distinguishable complements of the proviral loci. Jungle fowl appeared to have fewer copies than domestic chickens. For three randomly isolated proviral loci, domestic chickens (G. gallus subsp. domesticus) and red jungle fowl (G. gallus subsp. gallus) showed only a proviral state, whereas the most primitive and divergent of the jungle fowl, the green jungle fowl (G. varius), consistently demonstrated only preintegration states or disparate alleles. The presence of this family in all Gallus species and of related sequences in other genera suggests that a primordial founding integration event occurred prior to the evolutionary separation of Gallus species and possibly related genera. Additionally, at least one proviral locus has been acquired subsequent to speciation, indicating that this family was actively infectious after the primary founding event. This conserved, repetitive proviral family appears to represent the vestigial remnant of an avian retrovirus class related to and evolutionarily more ancient than the Rous-associated virus-0 family of avian endogenous retroviruses.     

Chicken domestication: an updated perspective based on mitochondrial genomes

Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A–I and W–Z. Common haplogroups A–G were shared by domestic chickens and red junglefowl. Rare haplogroups H–I and W–Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.     

家鸡腺苷琥珀酸裂解酶基因多态性与肌苷酸含量的关联及其与红原鸡的亲缘关系

根据腺苷琥珀酸裂解酶(adenylosuccinate lyase, ADSL)基因外显子2的序列设计引物, 用PCR-SSCP的方法对隐性白羽鸡、丝羽乌骨鸡、白耳鸡、藏鸡以及红色原鸡两个亚种进行了单核苷酸多态性分析, 并检测到了多态性, 表现为3种基因型, 对两种纯合子进行直接测序, 结果发现3484位碱基处发生C→T突变。对3种基因型的肌肉肌苷酸含量的最小二乘分析结果显示TT型(突变型)个体的肌肉肌苷酸含量极显著地高于CT型、显著地高于CC型个体, CT型个体也稍高于CC型, 但差异不显著, 初步推测该位点可能与肌肉肌苷酸含量有关。根据该多态位点的基因频率, 基于Nei氏的遗传距离运用NJ聚类法构建系统发生树, 进行家鸡与原鸡的亲缘关系分析, 结果发现, 丝羽乌骨鸡与白耳鸡的亲缘关系最近, 藏鸡和中国红原鸡亚种的亲缘关系也较近, 中国地方家鸡品种与中国红原鸡亚种的亲缘关系较近,而与泰国红色原鸡的亲缘关系较远,隐性白羽鸡与原鸡亲缘关系最远, 初步得出中国家鸡有自己独自的血缘来源的结论。     

Chicken domestication: from archeology to genomics

Current knowledge on chicken domestication is reviewed on the basis of archaeological, historical and molecular data. Several domestication centres have been identified in South and South-East Asia. Gallus?gallus is the major ancestor species, but Gallus?sonneratii has also contributed to the genetic make-up of the domestic chicken. Genetic diversity is now distributed among traditional populations, standardized breeds and highly selected lines. Knowing the genome sequence has accelerated the identification of causal mutations determining major morphological differences between wild Gallus and domestic breeds. Comparative genome resequencing between Gallus and domestic chickens has identified 21 selective sweeps, one involving a non-synonymous mutation in the TSHR gene, which functional consequences remain to be explored. The resequencing approach could also identify candidate genes responsible of quantitative traits loci (QTL) effects in selected lines. Genomics is opening new ways to understand major switches that took place during domestication and subsequent selection.     

The origin and genetic diversity of Chinese native chicken breeds

The first 539 bases of mitochondrial DNA D-loop region of six Chinese native chicken breeds (Gallus gallus domesticus) were sequenced and compared to those of the red junglefowl (Gallus gallus), the gray junglefowl (Gallus sonneratii), the green junglefowl (Gallus varius) and Lafayette's junglefowl (Gallus lafayettei) reported in GenBank, and the phylogenetic trees for the chickens were constructed based on the D-loop sequences. The results showed that the four species of the genus Gallus had great differences among each other, the G. g. domesticus was closest to the red junglefowl in Thailand and its adjacent regions, suggesting the Chinese domestic fowl probably originated from the red junglefowl in these regions. The two subs pecies of Thailand, G. g. gallus and G. g. spadiceus, should belong to one subspecies because of their resemblance. In the case of native breeds, there existed a great difference between the egg breeds and general purpose breeds, which suggested different maternal origins of the two types.     

Species-typical and Individually Distinctive Acoustic Features of Crow Calls of Red Jungle Fowl

Crow calls of red jungle fowl (Gallus gallus) were analyzed for the purposes of (a) determining the extent of commonality and variability of acoustic features within and between individual roosters, and (b) characterizing the modal crow call of this species. Comparisons were made between crow calls of jungle fowl and those of domestic fowl to assess the extent to which domestication has affected these motor patterns.