Genetic diversity of 21 experimental chicken lines with diverse origins and genetic backgrounds

Abstract

The genetic characteristics and diversity of 21 experimental chicken lines registered with the National BioResource Project of Japan were examined using mitochondrial D-loop sequences and 54 microsatellite DNA markers. A total of 12 haplotypes were detected in the 500-bp mitochondrial DNA sequences of the hypervariable segment I for 349 individuals of 21 lines. The 12 haplotypes belonged to three (A, D, and E) haplogroups, out of the eight (A‒H) common haplogroups in domestic chickens and red junglefowls. The haplogroups A and D were widely represented in indigenous chickens in the Asian and Pacific regions, and the haplogroup E was the most prevalent in domestic chickens. Genetic clustering by discriminant analysis of principal components with microsatellite markers divided 681 individuals of 21 lines into three groups that consisted of Fayoumi-, European-, and Asian- derived lines. In each of the cladograms constructed with Nei’s genetic distances based on allele frequencies and the membership coefficients provided by STRUCTURE and with the genetic distance based on the proportion of shared alleles, the genetic relationships coincided well with the breeding histories of the lines. Microsatellite markers showed remarkably lower genetic heterozygosities (less than 0.1 observed heterozygosity) for eight lines (GSP, GSN/1, YL, PNP, BM-C, WL-G, BL-E, and #413), which have been maintained as closed colonies for more than 40 years (except for #413), indicating their usefulness as experimental chicken lines in laboratory animal science research.

Combined deletions of IHH and NHEJ1 cause chondrodystrophy and embryonic lethality in the Creeper chicken

“…Both the JB and congenic GSP/Cp strains exhibited the Cp trait. The GSP/Cp strain expresses a Cp allele that was introduced from the JB strain into a highly inbred strain derived from the Fayoumi breed, GSP, whose average heterozygosity is <0.01 for >50 microsatellite DNA markers 17 ( Supplementary Figs. 1-4 and Supplementary Table 1).…”

“…The following three chicken strains were used for this study: the JB strain derived from the Japanese bantam breed "Chabo" that has the Creeper (Cp) trait ( Supplementary Fig. 1); and the GSP and PNP/DO strains, both of which are highly inbred strains derived from the Fayoumi breed 17,50,51 . All lines are maintained at the Avian Bioscience Research Center (ABRC), Nagoya University, Japan.…”

New Behavioral Handling Test Reveals Temperament Differences in Native Japanese Chickens

“…Remarkably, despite using dayold chicks, our handling test effectively revealed the aggressive nature of OSM. Another interesting breed is PNP, a highly inbred line derived from three roosters and two hens of the Fayoumi breed, which has been maintained as a closed breeding colony with several pairs per generation [18]. PNP exhibited more exploratory behavior and higher locomotor activity compared to other breeds, indicating a bustling nature.…”

Assessment of genetic diversity and genetic relationships of farm and laboratory quail populations in Japan using microsatellite DNA markers

“…The positions of the DY line and Saitama population and the monophyly of the six farm populations from Aichi prefecture on the Dc tree indicated that the Dc tree is more reliable. In our previous study on the genetic characterisation for laboratory chicken lines, the Dps genetic distance constructed less realistic phylogenetic trees than that of Da genetic distance (Nunome et al, 2019). The Dc and Da genetic distances are known to be better estimators for topology construction (Takezaki & Nei, 1996).…”