A few QTLs affecting red colour pigmentation in the chicken plumage have been identified. Unfortunately, none of them neither coincide nor closely located with the identified QTLs in this study. Surprisingly, no previous attempts were made to identify QTLs affecting metallic green colour pigmentation. However, some of the previously identified QTLs affecting other than colour pigmentation such as antibody response, growth etc. either closely located or perfectly coincide with the identified QTLs in this study. Interestingly, most of them are growth related QTLs. Therefore from the above observations it can be concluded that there is a strong correlation between colour and growth QTLs. In addition, colour loci have significant pleiotropic effect.

All of the four identified QTLs affecting red colour pigmentation all together can explain ~36% of the phenotypic variance of this trait. Whereas, the two identified QTLs affecting metallic green colour pigmentation all together can explain ~24% of the phenotypic variance of this trait. Therefore, it can be concluded that the chicken pigmentation mostly affected by epistatic interactions of QTLs with smaller effect.

Out of the four QTLs affecting Red colour pigmentation: 2 QTLs acted in Red Junglefowl direction and 2 in White Leghorn direction. Whereas, both of the two QTLs affecting metallic green colour pigmentation acted in the Red Junglefowl direction. Additionally, all the epistatic effect acted in the Red Junglefowl direction.

QTL located on chromosoeme 11 at 24 cM is about 5.14 Mbp long. Researchers have identified two selective sweeps within this region. A good candidate gene is located in this region, namely SLC6A2. Moreover, QTL located on chromosome 14 at 203 cM is about 3.8 Mbp long. A good candidate gene is located in this region such as A2BP1. In addition, QTL at locus 247 cM (on chromosoeme 3) is about 2.9 MB long and perfectly coincide with two selective sweeps indentified in different studies. Therefore some of the candidate genes found in this region likely to have effect on domestication traits includes, ESR1/ ESR2 and NR4A2/NR4A3 .