Pooled Sequencing Analysis of Geese (Anser cygnoides) Reveals Genomic Variations Associated With Feather Color

Abstract

During the domestication of the goose a change in its feather color took place, however, the molecular mechanisms responsible for this change are not completely understood. Here, we performed whole-genome resequencing on three pooled samples of geese (feral and domestic geese), with two distinct feather colors, to identify genes that might regulate feather color. We identified around 8 million SNPs within each of the three pools and validated allele frequencies for a subset of these SNPs using PCR and Sanger sequencing. Several genomic regions with signatures of differential selection were found when we compared the gray and white feather color populations using the FST and Hp approaches. When we combined previous functional studies with our genomic analyses we identified 26 genes (KITLG, MITF, TYRO3, KIT, AP3B1, SMARCA2, ROR2, CSNK1G3, CCDC112, VAMP7, SLC16A2, LOC106047519, RLIM, KIAA2022, ST8SIA4, LOC106044163, TRPM6, TICAM2, LOC106038556, LOC106038575, LOC106038574, LOC106038594, LOC106038573, LOC106038604, LOC106047489, and LOC106047492) that potentially regulate feather color in geese. These results substantially expand the catalog of potential feather color regulators in geese and provide a basis for further studies on domestication and avian feather coloration.

Morphological, anatomical and histological studies on knob and beak characters of six goose breeds from China

“…Packing characters such as feather color and shin color have been studied in various local geese ( Ren et al, 2021 ; Xu et al, 2022 ), but there is no detailed report on goose knob. The protrusion of the head is the most common in gallinales birds, and its formation is mainly concentrated in the skull.…”

Convergent evolution on oceanic islands: comparative genomics reveals species-specific processes in birds

“…Among the genes associated with outlier loci there were several involved in metabolism (i.e., fabp2, kars1, lipa, nfrkb, pdha1), five involved in pigmentation and six related to singing. Among the genes related to pigmentation, there were several related to avian plumage coloration, ap3b1 (Ren et al, 2021), hps6 (Domyan et al, 2019) and ric1 (Bruders et al, 2020), one was related to sexual dichromatism in birds (Gazda, 2019), and the atrn gene was related to melanin production and has also been associated with coat coloration in macaques (Bradley et al, 2013). Regarding the genes related to song, we detected, chrm2 and chrm5, which have shown differential expression associated with song learning and production in zebra finch (Osogwa, 2018), the mrps27 (Qi et al, 2012) and upf3b (Shi et al, 2021), which are involved in the song control system in the zebra finch, the paip1 gene, which has been associated with song learning (Lovell et al, 2008), and the ube2d3 gene, which was related to musical abilities using a convergent evidence method including data from humans, songbirds and other animals (Oikkonen et al, 2016).…”

Whole genome sequencing identifies candidate genes and mutations that can explain diluted and other colour varieties of domestic canaries (Serinus canaria)

“…For example, ASIP and TYRP1 emerged in several lines in the comparisons against WT or Black Frosted Yellow canaries that represent wild or wild‐like populations as well as in several other pairwise analyses (Figure 4). Additional genes ( DCT , KITLG and MITF ), that in other avian and mammalian species have been already shown to affect pigmentation (Liu et al, 2022; Ren et al, 2021; Stryjewski & Sorenson, 2017; Sultana et al, 2018), emerged in just one or a few comparisons involving canary DNA pools.…”