Genome-wide association study revealed the genomic regions associated with skin pigmentation in an Ogye x White Leghorn F2 chicken population

Cha, Jihye; Jin, Daehyeok; Kim, Jaehwan; Kim, Seung-Chang; Lim, Jin A; Chai, Han-Ha; Jung, Seul a; Lee, Jun Heon; Lee, Seung Hwan

doi:10.1016/j.psj.2023.102720

Cited by 8 publications

(7 citation statements)

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“…Similarly, R2, spanning from Z:81040000 to Z:82226500, encompasses a length of 1.18 Mb and hosts more than 15 protein-coding genes. Previous research (Cha et al, 2023; Li et al, 2014; Tian et al, 2014b; Xu et al, 2017), particularly concerning dermal pigmentation and plumage color variation, has highlighted several candidate genes predominantly located within the R1 region. Considering these earlier studies and our findings (discussed in the subsequent section), it becomes evident that the Id locus is co-localized with the Z-amplicon repeat units at the distal end of the q-arm of chromosome Z.…”

Section: Resultsmentioning

confidence: 99%

“…It has been reported that mutations in the MTAP gene are associated with nevus count and melanoma development (Kvaskoff et al, 2011). Genomic variants identified in the MTAP are associated with plumage and dermal pigmentation in the F2 population crossed from White Leghorn and the Yeonsan Ogye (Cha et al, 2023; Heo et al, 2023). Functional gene expression analysis of Silkie and White Leghorn chicken embryos during early embryonic stages indicated distinct patterns of MTAP expression.…”

Section: Discussionmentioning

confidence: 99%

“…Several studies have been undertaken involving crosses between BBC and non-BBC breeds, all in pursuit of identifying the candidate Id gene. These investigations have reported various potential genes which are associated with dermal and shank pigmentation variations (Arora et al, 2011; Cha et al, 2023; Li et al, 2014; Mcgibbon, 1978; Tian et al, 2014b; Xu et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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Common Ancestry of theIdLocus: Chromosomal Rearrangement and Polygenic Possibilities

Sharma,

Vijay

2023

Preprint

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The diversity of dermal pigmentation and plumage color in domestic chickens is intriguing. Black bone chickens (BBC) stand out with their intense melanin hyperpigmentation, driven by a complex chromosomal rearrangement on chromosome 20, specifically the Fm locus, causing overexpression of the EDN3 gene. In contrast, dermal pigmentation inhibition is regulated by the sex-linked Id locus. Previous studies have used crosses, GWAS and gene expression analysis to identify the genetic basis of the Id locus, but the puzzle remains unsolved. Our study seeks to precisely locate the Id locus, identify gene(s) inhibiting dermal pigmentation, and explore its ancestral state in BBC breeds. We analyzed public data from 270 chickens (42 BBC and 228 non-BBC) to refine the position of the Id locus to a ~1.6 Mb region between Z amplicon repeats on the distal end of q-arm and found that it shares a common ancestry among all BBC breeds, much like the Fm locus. The selection signatures and high fixation levels within MTAP, CCDC112 and a few other genes within this region support multiple candidates. Our results suggest that the Id locus is shared among BBC breeds and may have a polygenic nature, explaining the shank and dermal pigmentation variation.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Common Ancestry of theIdLocus: Chromosomal Rearrangement and Polygenic Possibilities

Sharma,

Vijay

2023

Preprint

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“…The MTAP gene encodes methyl-thioadenosine phosphorylase, acting in the methionine salvage pathway ( Kirovski et al, 2011 ). The MTAP gene has been already identified in chicken as main responsible of skin pigmentation ( Cha et al, 2023 ), hyperpigmentation in the Silkie chicken ( Tian et al, 2014 ), and pigmentation of Tibetan chicken shank ( Li et al, 2014 ). In particular, Li et al (2014) used the same DNA chip of the present study and found the QTL of MTAP and CDKN2A/B using the same GWAS approach.…”

Section: Discussionmentioning

confidence: 99%

Genomic insights into shank and eggshell color in Italian local chickens

Perini,

Cendron,

Lasagna

et al. 2024

Poultry Science

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“…The Fibromelanosis phenotype is found in Silkie and other black-bone chicken breeds, such as Yeonsan Ogye and Kadaknath. Study of this intriguing phenotype for over a century has gradually narrowed the genomic location of the underlying genetic mutation to a complex chromosomal rearrangement (Fm locus) on chromosome 20 [2][3][4][7][8][9] . Black-bone chicken breeds (which was not certified by peer review) is the author/funder.…”

Section: Introductionmentioning

confidence: 99%

What is the correct genomic structure of the complex chromosomal rearrangement at theFmlocus in Silkie chicken?

Sharma,

Vijay

2024

Preprint

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The availability of high-quality chromosome-level genome assemblies of an increasing number of avian species holds significant promise for addressing longstanding questions in bird evolution and biology. In a recent issue of Communications Biology, Zhu, F., Yin, ZT., Zhao, QS. et al. ( ZYZSJ) presented a chromosome-level assembly for the Silkie chicken using a multi-platform high-coverage dataset to obtain accurate and complete sequences spanning the chicken genome. A key finding from their genomic analysis is the reconstruction of the structure of the complex rearrangement at the Fm locus, the primary genetic change underlying the rare and conspicuous dermal hyperpigmentation phenotype generally called Fibromelanosis. However, in contrast to their identification of the *Fm_1 scenario (which the authors refer to as FM2) as the correct arrangement at the Fm locus, several previously published studies claim that *Fm_2 is the valid scenario. Our re-analysis of ZYZSJ's new genome assembly (CAU_Silkie) demonstrates that *Fm_2 is indeed the correct scenario, and the *Fm_1 scenario favoured by ZYZSJ results from an assembly error caused by mosaic haplotypes generated during the de novo assembly step. We recommend that genome projects perform post-assembly validation and correction to safeguard biological interpretations from the impact of assembly artefacts.

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Genome-wide association study revealed the genomic regions associated with skin pigmentation in an Ogye x White Leghorn F2 chicken population

Cited by 8 publications

References 50 publications

Common Ancestry of theIdLocus: Chromosomal Rearrangement and Polygenic Possibilities

Common Ancestry of theIdLocus: Chromosomal Rearrangement and Polygenic Possibilities

Genomic insights into shank and eggshell color in Italian local chickens

What is the correct genomic structure of the complex chromosomal rearrangement at theFmlocus in Silkie chicken?

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