A new dominant haplotype of <i><scp>MC</scp>1R</i> gene in Chinese black plumage chicken

Ten indigenous chicken breeds were originally distributed in Jiangxi Province, China, and they define a critical component of Chinese chicken genetic resources. We have investigated the population genetics of seven Jiangxi chicken breeds using 600K chicken BeadChip SNP data. To provide a genome-wide perspective for the population structure of all 10 Jiangxi chicken breeds, we herein genotyped 78 additional individuals from the seven breeds and 63 chickens from three uninvestigated breeds-Yugan Black (YG), Nancheng Black (NC) and Wanzai Yellow using 55K chicken SNP arrays. We then explored merged data of 17 101 SNPs from 235 individuals to infer the population structure of the 10 breeds. We showed that NC and YG are two regional populations of the same breed, as individuals from the two populations clustered together to form a branch separate from the other breeds in the neighbor-joining tree, they always grouped together in multidimensional principal component analyses and they displayed an identical pattern of ancestral lineage composition. Hence, NC and YG should be considered a single breed in the state-supported conservation scheme. Moreover, we conducted a genome scan for signatures of selection for black plumage. BAYESCAN and HAPFLK analyses of two contrasting groups (three blackfeathered breeds vs. six non-black-feathered breeds) consistently detected 25 putative regions under selection. Nine pigmentation-associated genes (DCT, SLC24A5, SLC30A4, MYO5A, CYP19A1, NADK2, SLC45A2, GNAQ and DCP2) reside within these regions, and these genes are interesting candidates for black plumage and provide a starting point for further identification of causative mutations for black feathers in chicken.

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“…; Zhang et al . ), and HOXB9 , HOXC8 , HOXA9 and HOXC9 are known to be involved in plumage melanogenesis in black‐bone chickens (Yu et al . ).…”

Section: Resultsmentioning

confidence: 99%

Whole‐genome SNP data unravel population structure and signatures of selection for black plumage of indigenous chicken breeds from Jiangxi province, China

et al. 2019

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“…a). Eight MC1R SNPs were identified in Line_B02 ( n = 520, Table ) and Line_W01 ( n = 122, Table ) using Sanger sequencing 3 . Complete LD was found for MC1R :c.‐37C>T, MC1R :c.69C>T, MC1R :c.212T>C and MC1R :c.274G>A in Line_B02 (Fig.…”

Section: Figurementioning

confidence: 99%

“…The dominant Extended Chinese black E C (CAA) haplotype of three non‐synonymous alleles, MC1R :c.212T>C (p.Met71Thr, rs312264213), MC1R :c.274G>A (p.Glu92Lys, rs314881228) and MC1R :c.644A>C (p.His215Pro, rs735789743), is different from the E (TAA) haplotype in non‐Chinese breeds 3 . This E C haplotype is dominant over the e bc (CAC) and e + (TGA) alleles 3 . In this study, we aimed to investigate if this Chinese E C haplotype can be applied to breeding black‐plumage Chinese chickens.…”

Section: Figurementioning

confidence: 99%

“…Melanocortin 1 receptor ( MC1R ) is the major gene that controls chicken plumage color, including extended black ( E ), birchen ( E R ), dominant wheaten ( e wh ), recessive wheaten ( e y ), brown ( e b ), buttercup ( e bc ) and wt ( e + ) alleles 1,2 . The dominant Extended Chinese black E C (CAA) haplotype of three non‐synonymous alleles, MC1R :c.212T>C (p.Met71Thr, rs312264213), MC1R :c.274G>A (p.Glu92Lys, rs314881228) and MC1R :c.644A>C (p.His215Pro, rs735789743), is different from the E (TAA) haplotype in non‐Chinese breeds 3 . This E C haplotype is dominant over the e bc (CAC) and e + (TGA) alleles 3 .…”

Section: Figurementioning

confidence: 99%

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Haplotypes of three missense mutations in Melanocortin 1 receptor serve as genetic markers for black plumage in Chinese chicken

Deng

Chen

et al. 2020

Animal Genetics

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“…The abundant polymorphism of the MC1R gene determined in local Chinese Hebei chicken strain was associated with their rich plumage pigmentation diversity (Guo et al, 2010). Zhang et al (2017) found that both the C allele of c.212T>C and the A allele of c.644A>C differentiates 39 homozygous and heterozygous individuals for breeding of pure black plumage Chinese chicken.…”

Section: Detection Of Snps In the Melanocortin 1-receptor (Mc1r) And mentioning

confidence: 99%

Detection of Snps in the Melanocortin 1-Receptor (MC1R) and Its Association with Shank Color Trait in Hs Chicken

Shen

Wang

Cui

et al. 2019

Braz. J. Poult. Sci.

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The melanocortin 1 receptor (MC1R) gene plays a key role in controlling the deposition of melanin. In mammals, the MC1Rgene is regarded as a major candidate gene in the control of melanin formation. In domestic animals, the MC1R gene mainly controls the expression of coat, skin, and plumage color in mammals and birds. In order to breed chickens with dark-green shank faster, we screened the molecular markers for shank color in a HS chicken population by exploring the relationship between polymorphism of the MC1R gene and three different shank colors (light green, dark green and yellow). Two primer pairs for code region of the MC1R gene were designed in the basic of chicken genomic sequence. DNA sequencing was performed to detect the polymorphisms and PCR was used to amplify DNA fragment. Sequences analysis indicated that 7 SNPs were predominant the three HS chicken populations with different shank color, including g.18,

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A new dominant haplotype of MC1R gene in Chinese black plumage chicken

Cited by 13 publications

References 4 publications

Whole‐genome SNP data unravel population structure and signatures of selection for black plumage of indigenous chicken breeds from Jiangxi province, China

Whole‐genome SNP data unravel population structure and signatures of selection for black plumage of indigenous chicken breeds from Jiangxi province, China

Haplotypes of three missense mutations in Melanocortin 1 receptor serve as genetic markers for black plumage in Chinese chicken

Detection of Snps in the Melanocortin 1-Receptor (MC1R) and Its Association with Shank Color Trait in Hs Chicken

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