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Piao chicken, a Chinese indigenous rumpless chicken breed, lacks pygostyle, caudal vertebra, uropygial gland and tail feathers. The rumplessness in Piao chicken presents an autosomal dominant inheritance pattern. However, the molecular genetic mechanisms underlying the rumplessness in Piao chicken remains unclear. In this study, whole-genome resequencing was performed for 146 individuals from 10 chicken breeds, including 9 tailed chicken breeds and Piao rumpless breed. Tailbone CT scan for Piao chickens and WL chickens, revealed that some Piao chicken tails were normal in number, and for a few Piao chickens tail length and tail bone numbers were between the rumpless and the normal tailed chickens. The results showed that the rumpless phenotype has not been completely fixed in Piao chicken breed. Using selection signature analysis and structural variation detection, we found a 4174 bp deletion located in the upstream region of IRX1 gene on chromosome 2 related to rumpless phenotype. Structural variation genotyping showed that the deletion was present in all 32 rumpless Piao chickens (del/del, wild/del) and absent from all 112 tailed chickens included in the dataset for the other 9 breeds and 2 tailed Piao chickens (wild/wild). In summary, all rumpless Piao chickens tested here carry this deletion mutation, to show a complete linkage association with rumplessness trait. We suggested that the 4174 bp deletion could be causative for rumpless phenotype in Piao chicken since this is the only mutation to show the complete linkage disequilibrium with rumplessness on whole genome level across all of 146 chickens from the 10 breeds. This study could facilitate a better understanding of the genetic characteristics of Piao chicken.

Under the pressure of natural and artificial selection, domestic animals, including chickens, have evolved unique mechanisms of genetic adaptations such as high-altitude adaptation, hot and arid climate adaptation, and desert adaptation. Here, we investigated the genetic basis of cold tolerance in chicken by integrating whole-genome and transcriptome sequencing technologies. Genome-wide comparative analyses of 118 chickens living in different latitudes showed 46 genes and several pathways that may be involved in cold adaptation. The results of the functional enrichment analysis of differentially expressed genes proved the important role of metabolic pathways and immune-related pathways in cold tolerance in chickens. The subsequent integration of whole genome and transcriptome sequencing technology further identified six genes - dnah5 (dynein axonemal heavy chain 5), ptgs2 (prostaglandin-endoperoxide synthase 2), inhba (inhibin beta A subunit), irx2 (iroquois homeobox 2), ensgalg00000054917, and ensgalg00000046652 - requiring more detailed studies. In addition, we also discovered different allele frequency distributions of five SNPs (single nucleotide polymorphisms) within ptgs2 and nine SNPs within dnah5 in chickens in different latitudes, suggesting strong selective pressure of these two genes in chickens. We provide a novel insight into the genetic adaptation in chickens to cold environments, and provide a reference for evaluating and developing adaptive chicken breeds in cold environments.

Background Since the domestication of chicken, various breeds have been developed for food production, entertainment, and so on. Compared to indigenous chicken breeds which generally do not show elite production performance, commercial breeds or lines are selected intensely for meat or egg production. In the present study, in order to understand the molecular mechanisms underlying the dramatic differences of egg number between commercial egg-type chickens and indigenous chickens, we performed a genome-wide association study (GWAS) in a mixed linear model. Results We obtained 148 single nucleotide polymorphisms (SNPs) associated with egg number traits (57 significantly, 91 suggestively). Among them, 4 SNPs overlapped with previously reported quantitative trait loci (QTL), including 2 for egg production and 2 for reproductive traits. Furthermore, we identified 32 candidate genes based on the function of the screened genes. These genes were found to be mainly involved in regulating hormones, playing a role in the formation, growth, and development of follicles, and in the development of the reproductive system. Some genes such as NELL2 (neural EGFL like 2), KITLG (KIT ligand), GHRHR (Growth hormone releasing hormone receptor), NCOA1 (Nuclear receptor coactivator 1), ITPR1 (inositol 1, 4, 5-trisphosphate receptor type 1), GAMT (guanidinoacetate N-methyltransferase), and CAMK4 (calcium/calmodulin-dependent protein kinase IV) deserve our attention and further study since they have been reported to be closely related to egg production, egg number and reproductive traits. In addition, the most significant genomic region obtained in this study was located at 48.61–48.84 Mb on GGA5. In this region, we have repeatedly identified four genes, in which YY1 (YY1 transcription factor) and WDR25 (WD repeat domain 25) have been shown to be related to oocytes and reproductive tissues, respectively, which implies that this region may be a candidate region underlying egg number traits. Conclusion Our study utilized the genomic information from various chicken breeds or populations differed in the average annual egg number to understand the molecular genetic mechanisms involved in egg number traits. We identified a series of SNPs, candidate genes, or genomic regions that associated with egg number, which could help us in developing the egg production trait in chickens.

The conservation and development of chicken have received considerable attention, but the admixture history of chicken breeds, especially Chinese indigenous breeds, has been poorly demonstrated. In this study, we aimed to evaluate the genetic diversity and population structure of eight chicken breeds (including conserved chicken breeds) from different geographic origin and to identify admixture within these breeds using a 600-K single-nucleotide polymorphism panel for genotyping. Using the genotype of 580,961 single-nucleotide polymorphism markers scored in 1,200 animals, we evaluated the genetic diversity (heterozygosity and proportion of polymorphic markers), linkage disequilibrium decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance), and migration events (TreeMix and f-statistics) of the eight domesticated chicken breeds. The results of population analytical methods revealed patterns of hybridization that occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture, followed by trade, have been important forces in shaping the genomic variation in modern Chinese chicken. Moreover, isolation by distance might play a critical role in shaping the genomic variation within Eurasia continent chicken breeds. Moreover, genetic information provided in this study is valuable resources for production applications (genomic prediction, and breeding strategy) and scientific research (genetic basis detection, studying evolution, or domestication).

Although many phenotypic traits of chickens have been well documented, the genetic patterns of gene expression levels in chickens remain to be determined. In the present study, we crossed two chicken breeds, White Leghorn (WL) and Cornish (Cor), which have been selected for egg and meat production, respectively, for a few hundred years. We evaluated transcriptome abundance in the brain, muscle, and liver from the day-old progenies of pure-bred WL and Cor, and the hybrids of these two breeds, by RNA-Seq in order to determine the inheritance patterns of gene expression. Comparison among expression levels in the different groups revealed that most of the genes showed conserved expression patterns in all three examined tissues and that brain had the highest number of conserved genes, which indicates that conserved genes are predominantly important compared to others. On the basis of allelic expression analysis, in addition to the conserved genes, we identified the extensive presence of additive, dominant (Cor dominant and WL dominant), over-dominant, and under-dominant genes in all three tissues in hybrids. Our study is the first to provide an overview of inheritance patterns of the transcriptome in layers and broilers, and we also provide insights into the genetics of chickens at the gene expression level.

Background: Since the domestication of chicken, various chicken breeds have been developed for food production, entertainment, and so on. Compared to indigenous chicken breeds which generally do not show elite production performance, commercial breeds or lines are selected intensely for meat or egg production. In the present study, in order to understand the molecular mechanisms underlying the dramatic egg yielding differences between commercial egg-type chickens and indigenous chickens, we performed a genome-wide association study (GWAS) in a mixed linear model. Results: We obtained 148 single nucleotide polymorphisms (SNPs) associated with egg production traits or reproductive traits (57 significantly, 91 suggestively). Among them, 18 SNPs overlapped with previously reported quantitative trait loci (QTL), including 13 for egg production and 5 for reproductive traits. Three SNPs were significantly associated with multiple egg production traits, such as egg number, age at first egg, and egg production rate in chickens. Furthermore, we identified 32 candidate genes based on the function of the screened genes. These genes were found to be mainly involved in regulating hormones, playing a role in the formation, growth, and development of follicles, and in the development of the reproductive system. Some genes such as NELL2, KITLG, GHRHR, NCOA1, ITPR1, GAMT, and CAMK4 deserve our attention and further study since they have been reported to be closely related to reproductive traits. In addition, the most significant genomic region obtained in this study was located at 48.61-48.84Mb on GGA5. In this region, we have repeatedly annotated four genes, in which YY1 and WDR25 have been shown to be related to oocytes and reproductive tissues, respectively, which implies that this region may be a candidate region underlying egg production traits. Conclusion: Our study utilized the genomic information from various chicken breeds or populations differed in egg production to understand the molecular genetic mechanisms involved in reproduction traits. We identified a series of SNPs, candidate genes, or genomic regions that associated with reproductive traits, which could help us in developing egg production in chickens.

Following chicken domestication, diversified chicken breeds were developed by both natural and artificial selection, which led to the accumulation of abundant genetic and phenotypic variations, making chickens an ideal genetic research model. To better understand the genetic structure of chicken breeds under different selection pressures, we genotyped various chicken populations with specific selection targets, including indigenous, commercial, gamecock, and wild ancestral chickens, using the 600K SNP array. We analyzed the population structure, genetic relationships, run of homozygosity (ROH), effective population number (Ne), and other genetic parameters. The wild ancestral population, red junglefowl (RJF), possessed the highest diversity, in comparison with all other domesticated populations, which was supported by linkage disequilibrium decay (LD), effective population number, and ROH analyses. The gamecock breeds, which were subjected to stronger male-biased selection for fighting-related traits, also presented higher variation than the commercial and indigenous breeds. Admixture analysis also indicated that game breed is a relatively independent branch of Chinese local breeds. Following intense selection for reproductive and productive traits, the commercial lines showed the least diversity. We also observed that the European local chickens had lower genetic variation than the Chinese local breeds, which could be attributed to the shorter history of the European breed. ROH were present in a breed specific manner and 191 ROH island were detected on four groups (commercial, local, game and wild chickens). These ROH islands were involved in egg production, growth and silky feathers and other traits. Moreover, we estimated the effective sex ratio of these breeds to demonstrate the change in the ratio of the two sexes. We found that commercial chickens had a greater sex imbalance between females and males. The commercial lines showed the highest female-to-male ratios. Interestingly, RJF comprised a greater proportion of males than females. Our results show the population genetics of chickens under selection pressures, and can aid in the development of better conservation strategies for different chicken breeds.

Although many phenotypic traits of chickens have been well documented, the genetic patterns of gene expression levels in chickens remain to be determined. In the present study, we crossed two chicken breeds, White Leghorn (WL) and Cornish (Cor), which have been selected for egg and meat production, respectively, for a few hundred years. We evaluated transcriptome abundance in the brain, muscle, and liver from the day-old progenies of pure-bred WL and Cor, and the hybrids of these two breeds, by RNA-Seq in order to determine the inheritance patterns of gene expression. Comparison among expression levels in the different groups revealed that most of the genes showed conserved expression patterns in all three examined tissues and that brain had the highest number of conserved genes, which indicates that conserved genes are predominantly important compared to others. On the basis of allelic expression analysis, in addition to the conserved genes, we identified the extensive presence of additive, dominant (Cor dominant and WL dominant), over-dominant, and under-dominant genes in all three tissues in hybrids. Our study is the first to provide an overview of inheritance patterns of the transcriptome in layers and broilers, and we also provide insights into the genetics of chickens at the gene expression level.

New-born chicks are vulnerable to bacterial infections and not good at regulating body temperature. There is a close relationship between thermal regulation and immunity, however, the underlying mechanism is not well understood. Salmonella Pullorum (SP) is a major concern in developing countries and causes significant economic losses in poultry industry. Early body temperature (EBT) has previously shown to be correlated with host immunity and resistance to pullorum disease. In this study, we challenged three independent chick populations (Beijing You, Dwarf and Rhode Island Red) with SP at 4 days of age, and rectal temperature was measured before and after the SP attack from 2 to 7 days of age. Host defense to SP was evaluated by survival and spleen SP carrier status. The results showed that chicks with higher EBT before SP infection tend to have higher resistance to later SP attack in two populations (Dwarf and Beijing You). The association between EBT before SP attack and SP resistance was non-significant in Rohde Island Red population (P = 0.06), but the trend was consistent with the other two populations. We also found low to moderate heritability in all three populations for EBT before and after the SP attack ranging from 0.14 to 0.20. Genome-wide association studies identified several genomic regions and biological pathways determining EBT before SP attack, which provides candidate functional genes of this trait. Our results reveal the genetic determination of EBT, and the relationship between EBT and SP resistance, providing an alternative strategy for improving SP resistant activities in chicken.

Background Salmonella infection is a serious concern in poultry farming because of its impact on both economic loss and human health. Chicks aged 20 days or less are extremely vulnerable to Salmonella pullorum (SP), which causes high mortality. Furthermore, an outbreak of SP infection can result in a considerable number of carriers that become potential transmitters, thus, threatening fellow chickens and offspring. In this study, we conducted a genome-wide association study (GWAS) to detect potential genomic loci and candidate genes associated with two disease-related traits: death and carrier state. Methods In total, 818 birds were phenotyped for death and carrier state traits through a SP challenge experiment, and genotyped by using a 600 K high-density single nucleotide polymorphism (SNP) array. A GWAS using a single-marker linear mixed model was performed with the GEMMA software. RNA-sequencing on spleen samples was carried out for further identification of candidate genes. Results We detected a region that was located between 33.48 and 34.03 Mb on chicken chromosome 4 and was significantly associated with death, with the most significant SNP (rs314483802) accounting for 11.73% of the phenotypic variation. Two candidate genes, FBXW7 and LRBA, were identified as the most promising genes involved in resistance to SP. The expression levels of FBXW7 and LRBA were significantly downregulated after SP infection, which suggests that they may have a role in controlling SP infections. Two other significant loci and related genes (TRAF3 and gga-mir-489) were associated with carrier state, which indicates a different polygenic determinism compared with that of death. In addition, genomic inbreeding coefficients showed no correlation with resistance to SP within each breed in our study. Conclusions The results of this GWAS with a carefully organized Salmonella challenge experiment represent an important milestone in understanding the genetics of infectious disease resistance, offer a theoretical basis for breeding SP-resistant chicken lines using marker-assisted selection, and provide new information for salmonellosis research in humans and other animals.

Background Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population divergence in chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibit major differences in body size and reproductive traits, and used them to determine the degree of cis versus trans variation in the brain, liver, and muscle tissue of male and female 1-day-old specimens. Results We provided an overview of how transcriptomes are regulated in hybrid progenies of two contrasting breeds based on allele specific expression analysis. Compared with cis-regulatory divergence, trans-acting genes were more extensive in the chicken genome. In addition, considerable compensatory cis- and trans-regulatory changes exist in the chicken genome. Most importantly, stronger purifying selection was observed on genes regulated by trans-variations than in genes regulated by the cis elements. Conclusions We present a pipeline to explore allele-specific expression in hybrid progenies of inbred lines without a specific reference genome. Our research is the first study to describe the regulatory divergence between two contrasting breeds. The results suggest that artificial selection associated with domestication in chicken could have acted more on trans-regulatory divergence than on cis-regulatory divergence.

Background: Gene expression variation is an important mechanism underlying phenotypic variation, and can occur via cis- and trans-regulation. In order to understand the role of cis- and trans-regulatory variation on population divergence of chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, with major differences in body size and reproductive traits, and used them to identify the degree of cis versus trans variation in brain, liver and muscle of both male and female samples at 1 day age. Results: We provided a landscape about how the transcriptomes are regulated in the hybrid progenies of two contrasted breeds by allele specific expression analysis. Our results showed that compared with the cis-regulatory divergence, trans-acted genes existed more extensively in the chicken genome. Furthermore, a widespread tendency of compensatory regulation exists in chicken genome. Most importantly, we found the evidence of stronger purifying selection on genes regulated by trans variations than the cis elements. Conclusions: We demonstrated a pipeline to explore the allele-specific expression in the hybrid progenies of inbred lines without specific reference genome. Our research performed the first study to describe the regulatory divergence between two contrasted breeds. The results suggested that artificial selection associated with domestication in chicken may have more often acted on trans-regulatory divergence than cis.

Background Gene expression variation is an important mechanism underlying phenotypic variation, and can occur via cis- and trans-regulation. In order to understand the role of cis- and trans-regulatory variation on population divergence of chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, with major differences in size and reproductive traits, and used them to identify the degree of cis versus trans variation in brain, liver and muscle of both male and female samples at 1-day age. Results We provided a landscape about how the transcriptomes are regulated between two contrasted breeds by allele specific expression analysis. Our results showed that compared with the cis-regulated genes, trans-acted genes existed more extensively in the chicken genome. Furthermore, a widespread compensatory tendency exists in chicken genome. Most importantly, we found the evidence of stronger purifying selection for trans-regulatory variation than the cis-elements. Conclusions Our research performed the first study to describe the transcriptome regulation between White Leghorn and Cornish Game breeds and suggests that artificial selection associated with domestication in chicken may have more often acted on trans-regulatory variation.

Background: The genetic foundation of chicken tail feather color is not very well studied to date, though that of body feather color is extensively explored. In the present study, we used a synthetic chicken dwarf line (DW), which was originated from the hybrids between a black tail chicken breed, Rhode Island Red (RIR) and a white tail breed, Dwarf Layer (DL), to understand the genetic rules of the white/black tail color. The DW line still contain the individuals with black or white tails, even if the body feather are predominantly red, after more than ten generation of self-crossing and being selected for the body feather color. We firstly performed four crosses using the DW line chickens including black tail male to female, reciprocal crosses between the black and white, and white male to female to elucidate the inheritance pattern of the white/black tail. Furtherly, we performed a genome-wide association (GWA) analysis to determine the candidate genomic regions underlying the tail feather color by using black tail chickens from the RIR and DW chickens and white individuals from DW lines. Results: In the cross experiment, we found that (i) the white/black tail feather colors are independent of body feather color and (ii) the phenotype are autosomal simple trait and (iii) the white are dominant to the black in the DW lines. The GWA results showed that seven Single-nucleotide polymorphism (SNP) on chromosome 24 were significantly correlated with tail feather color. The significant region (3.97-4.26 Mb) perches nine known genes and five anonymous genes. The nine genes were: NECTIN1, THY1, gga-mir-1466, USP2, C1QTNF5, RNF26, MCAM, CBL and CCDC153. Conclusions: The study has revealed the white/black tail feather trait is autosome-linked in Dwarf chickens. In the genome significant ~0.29 Mb region, fourteen genes were found and some of them could play critical roles in the formation of white/black tail feather color, especially gene MCAM. Taken together, our research is the first study on genetics of tail feather color and could help the more understanding of feather pigmentation in chicken.

In this study, we aimed to evaluate the genetic diversity and population structure of eight chicken breeds (including conserved chicken breeds) from different geographic origin and to identify admixture within these breeds using a 600-K SNP (single nucleotide polymorphism) panel for genotyping. Using the genotype of 580 961 single nucleotide polymorphism markers scored in 1 200 animals, we evaluated the genetic diversity (heterozygosity and proportion of polymorphic markers), linkage disequilibrium (LD) decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (FST and genetic distance), and migration events (TreeMix and f-statistics) of the eight domesticated chicken breeds.

calulate Fst between two populations (R code).

Aggression in chickens is a serious economic and welfare issue. Pigmentation traits have been well documented to be associated with animal behaviour. Previous studies have shown that chicken pecking behaviour is related to the feather colour and premelanosome protein 17 (PMEL17) is one of the candidate genes. In the present study, we performed a genotypic and phenotypic association analysis between chicken plumage colour (red and white) and aggressive behaviour in an F1 hybrid group, generated by crossing an autosome dominant white feather breed, White Leghorn (WL), and a red feathered breed, Rhode Island Red (RIR). In genetic theory, the progeny should all have white feathers since the WL are homozygous autosome dominant white. However, we found a few red-feathered female chickens. We compared aggressiveness between the red and white females to determine whether the feather colour alone affected the behaviour since the genetic background should be the same except for the feather colour. The aggressiveness was recorded 5 days after sex maturity at 26 weeks. Generally, white plumage hens showed significantly higher aggressiveness than the red ones did in chase, attack, peck, and threatening behaviour. We also detected three feather colour candidate genes, PMEL17, solute carrier family 45 member 2 (SLC45A2), and SRY-box 10 (SOX10) in determining the genetic foundation for the red and white feather colour in our hybrids population and there was no association between the three loci and the feather colour. Additional studies should be conducted to elucidate further the genetic or phenotypic mechanisms underlying the feather colours and the behaviour.

Additional file 1: Figure S1. Assessment of our analysis pipeline for estimating allele specific expression. Figure S2. Assessment of our local reads method for estimating allele specific expression. Figure S3. Classification of genes in brain. Figure S4. Classification of genes in liver. Figure S5. Classification of genes in muscle. Figure S6. Intersection of different groups of cis- and trans- regulatory genes. Figure S7. The ratio of the numbers of non-synonymous SNPs to the numbers of synonymous SNPs (pN/pS) in different groups of cross 2. Figure S8. The ratio of the numbers of non-synonymous SNPs to the numbers of synonymous SNPs (pN/pS) in different groups of cross 3. Table S1. The summary of differential expression genes in hybrid and purebred progenies Table S2. The difference of gene proportion of each categories between different groups Table S3. The gene list of intersection of each group

Aggression in chickens is a serious economic and animal welfare issue in poultry farming. Pigmentation traits have been documented to be associated with animal behaviour. Chicken pecking behaviour has been found to be related to feather colour, with premelanosome protein 17 (PMEL17) being one of the candidate genes. In the present study, we performed a genotypic and phenotypic association analysis between chicken plumage colour (red and white) and aggressive behaviour in an F1 hybrid group generated by crossing the autosomal dominant white-feathered breed White Leghorn (WL) and the red-feathered breed Rhode Island Red (RIR). In genetic theory, all the progeny should have white feathers because WL is homozygous autosomal dominant for white feathers. However, we found a few red-feathered female chickens. We compared the aggressiveness between the red and white females to determine whether the feather colour alone affected the behaviour, given that the genetic background should be the same except for feather colour. The aggressiveness was recorded 5 days after sexual maturity at 26 weeks. Generally, white plumage hens showed significantly higher aggressiveness compared to the red ones in chasing, attacking, pecking, and threatening behaviour traits. We assessed three candidate feather colour genes—PMEL17, solute carrier family 45 member 2 (SLC45A2), and SRY-box 10 (SOX10)—to determine the genetic basis for the red and white feather colour in our hybrid population; there was no association between the three loci and feather colour. The distinct behavioural findings observed herein provide clues to the mechanisms underlying the association between phenotype and behaviour in chickens. We suggest that mixing red and white chickens together might reduce the occurrence of aggressive behaviours.

Resistance to diseases varies considerably among populations of the same species and can be ascribed to both genetic and environmental factors. Salmonella Pullorum (SP) is responsible for significant losses in the poultry industry, especially in developing countries. To better understand SP resistance in chicken populations with different genetic backgrounds, we orally challenged 3 chicken lines with SP-a highly selected commercial breed (Rhode Island Red, RIR), a local Chinese chicken (Beijing You, BY), and a synthetic layer line (dwarf, DW)-at 4 d of age. Two traits related to SP resistance, survival, and bacterial carriage in the spleen were evaluated after infection. Survival rates were recorded up to 40 d of age when all chickens still alive were killed to verify the presence of SP in the spleen to determine carrier state. Mortalities for RIR, BY, and DW chicks were 25.1%, 8.3%, and 22.7%, respectively, and the corresponding carrier-states in the spleens were 17.9%, 0.6%, and 15.8%. Survival and carrier-state heritabilities were estimated using an animal threshold model. Survival heritability was 0.197, 0.091, and 0.167 in RIR, BY, and DW populations, respectively, and the heritabilities of carrier state for DW and RIR were 0.32 and 0.16, respectively. This is the first time that the heritability of the SP carrier state has been evaluated in chickens. Our study provides experimental evidence that chickens with various genetic background exhibited significantly different SP-resistant activities and heritabilities. These results may be useful for selecting lines with better disease resistance.

Suggestive SNPs associated with the earlobe color phenotype in Rhode Island Red chickens. (DOC 240 kb)

Polydactyly is one of the most common hereditary congenital limb malformations in chickens and other vertebrates. The zone of polarizing activity regulatory sequence (ZRS) is critical for the development of polydactyly. The causative mutation of polydactyly in the Silkie chicken has been mapped to the ZRS; however, the causative mutations of other chicken breeds are yet to be established. To understand whether the same mutation decides the polydactyly phenotype in other chicken breeds, we detected the single-nucleotide polymorphism in 26 different chicken breeds, specifically, 24 Chinese indigenous breeds and 2 European breeds. The mutation was found to have fully penetrated chickens with polydactyly in China, indicating that it is causative for polydactyly in Chinese indigenous chickens. In comparison, the mutation showed no association with polydactyly in Houdan chickens, which originate from France, Europe. Based on the different morphology of polydactyly in Chinese and European breeds, we assumed that the trait might be attributable to different genetic foundations. Therefore, we subsequently performed genome-wide association analysis (GWAS) to locate the region associated with polydactyly. As a result, a ~0.39 Mb genomic region on GGA2p was identified. The region contains six candidate genes, with the causative mutation found in Chinese indigenous breeds also being located in this region. Our results demonstrate that polydactyly in chickens from China and Europe is caused by two independent mutation events that are closely located in the chicken genome.

Background Earlobe color is a naturally and artificially selected trait in chicken. As a head furnishing trait, it has been selected as a breed characteristic. Research has demonstrated that white/red earlobe color was related to at least three loci and sex-linked. However, there has been little work to date to identify the specific genomic regions and genes response to earlobe color in Rhode Island Red chickens. Currently, it is possible to identify the genomic regions responsible for white/red earlobe in Rhode Island Red chicken to eliminate this gap in knowledge by using genome-wide association (GWA) analysis. Results In the present study, genome-wide association (GWA) analysis was conducted to explore the candidate genomic regions response to chicken earlobe color phenotype. Hens with red dominant and white dominant earlobe was used for case-control analysis by Illumina 600 K SNP arrays. The GWA results showed that 2.38 Mb genomic region (50.13 to 52.51 Mb) with 282 SNPs on chromosome Z were significantly correlated to earlobe color, including sixteen known genes and seven anonymous genes. The sixteen genes were PAM, SLCO4C1, ST8SIA4, FAM174A, CHD1, RGMB, RIOK2, LIX1, LNPEP, SHB, RNF38, TRIM14, NANS, CLTA, GNE, and CPLX1. Conclusions The study has revealed the white/red earlobe trait is polygenic and sex-linked in Rhode Island Red chickens. In the genome significant ~2.38 Mb region, twenty-three genes were found and some of them could play critical roles in the formation of white/red earlobe color, especially gene SLCO4C1. Taken together, the candidate genes findings herein can help elucidate the genomic architecture of response to white/red earlobe and provide a new insight on mechanisms underlying earlobe color in Rhode Island Red chickens and other breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0422-1) contains supplementary material, which is available to authorized users.