Browsing by Author "Li, Jingyi"

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    Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken
    Li, Jingyi; Davis, Brian W.; Jern, Patric; Dorshorst, Benjamin J.; Siegel, Paul B.; Andersson, Leif (2019-08-28)
    Background Henny feathering in chickens is determined by a dominant mutation that transforms male-specific plumage to female-like plumage. Previous studies indicated that this phenotype is caused by ectopic expression in skin of CYP19A1 encoding aromatase that converts androgens to estrogen and thereby inhibits the development of male-specific plumage. A long terminal repeat (LTR) from an uncharacterized endogenous retrovirus (ERV) insertion was found in an isoform of the CYP19A1 transcript from henny feathering chicken. However, the complete sequence and the genomic position of the insertion were not determined. Results We used publicly available whole genome sequence data to determine the flanking sequences of the ERV, and then PCR amplified the entire insertion and sequenced it using Nanopore long reads and Sanger sequencing. The 7524 bp insertion contains an intact endogenous retrovirus that was not found in chickens representing 31 different breeds not showing henny feathering or in samples of the ancestral red junglefowl. The sequence shows over 99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains, suggesting a recent integration. The ERV 3’LTR, containing a powerful transcriptional enhancer and core promoter with TATA box together with binding sites for EFIII and Ig/EBP inside the CYP19A1 5′ untranslated region, was detected partially in an aromatase transcript, which present a plausible explanation for ectopic expression of aromatase in non-ovarian tissues underlying the henny feathering phenotype. Conclusions We demonstrate that the henny feathering allele harbors an insertion of an intact avian leukosis virus at the 5’end of CYP19A1. The presence of this ERV showed complete concordance with the henny feathering phenotype both within a pedigree segregating for this phenotype and across breeds.
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    Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens
    Li, Jingyi; Lee, Mi-Ok; Chen, Junfeng; Davis, Brian W.; Dorshorst, Benjamin J.; Siegel, Paul B.; Inaba, Masafumi; Jiang, Tingxin; Chuong, Cheng-Ming; Andersson, Leif (2021-10-12)
    Melanotic (Ml) is a mutation in chickens that extends black (eumelanin) pigmentation in normally brown or red (pheomelanin) areas, thus affecting multiple within-feather patterns [J. W. Moore, J. R. Smyth Jr, J. Hered. 62, 215-219 (1971)]. In the present study, linkage mapping using a back-cross between Dark Cornish (Ml/Ml) and Partridge Plymouth Rock (ml(+)/ml(+)) chickens assigned Ml to an 820-kb region on chromosome 1. Identity-by-descent mapping, via whole-genome sequencing and diagnostic tests using a diverse set of chickens, refined the localization to the genomic region harboring GJA5 encoding gap-junction protein 5 (alias connexin 40) previously associated with pigmentation patterns in zebrafish. An insertion/deletion polymorphism located in the vicinity of the GJA5 promoter region was identified as the candidate causal mutation. Four different GJA5 transcripts were found to be expressed in feather follicles and at least two showed differential expression between genotypes. The results showed that Melanotic constitutes a cis-acting regulatory mutation affecting GJA5 expression. A recent study established the melanocortin-1 receptor (MC1R) locus and the interaction between the MC1R receptor and its antagonist agoutisignaling protein as the primary mechanism underlying variation in within-feather pigmentation patterns in chickens. The present study advances understanding the mechanisms underlying variation in plumage color in birds because it demonstrates that the activity of connexin 40/GJA5 can modulate the periodic pigmentation patterns within individual feathers.
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    Empathic vehicle design: Use cases and design directions from two workshops
    Nadri, Chihab; Alvarez, Ignacio; Bosch, Esther; Oehl, Michael; Braun, Michael; Healey, Jennifer; Jallais, Christophe; Ju, Wendy; Li, Jingyi; Jeon, Myounghoon (ACM, 2022-04-27)
    Empathic vehicles are expected to improve user experience in automated vehicles and to help increase user acceptance of technology. However, little is known about potential real-world implementations and designs using empathic interfaces in vehicles with higher levels of automation. Given advances in affect detection and emotion mitigation, we conducted two workshops (N1 =24, N2 = 22, Ntotal = 46) on the design of empathic vehicles and their potential utility in a variety of applications. This paper recapitulates key opportunities in the design and application of empathetic interfaces in automated vehicles which emerged from the two workshops hosted at the ACM AutoUI conferences.
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    The feather pattern autosomal barring in chicken is strongly associated with segregation at the MC1R locus
    Thalmann, Doreen Schwochow; Bornelov, Susanne; Jiang, Tingxin; Li, Jingyi; Gourichon, David; Bed'Hom, Bertrand; Dorshorst, Benjamin J.; Chuong, Cheng-Ming; Tixier-Boichard, Michele; Andersson, Leif (2021-04-01)
    Color patterns within individual feathers are common in birds but little is known about the genetic mechanisms causing such patterns. Here, we investigate the genetic basis for autosomal barring in chicken, a horizontal striping pattern on individual feathers. Using an informative backcross, we demonstrate that the MC1R locus is strongly associated with this phenotype. A deletion at SOX10, underlying the dark brown phenotype on its own, affects the manifestation of the barring pattern. The coding variant L133Q in MC1R is the most likely causal mutation for autosomal barring in this pedigree. Furthermore, a genetic screen across six different breeds showing different patterning phenotypes revealed that the most striking shared characteristics among these breeds were that they all carried the MC1R alleles Birchen or brown. Our data suggest that the presence of activating MC1R mutations enhancing pigment synthesis is an important mechanism underlying pigmentation patterns on individual feathers in chicken. We propose that MC1R and its antagonist ASIP play a critical role for determining within-feather pigmentation patterns in birds by acting as activator and inhibitor possibly in a Turing reaction-diffusion model.
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    Gene Mapping of Morphological Traits in Chickens
    Li, Jingyi (Virginia Tech, 2017-04-25)
    Chickens exhibit considerable variation in morphological traits, with some populations having undergone intensive selection for uniqueness and uniformity. These populations are a source of experimental material to study the genetics of morphological traits. An important first step in such studies is to map the genes and the causal mutations that influence these traits. This research focused on gene mapping of 12 morphological traits including 4 intra-feather color patterns (Pattern, Columbian, Melanotic, and mottling), 2 inter-feather color patterns (Blue and chocolate), 2 forms of feathered-legs, polydactyly, dark brown eggshell color, vulture hock, and creeper. Ten backcross and/or F2 populations were designed to produce 1,880 individuals. An additional 339 DNA samples from other populations were included. The procedures for gene mapping were: 1. Pooling of DNA samples of backcross or F2 individuals based on their shared phenotypes, followed by microarray assays for genotyping, a cost-effective initial screen for the candidate genomic regions, 2. Linkage mapping to narrow the range of candidate genes, 3. Sequencing to identify the candidate mutations, 4. Diagnostic tests to confirm the association between the candidate mutation and the phenotype. Of the 12 traits studied, 3 (mottling, Blue, and chocolate) made progress into step 4. Complexities due to genomic context, modifiers, and environmental factors precluded step 4 for the first form of the feathered-leg gene, step 3 for the mapping of Melanotic, and earlier stages for the mapping of Pattern, Columbian, dark brown egg, vulture hock, and the second form of feathered-leg. These findings provide insights of the complexity of how background genome can influence the phenotypic expression of single genes (gene genetic background interactions) and an understanding of cellular and molecular mechanisms involved in morphogenesis.
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    Mutations Upstream of the TBX5 and PITX1 Transcription Factor Genes Are Associated with Feathered Legs in the Domestic Chicken
    Li, Jingyi; Lee, Mi-Ok; Davis, Brian W.; Lamichhaney, Sangeet; Dorshorst, Benjamin J.; Siegel, Paul B.; Andersson, Leif (2020-09)
    Feathered leg is a trait in domestic chickens that has undergone intense selection by fancy breeders. Previous studies have shown that two major loci controlling feathered leg are located on chromosomes 13 and 15. Here, we present genetic evidence for the identification of candidate causal mutations at these loci. This was accomplished by combining classical linkage mapping using an experimental cross segregating for feathered leg and high-resolution identical-by-descent mapping using whole-genome sequence data from 167 samples of chicken with or without feathered legs. The first predicted causal mutation is a single-base change located 25 kb upstream of the gene for the forelimb-specific transcription factor TBX5 on chromosome 15. The second is a 17.7-kb deletion located similar to 200kb upstream of the gene for the hindlimb-specific transcription factor PITX1 on chromosome 13. These mutations are predicted to activate TBX5 and repress PITX1 expression, respectively. The study reveals a remarkable convergence in the evolution of the feathered-leg phenotype in domestic chickens and domestic pigeons, as this phenotype is caused by noncoding mutations upstream of the same two genes. Furthermore, the PITX1 causal variants are large overlapping deletions, 17.7 kb in chicken and 44 kb in pigeons. The results of the present study are consistent with the previously proposed model for pigeon that feathered leg is caused by reduced PITX1 expression and ectopic expression of TBX5 in hindlimb buds resulting in a shift of limb identity from hindlimb to more forelimb-like identity.
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    "Play Your Anger": A Report on the Empathic In-vehicle Interface Workshop
    Dong, Jiayuan; Nadri, Chihab; Alvarez, Ignacio; Diels, Cyriel; Lee, Myeongkyu; Li, Jingyi; Liao, Pei Hsuan; Manger, Carina; Sadeghian, Shadan; Schuß, Martina; Walker, Bruce N.; Walker, Francesco; Wang, Yiyuan; Jeon, Myounghoon (ACM, 2023-09-18)
    Empathic in-vehicle interfaces are critical in improving user safety and experiences. There has been much research on how to estimate drivers’ affective states, whereas little research has investigated intervention methods that mitigate potential impacts from the driver’s affective states on their driving performance and user experiences. To enhance the development of in-vehicle interfaces considering emotional aspects, we have organized a workshop series to gather automotive user interface experts to discuss this topic at the International ACM Conference on Automotive User Interfaces and Interactive Vehicular Applications (AutoUI). The present paper focuses particularly on the intervention methods created by the experts and proposes design recommendations for future empathic in-vehicle interfaces. We hope this work can spark lively discussions on the importance of drivers’ affective states in their user experience of automated vehicles and pose the right direction.