scholarly journals Mutations Upstream of the TBX5 and PITX1 Transcription Factor Genes Are Associated with Feathered Legs in the Domestic Chicken

2020 ◽  
Vol 37 (9) ◽  
pp. 2477-2486 ◽  
Author(s):  
Jingyi Li ◽  
MiOk Lee ◽  
Brian W Davis ◽  
Sangeet Lamichhaney ◽  
Ben J Dorshorst ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Sequence Data ◽  
Ectopic Expression ◽  
Base Change ◽  
Whole Genome Sequence ◽  
Chromosome 15 ◽  
Specific Transcription Factor ◽  
Proposed Model ◽  
Transcription Factor Genes ◽  
Causal Variants

Abstract 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 ∼200 kb 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.

Molecular and SNP characterization of two genome specific transcription factor genes GhMyb8 and GhMyb10 in cotton species

Euphytica ◽  
2007 ◽  
Vol 159 (1-2) ◽  
pp. 259-273 ◽  
Author(s):  
Chuan-Yu Hsu ◽  
Chuanfu An ◽  
Sukumar Saha ◽  
Din-Pow Ma ◽  
Johnie N. Jenkins ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Specific Transcription Factor ◽  
Cotton Species ◽  
Transcription Factor Genes

scholarly journals A conditional multi-trait sequence GWAS discovers pleiotropic candidate genes and variants for sheep wool, skin wrinkle and breech cover traits

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Sunduimijid Bolormaa ◽  
Andrew A. Swan ◽  
Paul Stothard ◽  
Majid Khansefid ◽  
Nasir Moghaddar ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Sequence ◽  
Sequence Data ◽  
Association Studies ◽  
Whole Genome Sequence ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Merino Wool ◽  
Causal Variants ◽  
Wool Proteins

Abstract Background Imputation to whole-genome sequence is now possible in large sheep populations. It is therefore of interest to use this data in genome-wide association studies (GWAS) to investigate putative causal variants and genes that underpin economically important traits. Merino wool is globally sought after for luxury fabrics, but some key wool quality attributes are unfavourably correlated with the characteristic skin wrinkle of Merinos. In turn, skin wrinkle is strongly linked to susceptibility to “fly strike” (Cutaneous myiasis), which is a major welfare issue. Here, we use whole-genome sequence data in a multi-trait GWAS to identify pleiotropic putative causal variants and genes associated with changes in key wool traits and skin wrinkle. Results A stepwise conditional multi-trait GWAS (CM-GWAS) identified putative causal variants and related genes from 178 independent quantitative trait loci (QTL) of 16 wool and skin wrinkle traits, measured on up to 7218 Merino sheep with 31 million imputed whole-genome sequence (WGS) genotypes. Novel candidate gene findings included the MAT1A gene that encodes an enzyme involved in the sulphur metabolism pathway critical to production of wool proteins, and the ESRP1 gene. We also discovered a significant wrinkle variant upstream of the HAS2 gene, which in dogs is associated with the exaggerated skin folds in the Shar-Pei breed. Conclusions The wool and skin wrinkle traits studied here appear to be highly polygenic with many putative candidate variants showing considerable pleiotropy. Our CM-GWAS identified many highly plausible candidate genes for wool traits as well as breech wrinkle and breech area wool cover.

scholarly journals Transcription factors involved in abiotic stress responses in maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era

2019 ◽  
Author(s):  
Roy Njoroge Kimotho ◽  
Elamin Hafiz Baillo ◽  
Zhengbin Zhang
Keyword(s):  
Zea Mays ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Target Genes ◽  
Animal Feed ◽  
Specific Transcription Factor ◽  
Transcription Factor Genes

Background: Maize (Zea mays L.) is a principal cereal crop cultivated worldwide for human food, animal feed, and more recently as a source of biofuel. However, as a direct consequence of water insufficiency and climate change, frequent occurrences of both biotic and abiotic stresses have been reported in different regions around the world, and recently, this has become a major threat in increasing global maize yields. Plants respond to abiotic stresses by utilizing the activity of transcription factors, which are families of genes coding for specific transcription factor proteins whose target genes form a regulon which is involved in the repression/ activation of genes associated with abiotic stress responses. Therefore, it is of uttermost importance to have a systematic study on each family of the transcription factors, the downstream target genes they regulate, and the specific transcription factor genes which are involved in multiple abiotic stress responses in maize and other main crops. Method: In this review, the main transcription factor families, the specific transcription factor genes and their regulons which are involved in abiotic stress regulation will be momentarily discussed. Great emphasis will be given on maize abiotic stress improvement throughout this review, although other examples from other plants like rice, Arabidopsis, wheat, and barley will be used. Results: We have described in detail the main transcription factor families in maize which take part in abiotic stress responses together with their regulons. Furthermore, we have also briefly described the utilization of high-efficiency technologies in the study and characterization of TFs involved in the abiotic stress regulatory networks in plants with an emphasis on increasing maize production. Examples of these technologies include next-generation sequencing, microarray analysis, machine learning and RNA-Seq technology. Conclusion: In conclusion, it is hoped that all the information provided in this review may in time contribute to the use of TF genes in the research, breeding, and development of new abiotic stress tolerant maize cultivars.

scholarly journals Transcription factors involved in abiotic stress responses in maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era

2019 ◽  
Author(s):  
Roy Njoroge Kimotho ◽  
Elamin Hafiz Baillo ◽  
Zhengbin Zhang
Keyword(s):  
Zea Mays ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Target Genes ◽  
Animal Feed ◽  
Specific Transcription Factor ◽  
Transcription Factor Genes

Background: Maize (Zea mays L.) is a principal cereal crop cultivated worldwide for human food, animal feed, and more recently as a source of biofuel. However, as a direct consequence of water insufficiency and climate change, frequent occurrences of both biotic and abiotic stresses have been reported in different regions around the world, and recently, this has become a major threat in increasing global maize yields. Plants respond to abiotic stresses by utilizing the activity of transcription factors, which are families of genes coding for specific transcription factor proteins whose target genes form a regulon which is involved in the repression/ activation of genes associated with abiotic stress responses. Therefore, it is of uttermost importance to have a systematic study on each family of the transcription factors, the downstream target genes they regulate, and the specific transcription factor genes which are involved in multiple abiotic stress responses in maize and other main crops. Method: In this review, the main transcription factor families, the specific transcription factor genes and their regulons which are involved in abiotic stress regulation will be momentarily discussed. Great emphasis will be given on maize abiotic stress improvement throughout this review, although other examples from other plants like rice, Arabidopsis, wheat, and barley will be used. Results: We have described in detail the main transcription factor families in maize which take part in abiotic stress responses together with their regulons. Furthermore, we have also briefly described the utilization of high-efficiency technologies in the study and characterization of TFs involved in the abiotic stress regulatory networks in plants with an emphasis on increasing maize production. Examples of these technologies include next-generation sequencing, microarray analysis, machine learning and RNA-Seq technology. Conclusion: In conclusion, it is hoped that all the information provided in this review may in time contribute to the use of TF genes in the research, breeding, and development of new abiotic stress tolerant maize cultivars.

scholarly journals The WRKY Transcription Factor Genes inLotus japonicus

2014 ◽  
Vol 2014 ◽  
pp. 1-15 ◽  
Author(s):  
Hui Song ◽  
Pengfei Wang ◽  
Zhibiao Nan ◽  
Xingjun Wang
Keyword(s):  
Transcription Factor ◽  
Stress Responses ◽  
Gene Clusters ◽  
Wrky Transcription Factor ◽  
Whole Genome Sequence ◽  
Gene Copy ◽  
Group I ◽  
A Genome ◽  
Transcription Factor Genes ◽  
Group Ii

WRKY transcription factor genes play critical roles in plant growth and development, as well as stress responses. WRKY genes have been examined in various higher plants, but they have not been characterized inLotus japonicus. The recent release of theL. japonicuswhole genome sequence provides an opportunity for a genome wide analysis of WRKY genes in this species. In this study, we identified 61 WRKY genes in theL. japonicusgenome. Based on the WRKY protein structure,L. japonicusWRKY (LjWRKY) genes can be classified into three groups (I–III). Investigations of gene copy number and gene clusters indicate that only one gene duplication event occurred on chromosome 4 and no clustered genes were detected on chromosomes 3 or 6. Researchers previously believed that group II and III WRKY domains were derived from the C-terminal WRKY domain of group I. Our results suggest that some WRKY genes in group II originated from the N-terminal domain of group I WRKY genes. Additional evidence to support this hypothesis was obtained byMedicago truncatulaWRKY (MtWRKY) protein motif analysis. We found that LjWRKY and MtWRKY group III genes are under purifying selection, suggesting that WRKY genes will become increasingly structured and functionally conserved.

scholarly journals Ectopic Overproduction of a Sporulation-Specific Transcription Factor Induces Assembly of Prespore-Like Membranous Compartments in Vegetative Cells of Fission Yeast

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 1195-1199 ◽  
Author(s):  
Yukiko Nakase ◽  
Aiko Hirata ◽  
Chikashi Shimoda ◽  
Taro Nakamura
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Fission Yeast ◽  
Nuclear Division ◽  
Ectopic Expression ◽  
Vegetative Cells ◽  
Common Features ◽  
Specific Transcription Factor

Mei4 is a key sporulation-specific transcription factor in fission yeast. Ectopic expression of Mei4 in vegetative cells caused formation of nucleated membranous compartments, which shared common features with normal forespore membranes, thereby perturbing nuclear division. These results suggest why expression of development-specific transcription factors must be strictly controlled.

scholarly journals Ectopic expression of the beta-cell specific transcription factor Pdx1 inhibits glucagon gene transcription

Diabetologia ◽  
2003 ◽  
Vol 46 (6) ◽  
pp. 810-821 ◽  
Author(s):  
B. Ritz-Laser ◽  
B. R. Gauthier ◽  
A. Estreicher ◽  
A. Mamin ◽  
T. Brun ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Beta Cell ◽  
Gene Transcription ◽  
Ectopic Expression ◽  
Specific Transcription Factor

Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR

FEBS Letters ◽  
2004 ◽  
Vol 573 (1-3) ◽  
pp. 214-218 ◽  
Author(s):  
Harukazu Suzuki ◽  
Rie Okunishi ◽  
Wataru Hashizume ◽  
Shintaro Katayama ◽  
Noriko Ninomiya ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Real Time ◽  
Mouse Brain ◽  
Adult Mouse ◽  
Rt Pcr ◽  
Adult Mouse Brain ◽  
Specific Transcription Factor ◽  
Medium Scale ◽  
Transcription Factor Genes
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