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Clites BL, Frohock B, Koury EJ, Andersen EC, Pierce JT. Natural variation in protein kinase D modifies alcohol sensitivity in Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.09.598102. [PMID: 38895441 PMCID: PMC11185769 DOI: 10.1101/2024.06.09.598102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Differences in naïve alcohol sensitivity between individuals are a strong predictor of later life alcohol use disorders (AUD). However, the genetic bases for alcohol sensitivity (beyond ethanol metabolism) and pharmacological approaches to modulate alcohol sensitivity remain poorly understood. We used a high-throughput behavioral screen to measure acute behavioral sensitivity to alcohol, a model of intoxication, in a genetically diverse set of over 150 wild strains of the nematode Caenorhabditis elegans. We performed a genome-wide association study to identify loci that underlie natural variation in alcohol sensitivity. We identified five quantitative trait loci (QTL) and further show that variants in the C. elegans ortholog of protein kinase D, dkf-2, likely underlie the chromosome V QTL. We found that resistance to intoxication was conferred by dkf-2 loss-of-function mutations as well as partly by a PKD inhibitor in a dkf-2-dependent manner. Protein kinase D might represent a conserved, druggable target to modify alcohol sensitivity with application towards AUD.
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Affiliation(s)
- Benjamin L Clites
- Waggoner Center for Alcohol & Addiction Research, Center for Learning and Memory, Department of Neuroscience, University of Texas at Austin, Austin TX
| | - Brooke Frohock
- Waggoner Center for Alcohol & Addiction Research, Center for Learning and Memory, Department of Neuroscience, University of Texas at Austin, Austin TX
| | - Emily J Koury
- Department of Biology, Johns Hopkins University, Baltimore MD
| | - Erik C Andersen
- Department of Biology, Johns Hopkins University, Baltimore MD
| | - Jonathan T Pierce
- Waggoner Center for Alcohol & Addiction Research, Center for Learning and Memory, Department of Neuroscience, University of Texas at Austin, Austin TX
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Sousa LPB, Pinto LFB, Cruz VAR, Oliveira GA, Rojas de Oliveira H, Chud TS, Pedrosa VB, Miglior F, Schenkel FS, Brito LF. Genome-wide association and functional genomic analyses for various hoof health traits in North American Holstein cattle. J Dairy Sci 2024; 107:2207-2230. [PMID: 37939841 DOI: 10.3168/jds.2023-23806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023]
Abstract
Hoof diseases are a major welfare and economic issue in the global dairy cattle production industry, which can be minimized through improved management and breeding practices. Optimal genetic improvement of hoof health could benefit from a deep understanding of the genetic background and biological underpinning of indicators of hoof health. Therefore, the primary objectives of this study were to perform genome-wide association studies, using imputed high-density genetic markers data from North American Holstein cattle, for 8 hoof-related traits: digital dermatitis, sole ulcer, sole hemorrhage, white line lesion, heel horn erosion, interdigital dermatitis, interdigital hyperplasia, and toe ulcer, and a hoof health index. De-regressed estimated breeding values from 25,580 Holstein animals were used as pseudo-phenotypes for the association analyses. The genomic quality control, genotype phasing, and genotype imputation were performed using the PLINK (version 1.9), Eagle (version 2.4.1), and Minimac4 software, respectively. The functional genomic analyses were performed using the GALLO R package and the DAVID platform. We identified 22, 34, 14, 22, 28, 33, 24, 43, and 15 significant markers for digital dermatitis, heel horn erosion, interdigital dermatitis, interdigital hyperplasia, sole hemorrhage, sole ulcer, toe ulcer, white line lesion disease, and the hoof health index, respectively. The significant markers were located across all autosomes, except BTA10, BTA12, BTA20, BTA26, BTA27, and BTA28. Moreover, the genomic regions identified overlap with various previously reported quantitative trait loci for exterior, health, meat and carcass, milk, production, and reproduction traits. The enrichment analyses identified 44 significant gene ontology terms. These enriched genomic regions harbor various candidate genes previously associated with bone development, metabolism, and infectious and immunological diseases. These findings indicate that hoof health traits are highly polygenic and influenced by a wide range of biological processes.
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Affiliation(s)
- Luis Paulo B Sousa
- Department of Animal Sciences, Federal University of Bahia, Salvador, BA, 40170-110, Brazil
| | - Luis Fernando B Pinto
- Department of Animal Sciences, Federal University of Bahia, Salvador, BA, 40170-110, Brazil
| | - Valdecy A R Cruz
- Department of Animal Sciences, Federal University of Bahia, Salvador, BA, 40170-110, Brazil
| | - Gerson A Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Hinayah Rojas de Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Tatiane S Chud
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; PEAK, Madison, WI 53718
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Lactanet Canada, Guelph, ON, N1K 1E5, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
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Heaton MP, Harhay GP, Bassett AS, Clark HJ, Carlson JM, Jobman EE, Sadd HR, Pelster MC, Workman AM, Kuehn LA, Kalbfleisch TS, Piscatelli H, Carrie M, Krafsur GM, Grotelueschen DM, Vander Ley BL. Association of ARRDC3 and NFIA variants with bovine congestive heart failure in feedlot cattle. F1000Res 2024; 11:385. [PMID: 38680232 PMCID: PMC11046187 DOI: 10.12688/f1000research.109488.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 06/24/2024] Open
Abstract
BACKGROUND Bovine congestive heart failure (BCHF) has become increasingly prevalent among feedlot cattle in the Western Great Plains of North America with up to 7% mortality in affected herds. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. Genes associated with BCHF in feedlot cattle have not been previously identified. Our aim was to search for genomic regions associated with this disease. METHODS A retrospective, matched case-control design with 102 clinical BCHF cases and their unaffected pen mates was used in a genome-wide association study. Paired nominal data from approximately 560,000 filtered single nucleotide polymorphisms (SNPs) were analyzed with McNemar's test. RESULTS Two independent genomic regions were identified as having the most significant association with BCHF: the arrestin domain-containing protein 3 gene ( ARRDC3), and the nuclear factor IA gene ( NFIA, mid- p-values, 1x10 -8 and 2x10 -7, respectively). Animals with two copies of risk alleles at either gene were approximately eight-fold more likely to have BCHF than their matched pen mates with either one or zero risk alleles at both genes (CI 95 = 3-17). Further, animals with two copies of risk alleles at both genes were 28-fold more likely to have BCHF than all others ( p-value = 1×10 -7, CI 95 = 4-206). A missense variant in ARRDC3 (C182Y) represents a potential functional variant since the C182 codon is conserved among all other jawed vertebrate species observed. A two-SNP test with markers in both genes showed 29% of 273 BCHF cases had homozygous risk genotypes in both genes, compared to 2.5% in 198 similar unaffected feedlot cattle. This and other DNA tests may be useful for identifying feedlot animals with the highest risk for BCHF in the environments described here. CONCLUSIONS Although pathogenic roles for variants in the ARRDC3 and NFIA genes are unknown, their discovery facilitates classifying animals by genetic risk and allows cattle producers to make informed decisions for selective breeding and animal health management.
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Affiliation(s)
- Michael P. Heaton
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Gregory P. Harhay
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Adam S. Bassett
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Halden J. Clark
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Jaden M. Carlson
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Erin E. Jobman
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Helen R. Sadd
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Madeline C. Pelster
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Aspen M. Workman
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Larry A. Kuehn
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | | | | | | | - Greta M. Krafsur
- Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado, 80045, USA
| | - Dale M. Grotelueschen
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Brian L. Vander Ley
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
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Heaton MP, Harhay GP, Bassett AS, Clark HJ, Carlson JM, Jobman EE, Sadd HR, Pelster MC, Workman AM, Kuehn LA, Kalbfleisch TS, Piscatelli H, Carrie M, Krafsur GM, Grotelueschen DM, Vander Ley BL. Association of ARRDC3 and NFIA variants with bovine congestive heart failure in feedlot cattle. F1000Res 2024; 11:385. [PMID: 38680232 PMCID: PMC11046187 DOI: 10.12688/f1000research.109488.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 05/01/2024] Open
Abstract
Background Bovine congestive heart failure (BCHF) has become increasingly prevalent among feedlot cattle in the Western Great Plains of North America with up to 7% mortality in affected herds. BCHF is an untreatable complex condition involving pulmonary hypertension that culminates in right ventricular failure and death. Genes associated with BCHF in feedlot cattle have not been previously identified. Our aim was to search for genomic regions associated with this disease. Methods A retrospective, matched case-control design with 102 clinical BCHF cases and their unaffected pen mates was used in a genome-wide association study. Paired nominal data from approximately 560,000 filtered single nucleotide polymorphisms (SNPs) were analyzed with McNemar's test. Results Two independent genomic regions were identified as having the most significant association with BCHF: the arrestin domain-containing protein 3 gene ( ARRDC3), and the nuclear factor IA gene ( NFIA, mid- p-values, 1x10 -8 and 2x10 -7, respectively). Animals with two copies of risk alleles at either gene were approximately eight-fold more likely to have BCHF than their matched pen mates with either one or zero risk alleles at both genes (CI 95 = 3-17). Further, animals with two copies of risk alleles at both genes were 28-fold more likely to have BCHF than all others ( p-value = 1×10 -7, CI 95 = 4-206). A missense variant in ARRDC3 (C182Y) represents a potential functional variant since the C182 codon is conserved among all other jawed vertebrate species observed. A two-SNP test with markers in both genes showed 29% of 273 BCHF cases had homozygous risk genotypes in both genes, compared to 2.5% in 198 similar unaffected feedlot cattle. This and other DNA tests may be useful for identifying feedlot animals with the highest risk for BCHF in the environments described here. Conclusions Although pathogenic roles for variants in the ARRDC3 and NFIA genes are unknown, their discovery facilitates classifying animals by genetic risk and allows cattle producers to make informed decisions for selective breeding and animal health management.
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Affiliation(s)
- Michael P. Heaton
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Gregory P. Harhay
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Adam S. Bassett
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Halden J. Clark
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Jaden M. Carlson
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Erin E. Jobman
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Helen R. Sadd
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Madeline C. Pelster
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Aspen M. Workman
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | - Larry A. Kuehn
- USDA, ARS, US Meat Animal Research Center, Clay Center, Nebraska, 68933, USA
| | | | | | | | - Greta M. Krafsur
- Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado, 80045, USA
| | - Dale M. Grotelueschen
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
| | - Brian L. Vander Ley
- University of Nebraska-Lincoln, Great Plains Veterinary Educational Center, Clay Center, Nebraska, 68933, USA
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Shilbayeh SAR, Adeen IS, Ghanem EH, Aljurayb H, Aldilaijan KE, AlDosari F, Fadda A. Exploratory focused pharmacogenetic testing reveals novel markers associated with risperidone pharmacokinetics in Saudi children with autism. Front Pharmacol 2024; 15:1356763. [PMID: 38375040 PMCID: PMC10875102 DOI: 10.3389/fphar.2024.1356763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024] Open
Abstract
Background: Autism spectrum disorders (ASDs) encompass a broad range of phenotypes characterized by diverse neurological alterations. Genomic studies have revealed considerable overlap between the molecular mechanisms implicated in the etiology of ASD and genes involved in the pharmacokinetic (PK) and pharmacodynamic (PD) pathways of antipsychotic drugs employed in ASD management. Given the conflicting data originating from candidate PK or PD gene association studies in diverse ethnogeographic ASD populations, dosage individualization based on "actionable" pharmacogenetic (PGx) markers has limited application in clinical practice. Additionally, off-label use of different antipsychotics is an ongoing practice, which is justified given the shortage of approved cures, despite the lack of satisfactory evidence for its safety according to precision medicine. This exploratory study aimed to identify PGx markers predictive of risperidone (RIS) exposure in autistic Saudi children. Methods: This prospective cohort study enrolled 89 Saudi children with ASD treated with RIS-based antipsychotic therapy. Plasma levels of RIS and 9-OH-RIS were measured using a liquid chromatography-tandem mass spectrometry system. To enable focused exploratory testing, genotyping was performed with the Axiom PharmacoFocus Array, which included a collection of probe sets targeting PK/PD genes. A total of 720 PGx markers were included in the association analysis. Results: A total of 27 PGx variants were found to have a prominent impact on various RIS PK parameters; most were not located within the genes involved in the classical RIS PK pathway. Specifically, 8 markers in 7 genes were identified as the PGx markers with the strongest impact on RIS levels (p < 0.01). Four PGx variants in 3 genes were strongly associated with 9-OH-RIS levels, while 5 markers in 5 different genes explained the interindividual variability in the total active moiety. Notably, 6 CYP2D6 variants exhibited strong linkage disequilibrium; however, they significantly influenced only the metabolic ratio and had no considerable effects on the individual estimates of RIS, 9-OH-RIS, or the total active moiety. After correction for multiple testing, rs78998153 in UGT2B17 (which is highly expressed in the brain) remained the most significant PGx marker positively adjusting the metabolic ratio. For the first time, certain human leukocyte antigen (HLA) markers were found to enhance various RIS exposure parameters, which reinforces the gut-brain axis theory of ASD etiology and its suggested inflammatory impacts on drug bioavailability through modulation of the brain, gastrointestinal tract and/or hepatic expression of metabolizing enzymes and transporters. Conclusion: Our hypothesis-generating approach identified a broad spectrum of PGx markers that interactively influence RIS exposure in ASD children, which indicated the need for further validation in population PK modeling studies to define polygenic scores for antipsychotic efficacy and safety, which could facilitate personalized therapeutic decision-making in this complex neurodevelopmental condition.
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Affiliation(s)
- Sireen Abdul Rahim Shilbayeh
- Department of Pharmacy Practice, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Iman Sharaf Adeen
- Department of Pediatric Behavior and Development and Adolescent Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ezzeldeen Hasan Ghanem
- Pharmaceutical Analysis Section, King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, Ministry of National Guard - Health Affairs, Riyadh, Saudi Arabia
| | - Haya Aljurayb
- Molecular Pathology Laboratory, Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Khawlah Essa Aldilaijan
- Health Sciences Research Center, King Abdullah Bin Abdulaziz University Hospital, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fatimah AlDosari
- Pharmaceutical Care Department, Ministry of National Guard-Health Affairs, Jeddah, Saudi Arabia
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Zhao X, Qiu Y, Meng F, Zhuang Z, Ruan D, Wu J, Ma F, Zheng E, Cai G, Yang J, Yang M, Wu Z. Genome-wide association studies for loin muscle area, loin muscle depth and backfat thickness in DLY pigs. Anim Genet 2024; 55:134-139. [PMID: 38098441 DOI: 10.1111/age.13386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 01/04/2024]
Abstract
This study aimed at identifying genes associated with loin muscle area (LMA), loin muscle depth (LMD) and backfat thickness (BFT). We performed single-trait and multi-trait genome-wide association studies (GWASs) after genotyping 685 Duroc × (Landrace × Yorkshire) (DLY) pigs using the Geneseek Porcine 50K SNP chip. In the single-trait GWASs, we identified two, eight and two significant SNPs associated with LMA, LMD and BFT, respectively, and searched genes within the 1 Mb region near the significant SNPs with relevant functions as candidate genes. Consequently, we identified one (DOCK5), three (PID1, PITX2, ELOVL6) and three (CCR1, PARP14, CASR) promising candidate genes for LMA, LMD and BFT, respectively. Moreover, the multi-trait GWAS identified four significant SNPs associated with the three traits. In conclusion, the GWAS analysis of LMA, LMD and BFT in a DLY pig population identified several associated SNPs and candidate genes, further deepening our understanding of the genetic basis of these traits, and they may be useful for marker-assisted selection to improve the three traits in DLY pigs.
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Affiliation(s)
- Xiang Zhao
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fanming Meng
- State Key Laboratory of Livestock and Poultry Breeding/Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fucai Ma
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Ming Yang
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
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Cesarani A, Corte Pause F, Hidalgo J, Garcia A, Degano L, Vicario D, Macciota NPP, Stradaioli G. Genetic background of semen parameters in Italian Simmental bulls. ITALIAN JOURNAL OF ANIMAL SCIENCE 2023. [DOI: 10.1080/1828051x.2022.2160665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Francesca Corte Pause
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Jorge Hidalgo
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Andre Garcia
- Angus Genetics Inc. - American Angus Association, Saint Joseph, MO, USA
| | - Lorenzo Degano
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | - Daniele Vicario
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | | | - Giuseppe Stradaioli
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
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Zhou F, Wang S, Qin H, Zeng H, Ye J, Yang J, Cai G, Wu Z, Zhang Z. Genome-wide association analysis unveils candidate genes and loci associated with aplasia cutis congenita in pigs. BMC Genomics 2023; 24:701. [PMID: 37990155 PMCID: PMC10664689 DOI: 10.1186/s12864-023-09803-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/11/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Aplasia cutis congenita (ACC) is a rare genetic disorder characterized by the localized or widespread absence of skin in humans and animals. Individuals with ACC may experience developmental abnormalities in the skeletal and muscular systems, as well as potential complications. Localized and isolated cases of ACC can be treated through surgical and medical interventions, while extensive cases of ACC may result in neonatal mortality. The presence of ACC in pigs has implications for animal welfare. It contributes to an elevated mortality rate among piglets at birth, leading to substantial economic losses in the pig farming industry. In order to elucidate candidate genetic loci associated with ACC, we performed a Genome-Wide Association Study analysis on 216 Duroc pigs. The primary goal of this study was to identify candidate genes that associated with ACC. RESULTS This study identified nine significant SNPs associated with ACC. Further analysis revealed the presence of two quantitative trait loci, 483 kb (5:18,196,971-18,680,098) on SSC 5 and 159 kb (13:20,713,440-207294431 bp) on SSC13. By annotating candidate genes within a 1 Mb region surrounding the significant SNPs, a total of 11 candidate genes were identified on SSC5 and SSC13, including KRT71, KRT1, KRT4, ITGB7, CSAD, RARG, SP7, PFKL, TRPM2, SUMO3, and TSPEAR. CONCLUSIONS The results of this study further elucidate the potential mechanisms underlying and genetic architecture of ACC and identify reliable candidate genes. These results lay the foundation for treating and understanding ACC in humans.
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Affiliation(s)
- Fuchen Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Shenghui Wang
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Haojun Qin
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Haiyu Zeng
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Jian Ye
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.
- Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527400, P.R. China.
| | - Zebin Zhang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.
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Sanchez DL, Samonte SOPB, Wilson LT. Genetic architecture of head rice and rice chalky grain percentages using genome-wide association studies. FRONTIERS IN PLANT SCIENCE 2023; 14:1274823. [PMID: 38046607 PMCID: PMC10691675 DOI: 10.3389/fpls.2023.1274823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
High head rice and low chalky grain percentages are key grain quality traits selected in developing rice cultivars. The objectives of this research were to characterize the phenotypic variation of head rice and chalky grain percentages in a diverse collection of rice accessions, identify single nucleotide polymorphism (SNP) markers associated with each of these traits using genome-wide association studies (GWAS), and identify putative candidate genes linked to the SNPs identified by GWAS. Diverse rice varieties, landraces, and breeding lines were grown at the Texas A&M AgriLife Research Center in Beaumont. Head rice percentages (HRP) and chalky grain percentages (CGP) of 195 and 199 non-waxy accessions were estimated in 2018 and 2019, respectively. Phenotypic data were analyzed along with 854,832 SNPs using three statistical models: mixed linear model (MLM), multi-locus mixed model (MLMM), and fixed and random model circulating probability unification (FarmCPU). Significant variations in HRP and CGP were observed between rice accessions. Two significant marker-trait associations (MTAs) were detected on chromosomes 1 and 2, respectively, based on best linear unbiased prediction (BLUP) values in 2018, while in 2019, one SNP was significantly associated with HRP in each of chromosomes 6, 8, 9, and 11, and two in chromosome 7. CGP was significantly associated with five SNPs located in chromosomes 2, 4, 6, and 8 in the 2018 study and ten SNPs in chromosomes 1, 2, 3, 4, 7, 8, 11, and 12 in the 2019 study. The SNPs are located within or linked to putative candidate genes involved in HRP and CGP. This study reports five and ten novel MTAs for HRP and CGP, respectively, while three and five MTAs co-located with previously reported quantitative trait loci for HRP and CGP, respectively. The validation of candidate genes for their roles in determining HRP and CGP is necessary to design functional molecular markers that can be used to effectively develop rice cultivars with desirable grain quality.
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Nyangiri OA, Mulindwa J, Namulondo J, Kitibwa A, Nassuuna J, Elliott A, Kimuda MP, Boobo A, Nerima B, Adriko M, Dunton NJ, Madhan GK, Kristiansen M, Casacuberta-Partal M, Noyes H, Matovu E. Variants of IL6, IL10, FCN2, RNASE3, IL12B and IL17B loci are associated with Schistosoma mansoni worm burden in the Albert Nile region of Uganda. PLoS Negl Trop Dis 2023; 17:e0011796. [PMID: 38033168 PMCID: PMC10715658 DOI: 10.1371/journal.pntd.0011796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 12/12/2023] [Accepted: 11/14/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Individuals genetically susceptible to high schistosomiasis worm burden may contribute disproportionately to transmission and could be prioritized for control. Identifying genes involved may guide development of therapy. METHODOLOGY/PRINCIPAL FINDINGS A cohort of 606 children aged 10-15 years were recruited in the Albert Nile region of Uganda and assessed for Schistosoma mansoni worm burden using the Up-Converting Particle Lateral Flow (UCP-LF) test detecting circulating anodic antigen (CAA), point-of-care Circulating Cathodic Antigen (POC-CCA) and Kato-Katz tests. Whole genome genotyping was conducted on 326 children comprising the top and bottom 25% of worm burden. Linear models were fitted to identify variants associated with worm burden in preselected candidate genes. Expression quantitative trait locus (eQTL) analysis was conducted for candidate genes with UCP-LF worm burden included as a covariate. Single Nucleotide Polymorphism loci associated with UCP-LF CAA included IL6 rs2066992 (OR = 0.43, p = 0.0006) and rs7793163 (OR = 2.0, p = 0.0007); IL21 SNP kgp513476 (OR 1.79, p = 0.0025) and IL17B SNP kgp708159 (OR = 0.35, p = 0.0028). A haplotype in the IL10 locus was associated with lower worm burden (OR = 0.53, p = 0.015) and overlapped SNPs rs1800896, rs1800871 and rs1800872. Significant haplotypes (p<0.05, overlapping significant SNP) associated with worm burden were observed in IL6 and the Th17 pathway IL12B and IL17B genes. There were significant eQTL in the IL6, IL5, IL21, IL25 and IFNG regions. CONCLUSIONS Variants associated with S. mansoni worm burden were in IL6, FCN2, RNASE3, IL10, IL12B and IL17B gene loci. However only eQTL associations remained significant after Bonferroni correction. In summary, immune balance, pathogen recognition and Th17 pathways may play a role in modulating Schistosoma worm burden. Individuals carrying risk variants may be targeted first in allocation of control efforts to reduce the burden of schistosomiasis in the community.
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Affiliation(s)
- Oscar Asanya Nyangiri
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Julius Mulindwa
- Department of Biochemistry and Sports Sciences, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Joyce Namulondo
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Anna Kitibwa
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Jacent Nassuuna
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Alison Elliott
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Magambo Phillip Kimuda
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Alex Boobo
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Barbara Nerima
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Moses Adriko
- Vector Borne & NTD Control Division, Ministry of Health, Uganda
| | - Nathan J. Dunton
- UCL Genomics core facility, University College London, London, United Kingdom
| | | | - Mark Kristiansen
- UCL Genomics core facility, University College London, London, United Kingdom
| | | | - Harry Noyes
- Centre for Genomic Research, University of Liverpool, Liverpool, United Kingdom
| | - Enock Matovu
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
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Ettetuani B, Chahboune R, Moussa A. Adjustment of p-value expression to ontology using machine learning for genetic prediction, prioritization, interaction, and its validation in glomerular disease. Front Genet 2023; 14:1215232. [PMID: 37900183 PMCID: PMC10603191 DOI: 10.3389/fgene.2023.1215232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/28/2023] [Indexed: 10/31/2023] Open
Abstract
The results of gene expression analysis based on p-value can be extracted and sorted by their absolute statistical significance and then applied to multiple similarity scores of their gene ontology (GO) terms to promote the combination and adjustment of these scores as essential predictive tasks for understanding biological/clinical pathways. The latter allows the possibility to assess whether certain aspects of gene function may be associated with other varieties of genes, to evaluate regulation, and to link them into networks that prioritize candidate genes for classification by applying machine learning techniques. We then detect significant genetic interactions based on our algorithm to validate the results. Finally, based on specifically selected tissues according to their normalized gene expression and frequencies of occurrence from their different biological and clinical inputs, a reported classification of genes under the subject category has validated the abstract (glomerular diseases) as a case study.
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Affiliation(s)
- Boutaina Ettetuani
- Systems and Data Engineering Team, National School of Applied Sciences, Abdelmalek Essaadi University, Tétouan, Morocco
| | - Rajaa Chahboune
- Life and Health Sciences Team, Faculty of Medicine and Pharmacy, Abdelmalek Essaadi University, Tétouan, Morocco
| | - Ahmed Moussa
- Systems and Data Engineering Team, National School of Applied Sciences, Abdelmalek Essaadi University, Tétouan, Morocco
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Sanchez DL, Santana AS, Morais PIC, Peterlini E, De La Fuente G, Castellano MJ, Blanco M, Lübberstedt T. Phenotypic and genome-wide association analyses for nitrogen use efficiency related traits in maize ( Zea mays L.) exotic introgression lines. FRONTIERS IN PLANT SCIENCE 2023; 14:1270166. [PMID: 37877090 PMCID: PMC10590880 DOI: 10.3389/fpls.2023.1270166] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/18/2023] [Indexed: 10/26/2023]
Abstract
Nitrogen (N) limits crop production, yet more than half of N fertilizer inputs are lost to the environment. Developing maize hybrids with improved N use efficiency can help minimize N losses and in turn reduce adverse ecological, economical, and health consequences. This study aimed to identify single nucleotide polymorphisms (SNPs) associated with agronomic traits (plant height, grain yield, and anthesis to silking interval) under high and low N conditions. A genome-wide association study (GWAS) was conducted using 181 doubled haploid (DH) lines derived from crosses between landraces from the Germplasm Enhancement of Maize (BGEM lines) project and two inbreds, PHB47 and PHZ51. These DH lines were genotyped using 62,077 SNP markers. The same lines from the per se trials were used as parental lines for the testcross field trials. Plant height, anthesis to silking interval, and grain yield were collected from high and low N conditions in three environments for both per se and testcross trials. We used three GWAS models, namely, general linear model (GLM), mixed linear model (MLM), and Fixed and Random model Circulating Probability Unification (FarmCPU) model. We observed significant genetic variation among the DH lines and their derived testcrosses. Interestingly, some testcrosses of exotic introgression lines were superior under high and low N conditions compared to the check hybrid, PHB47/PHZ51. We detected multiple SNPs associated with agronomic traits under high and low N, some of which co-localized with gene models associated with stress response and N metabolism. The BGEM panel is, thus, a promising source of allelic diversity for genes controlling agronomic traits under different N conditions.
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Affiliation(s)
| | | | | | | | | | | | - Michael Blanco
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Department of Agriculture, Agricultural Research Service (USDA-ARS), Ames, IA, United States
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Xie L, Qin J, Rao L, Cui D, Tang X, Chen L, Xiao S, Zhang Z, Huang L. Genetic dissection and genomic prediction for pork cuts and carcass morphology traits in pig. J Anim Sci Biotechnol 2023; 14:116. [PMID: 37660101 PMCID: PMC10475202 DOI: 10.1186/s40104-023-00914-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/02/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND As pre-cut and pre-packaged chilled meat becomes increasingly popular, integrating the carcass-cutting process into the pig industry chain has become a trend. Identifying quantitative trait loci (QTLs) of pork cuts would facilitate the selection of pigs with a higher overall value. However, previous studies solely focused on evaluating the phenotypic and genetic parameters of pork cuts, neglecting the investigation of QTLs influencing these traits. This study involved 17 pork cuts and 12 morphology traits from 2,012 pigs across four populations genotyped using CC1 PorcineSNP50 BeadChips. Our aim was to identify QTLs and evaluate the accuracy of genomic estimated breed values (GEBVs) for pork cuts. RESULTS We identified 14 QTLs and 112 QTLs for 17 pork cuts by GWAS using haplotype and imputation genotypes, respectively. Specifically, we found that HMGA1, VRTN and BMP2 were associated with body length and weight. Subsequent analysis revealed that HMGA1 primarily affects the size of fore leg bones, VRTN primarily affects the number of vertebrates, and BMP2 primarily affects the length of vertebrae and the size of hind leg bones. The prediction accuracy was defined as the correlation between the adjusted phenotype and GEBVs in the validation population, divided by the square root of the trait's heritability. The prediction accuracy of GEBVs for pork cuts varied from 0.342 to 0.693. Notably, ribs, boneless picnic shoulder, tenderloin, hind leg bones, and scapula bones exhibited prediction accuracies exceeding 0.600. Employing better models, increasing marker density through genotype imputation, and pre-selecting markers significantly improved the prediction accuracy of GEBVs. CONCLUSIONS We performed the first study to dissect the genetic mechanism of pork cuts and identified a large number of significant QTLs and potential candidate genes. These findings carry significant implications for the breeding of pork cuts through marker-assisted and genomic selection. Additionally, we have constructed the first reference populations for genomic selection of pork cuts in pigs.
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Affiliation(s)
- Lei Xie
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Jiangtao Qin
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Lin Rao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Dengshuai Cui
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Xi Tang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Liqing Chen
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Zhiyan Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045 China
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Lee YS, Oh JD, Lee JY, Shin D. A genomic estimated breeding value-assisted reduction method of single nucleotide polymorphism sets: a novel approach for determining the cutoff thresholds in genome-wide association studies and best linear unbiased prediction. Anim Cells Syst (Seoul) 2023; 27:180-186. [PMID: 37674816 PMCID: PMC10478620 DOI: 10.1080/19768354.2023.2250841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/16/2023] [Accepted: 07/20/2023] [Indexed: 09/08/2023] Open
Abstract
Traditionally, the p-value is the criterion for the cutoff threshold to determine significant markers in genome-wide association studies (GWASs). Choosing the best subset of markers for the best linear unbiased prediction (BLUP) for improved prediction ability (PA) has become an interesting issue. However, when dealing with many traits having the same marker information, the p-values' themselves cannot be used as an obvious solution for having a confidence in GWAS and BLUP. We thus suggest a genomic estimated breeding value-assisted reduction method of the single nucleotide polymorphism (SNP) set (GARS) to address these difficulties. GARS is a BLUP-based SNP set decision presentation. The samples were Landrace pigs and the traits used were back fat thickness (BF) and daily weight gain (DWG). The prediction abilities (PAs) for BF and DWG for the entire SNP set were 0.8 and 0.8, respectively. By using the correlation between genomic estimated breeding values (GEBVs) and phenotypic values, selecting the cutoff threshold in GWAS and the best SNP subsets in BLUP was plausible as defined by GARS method. 6,000 SNPs in BF and 4,000 SNPs in DWG were considered as adequate thresholds. Gene Ontology (GO) analysis using the GARS results of the BF indicated neuron projection development as the notable GO term, whereas for the DWG, the main GO terms were nervous system development and cell adhesion.
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Affiliation(s)
- Young-Sup Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Jae-Don Oh
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Jun-Yeong Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
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Quarto T, Lella A, Di Carlo P, Rampino A, Paladini V, Papalino M, Romano R, Fazio L, Marvulli D, Popolizio T, Blasi G, Pergola G, Bertolino A. Heritability of amygdala reactivity to angry faces and its replicable association with the schizophrenia risk locus of miR-137. J Psychiatry Neurosci 2023; 48:E357-E366. [PMID: 37751917 PMCID: PMC10521919 DOI: 10.1503/jpn.230013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 07/11/2023] [Accepted: 07/30/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Among healthy participants, the interindividual variability of brain response to facial emotions is associated with genetic variation, including common risk variants for schizophrenia, a heritable brain disorder characterized by anomalies in emotion processing. We aimed to identify genetic variants associated with heritable brain activity during processing of facial emotions among healthy participants and to explore the impact of these identified variants among patients with schizophrenia. METHODS We conducted a data-driven stepwise study including samples of healthy twins, unrelated healthy participants and patients with schizophrenia. Participants approached or avoided pictures of faces with negative emotional valence during functional magnetic resonance imaging (fMRI). RESULTS We investigated 3 samples of healthy participants - including 28 healthy twin pairs, 289 unrelated healthy participants (genome-wide association study [GWAS] discovery sample) and 90 unrelated healthy participants (replication sample) - and 1 sample of 48 patients with schizophrenia. Among healthy twins, we identified the amygdala as the brain region with the highest heritability during processing of angry faces (heritability estimate 0.54, p < 0.001). Subsequent GWAS in both discovery and replication samples of healthy non-twins indicated that amygdala activity was associated with a polymorphism in the miR-137 locus (rs1198575), a micro-RNA strongly involved in risk for schizophrenia. A significant effect in the same direction was found among patients with schizophrenia (p = 0.03). LIMITATIONS The limited sample size available for GWAS analyses may require further replication of results. CONCLUSION Our data-driven approach shows preliminary evidence that amygdala activity, as evaluated with our task, is heritable. Our genetic associations preliminarily suggest a role for miR-137 in brain activity during explicit processing of facial emotions among healthy participants and patients with schizophrenia, pointing to the amygdala as a brain region whose activity is related to miR-137.
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Affiliation(s)
- Tiziana Quarto
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
| | - Annalisa Lella
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
| | - Pasquale Di Carlo
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
| | - Antonio Rampino
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
| | - Vittoria Paladini
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
| | - Marco Papalino
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
| | - Raffaella Romano
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
| | - Leonardo Fazio
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
| | - Daniela Marvulli
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
| | - Teresa Popolizio
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
| | - Giuseppe Blasi
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
| | - Giulio Pergola
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
| | - Alessandro Bertolino
- From the Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy (Quarto, Lella, Di Carlo, Rampino, Paladini, Papalino, Romano, Fazio, Marvulli, Blasi, Pergola, Bertolino); the Department of Humanities, University of Foggia, Foggia, Italy (Quarto); the Psychiatry Unit, Bari University Hospital, Bari, Italy (Rampino, Blasi, Bertolino); the LUM (Fazio); the IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy (Popolizio); the Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD (Pergola)
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Pasam RK, Kant S, Thoday-Kennedy E, Dimech A, Joshi S, Keeble-Gagnere G, Forrest K, Tibbits J, Hayden M. Haplotype-Based Genome-Wide Association Analysis Using Exome Capture Assay and Digital Phenotyping Identifies Genetic Loci Underlying Salt Tolerance Mechanisms in Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2367. [PMID: 37375992 DOI: 10.3390/plants12122367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
Soil salinity can impose substantial stress on plant growth and cause significant yield losses. Crop varieties tolerant to salinity stress are needed to sustain yields in saline soils. This requires effective genotyping and phenotyping of germplasm pools to identify novel genes and QTL conferring salt tolerance that can be utilised in crop breeding schemes. We investigated a globally diverse collection of 580 wheat accessions for their growth response to salinity using automated digital phenotyping performed under controlled environmental conditions. The results show that digitally collected plant traits, including digital shoot growth rate and digital senescence rate, can be used as proxy traits for selecting salinity-tolerant accessions. A haplotype-based genome-wide association study was conducted using 58,502 linkage disequilibrium-based haplotype blocks derived from 883,300 genome-wide SNPs and identified 95 QTL for salinity tolerance component traits, of which 54 were novel and 41 overlapped with previously reported QTL. Gene ontology analysis identified a suite of candidate genes for salinity tolerance, some of which are already known to play a role in stress tolerance in other plant species. This study identified wheat accessions that utilise different tolerance mechanisms and which can be used in future studies to investigate the genetic and genic basis of salinity tolerance. Our results suggest salinity tolerance has not arisen from or been bred into accessions from specific regions or groups. Rather, they suggest salinity tolerance is widespread, with small-effect genetic variants contributing to different levels of tolerance in diverse, locally adapted germplasm.
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Affiliation(s)
- Raj K Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Surya Kant
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | | | - Adam Dimech
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Sameer Joshi
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400, Australia
| | | | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
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Miranda J, Horvat N, Assuncao AN, de M Machado FA, Chakraborty J, Pandini RV, Saraiva S, Nahas CSR, Nahas SC, Nomura CH. MRI-based radiomic score increased mrTRG accuracy in predicting rectal cancer response to neoadjuvant therapy. Abdom Radiol (NY) 2023; 48:1911-1920. [PMID: 37004557 PMCID: PMC10942660 DOI: 10.1007/s00261-023-03898-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/04/2023]
Abstract
PURPOSE To develop a magnetic resonance imaging (MRI)-based radiomics score, i.e., "rad-score," and to investigate the performance of rad-score alone and combined with mrTRG in predicting pathologic complete response (pCR) in patients with locally advanced rectal cancer following neoadjuvant chemoradiation therapy. METHODS This retrospective study included consecutive patients with LARC who underwent neoadjuvant chemoradiotherapy followed by surgery from between July 2011 to November 2015. Volumes of interest of the entire tumor on baseline rectal MRI and of the tumor bed on restaging rectal MRI were manually segmented on T2-weighted images. The radiologist also provided the ymrTRG score on the restaging MRI. Radiomic score (rad-score) was calculated and optimal cut-off points for both mrTRG and rad-score to predict pCR were selected using Youden's J statistic. RESULTS Of 180 patients (mean age = 63 years; 60% men), 33/180 (18%) achieved pCR. High rad-score (> - 1.49) yielded an area under the curve (AUC) of 0.758, comparable to ymrTRG 1-2 which yielded an AUC of 0.759. The combination of high rad-score and ymrTRG 1-2 yielded a significantly higher AUC of 0.836 compared with ymrTRG 1-2 and high rad-score alone (p < 0.001). A logistic regression model incorporating both high rad-score and mrTRG 1-2 was built to calculate adjusted odds ratios for pCR, which was 4.85 (p < 0.001). CONCLUSION Our study demonstrates that a rectal restaging MRI-based rad-score had comparable diagnostic performance to ymrTRG. Moreover, the combined rad-score and ymrTRG model yielded a significant better diagnostic performance for predicting pCR.
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Affiliation(s)
- Joao Miranda
- Department of Radiology, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Natally Horvat
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 29, New York, NY, 10065, USA.
| | - Antonildes N Assuncao
- Department of Radiology, University of Sao Paulo, Sao Paulo, SP, Brazil
- Research and Education Institute, Hospital Sirio-Libanes, Sao Paulo, SP, Brazil
| | | | - Jayasree Chakraborty
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Samya Saraiva
- Department of Radiology, Hospital Sirio-Libanes, Sao Paulo, SP, Brazil
| | | | | | - Cesar Higa Nomura
- Department of Radiology, University of Sao Paulo, Sao Paulo, SP, Brazil
- Department of Radiology, Hospital Sirio-Libanes, Sao Paulo, SP, Brazil
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18
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Adeniyi OO, Medugorac I, Grochowska E, Düring RA, Lühken G. Single-Locus and Multi-Locus Genome-Wide Association Studies Identify Genes Associated with Liver Cu Concentration in Merinoland Sheep. Genes (Basel) 2023; 14:genes14051053. [PMID: 37239413 DOI: 10.3390/genes14051053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Economic losses due to copper intoxication or deficiency is a problem encountered by sheep farmers. The aim of this study was to investigate the ovine genome for genomic regions and candidate genes responsible for variability in liver copper concentration. Liver samples were collected from slaughtered lambs of the Merinoland breed from two farms, and used for measurement of copper concentration and genome-wide association study (GWAS). A total of 45,511 SNPs and 130 samples were finally used for analysis, in which single-locus and several multi-locus GWAS (SL-GWAS; ML-GWAS) methods were employed. Gene enrichment analysis was performed for identified candidate genes to detect gene ontology (GO) terms significantly associated with hepatic copper levels. The SL-GWAS and a minimum of two ML-GWAS identified two and thirteen significant SNPs, respectively. Within genomic regions surrounding identified SNPs, we observed nine promising candidate genes such as DYNC1I2, VPS35, SLC38A9 and CHMP1A. GO terms such as lysosomal membrane, mitochondrial inner membrane and sodium:proton antiporter activity were significantly enriched. Genes involved in these identified GO terms mediate multivesicular body (MVB) fusion with lysosome for degradation and control mitochondrial membrane permeability. This reveals the polygenic status of this trait and candidate genes for further studies on breeding for copper tolerance in sheep.
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Affiliation(s)
- Olusegun O Adeniyi
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Ludwigstrasse 21, 35390 Giessen, Germany
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Ludwig Maximilian University Munich, Lena-Christ-Str. 48, 82152 Martinsried, Germany
| | - Ewa Grochowska
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka 28 St., 85-084 Bydgoszcz, Poland
| | - Rolf-Alexander Düring
- Institute of Soil Science and Soil Conservation, Interdisciplinary Research Center for Biosystems, Land Use and Nutrition (IFZ), Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Ludwigstrasse 21, 35390 Giessen, Germany
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Ribeiro CAG, de Sousa Tinoco SM, de Souza VF, Negri BF, Gault CM, Pastina MM, Magalhaes JV, Guimarães LJM, de Barros EG, Buckler ES, Guimaraes CT. Genome-Wide Association Study for Root Morphology and Phosphorus Acquisition Efficiency in Diverse Maize Panels. Int J Mol Sci 2023; 24:ijms24076233. [PMID: 37047206 PMCID: PMC10094163 DOI: 10.3390/ijms24076233] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Maximizing soil exploration through modifications of the root system is a strategy for plants to overcome phosphorus (P) deficiency. Genome-wide association with 561 tropical maize inbred lines from Embrapa and DTMA panels was undertaken for root morphology and P acquisition traits under low- and high-P concentrations, with 353,540 SNPs. P supply modified root morphology traits, biomass and P content in the global maize panel, but root length and root surface area changed differentially in Embrapa and DTMA panels. This suggests that different root plasticity mechanisms exist for maize adaptation to low-P conditions. A total of 87 SNPs were associated to phenotypic traits in both P conditions at −log10(p-value) ≥ 5, whereas only seven SNPs reached the Bonferroni significance. Among these SNPs, S9_137746077, which is located upstream of the gene GRMZM2G378852 that encodes a MAPKKK protein kinase, was significantly associated with total seedling dry weight, with the same allele increasing root length and root surface area under P deficiency. The C allele of S8_88600375, mapped within GRMZM2G044531 that encodes an AGC kinase, significantly enhanced root length under low P, positively affecting root surface area and seedling weight. The broad genetic diversity evaluated in this panel suggests that candidate genes and favorable alleles could be exploited to improve P efficiency in maize breeding programs of Africa and Latin America.
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Affiliation(s)
- Carlos Alexandre Gomes Ribeiro
- Programa de Pós-Graduação em Genética e Melhoramento, Universidade Federal de Viçosa, Viçosa 36570-000, Minas Gerais, Brazil
| | | | - Vander Fillipe de Souza
- Programa de Pós-Graduação em Bioengenharia, Universidade Federal de São João del-Rei, São João del-Rei 36301-160, Minas Gerais, Brazil
| | - Barbara França Negri
- Programa de Pós-Graduação em Bioengenharia, Universidade Federal de São João del-Rei, São João del-Rei 36301-160, Minas Gerais, Brazil
| | | | | | | | | | - Everaldo Gonçalves de Barros
- Programa de Pós-Graduação em Genética e Melhoramento, Universidade Federal de Viçosa, Viçosa 36570-000, Minas Gerais, Brazil
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
- USDA-ARS, Robert Holley Center, Ithaca, NY 14853, USA
| | - Claudia Teixeira Guimaraes
- Embrapa Milho e Sorgo, Sete Lagoas 35701-970, Minas Gerais, Brazil
- Programa de Pós-Graduação em Bioengenharia, Universidade Federal de São João del-Rei, São João del-Rei 36301-160, Minas Gerais, Brazil
- Correspondence: ; Tel.: +55-31-3027-1300
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Heritable Risk and Protective Genetic Components of Glaucoma Medication Non-Adherence. Int J Mol Sci 2023; 24:ijms24065636. [PMID: 36982708 PMCID: PMC10058353 DOI: 10.3390/ijms24065636] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Glaucoma is the leading cause of irreversible blindness, affecting 76 million globally. It is characterized by irreversible damage to the optic nerve. Pharmacotherapy manages intraocular pressure (IOP) and slows disease progression. However, non-adherence to glaucoma medications remains problematic, with 41–71% of patients being non-adherent to their prescribed medication. Despite substantial investment in research, clinical effort, and patient education protocols, non-adherence remains high. Therefore, we aimed to determine if there is a substantive genetic component behind patients’ glaucoma medication non-adherence. We assessed glaucoma medication non-adherence with prescription refill data from the Marshfield Clinic Healthcare System’s pharmacy dispensing database. Two standard measures were calculated: the medication possession ratio (MPR) and the proportion of days covered (PDC). Non-adherence on each metric was defined as less than 80% medication coverage over 12 months. Genotyping was done using the Illumina HumanCoreExome BeadChip in addition to exome sequencing on the 230 patients (1) to calculate the heritability of glaucoma medication non-adherence and (2) to identify SNPs and/or coding variants in genes associated with medication non-adherence. Ingenuity pathway analysis (IPA) was utilized to derive biological meaning from any significant genes in aggregate. Over 12 months, 59% of patients were found to be non-adherent as measured by the MPR80, and 67% were non-adherent as measured by the PDC80. Genome-wide complex trait analysis (GCTA) suggested that 57% (MPR80) and 48% (PDC80) of glaucoma medication non-adherence could be attributed to a genetic component. Missense mutations in TTC28, KIAA1731, ADAMTS5, OR2W3, OR10A6, SAXO2, KCTD18, CHCHD6, and UPK1A were all found to be significantly associated with glaucoma medication non-adherence by whole exome sequencing after Bonferroni correction (p < 10−3) (PDC80). While missense mutations in TINAG, CHCHD6, GSTZ1, and SEMA4G were found to be significantly associated with medication non-adherence by whole exome sequencing after Bonferroni correction (p < 10−3) (MPR80). The same coding SNP in CHCHD6 which functions in Alzheimer’s disease pathophysiology was significant by both measures and increased risk for glaucoma medication non-adherence by three-fold (95% CI, 1.62–5.8). Although our study was underpowered for genome-wide significance, SNP rs6474264 within ZMAT4 (p = 5.54 × 10–6) was found to be nominally significant, with a decreased risk for glaucoma medication non-adherence (OR, 0.22; 95% CI, 0.11–0.42)). IPA demonstrated significant overlap, utilizing, both standard measures including opioid signaling, drug metabolism, and synaptogenesis signaling. CREB signaling in neurons (which is associated with enhancing the baseline firing rate for the formation of long-term potentiation in nerve fibers) was shown to have protective associations. Our results suggest a substantial heritable genetic component to glaucoma medication non-adherence (47–58%). This finding is in line with genetic studies of other conditions with a psychiatric component (e.g., post-traumatic stress disorder (PTSD) or alcohol dependence). Our findings suggest both risk and protective statistically significant genes/pathways underlying glaucoma medication non-adherence for the first time. Further studies investigating more diverse populations with larger sample sizes are needed to validate these findings.
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21
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Wang J, Zhang J, Wang Q, Zhang Q, Thiam M, Zhu B, Ying F, Elsharkawy MS, Zheng M, Wen J, Li Q, Zhao G. A heterophil/lymphocyte-selected population reveals the phosphatase PTPRJ is associated with immune defense in chickens. Commun Biol 2023; 6:196. [PMID: 36807561 PMCID: PMC9938895 DOI: 10.1038/s42003-023-04559-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 02/06/2023] [Indexed: 02/20/2023] Open
Abstract
Quantification of leukocyte profiles is among the simplest measures of animal immune function. However, the relationship between H/L ratio and innate immunity and the measure's utility as an index for heterophil function remains to be analyzed. Variants associated with H/L ratio were fine-mapped based on the resequencing of 249 chickens of different generations and an F2 segregating population generated by crossing selection and control lines. H/L ratio in the selection line was associated with a selective sweep of mutations in protein tyrosine phosphatase, receptor type J (PTPRJ), which affects proliferation and differentiation of heterophils through its downstream regulatory genes. The SNP downstream of PTPRJ (rs736799474) have a universal effect on H/L, with CC homozygotes exhibiting improved heterophil function because of downregulated PTPRJ expression. In short, we systematically elucidated the genetic basis of the change in heterophil function resulting from H/L selection by identifying the regulatory gene (PTPRJ) and causative SNP.
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Affiliation(s)
- Jie Wang
- grid.464332.4Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, 100193 China ,grid.452757.60000 0004 0644 6150Poultry Institute, Shandong Academy of Agricultural Sciences, Ji’nan, 250100 P. R. China
| | - Jin Zhang
- grid.464332.4Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, 100193 China
| | - Qiao Wang
- grid.464332.4Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, 100193 China
| | - Qi Zhang
- grid.464332.4Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, 100193 China
| | - Mamadou Thiam
- grid.464332.4Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, 100193 China
| | - Bo Zhu
- grid.464332.4Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, 100193 China
| | - Fan Ying
- grid.464332.4Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, 100193 China
| | - Mohamed Shafey Elsharkawy
- grid.464332.4Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, 100193 China
| | - Maiqing Zheng
- grid.464332.4Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, 100193 China
| | - Jie Wen
- grid.464332.4Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, 100193 China
| | - Qinghe Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, 100193, China.
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, 100193, China.
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22
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Big Data in Gastroenterology Research. Int J Mol Sci 2023; 24:ijms24032458. [PMID: 36768780 PMCID: PMC9916510 DOI: 10.3390/ijms24032458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Studying individual data types in isolation provides only limited and incomplete answers to complex biological questions and particularly falls short in revealing sufficient mechanistic and kinetic details. In contrast, multi-omics approaches to studying health and disease permit the generation and integration of multiple data types on a much larger scale, offering a comprehensive picture of biological and disease processes. Gastroenterology and hepatobiliary research are particularly well-suited to such analyses, given the unique position of the luminal gastrointestinal (GI) tract at the nexus between the gut (mucosa and luminal contents), brain, immune and endocrine systems, and GI microbiome. The generation of 'big data' from multi-omic, multi-site studies can enhance investigations into the connections between these organ systems and organisms and more broadly and accurately appraise the effects of dietary, pharmacological, and other therapeutic interventions. In this review, we describe a variety of useful omics approaches and how they can be integrated to provide a holistic depiction of the human and microbial genetic and proteomic changes underlying physiological and pathophysiological phenomena. We highlight the potential pitfalls and alternatives to help avoid the common errors in study design, execution, and analysis. We focus on the application, integration, and analysis of big data in gastroenterology and hepatobiliary research.
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23
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Huang Y, Cai L, Duan Y, Zeng Q, He M, Wu Z, Zou X, Zhou M, Zhang Z, Xiao S, Yang B, Ma J, Huang L. Whole-genome sequence-based association analyses on an eight-breed crossed heterogeneous stock of pigs reveal the genetic basis of skeletal muscle fiber characteristics. Meat Sci 2022; 194:108974. [PMID: 36167013 DOI: 10.1016/j.meatsci.2022.108974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 08/02/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
Skeletal muscle fiber characteristics (MFCs) have been extensively studied due to their importance to human health and athletic ability, as well as to the quantity and quality of livestock meat production. Hence, we performed a genome-wide association study (GWAS) on nine muscle fiber traits by using whole genome sequence data in an eight-breed crossed heterogeneous stock pig population. This GWAS revealed 67 quantitative trait loci (QTLs) for these traits. The most significant GWAS signal was detected in the region of Sus scrofa chromosome 12 (SSC12) containing the MYH gene family. Notably, we identified a significant SNP rs322008693 (P = 7.52E-09) as the most likely causal mutation for the total number of muscle fibers (TNMF) QTL on SSC1. The results of EMSA and luciferase assays indicated that the rs322008693 SNP resided in a functional element. These findings provide valuable molecular markers for pig meat production selection as well as for deciphering the genetic mechanisms of the muscle fiber physiology.
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Affiliation(s)
- Yizhong Huang
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Liping Cai
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yanyu Duan
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qingjie Zeng
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Maozhang He
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhongping Wu
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoxiao Zou
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Mengqing Zhou
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhou Zhang
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shijun Xiao
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bin Yang
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Junwu Ma
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Lusheng Huang
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China.
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Anderegg J, Kirchgessner N, Kronenberg L, McDonald BA. Automated Quantitative Measurement of Yellow Halos Suggests Activity of Necrotrophic Effectors in Septoria tritici Blotch. PHYTOPATHOLOGY 2022; 112:2560-2573. [PMID: 35793150 DOI: 10.1094/phyto-11-21-0465-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Many necrotrophic plant pathogens utilize host-selective toxins or necrotrophic effectors during the infection process. We hypothesized that the chlorotic yellow halos frequently observed around necrotic lesions caused by the wheat pathogen Zymoseptoria tritici could result from the activity of necrotrophic effectors interacting with the products of toxin sensitivity genes. As an initial step toward testing this hypothesis, we developed an automated image analysis (AIA) workflow that could quantify the degree of yellow halo formation occurring in wheat leaves naturally infected by a highly diverse pathogen population under field conditions. This AIA based on statistical learning was applied to more than 10,000 naturally infected leaves collected from 335 wheat cultivars grown in a replicated field experiment. We estimated a high heritability (h2 = 0.71) for the degree of yellow halo formation, suggesting that this quantitative trait has a significant genetic component. Using genome-wide association mapping, we identified six chromosome segments significantly associated with the yellow halo phenotype. Most of these segments contained candidate genes associated with targets of necrotrophic effectors in other necrotrophic pathogens. Our findings conform with the hypothesis that toxin sensitivity genes could account for a significant fraction of the observed variation in quantitative resistance to Septoria tritici blotch. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Jonas Anderegg
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Norbert Kirchgessner
- Crop Science Group, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Lukas Kronenberg
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Bruce A McDonald
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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D’Ascenzo N, Antonecchia E, Angiolillo A, Bender V, Camerlenghi M, Xie Q, Di Costanzo A. Metabolomics of blood reveals age-dependent pathways in Parkinson’s Disease. Cell Biosci 2022; 12:102. [PMID: 35794650 PMCID: PMC9258166 DOI: 10.1186/s13578-022-00831-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/08/2022] [Indexed: 01/01/2023] Open
Abstract
Background Parkinson’s Disease (PD) is the second most frequent degenerative disorder, the risk of which increases with age. A preclinical PD diagnostic test does not exist. We identify PD blood metabolites and metabolic pathways significantly correlated with age to develop personalized age-dependent PD blood biomarkers. Results We found 33 metabolites producing a receiver operating characteristic (ROC) area under the curve (AUC) value of 97%. PCA revealed that they belong to three pathways with distinct age-dependent behavior: glycine, threonine and serine metabolism correlates with age only in PD patients; unsaturated fatty acids biosynthesis correlates with age only in a healthy control group; and, finally, tryptophan metabolism characterizes PD but does not correlate with age. Conclusions The targeted analysis of the blood metabolome proposed in this paper allowed to find specific age-related metabolites and metabolic pathways. The model offers a promising set of blood biomarkers for a personalized age-dependent approach to the early PD diagnosis. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00831-5.
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Li H, Xu C, Meng F, Yao Z, Fan Z, Yang Y, Meng X, Zhan Y, Sun Y, Ma F, Yang J, Yang M, Yang J, Wu Z, Cai G, Zheng E. Genome-Wide Association Studies for Flesh Color and Intramuscular Fat in (Duroc × Landrace × Large White) Crossbred Commercial Pigs. Genes (Basel) 2022; 13:2131. [PMID: 36421806 PMCID: PMC9690869 DOI: 10.3390/genes13112131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/12/2022] [Accepted: 11/12/2022] [Indexed: 07/30/2023] Open
Abstract
The intuitive impression of pork is extremely important in terms of whether consumers are enthusiastic about purchasing it. Flesh color and intramuscular fat (IMF) are indispensable indicators in meat quality assessment. In this study, we determined the flesh color and intramuscular fat at 45 min and 12 h after slaughter (45 mFC, 45 mIMF, 12 hFC, and 12 hIMF) of 1518 commercial Duroc × Landrace × Large White (DLY) pigs. We performed a single nucleotide polymorphism (SNP) genome-wide association study (GWAS) analysis with 28,066 SNPs. This experiment found that the correlation between 45 mFC and 12 hFC was 0.343. The correlation between 45 mIMF and 12 hIMF was 0.238. The heritability of the traits 45 mFC, 12 hFC, 45 mIMF, and 12 hIMF was 0.112, 0.217, 0.139, and 0.178, respectively, and we identified seven SNPs for flesh color and three SNPs for IMF. Finally, several candidate genes regulating these four traits were identified. Three candidate genes related to flesh color were provided: SNCAIP and PRR16 on SSC2, ST3GAL4 on SSC5, and GALR1 on SSC1. A total of three candidate genes related to intramuscular fat were found, including ABLIM3 on SSC2, DPH5 on SSC4, and DOCK10 on SSC15. Furthermore, GO and KEGG analysis revealed that these genes are involved in the regulation of apoptosis and are implicated in functions such as pigmentation and skeletal muscle metabolism. This study applied GWAS to analyze the scoring results of flesh color and IMF in different time periods, and it further revealed the genetic structure of flesh color and IMF traits, which may provide important genetic loci for the subsequent improvement of pig meat quality traits.
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Affiliation(s)
- Hao Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Fanming Meng
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zekai Yao
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhenfei Fan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Yingshan Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Xianglun Meng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Yuexin Zhan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Ying Sun
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Fucai Ma
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Jifei Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
| | - Ming Yang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527400, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China
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Elghzaly AA, Sun C, Looger LL, Hirose M, Salama M, Khalil NM, Behiry ME, Hegazy MT, Hussein MA, Salem MN, Eltoraby E, Tawhid Z, Alwasefy M, Allam W, El-Shiekh I, Elserafy M, Abdelnaser A, Hashish S, Shebl N, Shahba AA, Elgirby A, Hassab A, Refay K, El-Touchy HM, Youssef A, Shabacy F, Hashim AA, Abdelzaher A, Alshebini E, Fayez D, El-Bakry SA, Elzohri MH, Abdelsalam EN, El-Khamisy SF, Ibrahim S, Ragab G, Nath SK. Genome-wide association study for systemic lupus erythematosus in an egyptian population. Front Genet 2022; 13:948505. [PMID: 36324510 PMCID: PMC9619055 DOI: 10.3389/fgene.2022.948505] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/30/2022] [Indexed: 04/11/2024] Open
Abstract
Systemic lupus erythematosus (SLE) susceptibility has a strong genetic component. Genome-wide association studies (GWAS) across trans-ancestral populations show both common and distinct genetic variants of susceptibility across European and Asian ancestries, while many other ethnic populations remain underexplored. We conducted the first SLE GWAS on Egyptians-an admixed North African/Middle Eastern population-using 537 patients and 883 controls. To identify novel susceptibility loci and replicate previously known loci, we performed imputation-based association analysis with 6,382,276 SNPs while accounting for individual admixture. We validated the association analysis using adaptive permutation tests (n = 109). We identified a novel genome-wide significant locus near IRS1/miR-5702 (Pcorrected = 1.98 × 10-8) and eight novel suggestive loci (Pcorrected < 1.0 × 10-5). We also replicated (Pperm < 0.01) 97 previously known loci with at least one associated nearby SNP, with ITGAM, DEF6-PPARD and IRF5 the top three replicated loci. SNPs correlated (r 2 > 0.8) with lead SNPs from four suggestive loci (ARMC9, DIAPH3, IFLDT1, and ENTPD3) were associated with differential gene expression (3.5 × 10-95 < p < 1.0 × 10-2) across diverse tissues. These loci are involved in cellular proliferation and invasion-pathways prominent in lupus and nephritis. Our study highlights the utility of GWAS in an admixed Egyptian population for delineating new genetic associations and for understanding SLE pathogenesis.
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Affiliation(s)
- Ashraf A. Elghzaly
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, El-Mansoura, Egypt
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Loren L. Looger
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, San Diego, CA, United States
| | - Misa Hirose
- Division of Genetics, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Mohamed Salama
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
| | - Noha M. Khalil
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mervat Essam Behiry
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed Tharwat Hegazy
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed Ahmed Hussein
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamad Nabil Salem
- Department of Internal Medicine, Faculty of Medicine, Beni-Suef University, Beni Suef, Egypt
| | - Ehab Eltoraby
- Department of Internal Medicine, Faculty of Medicine, Mansoura University, El-Mansoura, Egypt
| | - Ziyad Tawhid
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, El-Mansoura, Egypt
| | - Mona Alwasefy
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, El-Mansoura, Egypt
| | - Walaa Allam
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Iman El-Shiekh
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Anwar Abdelnaser
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
| | - Sara Hashish
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
| | - Nourhan Shebl
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
| | | | - Amira Elgirby
- Department of Internal Medicine, Faculty of Medicine, Alexandria University, Bab Sharqi, Egypt
| | - Amina Hassab
- Department of Clinical Pathology, Faculty of Medicine, Alexandria University, Bab Sharqi, Egypt
| | - Khalida Refay
- Department of Internal Medicine, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | | | - Ali Youssef
- Department of Rheumatology and Immunology, Faculty of Medicine, Benha University Hospital, Benha, Egypt
| | - Fatma Shabacy
- Department of Rheumatology and Immunology, Faculty of Medicine, Benha University Hospital, Benha, Egypt
| | | | - Asmaa Abdelzaher
- Department of Clinical Pathology, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Emad Alshebini
- Department of Internal Medicine, Faculty of Medicine, Menoufia University, Al Minufiyah, Egypt
| | - Dalia Fayez
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Samah A. El-Bakry
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mona H. Elzohri
- Department of Internal Medicine, Faculty of Medicine, Assiut University, Asyut, Egypt
| | | | - Sherif F. El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- The Healthy Lifespan Institute, University of Sheffield, Sheffield, United Kingdom
- The Institute of Cancer Therapeutics, University of Bradford, Bradford, United Kingdom
| | - Saleh Ibrahim
- Division of Genetics, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Gaafar Ragab
- Rheumatology and Clinical Immunology Unit, Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
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Cho E, Cho S, Kim M, Ediriweera TK, Seo D, Lee SS, Cha J, Jin D, Kim YK, Lee JH. Single nucleotide polymorphism marker combinations for classifying Yeonsan Ogye chicken using a machine learning approach. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2022; 64:830-841. [PMID: 36287747 PMCID: PMC9574617 DOI: 10.5187/jast.2022.e64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/15/2022] [Accepted: 08/01/2022] [Indexed: 11/27/2022]
Abstract
Genetic analysis has great potential as a tool to differentiate between different species and breeds of livestock. In this study, the optimal combinations of single nucleotide polymorphism (SNP) markers for discriminating the Yeonsan Ogye chicken (Gallus gallus domesticus) breed were identified using high-density 600K SNP array data. In 3,904 individuals from 198 chicken breeds, SNP markers specific to the target population were discovered through a case-control genome-wide association study (GWAS) and filtered out based on the linkage disequilibrium blocks. Significant SNP markers were selected by feature selection applying two machine learning algorithms: Random Forest (RF) and AdaBoost (AB). Using a machine learning approach, the 38 (RF) and 43 (AB) optimal SNP marker combinations for the Yeonsan Ogye chicken population demonstrated 100% accuracy. Hence, the GWAS and machine learning models used in this study can be efficiently utilized to identify the optimal combination of markers for discriminating target populations using multiple SNP markers.
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Affiliation(s)
- Eunjin Cho
- Department of Bio-AI Convergence, Chungnam
National University, Daejeon 34134, Korea
| | - Sunghyun Cho
- Research and Development Center,
Insilicogen Inc., Yongin 19654, Korea
| | - Minjun Kim
- Division of Animal and Dairy Science,
Chungnam National University, Daejeon 34134, Korea
| | | | - Dongwon Seo
- Department of Bio-AI Convergence, Chungnam
National University, Daejeon 34134, Korea,Research Institute TNT Research
Company, Jeonju 54810, Korea
| | | | - Jihye Cha
- Animal Genome & Bioinformatics,
National Institute of Animal Science, Rural Development
Administration, Wanju 55365, Korea
| | - Daehyeok Jin
- Animal Genetic Resources Research Center,
National Institute of Animal Science, Rural Development
Administration, Hamyang 50000, Korea
| | - Young-Kuk Kim
- Department of Bio-AI Convergence, Chungnam
National University, Daejeon 34134, Korea
| | - Jun Heon Lee
- Department of Bio-AI Convergence, Chungnam
National University, Daejeon 34134, Korea,Division of Animal and Dairy Science,
Chungnam National University, Daejeon 34134, Korea,Corresponding author: Jun Heon Lee,
Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134,
Korea. Tel: +82-42-821-5779, E-mail:
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Yuan X, Cui H, Jin Y, Zhao W, Liu X, Wang Y, Ding J, Liu L, Wen J, Zhao G. Fatty acid metabolism-related genes are associated with flavor-presenting aldehydes in Chinese local chicken. Front Genet 2022; 13:902180. [PMID: 36035160 PMCID: PMC9412053 DOI: 10.3389/fgene.2022.902180] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Aldehydes are primary volatile organic compounds (VOCs) in local Chinese chicken meat and contribute green grass, fatty, citrus, and bitter almond aromas to chicken meat. To understand the genetic basis of these aldehyde VOC aromas, we used approximately 500 Chinese Jingxing Yellow (JXY) chickens to conduct genome-wide association studies (GWAS) on the flavor traits with the data of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs). In total, 501 association variants (253 SNPs and 248 INDELs) were found to be suggestively (SNPs: p-value < 2.77e-06 and INDELs: p-value < 3.78e-05) associated with total aldehydes (the sum of nine aldehydes), hexanal, heptanal, benzaldehyde, (E,E)-2,4-nonadienal, octanal, (E)-2-decenal, nonanal, decanal, and octadecanal. Of them, six SNPs and 23 INDELs reached a genome-wide significance level (SNPs: p-value < 1.38e-07 and INDELs: p-value < 1.89e-06). Potential candidate aldehyde genes were functionally annotated for lipid metabolism, especially fatty acid-related pathways and phospholipid-related gene ontology (GO) terms. Moreover, the GWAS analysis of total aldehydes, hexanal, and nonanal generated the most significant signals, and phenotypic content differed between different genotypes at candidate gene-related loci. For total aldehydes and hexanal traits, candidate genes were annotated based on the significant and suggestive variants on chromosomes 3 and 8 with highly polymorphic linkage blocks. The following candidate genes were also identified: GALM, MAP4K3, GPCPD1, RPS6KA2, CRLS1, ASAP1, TRMT6, SDC1, PUM2, ALDH9A1, MGST3, GMEB1, MECR, LDLRAP1, GPAM and ACSL5. We also found that polyunsaturated fatty acids (PUFAs) (C18:2n6c linoleic acid and C18:3n3 linolenic acid) were significantly correlated with total aldehydes and hexanal contents. PUFAs are important aldehyde precursors, and consistently, our results suggested that candidate genes involved in fatty acid pathways and phospholipid GO terms were identified in association loci. This work provides an understanding of the genetic basis of aldehyde formation, which is a key flavor-forming compound.
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Genome-Wide Association Study Reveals the Genetic Basis of Kernel and Cob Moisture Changes in Maize at Physiological Maturity Stage. PLANTS 2022; 11:plants11151989. [PMID: 35956467 PMCID: PMC9370647 DOI: 10.3390/plants11151989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/24/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022]
Abstract
Low moisture content (MC) and high dehydration rate (DR) at physiological maturity affect grain mechanical harvest, transport, and storage. In this study, we used an association panel composed of 241 maize inbred lines to analyze ear moisture changes at physiological maturity stage. A genome-wide association study revealed nine significant SNPs and 91 candidate genes. One SNP (SYN38588) was repeatedly detected for two traits, and 15 candidate genes were scanned in the linkage disequilibrium regions of this SNP. Of these, genes Zm00001d020615 and Zm00001d020623 were individually annotated as a polygalacturonase (PG) and a copper transporter 5.1 (COPT5.1), respectively. Candidate gene association analysis showed that three SNPs located in the exons of Zm00001d020615 were significantly associated with the dehydration rate, and AATTAA was determined as the superior haplotype. All these findings suggested that Zm00001d020615 was a key gene affecting moisture changes of maize at the physiological maturity stage. These results have demonstrated the genetic basis of ear moisture changes in maize and indicated a superior haplotype for cultivating maize varieties with low moisture content and high dehydration rates.
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31
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Is my PET in my genes? Pediatr Nephrol 2022; 37:1175-1178. [PMID: 35079873 DOI: 10.1007/s00467-022-05452-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 10/19/2022]
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32
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Sanchez DL, Samonte SOP, Alpuerto JBB, Croaker PA, Morales KY, Yang Y, Wilson LT, Tabien RE, Yan Z, Thomson MJ, Septiningsih EM. Phenotypic variation and genome-wide association studies of main culm panicle node number, maximum node production rate, and degree-days to heading in rice. BMC Genomics 2022; 23:390. [PMID: 35606708 PMCID: PMC9125873 DOI: 10.1186/s12864-022-08629-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Grain yield is a complex trait that results from interaction between underlying phenotypic traits and climatic, edaphic, and biotic variables. In rice, main culm panicle node number (MCPNN; the node number on which the panicle is borne) and maximum node production rate (MNPR; the number of leaves that emerge per degree-day > 10°C) are primary phenotypic plant traits that have significant positive direct effects on yield-related traits. Degree-days to heading (DDTH), which has a significant positive effect on grain yield, is influenced by the interaction between MCPNN and MNPR. The objective of this research is to assess the phenotypic variation of MCPNN, MNPR, and DDTH in a panel of diverse rice accessions, determine regions in the rice genome associated with these traits using genome-wide association studies (GWAS), and identify putative candidate genes that control these traits. Results Considerable variation was observed for the three traits in a 220-genotype diverse rice population. MCPNN ranged from 8.1 to 20.9 nodes in 2018 and from 9.9 to 21.0 nodes in 2019. MNPR ranged from 0.0097 to 0.0214 nodes/degree day > 10°C in 2018 and from 0.0108 to 0.0193 nodes/degree-day > 10°C in 2019. DDTH ranged from 713 to 2,345 degree-days > 10°C in 2018 and from 778 to 2,404 degree-days > 10°C in 2019. Thirteen significant (P < 2.91 x 10-7) trait-single nucleotide polymorphism (SNP) associations were identified using the multilocus mixed linear model for GWAS. Significant associations between MCPNN and three SNPs in chromosome 2 (S02_12032235, S02_11971745, and S02_12030176) were detected with both the 2018 and best linear unbiased prediction (BLUP) datasets. Nine SNPs in chromosome 6 (S06_1970442, S06_2310856, S06_2550351, S06_1968653, S06_2296852, S06_1968680, S06_1968681, S06_1970597, and S06_1970602) were significantly associated with MNPR in the 2019 dataset. One SNP in chromosome 11 (S11_29358169) was significantly associated with the DDTH in the BLUP dataset. Conclusions This study identifies SNP markers that are putatively associated with MCPNN, MNPR, and DDTH. Some of these SNPs were located within or near gene models, which identify possible candidate genes involved in these traits. Validation of the putative candidate genes through expression and gene editing analyses are necessary to confirm their roles in regulating MCPNN, MNPR, and DDTH. Identifying the underlying genetic basis for primary phenotypic traits MCPNN and MNPR could lead to the development of fast and efficient approaches for their estimation, such as marker-assisted selection and gene editing, which is essential in increasing breeding efficiency and enhancing grain yield in rice. On the other hand, DDTH is a resultant variable that is highly affected by nitrogen and water management, plant density, and several other factors. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08629-y.
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Affiliation(s)
- Darlene L Sanchez
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA.
| | | | - Jasper Benedict B Alpuerto
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA.,Bayer Research and Development Services (Bayer Crop Science), Chesterfield, Missouri, 63017, USA
| | - Peyton A Croaker
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Karina Y Morales
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, 77843, USA
| | - Yubin Yang
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Lloyd T Wilson
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Rodante E Tabien
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Zongbu Yan
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Michael J Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, 77843, USA
| | - Endang M Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, 77843, USA
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Cinar O, Viechtbauer W. A Comparison of Methods for Gene-Based Testing That Account for Linkage Disequilibrium. Front Genet 2022; 13:867724. [PMID: 35601489 PMCID: PMC9117705 DOI: 10.3389/fgene.2022.867724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/07/2022] [Indexed: 11/16/2022] Open
Abstract
Controlling the type I error rate while retaining sufficient power is a major concern in genome-wide association studies, which nowadays often examine more than a million single-nucleotide polymorphisms (SNPs) simultaneously. Methods such as the Bonferroni correction can lead to a considerable decrease in power due to the large number of tests conducted. Shifting the focus to higher functional structures (e.g., genes) can reduce the loss of power. This can be accomplished via the combination of p-values of SNPs that belong to the same structural unit to test their joint null hypothesis. However, standard methods for this purpose (e.g., Fisher’s method) do not account for the dependence among the tests due to linkage disequilibrium (LD). In this paper, we review various adjustments to methods for combining p-values that take LD information explicitly into consideration and evaluate their performance in a simulation study based on data from the HapMap project. The results illustrate the importance of incorporating LD information into the methods for controlling the type I error rate at the desired level. Furthermore, some methods are more successful in controlling the type I error rate than others. Among them, Brown’s method was the most robust technique with respect to the characteristics of the genes and outperformed the Bonferroni method in terms of power in many scenarios. Examining the genetic factors of a phenotype of interest at the gene-rather than SNP-level can provide researchers benefits in terms of the power of the study. While doing so, one should be careful to account for LD in SNPs belonging to the same gene, for which Brown’s method seems the most robust technique.
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34
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Ma L, Wang C, Hu Y, Dai W, Liang Z, Zou C, Pan G, Lübberstedt T, Shen Y. GWAS and transcriptome analysis reveal MADS26 involved in seed germination ability in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1717-1730. [PMID: 35247071 DOI: 10.1007/s00122-022-04065-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/15/2022] [Indexed: 05/09/2023]
Abstract
MADS26 affecting maize seed germination was identified by GWAS and transcriptomics. Gene-based association analyses revealed three variations within MADS26 regulating seed germination traits. Overexpressed MADS26 in Arabidopsis improved seed germination. Seed germination ability is extremely important for maize production. Exploring the genetic control of seed germination ability is useful for improving maize yield. In this study, a genome-wide association study (GWAS) was conducted to excavate the significant SNPs involved in seed germination ability based on an association panel consisting of 300 lines. A total of 11 SNPs and 75 candidate genes were significantly associated with the seed germination traits. In addition, we constructed 24 transcriptome libraries from maize seeds at four germination stages using two inbred lines with contrasting germination rates. In total, 15,865 differentially expressed genes were induced during seed germination. Integrating the results of GWAS and transcriptome analysis uncovered four prioritized genes underlying maize seed germination. The variations located in the promoter of Zm00001d017932, a MADS-transcription factor 26 (MADS26), were verified to affect the seed germination, and the haplotype TAT was determined as a favorable haplotype for high-germination capability. MADS26 was induced to express by ethylene during seed germination in maize and overexpressing MADS26 increased the seed germination ability in Arabidopsis. These findings will contribute to understanding of the genetic and molecular mechanisms on seed germination and the genetic modification of seed germination ability in maize.
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Affiliation(s)
- Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chen Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Hu
- Zigong Research Institute of Agricultural Sciences, Zigong, 643002, China
| | - Wei Dai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhenjuan Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | | | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Lin A, Kolossváry M, Cadet S, McElhinney P, Goeller M, Han D, Yuvaraj J, Nerlekar N, Slomka PJ, Marwan M, Nicholls SJ, Achenbach S, Maurovich-Horvat P, Wong DTL, Dey D. Radiomics-Based Precision Phenotyping Identifies Unstable Coronary Plaques From Computed Tomography Angiography. JACC Cardiovasc Imaging 2022; 15:859-871. [PMID: 35512957 PMCID: PMC9072980 DOI: 10.1016/j.jcmg.2021.11.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVES The aim of this study was to precisely phenotype culprit and nonculprit lesions in myocardial infarction (MI) and lesions in stable coronary artery disease (CAD) using coronary computed tomography angiography (CTA)-based radiomic analysis. BACKGROUND It remains debated whether any single coronary atherosclerotic plaque within the vulnerable patient exhibits unique morphology conferring an increased risk of clinical events. METHODS A total of 60 patients with acute MI prospectively underwent coronary CTA before invasive angiography and were matched to 60 patients with stable CAD. For all coronary lesions, high-risk plaque (HRP) characteristics were qualitatively assessed, followed by semiautomated plaque quantification and extraction of 1,103 radiomic features. Machine learning models were built to examine the additive value of radiomic features for discriminating culprit lesions over and above HRP and plaque volumes. RESULTS Culprit lesions had higher mean volumes of noncalcified plaque (NCP) and low-density noncalcified plaque (LDNCP) compared with the highest-grade stenosis nonculprits and highest-grade stenosis stable CAD lesions (NCP: 138.1 mm3 vs 110.7 mm3 vs 102.7 mm3; LDNCP: 14.2 mm3 vs 9.8 mm3 vs 8.4 mm3; both Ptrend < 0.01). In multivariable linear regression adjusted for NCP and LDNCP volumes, 14.9% (164 of 1,103) of radiomic features were associated with culprits and 9.7% (107 of 1,103) were associated with the highest-grade stenosis nonculprits (critical P < 0.0007) when compared with highest-grade stenosis stable CAD lesions as reference. Hierarchical clustering of significant radiomic features identified 9 unique data clusters (latent phenotypes): 5 contained radiomic features specific to culprits, 1 contained features specific to highest-grade stenosis nonculprits, and 3 contained features associated with either lesion type. Radiomic features provided incremental value for discriminating culprit lesions when added to a machine learning model containing HRP and plaque volumes (area under the receiver-operating characteristic curve 0.86 vs 0.76; P = 0.004). CONCLUSIONS Culprit lesions and highest-grade stenosis nonculprit lesions in MI have distinct radiomic signatures compared with lesions in stable CAD. Within the vulnerable patient may exist individual vulnerable plaques identifiable by coronary CTA-based precision phenotyping.
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Affiliation(s)
- Andrew Lin
- Biomedical Imaging Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA; Monash Cardiovascular Research Centre, Victorian Heart Institute, Monash University and MonashHeart, Monash Health, Melbourne, Victoria, Australia
| | - Márton Kolossváry
- Cardiovascular Imaging Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sebastien Cadet
- Department of Imaging and Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Priscilla McElhinney
- Biomedical Imaging Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Markus Goeller
- Department of Cardiology, Friedrich-Alexander-University Erlangen-Nürnberg, Faculty of Medicine, Erlangen, Germany
| | - Donghee Han
- Department of Imaging and Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jeremy Yuvaraj
- Monash Cardiovascular Research Centre, Victorian Heart Institute, Monash University and MonashHeart, Monash Health, Melbourne, Victoria, Australia
| | - Nitesh Nerlekar
- Monash Cardiovascular Research Centre, Victorian Heart Institute, Monash University and MonashHeart, Monash Health, Melbourne, Victoria, Australia
| | - Piotr J Slomka
- Artificial Intelligence in Medicine Program, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Mohamed Marwan
- Department of Cardiology, Friedrich-Alexander-University Erlangen-Nürnberg, Faculty of Medicine, Erlangen, Germany
| | - Stephen J Nicholls
- Monash Cardiovascular Research Centre, Victorian Heart Institute, Monash University and MonashHeart, Monash Health, Melbourne, Victoria, Australia
| | - Stephan Achenbach
- Department of Cardiology, Friedrich-Alexander-University Erlangen-Nürnberg, Faculty of Medicine, Erlangen, Germany
| | - Pál Maurovich-Horvat
- Medical Imaging Centre, Semmelweis University, Budapest, Hungary; MTA-SE Cardiovascular Imaging Research Group, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Dennis T L Wong
- Monash Cardiovascular Research Centre, Victorian Heart Institute, Monash University and MonashHeart, Monash Health, Melbourne, Victoria, Australia
| | - Damini Dey
- Biomedical Imaging Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA.
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Lin S, Ke C, Liu L, Gao Y, Xu L, Han B, Zhao Y, Zhang S, Sun D. Genome-wide association studies for immunoglobulin concentrations in colostrum and serum in Chinese Holstein. BMC Genomics 2022; 23:41. [PMID: 35012443 PMCID: PMC8744259 DOI: 10.1186/s12864-021-08250-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/13/2021] [Indexed: 11/24/2022] Open
Abstract
Background The early death and health problems of calves caused substantial economic losses in the dairy industry. As the immune system of neonates has not been fully developed, the absorption of maternal immunoglobulin (Ig) from colostrum is essential in protecting newborn calves against common disease organisms in their early life. The overwhelming majority of Ig in bovine whey is transported from the serum. Therefore, Ig concentration in the colostrum and serum of dairy cows are critical traits when estimating the potential disease resistance of its offspring. Results Colostrum, blood, and hair follicle samples were collected from 588 Chinese Holstein cows within 24 h after calving. The concentration of total IgG, IgG1, IgG2, IgA and IgM in both colostrum and serum were detected via ELISA methods. With GCTA software, genome-wide association studies (GWASs) were performed with 91,620 SNPs genotyped by GeneSeek 150 K (140,668 SNPs) chips. As a result, 1, 5, 1 and 29 significant SNPs were detected associated with the concentrations of colostrum IgG1, IgG2, IgA IgM, and serum IgG2 at the genome-wide level (P < 3.08E–6); 11, 2, 13, 2, 12, 8, 2, 27, 1 and 4 SNPs were found significantly associated with total IgG, IgG1, IgG2, IgA and IgM in colostrum and serum at the suggestive level (P < 6.15E–5). Such SNPs located in or proximate to (±1 Mb) 423 genes, which were functionally implicated in biological processes and pathways, such as immune response, B cell activation, inflammatory response and NF-kappaB signaling pathways. By combining the biological functions and the known QTL data for immune traits in bovine, 14 promising candidate functional genes were identified for immunoglobulin concentrations in colostrum and serum in dairy cattle, they were FGFR4, FGFR2, NCF1, IKBKG, SORBS3, IGHV1S18, KIT, PTGS2, BAX, GRB2, TAOK1, ICAM1, TGFB1 and RAC3. Conclusions In this study, we identified 14 candidate genes related to concentrations of immunoglobulins in colostrum and serum in dairy cattle by performing GWASs. Our findings provide a groundwork for unraveling the key genes and causal mutations affecting immunoglobulin concentrations in colostrum and important information for genetic improvement of such traits in dairy cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08250-5.
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Affiliation(s)
- Shan Lin
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Cuncun Ke
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Lin Liu
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - Yahui Gao
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Lingna Xu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Bo Han
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Shengli Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Dongxiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
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Diaz S, Polania J, Ariza-Suarez D, Cajiao C, Grajales M, Raatz B, Beebe SE. Genetic Correlation Between Fe and Zn Biofortification and Yield Components in a Common Bean ( Phaseolus vulgaris L.). FRONTIERS IN PLANT SCIENCE 2022; 12:739033. [PMID: 35046970 PMCID: PMC8761845 DOI: 10.3389/fpls.2021.739033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/08/2021] [Indexed: 05/05/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is the most important legume for direct human consumption worldwide. It is a rich and relatively inexpensive source of proteins and micronutrients, especially iron and zinc. Bean is a target for biofortification to develop new cultivars with high Fe/Zn levels that help to ameliorate malnutrition mainly in developing countries. A strong negative phenotypic correlation between Fe/Zn concentration and yield is usually reported, posing a significant challenge for breeders. The objective of this study was to investigate the genetic relationship between Fe/Zn. We used Quantitative Trait Loci (QTLs) mapping and Genome-Wide Association Studies (GWAS) analysis in three bi-parental populations that included biofortified parents, identifying genomic regions associated with yield and micromineral accumulation. Significant negative correlations were observed between agronomic traits (pod harvest index, PHI; pod number, PdN; seed number, SdN; 100 seed weight, 100SdW; and seed per pod, Sd/Pd) and micronutrient concentration traits (SdFe and SdZn), especially between pod harvest index (PHI) and SdFe and SdZn. PHI presented a higher correlation with SdN than PdN. Seventy-nine QTLs were identified for the three populations: 14 for SdFe, 12 for SdZn, 13 for PHI, 11 for SdN, 14 for PdN, 6 for 100SdW, and 9 for Sd/Pd. Twenty-three hotspot regions were identified in which several QTLs were co-located, of which 13 hotpots displayed QTL of opposite effect for yield components and Fe/Zn accumulation. In contrast, eight QTLs for SdFe and six QTLs for SdZn were observed that segregated independently of QTL of yield components. The selection of these QTLs will enable enhanced levels of Fe/Zn and will not affect the yield performance of new cultivars focused on biofortification.
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Affiliation(s)
| | | | | | | | | | | | - Stephen E. Beebe
- Bean Program, Crops for Health and Nutrition Area, Alliance Bioversity International – CIAT, Cali, Colombia
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Hu X, Liang X, Antonecchia E, Chiaravallotti A, Chu Q, Han S, Li Z, Wan L, D'Ascenzo N, Schillaci O, Xie Q. 3-D Textural Analysis of 2-[¹⁸F]FDG PET and Ki67 Expression in Nonsmall Cell Lung Cancer. IEEE TRANSACTIONS ON RADIATION AND PLASMA MEDICAL SCIENCES 2022. [DOI: 10.1109/trpms.2021.3051376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Pedrosa VB, Schenkel FS, Chen SY, Oliveira HR, Casey TM, Melka MG, Brito LF. Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data. Genes (Basel) 2021; 12:genes12111830. [PMID: 34828436 PMCID: PMC8624223 DOI: 10.3390/genes12111830] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 12/22/2022] Open
Abstract
Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1, ZMIZ1, PPIF, LDB2, ABI3, SERPINB6, and SERPINB9 for LP; NIM1K, ZNF131, GABRG1, GABRA2, DCHS1, and SPIDR for MILK; NR6A1, OLFML2A, EXT2, POLD1, GOT1, and ETV6 for FAT; DPP6, LRRC26, and the KCN gene family for FAT%; CDC14A, RTCA, HSTN, and ODAM for PROT; and HERC3, HERC5, LALBA, CCL28, and NEURL1 for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.
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Affiliation(s)
- Victor B. Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, Brazil
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada;
| | - Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada;
| | - Theresa M. Casey
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
| | - Melkaye G. Melka
- Department of Animal and Food Science, University of Wisconsin River Falls, River Falls, WI 54022, USA;
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Correspondence:
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40
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Kreiner JM, Tranel PJ, Weigel D, Stinchcombe JR, Wright SI. The genetic architecture and population genomic signatures of glyphosate resistance in Amaranthus tuberculatus. Mol Ecol 2021; 30:5373-5389. [PMID: 33853196 DOI: 10.1111/mec.15920] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/15/2021] [Accepted: 04/06/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about the genetic basis of herbicide resistance has come from detailed investigations of monogenic adaptation at known target-sites, despite the increasingly recognized importance of polygenic resistance. Little work has been done to characterize the broader genomic basis of herbicide resistance, including the number and distribution of genes involved, their effect sizes, allele frequencies and signatures of selection. In this work, we implemented genome-wide association (GWA) and population genomic approaches to examine the genetic architecture of glyphosate (Round-up) resistance in the problematic agricultural weed Amaranthus tuberculatus. A GWA was able to correctly identify the known target-gene but statistically controlling for two causal target-site mechanisms revealed an additional 250 genes across all 16 chromosomes associated with non-target-site resistance (NTSR). The encoded proteins had functions that have been linked to NTSR, the most significant of which is response to chemicals, but also showed pleiotropic roles in reproduction and growth. Compared to an empirical null that accounts for complex population structure, the architecture of NTSR was enriched for large effect sizes and low allele frequencies, suggesting the role of pleiotropic constraints on its evolution. The enrichment of rare alleles also suggested that the genetic architecture of NTSR may be population-specific and heterogeneous across the range. Despite their rarity, we found signals of recent positive selection on NTSR-alleles by both window- and haplotype-based statistics, and an enrichment of amino acid changing variants. In our samples, genome-wide single nucleotide polymorphisms explain a comparable amount of the total variation in glyphosate resistance to monogenic mechanisms, even in a collection of individuals where 80% of resistant individuals have large-effect TSR mutations, indicating an underappreciated polygenic contribution to the evolution of herbicide resistance in weed populations.
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Affiliation(s)
- Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Koffler Scientific Reserve, University of Toronto, King City, ON, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
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Tietgen L, Hagen IJ, Kleven O, Bernardi CD, Kvalnes T, Norén K, Hasselgren M, Wallén JF, Angerbjörn A, Landa A, Eide NE, Flagstad Ø, Jensen H. Fur colour in the Arctic fox: genetic architecture and consequences for fitness. Proc Biol Sci 2021; 288:20211452. [PMID: 34583587 PMCID: PMC8479361 DOI: 10.1098/rspb.2021.1452] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies provide good opportunities for studying the genetic basis of adaptive traits in wild populations. Yet, previous studies often failed to identify major effect genes. In this study, we used high-density single nucleotide polymorphism and individual fitness data from a wild non-model species. Using a whole-genome approach, we identified the MC1R gene as the sole causal gene underlying Arctic fox Vulpes lagopus fur colour. Further, we showed the adaptive importance of fur colour genotypes through measures of fitness that link ecological and evolutionary processes. We found a tendency for blue foxes that are heterozygous at the fur colour locus to have higher fitness than homozygous white foxes. The effect of genotype on fitness was independent of winter duration but varied with prey availability, with the strongest effect in years of increasing rodent populations. MC1R is located in a genomic region with high gene density, and we discuss the potential for indirect selection through linkage and pleiotropy. Our study shows that whole-genome analyses can be successfully applied to wild species and identify major effect genes underlying adaptive traits. Furthermore, we show how this approach can be used to identify knowledge gaps in our understanding of interactions between ecology and evolution.
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Affiliation(s)
- Lukas Tietgen
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.,Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Ingerid J Hagen
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.,Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Oddmund Kleven
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Cecilia Di Bernardi
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway.,Department of Biology and Biotechnologies 'Charles Darwin', University of Rome La Sapienza, Viale dell' Università 32, Rome 00185, Italy
| | - Thomas Kvalnes
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Malin Hasselgren
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Johan Fredrik Wallén
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden.,Swedish Museum of Natural History, Stockholm 10405, Sweden
| | - Anders Angerbjörn
- Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Arild Landa
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Nina E Eide
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Øystein Flagstad
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway
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A major quantitative trait locus affecting resistance to Tilapia lake virus in farmed Nile tilapia (Oreochromis niloticus). Heredity (Edinb) 2021; 127:334-343. [PMID: 34262170 PMCID: PMC8405827 DOI: 10.1038/s41437-021-00447-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/31/2021] [Accepted: 05/31/2021] [Indexed: 02/06/2023] Open
Abstract
Enhancing host resistance to infectious disease has received increasing attention in recent years as a major goal of farm animal breeding programs. Combining field data with genomic tools can provide opportunities to understand the genetic architecture of disease resistance, leading to new opportunities for disease control. In the current study, a genome-wide association study was performed to assess resistance to the Tilapia lake virus (TiLV), one of the biggest threats affecting Nile tilapia (Oreochromis niloticus); a key aquaculture species globally. A pond outbreak of TiLV in a pedigreed population of the GIFT strain was observed, with 950 fish classified as either survivor or mortality, and genotyped using a 65 K SNP array. A significant QTL of large effect was identified on chromosome Oni22. The average mortality rate of tilapia homozygous for the resistance allele at the most significant SNP (P value = 4.51E-10) was 11%, compared to 43% for tilapia homozygous for the susceptibility allele. Several candidate genes related to host response to viral infection were identified within this QTL, including lgals17, vps52, and trim29. These results provide a rare example of a major QTL affecting a trait of major importance to a farmed animal. Genetic markers from the QTL region have potential in marker-assisted selection to improve host resistance, providing a genetic solution to an infectious disease where few other control or mitigation options currently exist.
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Yan G, Liu X, Xiao S, Xin W, Xu W, Li Y, Huang T, Qin J, Xie L, Ma J, Zhang Z, Huang L. An imputed whole-genome sequence-based GWAS approach pinpoints causal mutations for complex traits in a specific swine population. SCIENCE CHINA-LIFE SCIENCES 2021; 65:781-794. [PMID: 34387836 DOI: 10.1007/s11427-020-1960-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/19/2021] [Indexed: 01/08/2023]
Abstract
Sequencing-based genome-wide association studies (GWAS) have facilitated the identification of causal associations between genetic variants and traits in diverse species. However, it is cost-prohibitive for the majority of research groups to sequence a large number of samples. Here, we carried out genotype imputation to increase the density of single nucleotide polymorphisms in a large-scale Swine F2 population using a reference panel including 117 individuals, followed by a series of GWAS analyses. The imputation accuracies reached 0.89 and 0.86 for allelic concordance and correlation, respectively. A quantitative trait nucleotide (QTN) affecting the chest vertebrate was detected directly, while the investigation of another QTN affecting the residual glucose failed due to the presence of similar haplotypes carrying wild-type and mutant allelesin the reference panel used in this study. A high imputation accuracy was confirmed by Sanger sequencing technology for the most significant loci. Two candidate genes, CPNE5 and MYH3, affecting meat-related traits were proposed. Collectively, we illustrated four scenarios in imputation-based GWAS that may be encountered by researchers, and our results will provide an extensive reference for future genotype imputation-based GWAS analyses in the future.
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Affiliation(s)
- Guorong Yan
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
- Institute of Photomedicine, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xianxian Liu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wenshui Xin
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Wenwu Xu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yiping Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Tao Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jiangtao Qin
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Lei Xie
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junwu Ma
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Zhiyan Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
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Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance. Sci Rep 2021; 11:15730. [PMID: 34344928 PMCID: PMC8333424 DOI: 10.1038/s41598-021-95116-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/19/2021] [Indexed: 11/10/2022] Open
Abstract
Sugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV) is a major disease affecting sugarcane, a leading sugar and energy crop. Despite damages caused by SCYLV, the genetic base of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic base of SCYLV resistance using dominant and codominant markers and genotypes of interest for sugarcane breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them and demonstrated their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.
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Ma L, Qing C, Zhang M, Zou C, Pan G, Shen Y. GWAS with a PCA uncovers candidate genes for accumulations of microelements in maize seedlings. PHYSIOLOGIA PLANTARUM 2021; 172:2170-2180. [PMID: 34028036 DOI: 10.1111/ppl.13466] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/03/2021] [Accepted: 05/18/2021] [Indexed: 05/13/2023]
Abstract
Microelements are necessary for plant growth and development, they control key processes of physiological metabolism. Herein, we evaluated three accumulation-related performances for each of the four microelements (Fe, Zn, Cu, and Mn) among 305 inbred maize lines. Quantification of these microelements in maize roots and shoots revealed abundant phenotypic variations in the association panel, with the variation coefficients ranging from 0.31 to 0.76. Principal component analysis (PCA) of the three related traits (concentration in root, concentration in shoot, and transport coefficient) showed that PC1 and PC2 explained >95% of phenotypic variations for each element. The scores of PC1 and PC2 were thereby used for a genome-wide association study by combining 44,134 SNPs of this panel. A total of 27, 1, 5, and 3 SNPs were significantly (P < .05) associated with Zn-PC1, Zn-PC2, Cu-PC1, and Mn-PC2, respectively, with 11 genes closely linked (r2 > 0.8) to these SNPs. Of them, GRMZM2G142870, GRMZM2G045531, and GRMZM2G143512 were individually annotated as ABC transporter C family member 14, zinc transporter 3, and heavy metal ATPase10. A candidate gene association analysis further verified that GRMZM2G142870 and GRMZM2G045531 affect Zn and Mn accumulations, respectively. Evaluation of contrasting allele ratios in elite lines indicated that the majority of the alleles correlating with higher Zn or Cu had not been utilized in maize breeding. Integration of more "higher-accumulation" alleles in the elite lines will be practical for improving Zn and Cu accumulations in maize. Our findings contribute to genetic revelation and molecular marker-assisted selection of microelement accumulations in maize.
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Affiliation(s)
- Langlang Ma
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chunyan Qing
- Mianyang Academy of Agricultural Sciences, Mianyang, China
| | - Minyan Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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Hirtz R, Zheng Y, Rajcsanyi LS, Libuda L, Antel J, Peters T, Hebebrand J, Hinney A. [Genetic Analyses of Complex Phenotypes Through the Example of Anorexia Nervosa and Bodyweight Regulation]. ZEITSCHRIFT FUR KINDER-UND JUGENDPSYCHIATRIE UND PSYCHOTHERAPIE 2021; 50:175-185. [PMID: 34328348 DOI: 10.1024/1422-4917/a000829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Genetic Analyses of Complex Phenotypes Through the Example of Anorexia Nervosa and Bodyweight Regulation Abstract. Genetics variants are important for the regulation of bodyweight and also contribute to the genetic architecture of eating disorders. For many decades, family studies, a subentity of so-called formal genetic studies, were employed to determine the genetic share of bodyweight and eating disorders and found heritability rates exceeding 50 % with both phenotypes. Because of this significant contribution of genetics, the search for those genes and their variants related to the variance in bodyweight and the etiology of eating disorders - or both - was commenced by the early 1990s. Initially, candidate genes studies were conducted targeting those genes most plausibly related to either phenotype, especially based on pathophysiological considerations. This approach, however, implicated only a few genes in the regulation of bodyweight and did not provide significant insights into the genetics of eating disorders. Driven by considerable methodological advances in genetic research, especially related to the introduction of so-called genome-wide association studies by the beginning of the 21st century, today more than 1,000 variants/loci have been detected that affect the regulation of bodyweight. Eight such loci have been identified regarding anorexia nervosa (AN). These results as well as those from cross-disorder analyses provide insights into the complex regulation of bodyweight and demonstrated unforeseen pathomechanisms for AN.
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Affiliation(s)
- Raphael Hirtz
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, LVR-Klinikum Essen, Kliniken und Institut der Universität Duisburg-Essen, Universitätsklinikum Essen.,Abteilung für Pädiatrische Endokrinologie und Diabetologie, Kinderklinik II, Universitätsklinikum Essen
| | - Yiran Zheng
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, LVR-Klinikum Essen, Kliniken und Institut der Universität Duisburg-Essen, Universitätsklinikum Essen
| | - Luisa S Rajcsanyi
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, LVR-Klinikum Essen, Kliniken und Institut der Universität Duisburg-Essen, Universitätsklinikum Essen
| | - Lars Libuda
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, LVR-Klinikum Essen, Kliniken und Institut der Universität Duisburg-Essen, Universitätsklinikum Essen.,Institut für Ernährung, Konsum und Gesundheit, Fakultät für Naturwissenschaften, Universität Paderborn
| | - Jochen Antel
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, LVR-Klinikum Essen, Kliniken und Institut der Universität Duisburg-Essen, Universitätsklinikum Essen
| | - Triinu Peters
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, LVR-Klinikum Essen, Kliniken und Institut der Universität Duisburg-Essen, Universitätsklinikum Essen
| | - Johannes Hebebrand
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, LVR-Klinikum Essen, Kliniken und Institut der Universität Duisburg-Essen, Universitätsklinikum Essen
| | - Anke Hinney
- Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, LVR-Klinikum Essen, Kliniken und Institut der Universität Duisburg-Essen, Universitätsklinikum Essen
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McInnes G, Yee SW, Pershad Y, Altman RB. Genomewide Association Studies in Pharmacogenomics. Clin Pharmacol Ther 2021; 110:637-648. [PMID: 34185318 PMCID: PMC8376796 DOI: 10.1002/cpt.2349] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/15/2021] [Indexed: 12/24/2022]
Abstract
The increasing availability of genotype data linked with information about drug-response phenotypes has enabled genomewide association studies (GWAS) that uncover genetic determinants of drug response. GWAS have discovered associations between genetic variants and both drug efficacy and adverse drug reactions. Despite these successes, the design of GWAS in pharmacogenomics (PGx) faces unique challenges. In this review, we analyze the last decade of GWAS in PGx. We review trends in publications over time, including the drugs and drug classes studied and the clinical phenotypes used. Several data sharing consortia have contributed substantially to the PGx GWAS literature. We anticipate increased focus on biobanks and highlight phenotypes that would best enable future PGx discoveries.
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Affiliation(s)
- Gregory McInnes
- Biomedical Informatics Training Program, Stanford University, Stanford, California, USA
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, California, USA
| | - Yash Pershad
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Russ B Altman
- Department of Bioengineering, Stanford University, Stanford, California, USA.,Departments of Genetics, Medicine, Biomedical Data Science, Stanford, California, USA
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Liu N, Du Y, Warburton ML, Xiao Y, Yan J. Phenotypic Plasticity Contributes to Maize Adaptation and Heterosis. Mol Biol Evol 2021; 38:1262-1275. [PMID: 33212480 PMCID: PMC8480182 DOI: 10.1093/molbev/msaa283] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in this area to date. In the present study, we established a population of 976 maize F1 hybrids by crossing 488 diverse inbred lines with two elite testers. Genome-wide association study identified hundreds of quantitative trait loci associated with phenotypic plasticity variation across diverse F1 hybrids, the majority of which contributed very little variance, in accordance with the polygenic nature of these traits. We identified several quantitative trait locus regions that may have been selected during the tropical-temperate adaptation process. We also observed heterosis in terms of phenotypic plasticity, in addition to the traditional genetic value differences measured between hybrid and inbred lines, and the pattern of which was affected by genetic background. Our results demonstrate a landscape of phenotypic plasticity in maize, which will aid in the understanding of its genetic architecture, its contribution to adaptation and heterosis, and how it may be exploited for future maize breeding in a rapidly changing environment.
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Affiliation(s)
- Nannan Liu
- Horticulture Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuanhao Du
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Marilyn L Warburton
- United States Department of Agriculture-Agricultural Research Service: Corn Host Plant Resistance Research Unit, Mississippi State, MS
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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Zhang Y, Liu P, Wang C, Zhang N, Zhu Y, Zou C, Yuan G, Yang C, Gao S, Pan G, Ma L, Shen Y. Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize. PeerJ 2021; 9:e11707. [PMID: 34249517 PMCID: PMC8247712 DOI: 10.7717/peerj.11707] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
As one of the major crops, maize (Zea mays L.) is mainly distributed in tropical and temperate regions. However, with the changes of the environments, chilling stress has become a significantly abiotic stress affecting seed germination and thus the reproductive and biomass accumulation of maize. Herein, we investigated five seed germination-related phenotypes among 300 inbred lines under low-temperature condition (10 °C). By combining 43,943 single nucleotide polymorphisms (SNPs), a total of 15 significant (P < 2.03 × 10-6) SNPs were identified to correlate with seed germination under cold stress based on the FarmCPU model in GWAS, among which three loci were repeatedly associated with multiple traits. Ten gene models were closely linked to these three variations, among which Zm00001d010454, Zm00001d010458, Zm00001d010459, and Zm00001d050021 were further verified by candidate gene association study and expression pattern analysis. Importantly, these candidate genes were previously reported to involve plant tolerance to chilling stress and other abiotic stress. Our findings contribute to the understanding of the genetic and molecular mechanisms underlying chilling germination in maize.
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Affiliation(s)
- Yinchao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peng Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Chen Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Na Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuxiao Zhu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Chaoying Zou
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guangsheng Yuan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Cong Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shibin Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guangtang Pan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Langlang Ma
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yaou Shen
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
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50
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Nie C, Qu L, Li X, Jiang Z, Wang K, Li H, Wang H, Qu C, Qu L, Ning Z. Genomic Regions Related to White/Black Tail Feather Color in Dwarf Chickens Identified Using a Genome-Wide Association Study. Front Genet 2021; 12:566047. [PMID: 33995468 PMCID: PMC8120320 DOI: 10.3389/fgene.2021.566047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/21/2021] [Indexed: 11/13/2022] Open
Abstract
Although the genetic foundation of chicken body feather color has been extensively explored, that of tail feather color remains poorly understood. In the present study, we used a synthetic chicken dwarf line (DW), derived from hybrids bred between a black tail chicken breed, Rhode Island Red (RIR), and a white tail breed, dwarf layer (DL), to investigate the genetic rules associated white/black tail color. Even though the body feathers are predominantly red, the DW line still comprises individuals with black or white tails after more than 10 generations of self-crossing and selection for the body feather color. We first performed four crosses using the DW chickens, including black-tailed males to females, reciprocal crosses between the black and white, and white males to females to elucidate the inheritance pattern of the white/black tail. We also performed a genome-wide association (GWA) analysis to determine the candidate genomic regions underlying the tail feather color using black tail chickens from the RIR and DW lines and white individuals from the DW line. In the crossing experiment, we found that (i) the white/black tail feather color is independent of body feather color; (ii) the phenotype is a simple autosomal trait; and (iii) the white is dominant to the black in the DW line. The GWA results showed that seven single-nucleotide polymorphisms (SNPs) on chromosome 24 were significantly correlated with tail feather color. The significant region (3.97-4.26 Mb) comprises nine known genes (NECTIN1, THY1, gga-mir-1466, USP2, C1QTNF5, RNF26, MCAM, CBL, and CCDC153) and five anonymous genes. This study revealed that the white/black tail feather trait is autosome-linked in DW chickens. Fourteen genes were found in the significant ~0.29 Mb genomic region, and some, especially MCAM, are suggested to play critical roles in the determination of white/black tail feather color. Our research is the first study on the genetics underlying tail feather color and could help further the understanding of feather pigmentation in chickens.
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Affiliation(s)
- Changsheng Nie
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Liang Qu
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, China
| | - Xinghua Li
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Kehua Wang
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, China
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Huie Wang
- College of Animal Science, Tarim University, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xinjiang, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, China
| | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhonghua Ning
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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