1
|
Tilhou N, Kissing Kucek L, Carr B, Douglas J, Englert J, Ali S, Raasch J, Bhamidimarri S, Mirsky S, Monteros MJ, Hayes R, Riday H. Pooled DNA sequencing in hairy vetch ( Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscence. Front Plant Sci 2024; 15:1384596. [PMID: 38638346 PMCID: PMC11024373 DOI: 10.3389/fpls.2024.1384596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024]
Abstract
Introduction Hairy vetch (Vicia villosa Roth) is a promising legume cover crop, but its use is limited by high rates of pod dehiscence and seed dormancy. Methods We used phenotypically contrasting pooled DNA samples (n=24 with 29-74 individuals per sample) from an ongoing cover crop breeding program across four environments (site-year combinations: Maryland 2020, Maryland 2022, Wisconsin 2021, Wisconsin 2022) to find genetic associations and genomic prediction accuracies for pod dehiscence and seed dormancy. We also combined pooled DNA sample genetic association results with the results of a prior genome-wide association study. Results and discussion Genomic prediction resulted in positive predictive abilities for both traits between environments and with an independent dataset (0.34-0.50), but reduced predictive ability for DNA pools with divergent seed dormancy in the Maryland environments (0.07-0.15). The pooled DNA samples found six significant (false discovery rate q-value<0.01) quantitative trait loci (QTL) for seed dormancy and four significant QTL for pod dehiscence. Unfortunately, the minor alleles of the pod dehiscence QTL increased the rate of pod dehiscence and are not useful for marker-assisted selection. When combined with a prior association study, sixteen seed dormancy QTL and zero pod dehiscence QTL were significant. Combining the association studies did not increase the detection of useful QTL.
Collapse
Affiliation(s)
- Neal Tilhou
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - Lisa Kissing Kucek
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - Brandon Carr
- United States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), James E. “Bud” Smith Plant Materials Center, Knox City, TX, United States
| | - Joel Douglas
- United States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), Central National Technology Support Center, Fort Worth, TX, United States
| | - John Englert
- United States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), National Plant Materials Program, Washington, DC, United States
| | - Shahjahan Ali
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - John Raasch
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | | | - Steven Mirsky
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD, United States
| | - Maria J. Monteros
- Bayer Crop Science, North America (NA) Breeding, Chesterfield, MO, United States
| | - Ryan Hayes
- Forage Seed and Cereal Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Corvallis, OR, United States
| | - Heathcliffe Riday
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| |
Collapse
|
2
|
Akenroye AT, Brunetti T, Romero K, Daya M, Kanchan K, Shankar G, Chavan S, Preethi Boorgula M, Ampleford EA, Fonseca HF, Hawkins GA, Pitangueira Teixeira HM, Campbell M, Rafaels N, Winters A, Bleecker ER, Cruz AA, Barreto ML, Meyers DA, Ortega VE, Figueiredo CA, Barnes KC, Checkley W, Hansel NN, Mathias RA. Genome-wide association study of asthma, total IgE, and lung function in a cohort of Peruvian children. J Allergy Clin Immunol 2021; 148:1493-1504. [PMID: 33713768 PMCID: PMC8429514 DOI: 10.1016/j.jaci.2021.02.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Genetic ancestry plays a role in asthma health disparities. OBJECTIVE Our aim was to evaluate the impact of ancestry on and identify genetic variants associated with asthma, total serum IgE level, and lung function. METHODS A total of 436 Peruvian children (aged 9-19 years) with asthma and 291 without asthma were genotyped by using the Illumina Multi-Ethnic Global Array. Genome-wide proportions of indigenous ancestry populations from continental America (NAT) and European ancestry from the Iberian populations in Spain (IBS) were estimated by using ADMIXTURE. We assessed the relationship between ancestry and the phenotypes and performed a genome-wide association study. RESULTS The mean ancestry proportions were 84.7% NAT (case patients, 84.2%; controls, 85.4%) and 15.3% IBS (15.8%; 14.6%). With adjustment for asthma, NAT was associated with higher total serum IgE levels (P < .001) and IBS was associated with lower total serum IgE levels (P < .001). NAT was associated with higher FEV1 percent predicted values (P < .001), whereas IBS was associated with lower FEV1 values in the controls but not in the case patients. The HLA-DR/DQ region on chromosome 6 (Chr6) was strongly associated with total serum IgE (rs3135348; P = 3.438 × 10-10) and was independent of an association with the haplotype HLA-DQA1∼HLA-DQB1:04.01∼04.02 (P = 1.55 × 10-05). For lung function, we identified a locus (rs4410198; P = 5.536 × 10-11) mapping to Chr19, near a cluster of zinc finger interacting genes that colocalizes to the long noncoding RNA CTD-2537I9.5. This novel locus was replicated in an independent sample of pediatric case patients with asthma with similar admixture from Brazil (P = .005). CONCLUSION This study confirms the role of HLA in atopy, and identifies a novel locus mapping to a long noncoding RNA for lung function that may be specific to children with NAT.
Collapse
Affiliation(s)
- Ayobami T Akenroye
- Division of Pediatric Allergy and Immunology, Johns Hopkins University School of Medicine, Baltimore, Md
| | - Tonya Brunetti
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - Karina Romero
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Md; A.B. PRISMA, Lima, Peru
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - Kanika Kanchan
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Md
| | - Gautam Shankar
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Md
| | - Sameer Chavan
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - Meher Preethi Boorgula
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - Elizabeth A Ampleford
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC
| | | | - Gregory A Hawkins
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | | | - Monica Campbell
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - Nicholas Rafaels
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - Alexandra Winters
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Md
| | | | | | - Mauricio L Barreto
- Centro de Integração de Dados e Conhecimento para Saúde, Fiocruz, Salvador, Brazil
| | | | - Victor E Ortega
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC
| | - Camila A Figueiredo
- Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador, Brazil
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - William Checkley
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Md; Department of International Health, Program in Global Disease Epidemiology and Control, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md
| | - Nadia N Hansel
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Md.
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Md.
| |
Collapse
|