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Johnson JP, Piche L, Worral H, Atanda SA, Coyne CJ, McGee RJ, McPhee K, Bandillo N. Effective population size in field pea. BMC Genomics 2024; 25:695. [PMID: 39009980 PMCID: PMC11251210 DOI: 10.1186/s12864-024-10587-6] [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: 02/02/2024] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Effective population size (Ne) is a pivotal parameter in population genetics as it can provide information on the rate of inbreeding and the contemporary status of genetic diversity in breeding populations. The population with smaller Ne can lead to faster inbreeding, with little potential for genetic gain making selections ineffective. The importance of Ne has become increasingly recognized in plant breeding, which can help breeders monitor and enhance the genetic variability or redesign their selection protocols. Here, we present the first Ne estimates based on linkage disequilibrium (LD) in the pea genome. RESULTS We calculated and compared Ne using SNP markers from North Dakota State University (NDSU) modern breeding lines and United States Department of Agriculture (USDA) diversity panel. The extent of LD was highly variable not only between populations but also among different regions and chromosomes of the genome. Overall, NDSU had a higher and longer-range LD than the USDA that could extend up to 500 Kb, with a genome-wide average r2 of 0.57 (vs 0.34), likely due to its lower recombination rates and the selection background. The estimated Ne for the USDA was nearly three-fold higher (Ne = 174) than NDSU (Ne = 64), which can be confounded by a high degree of population structure due to the selfing nature of pea. CONCLUSIONS Our results provided insights into the genetic diversity of the germplasm studied, which can guide plant breeders to actively monitor Ne in successive cycles of breeding to sustain viability of the breeding efforts in the long term.
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Affiliation(s)
| | - Lisa Piche
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Hannah Worral
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Sikiru Adeniyi Atanda
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Clarice J Coyne
- USDA-ARS Plant Germplasm Introduction and Testing, Washington State University, Pullman, WA, 99164, USA
| | - Rebecca J McGee
- USDA-ARS Grain Legume Genetics and Physiology Research, Pullman, WA, 99164, USA
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Kevin McPhee
- Department of Plant Science and Plant Pathology, Montana State University, 119 Plant Bioscience Building, Bozeman, MT, 59717-3150, USA
| | - Nonoy Bandillo
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
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Xiong H, Chen Y, Ravelombola W, Mou B, Sun X, Zhang Q, Xiao Y, Tian Y, Luo Q, Alatawi I, Chiwina KE, Alkabkabi HM, Shi A. Genetic Dissection of Diverse Seed Coat Patterns in Cowpea through a Comprehensive GWAS Approach. PLANTS (BASEL, SWITZERLAND) 2024; 13:1275. [PMID: 38732490 PMCID: PMC11085092 DOI: 10.3390/plants13091275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/27/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
This study investigates the genetic determinants of seed coat color and pattern variations in cowpea (Vigna unguiculata), employing a genome-wide association approach. Analyzing a mapping panel of 296 cowpea varieties with 110,000 single nucleotide polymorphisms (SNPs), we focused on eight unique coat patterns: (1) Red and (2) Cream seed; (3) White and (4) Brown/Tan seed coat; (5) Pink, (6) Black, (7) Browneye and (8) Red/Brown Holstein. Across six GWAS models (GLM, SRM, MLM, MLMM, FarmCPU from GAPIT3, and TASSEL5), 13 significant SNP markers were identified and led to the discovery of 23 candidate genes. Among these, four specific genes may play a direct role in determining seed coat pigment. These findings lay a foundational basis for future breeding programs aimed at creating cowpea varieties aligned with consumer preferences and market requirements.
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Affiliation(s)
- Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.C.)
| | - Yilin Chen
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.C.)
| | | | - Beiquan Mou
- Sam Farr U.S. Crop Improvement and Protection Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Salinas, CA 93905, USA
| | - Xiaolun Sun
- Department of Poultry Science & The Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Qingyang Zhang
- Mathematical Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Yiting Xiao
- Biological Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Yang Tian
- Program of Material Science and Engineering, Fayetteville, AR 72701, USA
| | - Qun Luo
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.C.)
| | - Ibtisam Alatawi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.C.)
| | - Kenani Edward Chiwina
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.C.)
| | | | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.C.)
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Li Y, Lei H, Wen X, Cao H. A powerful approach to identify replicable variants in genome-wide association studies. Am J Hum Genet 2024; 111:966-978. [PMID: 38701746 PMCID: PMC11080610 DOI: 10.1016/j.ajhg.2024.04.004] [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: 08/19/2023] [Revised: 04/04/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024] Open
Abstract
Replicability is the cornerstone of modern scientific research. Reliable identifications of genotype-phenotype associations that are significant in multiple genome-wide association studies (GWASs) provide stronger evidence for the findings. Current replicability analysis relies on the independence assumption among single-nucleotide polymorphisms (SNPs) and ignores the linkage disequilibrium (LD) structure. We show that such a strategy may produce either overly liberal or overly conservative results in practice. We develop an efficient method, ReAD, to detect replicable SNPs associated with the phenotype from two GWASs accounting for the LD structure. The local dependence structure of SNPs across two heterogeneous studies is captured by a four-state hidden Markov model (HMM) built on two sequences of p values. By incorporating information from adjacent locations via the HMM, our approach provides more accurate SNP significance rankings. ReAD is scalable, platform independent, and more powerful than existing replicability analysis methods with effective false discovery rate control. Through analysis of datasets from two asthma GWASs and two ulcerative colitis GWASs, we show that ReAD can identify replicable genetic loci that existing methods might otherwise miss.
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Affiliation(s)
- Yan Li
- School of Computer Science and Technology, Changchun University of Science and Technology, Changchun, Jilin 130022, China; School of Mathematics, Jilin University, Changchun, Jilin 130012, China
| | - Haochen Lei
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hongyuan Cao
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA.
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Chen Z, Zhu M, Wu Q, Lu H, Lei C, Ahmed Z, Sun J. Analysis of genetic diversity and selection characteristics using the whole genome sequencing data of five buffaloes, including Xilin buffalo, in Guangxi, China. Front Genet 2023; 13:1084824. [PMID: 36699455 PMCID: PMC9869173 DOI: 10.3389/fgene.2022.1084824] [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: 10/31/2022] [Accepted: 12/27/2022] [Indexed: 01/12/2023] Open
Abstract
Buffalo is an economically important livestock that renders useful services to manhood in terms of meat, milk, leather, and draught. The Xilin buffalo is among the native buffalo breeds of China. In the present study, the genetic architecture and selection signature signals of Xilin buffalo have been explored. Correlation analysis of the population structure of Xilin buffalo was conducted by constructing NJ tree, PCA, ADMIXTURE and other methods. A total of twenty-five (n = 25) Xilin buffalo whole genome data and data of forty-six (n = 46) buffaloes published data were used. The population structure analysis showed that the Xilin buffalo belong to the Middle-Lower Yangtze. The genome diversity of Xilin buffalo was relatively high. The CLR, π ratio, F ST, and XP-EHH were used to detect the candidate genes characteristics of positive selection in Xilin buffalo. Among the identified genes, most of the enriched signal pathways were related to the nervous system and metabolism. The mainly reported genes were related to the nervous system (GRM5, GRIK2, GRIA4), reproductive genes (CSNK1G2, KCNIP4), and lactation (TP63). The results of this study are of great significance for understanding the molecular basis of phenotypic variation of related traits of Xilin buffalo. We provide a comprehensive overview of sequence variations in Xilin buffalo genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Xilin buffalo and help in future breeding and conservation programs of this important livestock genetic resource.
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Affiliation(s)
- Zhefu Chen
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China,College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Min Zhu
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qiang Wu
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Huilin Lu
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot, China
| | - Junli Sun
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China,*Correspondence: Junli Sun,
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Wei S, Yu X, Wen X, Zhang M, Lang Q, Zhong P, Huang B. Genetic Variations in Metallothionein Genes and Susceptibility to Hypertensive Disorders of Pregnancy: A Case-Control Study. Front Genet 2022; 13:830446. [PMID: 35734434 PMCID: PMC9208279 DOI: 10.3389/fgene.2022.830446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/19/2022] [Indexed: 01/07/2023] Open
Abstract
Background: The involvement of oxidative stress in the pathological process of hypertensive disorders of pregnancy (HDP) gives rise to the interest in exploring the association of genetic variations in antioxidant metallothionein (MT) genes with HDP susceptibility. Methods: Seventeen single-nucleotide polymorphisms(SNPs) in MT genes were selected to conduct genotyping based on a case-control study consisting of 371 HDP cases (pregnancy with chronic hypertension (66), gestational hypertension (172), and preeclampsia or preeclampsia superimposed on chronic hypertension (133)) and 479 controls. The association between SNPs in MTs and the risk of HDP was estimated with unconditional logistic regression analysis and further tested with the false-positive report probability (FPRP) procedure. The joint effects of SNPs on the HDP risk were assessed by haplotype analysis. Results: After the adjustment for age and pre-pregnancy body mass index (pre-BMI) in the logistic regress analysis and followed by the FPRP test, the genetic variation rs10636 (OR = 0.46, 95% CI: 0.30–0.71 for GG vs. CC, p = 0.000 and OR = 0.48, 95% CI: 0.32–0.73 for GG vs. CG/CC, p = 0.001) in MT2A was associated with gestational hypertension. Other four SNPs, that is, rs11076161 (OR = 1.89, 95% CI: 1.35–2.63 for GG vs. GA/AA, p = 0.000) in MT1A; rs7191779 (OR = 1.54, 95% CI: 1.11–2.13 for CC vs. CG/GG, p = 0.010) in MT1B; rs8044719 (OR = 0.57, 95% CI: 0.40–0.80 for GT vs. GG, p = 0.001) in MT1DP; and rs8052334 (OR = 1.52, 95% CI: 1.10–2.11 for TT vs. TC/CC, p = 0.012) in MT1B were significantly associated with the susceptibility of HDP. The haplotype analysis among 11, 10, 10, and seven SNPs in MT (MT1A, MT2A, MT1M, MT1B, and MT1DP) genes showed that eight (A-C-G-T-C-G-A-G-C-G-C, OR = 4.559; A-C-T-C-C-C-A-G-C-G-C, OR = 5.777; A-C-T-T-C-G-A-G-C-G-C, OR = 4.590; G-A-T-C-C-G-C-G-G-C-C, OR = 4.065; G-A-T-C-G-C-C-G-G-C-C, OR = 4.652; G-A-T-T-C-C-C-G-G-C-C, OR = 0.404; G-C-T-C-C-C-A-G-G-C-C, OR = 1.901; G-C-T-T-C-C-A-G-G-C-C, and OR = 3.810), five (C-G-A-T-C-A-C-C-G-G, OR = 2.032; C-G-A-T-C-G-C-C-G-G, OR = 2.077; G-A-C-T-C-A-C-C-T-G, OR = 0.564; G-G-A-G-C-A-C-C-G-G, OR = 5.466; G-G-A-T-T-A-G-C-G-G, and OR = 0.284), five (A-C-G-T-C-G-A-G-C-C, OR = 2.399; A-C-T-C-C-C-C-T-G-G, OR = 0.259; G-A-T-C-C-C-C-G-G-C, OR = 1.572; G-A-T-C-G-C-C-G-G-C, OR = 0.001; G-C-T-C-G-C-A-G-G-C, and OR = 2.512), and five (A-C-T-C-C-C-G, OR = 0.634; G-A-G-C-C-C-G, OR = 4.047; G-A-T-T-G-C-G, OR = 0.499; G-C-G-T-C-A-G, and OR = 7.299; G-C-T-C-C-A-G, OR = 1.434) haplotypes were significantly associated with pregnancy with chronic hypertension, gestational hypertension, preeclampsia, or preeclampsia superimposed on chronic hypertension and HDP. Conclusion: These variant MT alleles and their combination patterns may be used as genetic markers for predicting HDP susceptibility.
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Affiliation(s)
- Shudan Wei
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, Guilin Medical University, Guilin, China
| | - Xiangyuan Yu
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, Guilin Medical University, Guilin, China
| | - Xiaolan Wen
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, Guilin Medical University, Guilin, China
| | - Min Zhang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, Guilin Medical University, Guilin, China
| | - Qi Lang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, Guilin Medical University, Guilin, China
| | - Ping Zhong
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Bo Huang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, Guilin Medical University, Guilin, China
- *Correspondence: Bo Huang,
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