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Yang S, Chen J, Fu J, Huang J, Li T, Yao Z, Ye X. Disease-Associated Streptococcus pneumoniae Genetic Variation. Emerg Infect Dis 2024; 30:39-49. [PMID: 38146979 PMCID: PMC10756394 DOI: 10.3201/eid3001.221927] [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] [Indexed: 12/27/2023] Open
Abstract
Streptococcus pneumoniae is an opportunistic pathogen that causes substantial illness and death among children worldwide. The genetic backgrounds of pneumococci that cause infection versus asymptomatic carriage vary substantially. To determine the evolutionary mechanisms of opportunistic pathogenicity, we conducted a genomic surveillance study in China. We collected 783 S. pneumoniae isolates from infected and asymptomatic children. By using a 2-stage genomewide association study process, we compared genomic differences between infection and carriage isolates to address genomic variation associated with pathogenicity. We identified 8 consensus k-mers associated with adherence, antimicrobial resistance, and immune modulation, which were unevenly distributed in the infection isolates. Classification accuracy of the best k-mer predictor for S. pneumoniae infection was good, giving a simple target for predicting pathogenic isolates. Our findings suggest that S. pneumoniae pathogenicity is complex and multifactorial, and we provide genetic evidence for precise targeted interventions.
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Dutta A, McDonald BA, Croll D. Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen. PLoS Pathog 2023; 19:e1011801. [PMID: 37972199 PMCID: PMC10688896 DOI: 10.1371/journal.ppat.1011801] [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: 05/10/2023] [Revised: 11/30/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Microbial pathogens often harbor substantial functional diversity driven by structural genetic variation. Rapid adaptation from such standing variation threatens global food security and human health. Genome-wide association studies (GWAS) provide a powerful approach to identify genetic variants underlying recent pathogen adaptation. However, the reliance on single reference genomes and single nucleotide polymorphisms (SNPs) obscures the true extent of adaptive genetic variation. Here, we show quantitatively how a combination of multiple reference genomes and reference-free approaches captures substantially more relevant genetic variation compared to single reference mapping. We performed reference-genome based association mapping across 19 reference-quality genomes covering the diversity of the species. We contrasted the results with a reference-free (i.e., k-mer) approach using raw whole-genome sequencing data in a panel of 145 strains collected across the global distribution range of the fungal wheat pathogen Zymoseptoria tritici. We mapped the genetic architecture of 49 life history traits including virulence, reproduction and growth in multiple stressful environments. The inclusion of additional reference genome SNP datasets provides a nearly linear increase in additional loci mapped through GWAS. Variants detected through the k-mer approach explained a higher proportion of phenotypic variation than a reference genome-based approach and revealed functionally confirmed loci that classic GWAS approaches failed to map. The power of GWAS in microbial pathogens can be significantly enhanced by comprehensively capturing structural genetic variation. Our approach is generalizable to a large number of species and will uncover novel mechanisms driving rapid adaptation of pathogens.
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Affiliation(s)
- Anik Dutta
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Bruce A. McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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Kaur H, Sharma P, Kumar J, Singh VK, Vasistha NK, Gahlaut V, Tyagi V, Verma SK, Singh S, Dhaliwal HS, Sheikh I. Genetic analysis of iron, zinc and grain yield in wheat-Aegilops derivatives using multi-locus GWAS. Mol Biol Rep 2023; 50:9191-9202. [PMID: 37776411 DOI: 10.1007/s11033-023-08800-y] [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: 04/20/2023] [Accepted: 09/05/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Wheat is a major staple crop and helps to reduce worldwide micronutrient deficiency. Investigating the genetics that control the concentrations of iron (Fe) and zinc (Zn) in wheat is crucial. Hence, we undertook a comprehensive study aimed at elucidating the genomic regions linked to the contents of Fe and Zn in the grain. METHODS AND RESULTS We performed the multi-locus genome-wide association (ML-GWAS) using a panel of 161 wheat-Aegilops substitution and addition lines to dissect the genomic regions controlling grain iron (GFeC), and grain zinc (GZnC) contents. The wheat panel was genotyped using 10,825 high-quality SNPs and phenotyped in three different environments (E1-E3) during 2017-2019. A total of 111 marker-trait associations (MTAs) (at p-value < 0.001) were detected that belong to all three sub-genomes of wheat. The highest number of MTAs were identified for GFeC (58), followed by GZnC (44) and yield (9). Further, six stable MTAs were identified for these three traits and also two pleiotropic MTAs were identified for GFeC and GZnC. A total of 1291 putative candidate genes (CGs) were also identified for all three traits. These CGs encode a diverse set of proteins, including heavy metal-associated (HMA), bZIP family protein, AP2/ERF, and protein previously associated with GFeC, GZnC, and grain yield. CONCLUSIONS The significant MTAs and CGs pinpointed in this current study are poised to play a pivotal role in enhancing both the nutritional quality and yield of wheat, utilizing marker-assisted selection (MAS) techniques.
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Affiliation(s)
- Harneet Kaur
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
| | - Prachi Sharma
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali, Punjab, 140306, India
| | - Vikas Kumar Singh
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P., 250004, India
| | - Neeraj Kumar Vasistha
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
- Department of Genetics and Plant Breeding, Rajiv Gandhi University, Itanagar, India
| | - Vijay Gahlaut
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India.
- University Center for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India.
| | - Vikrant Tyagi
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
| | | | - Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Mexico
- USDA-ARS, Southeast Area, Subtropical Horticulture Research Station, 13601 Old Cutler Road, Miami, FL, 33158, USA
| | - H S Dhaliwal
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
| | - Imran Sheikh
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India.
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Li S, Kong L, Xiao X, Li P, Liu A, Li J, Gong J, Gong W, Ge Q, Shang H, Pan J, Chen H, Peng Y, Zhang Y, Lu Q, Shi Y, Yuan Y. Genome-wide artificial introgressions of Gossypium barbadense into G. hirsutum reveal superior loci for simultaneous improvement of cotton fiber quality and yield traits. J Adv Res 2023; 53:1-16. [PMID: 36460274 PMCID: PMC10658236 DOI: 10.1016/j.jare.2022.11.009] [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: 04/18/2022] [Revised: 10/31/2022] [Accepted: 11/24/2022] [Indexed: 12/02/2022] Open
Abstract
INTRODUCTION The simultaneous improvement of fiber quality and yield for cotton is strongly limited by the narrow genetic backgrounds of Gossypium hirsutum (Gh) and the negative genetic correlations among traits. An effective way to overcome the bottlenecks is to introgress the favorable alleles of Gossypium barbadense (Gb) for fiber quality into Gh with high yield. OBJECTIVES This study was to identify superior loci for the improvement of fiber quality and yield. METHODS Two sets of chromosome segment substitution lines (CSSLs) were generated by crossing Hai1 (Gb, donor-parent) with cultivar CCRI36 (Gh) and CCRI45 (Gh) as genetic backgrounds, and cultivated in 6 and 8 environments, respectively. The kmer genotyping strategy was improved and applied to the population genetic analysis of 743 genomic sequencing data. A progeny segregating population was constructed to validate genetic effects of the candidate loci. RESULTS A total of 68,912 and 83,352 genome-wide introgressed kmers were identified in the CCRI36 and CCRI45 populations, respectively. Over 90 % introgressions were homologous exchanges and about 21 % were reverse insertions. In total, 291 major introgressed segments were identified with stable genetic effects, of which 66(22.98 %), 64(21.99 %), 35(12.03 %), 31(10.65 %) and 18(6.19 %) were beneficial for the improvement of fiber length (FL), strength (FS), micronaire, lint-percentage (LP) and boll-weight, respectively. Thirty-nine introgression segments were detected with stable favorable additive effects for simultaneous improvement of 2 or more traits in Gh genetic background, including 6 could increase FL/FS and LP. The pyramiding effects of 3 pleiotropic segments (A07:C45Clu-081, D06:C45Clu-218, D02:C45Clu-193) were further validated in the segregating population. CONCLUSION The combining of genome-wide introgressions and kmer genotyping strategy showed significant advantages in exploring genetic resources. Through the genome-wide comprehensive mining, a total of 11 clusters (segments) were discovered for the stable simultaneous improvement of FL/FS and LP, which should be paid more attention in the future.
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Affiliation(s)
- Shaoqi Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Linglei Kong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xianghui Xiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Pengtao Li
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jingtao Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hong Chen
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, China
| | - Yan Peng
- Third Division of the Xinjiang Production and Construction Corps Agricultural Research Institute, Tumushuke 843900, China
| | - Yuanming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Quanwei Lu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China.
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Karikari B, Lemay MA, Belzile F. k-mer-Based Genome-Wide Association Studies in Plants: Advances, Challenges, and Perspectives. Genes (Basel) 2023; 14:1439. [PMID: 37510343 PMCID: PMC10379394 DOI: 10.3390/genes14071439] [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: 06/13/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Genome-wide association studies (GWAS) have allowed the discovery of marker-trait associations in crops over recent decades. However, their power is hampered by a number of limitations, with the key one among them being an overreliance on single-nucleotide polymorphisms (SNPs) as molecular markers. Indeed, SNPs represent only one type of genetic variation and are usually derived from alignment to a single genome assembly that may be poorly representative of the population under study. To overcome this, k-mer-based GWAS approaches have recently been developed. k-mer-based GWAS provide a universal way to assess variation due to SNPs, insertions/deletions, and structural variations without having to specifically detect and genotype these variants. In addition, k-mer-based analyses can be used in species that lack a reference genome. However, the use of k-mers for GWAS presents challenges such as data size and complexity, lack of standard tools, and potential detection of false associations. Nevertheless, efforts are being made to overcome these challenges and a general analysis workflow has started to emerge. We identify the priorities for k-mer-based GWAS in years to come, notably in the development of user-friendly programs for their analysis and approaches for linking significant k-mers to sequence variation.
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Affiliation(s)
- Benjamin Karikari
- Département de Phytologie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale P.O. Box TL 1882, Ghana
| | - Marc-André Lemay
- Département de Phytologie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada
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Vallarino JG, Jun H, Wang S, Wang X, Sade N, Orf I, Zhang D, Shi J, Shen S, Cuadros-Inostroza Á, Xu Q, Luo J, Fernie AR, Brotman Y. Limitations and advantages of using metabolite-based genome-wide association studies: focus on fruit quality traits. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 333:111748. [PMID: 37230189 DOI: 10.1016/j.plantsci.2023.111748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 05/27/2023]
Abstract
In the last decades, linkage mapping has help in the location of metabolite quantitative trait loci (QTL) in many species; however, this approach shows some limitations. Recently, thanks to the most recent advanced in high-throughput genotyping technologies like next-generation sequencing, metabolite genome-wide association study (mGWAS) has been proposed a powerful tool to identify the genetic variants in polygenic agrinomic traits. Fruit flavor is a complex interaction of aroma volatiles and taste being sugar and acid ratio key parameter for flavor acceptance. Here, we review recent progress of mGWAS in pinpoint gene polymorphisms related to flavor-related metabolites in fruits. Despite clear successes in discovering novel genes or regions associated with metabolite accumulation affecting sensory attributes in fruits, GWAS incurs in several limitations summarized in this review. In addition, in our own work, we performed mGWAS on 194 Citrus grandis accessions to investigate the genetic control of individual primary and lipid metabolites in ripe fruit. We have identified a total of 667 associations for 14 primary metabolites including amino acids, sugars, and organic acids, and 768 associations corresponding to 47 lipids. Furthermore, candidate genes related to important metabolites related to fruit quality such as sugars, organic acids and lipids were discovered.
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Affiliation(s)
- José G Vallarino
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Campus de Teatinos, 29071 Málaga, Spain
| | - Hong Jun
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | | | - Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Isabel Orf
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Dabing Zhang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Jianxin Shi
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | | | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Alisdair R Fernie
- Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Mühlenberg, Golm, Potsdam 14476, Germany; Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria.
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel.
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Leonard AS, Crysnanto D, Fang ZH, Heaton MP, Vander Ley BL, Herrera C, Bollwein H, Bickhart DM, Kuhn KL, Smith TPL, Rosen BD, Pausch H. Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies. Nat Commun 2022; 13:3012. [PMID: 35641504 PMCID: PMC9156671 DOI: 10.1038/s41467-022-30680-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 05/10/2022] [Indexed: 12/12/2022] Open
Abstract
Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.
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Affiliation(s)
- Alexander S Leonard
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
| | - Danang Crysnanto
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Zih-Hua Fang
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Michael P Heaton
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Carolina Herrera
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057, Zurich, Switzerland
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057, Zurich, Switzerland
| | - Derek M Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA
| | - Kristen L Kuhn
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD, 20705, USA.
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
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Shen Y, Zhou G, Liang C, Tian Z. Omics-based interdisciplinarity is accelerating plant breeding. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102167. [PMID: 35016139 DOI: 10.1016/j.pbi.2021.102167] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/08/2021] [Accepted: 12/07/2021] [Indexed: 05/09/2023]
Abstract
Plant breeding is one of the oldest and most important activities accompanying human civilization. During the past thousand years, plant breeding has achieved three significant innovations, each of which derives from introgression of new theories or technologies. These innovations have significantly increased the food supply and allowed for population development. However, with population increases and resource shortages, the world is continuously facing the challenge of food security, which calls for next innovation in plant breeding. Recent technological advances in multiple disciplines have boosted the development of omics, which is accelerating plant breeding. Here, we review the recent advances in omics and discuss our understanding of how interdisciplinary researches will prompt new innovations in plant breeding.
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Affiliation(s)
- Yanting Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Guoan Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Gupta PK. GWAS for genetics of complex quantitative traits: Genome to pangenome and SNPs to SVs and k-mers. Bioessays 2021; 43:e2100109. [PMID: 34486143 DOI: 10.1002/bies.202100109] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 12/22/2022]
Abstract
The development of improved methods for genome-wide association studies (GWAS) for genetics of quantitative traits has been an active area of research during the last 25 years. This activity initially started with the use of mixed linear model (MLM), which was variously modified. During the last decade, however, with the availability of high throughput next generation sequencing (NGS) technology, development and use of pangenomes and novel markers including structural variations (SVs) and k-mers for GWAS has taken over as a new thrust area of research. Pangenomes and SVs are now available in humans, livestock, and a number of plant species, so that these resources along with k-mers are being used in GWAS for exploring additional genetic variation that was hitherto not available for analysis. These developments have resulted in significant improvement in GWAS methodology for detection of marker-trait associations (MTAs) that are relevant to human healthcare and crop improvement.
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Affiliation(s)
- Pushpendra K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University Meerut, Meerut, Uttar Pradesh, India
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