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Mukherjee A, Cai Z, Mukherjee S. Editorial: Application of genomics in livestock populations under selection or conservation. Front Genet 2024; 15:1363839. [PMID: 38327831 PMCID: PMC10847554 DOI: 10.3389/fgene.2024.1363839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Affiliation(s)
| | - Zexi Cai
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
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Yang CJ, Ladejobi O, Mott R, Powell W, Mackay I. Analysis of historical selection in winter wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3005-3023. [PMID: 35864201 PMCID: PMC9482581 DOI: 10.1007/s00122-022-04163-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
KEY MESSAGE Modeling of the distribution of allele frequency over year of variety release identifies major loci involved in historical breeding of winter wheat. Winter wheat is a major crop with a rich selection history in the modern era of crop breeding. Genetic gains across economically important traits like yield have been well characterized and are the major force driving its production. Winter wheat is also an excellent model for analyzing historical genetic selection. As a proof of concept, we analyze two major collections of winter wheat varieties that were bred in Western Europe from 1916 to 2010, namely the Triticeae Genome (TG) and WAGTAIL panels, which include 333 and 403 varieties, respectively. We develop and apply a selection mapping approach, Regression of Alleles on Years (RALLY), in these panels, as well as in simulated populations. RALLY maps loci under sustained historical selection by using a simple logistic model to regress allele counts on years of variety release. To control for drift-induced allele frequency change, we develop a hybrid approach of genomic control and delta control. Within the TG panel, we identify 22 significant RALLY quantitative selection loci (QSLs) and estimate the local heritabilities for 12 traits across these QSLs. By correlating predicted marker effects with RALLY regression estimates, we show that alleles whose frequencies have increased over time are heavily biased toward conferring positive yield effect, but negative effects in flowering time, lodging, plant height and grain protein content. Altogether, our results (1) demonstrate the use of RALLY to identify selected genomic regions while controlling for drift, and (2) reveal key patterns in the historical selection in winter wheat and guide its future breeding.
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Affiliation(s)
- Chin Jian Yang
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Olufunmilayo Ladejobi
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Richard Mott
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Wayne Powell
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Ian Mackay
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK.
- IMplant Consultancy Ltd, Chelmsford, UK.
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Bohra A, Kilian B, Sivasankar S, Caccamo M, Mba C, McCouch SR, Varshney RK. Reap the crop wild relatives for breeding future crops. Trends Biotechnol 2021; 40:412-431. [PMID: 34629170 DOI: 10.1016/j.tibtech.2021.08.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023]
Abstract
Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that have boosted crop resilience and global agricultural production. Advances in breeding and genomics have accelerated the identification of valuable CWRs for use in crop improvement. The enhanced genetic diversity of breeding pools carrying optimum combinations of favorable alleles for targeted crop-growing regions is crucial to sustain genetic gain. In parallel, growing sequence information on wild genomes in combination with precise gene-editing tools provide a fast-track route to transform CWRs into ideal future crops. Data-informed germplasm collection and management strategies together with adequate policy support will be equally important to improve access to CWRs and their sustainable use to meet food and nutrition security targets.
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Affiliation(s)
- Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), 208024 Kanpur, India
| | | | - Shoba Sivasankar
- International Atomic Energy Agency (IAEA), Vienna International Centre, 1400 Vienna, Austria
| | | | - Chikelu Mba
- Food and Agriculture Organization of the United Nations (FAO), Rome 00153, Italy
| | - Susan R McCouch
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA.
| | - Rajeev K Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA 6150, Australia.
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Beche E, Gillman JD, Song Q, Nelson R, Beissinger T, Decker J, Shannon G, Scaboo AM. Genomic prediction using training population design in interspecific soybean populations. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:15. [PMID: 37309481 PMCID: PMC10236090 DOI: 10.1007/s11032-021-01203-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/11/2021] [Indexed: 06/14/2023]
Abstract
Agronomically important traits generally have complex genetic architecture, where many genes have a small and largely additive effect. Genomic prediction has been demonstrated to increase genetic gain and efficiency in plant breeding programs beyond marker-assisted selection and phenotypic selection. The objective of this study was to evaluate the impact of allelic origin, marker density, training population size, and cross-validation schemes on the accuracy of genomic prediction models in an interspecific soybean nested association mapping (NAM) panel. Three cross-validation schemes were used: (a) Within-Family (WF): training population and predictions are made exclusively within each family; (b) Across All families (AF): all the individuals from the three families were randomly assigned to either the training or validation set; (c) Leave one Family out (LFO): each family is predicted using a training set that contains the other two families. Predictive abilities increased with training population size up to 350 individuals, but no significant gains were noted beyond 250 individuals in the training population. The number of markers had a limited impact on the observed predictive ability across traits; increasing markers used in the model above 1000 revealed no significant increases in prediction accuracy. Predictive abilities for AF were not significantly different from the WF method, and predictive abilities across populations for the WF method had a range of 0.58 to 0.70 for maturity, protein, meal, and oil. Our results also showed encouraging prediction accuracies for grain yield (0.58-0.69) using the WF method. Partitioning genomic prediction between G. max and G. soja alleles revealed useful information to select material with a larger allele contribution from both parents and could accelerate allele introgression from exotic germplasm into the elite soybean gene pool. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01203-6.
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Affiliation(s)
- Eduardo Beche
- Division of Plant Science, University of Missouri, Columbia, MO USA
| | | | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD USA
| | - Randall Nelson
- Department of Crop Sciences, University of Illinois, and USDA-Agricultural Research Service (retired), 1101 W. Peabody Dr., Urbana, IL 61801 USA
| | - Tim Beissinger
- Division of Plant Breeding Methodology, Department of Crop Sciences, Georg-August-Universität, Göttingen, Germany
| | - Jared Decker
- Division of Animal Science, University of Missouri, Columbia, MO USA
| | - Grover Shannon
- Division of Plant Science, University of Missouri, Columbia, MO USA
| | - Andrew M. Scaboo
- Division of Plant Science, University of Missouri, Columbia, MO USA
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Scott MF, Ladejobi O, Amer S, Bentley AR, Biernaskie J, Boden SA, Clark M, Dell'Acqua M, Dixon LE, Filippi CV, Fradgley N, Gardner KA, Mackay IJ, O'Sullivan D, Percival-Alwyn L, Roorkiwal M, Singh RK, Thudi M, Varshney RK, Venturini L, Whan A, Cockram J, Mott R. Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding. Heredity (Edinb) 2020; 125:396-416. [PMID: 32616877 PMCID: PMC7784848 DOI: 10.1038/s41437-020-0336-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 11/21/2022] Open
Abstract
Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.
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Affiliation(s)
| | | | - Samer Amer
- University of Reading, Reading, RG6 6AH, UK
- Faculty of Agriculture, Alexandria University, Alexandria, 23714, Egypt
| | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Jay Biernaskie
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Scott A Boden
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | | | | | - Laura E Dixon
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Carla V Filippi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Nicolas Repetto y Los Reseros s/n, 1686, Hurlingham, Buenos Aires, Argentina
| | - Nick Fradgley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Keith A Gardner
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Ian J Mackay
- SRUC, West Mains Road, Kings Buildings, Edinburgh, EH9 3JG, UK
| | | | | | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rakesh Kumar Singh
- International Center for Biosaline Agriculture, Academic City, Dubai, United Arab Emirates
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev Kumar Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Alex Whan
- CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - James Cockram
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Richard Mott
- UCL Genetics Institute, Gower Street, London, WC1E 6BT, UK
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