1
|
Desbiez-Piat A, Ressayre A, Marchadier E, Noly A, Remoué C, Vitte C, Belcram H, Bourgais A, Galic N, Le Guilloux M, Tenaillon MI, Dillmann C. Pervasive G × E interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments. Genetics 2023; 225:iyad186. [PMID: 37824828 DOI: 10.1093/genetics/iyad186] [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: 07/27/2023] [Revised: 07/27/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
Quantitative genetics models have shown that long-term selection responses depend on initial variance and mutational influx. Understanding limits of selection requires quantifying the role of mutational variance. However, correlative responses to selection on nonfocal traits can perturb the selection response on the focal trait; and generations are often confounded with selection environments so that genotype by environment (G×E) interactions are ignored. The Saclay divergent selection experiments (DSEs) on maize flowering time were used to track the fate of individual mutations combining genotyping data and phenotyping data from yearly measurements (DSEYM) and common garden experiments (DSECG) with four objectives: (1) to quantify the relative contribution of standing and mutational variance to the selection response, (2) to estimate genotypic mutation effects, (3) to study the impact of G×E interactions in the selection response, and (4) to analyze how trait correlations modulate the exploration of the phenotypic space. We validated experimentally the expected enrichment of fixed beneficial mutations with an average effect of +0.278 and +0.299 days to flowering, depending on the genetic background. Fixation of unfavorable mutations reached up to 25% of incoming mutations, a genetic load possibly due to antagonistic pleiotropy, whereby mutations fixed in the selection environment (DSEYM) turned to be unfavorable in the evaluation environment (DSECG). Global patterns of trait correlations were conserved across genetic backgrounds but exhibited temporal patterns. Traits weakly or uncorrelated with flowering time triggered stochastic exploration of the phenotypic space, owing to microenvironment-specific fixation of standing variants and pleiotropic mutational input.
Collapse
Affiliation(s)
- Arnaud Desbiez-Piat
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
- Université Montpellier, INRAE, Institut Agro Montpellier, LEPSE, Montpellier 34000, France
| | - Adrienne Ressayre
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Elodie Marchadier
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Alicia Noly
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institut of Plants Sciences Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Carine Remoué
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Clémentine Vitte
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Harry Belcram
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Aurélie Bourgais
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Nathalie Galic
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Martine Le Guilloux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Maud I Tenaillon
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Christine Dillmann
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| |
Collapse
|
2
|
Choquette NE, Weldekidan T, Brewer J, Davis SB, Wisser RJ, Holland JB. Enhancing adaptation of tropical maize to temperate environments using genomic selection. G3 (BETHESDA, MD.) 2023; 13:jkad141. [PMID: 37368984 PMCID: PMC10468305 DOI: 10.1093/g3journal/jkad141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023]
Abstract
Tropical maize can be used to diversify the genetic base of temperate germplasm and help create climate-adapted cultivars. However, tropical maize is unadapted to temperate environments, in which sensitivities to long photoperiods and cooler temperatures result in severely delayed flowering times, developmental defects, and little to no yield. Overcoming this maladaptive syndrome can require a decade of phenotypic selection in a targeted, temperate environment. To accelerate the incorporation of tropical diversity in temperate breeding pools, we tested if an additional generation of genomic selection can be used in an off-season nursery where phenotypic selection is not very effective. Prediction models were trained using flowering time recorded on random individuals in separate lineages of a heterogenous population grown at two northern U.S. latitudes. Direct phenotypic selection and genomic prediction model training was performed within each target environment and lineage, followed by genomic prediction of random intermated progenies in the off-season nursery. Performance of genomic prediction models was evaluated on self-fertilized progenies of prediction candidates grown in both target locations in the following summer season. Prediction abilities ranged from 0.30 to 0.40 among populations and evaluation environments. Prediction models with varying marker effect distributions or spatial field effects had similar accuracies. Our results suggest that genomic selection in a single off-season generation could increase genetic gains for flowering time by more than 50% compared to direct selection in summer seasons only, reducing the time required to change the population mean to an acceptably adapted flowering time by about one-third to one-half.
Collapse
Affiliation(s)
- Nicole E Choquette
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Jason Brewer
- USDA-ARS Plant Science Research Unit, Raleigh, NC 27695, USA
| | - Scott B Davis
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Randall J Wisser
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environmentaux, INRAE, University of Montpellier, L’Institut Agro, Montpellier, FR 34000, USA
| | - James B Holland
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
- USDA-ARS Plant Science Research Unit, Raleigh, NC 27695, USA
| |
Collapse
|
3
|
Choquette NE, Holland JB, Weldekidan T, Drouault J, de Leon N, Flint-Garcia S, Lauter N, Murray SC, Xu W, Wisser RJ. Environment-specific selection alters flowering-time plasticity and results in pervasive pleiotropic responses in maize. THE NEW PHYTOLOGIST 2023; 238:737-749. [PMID: 36683443 DOI: 10.1111/nph.18769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Crop genetic diversity for climate adaptations is globally partitioned. We performed experimental evolution in maize to understand the response to selection and how plant germplasm can be moved across geographical zones. Initialized with a common population of tropical origin, artificial selection on flowering time was performed for two generations at eight field sites spanning 25° latitude, a 2800 km transect. We then jointly tested all selection lineages across the original sites of selection, for the target trait and 23 other traits. Modeling intergenerational shifts in a physiological reaction norm revealed separate components for flowering-time plasticity. Generalized and local modes of selection altered the plasticity of each lineage, leading to a latitudinal pattern in the responses to selection that were strongly driven by photoperiod. This transformation led to widespread changes in developmental, architectural, and yield traits, expressed collectively in an environment-dependent manner. Furthermore, selection for flowering time alone alleviated a maladaptive syndrome and improved yields for tropical maize in the temperate zone. Our findings show how phenotypic selection can rapidly shift the flowering phenology and plasticity of maize. They also demonstrate that selecting crops to local conditions can accelerate adaptation to climate change.
Collapse
Affiliation(s)
- Nicole E Choquette
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - James B Holland
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
- USDA-ARS Plant Science Research Unit, Raleigh, NC, 27695, USA
| | | | - Justine Drouault
- Laboratoire d'Ecophysiologie des Plantes sous Stress Environmentaux, INRAE, University of Montpellier, L'Institut Agro, Montpellier, 34000, France
| | - Natalia de Leon
- Deptartment of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | | | - Nick Lauter
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Seth C Murray
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Wenwei Xu
- Agricultural Research and Extension Center, Texas A&M AgriLife Research, Lubbock, TX, 79403, USA
| | - Randall J Wisser
- Deptartment of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
- Laboratoire d'Ecophysiologie des Plantes sous Stress Environmentaux, INRAE, University of Montpellier, L'Institut Agro, Montpellier, 34000, France
| |
Collapse
|
4
|
Cooper M, Messina CD. Breeding crops for drought-affected environments and improved climate resilience. THE PLANT CELL 2023; 35:162-186. [PMID: 36370076 PMCID: PMC9806606 DOI: 10.1093/plcell/koac321] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/01/2022] [Indexed: 05/12/2023]
Abstract
Breeding climate-resilient crops with improved levels of abiotic and biotic stress resistance as a response to climate change presents both opportunities and challenges. Applying the framework of the "breeder's equation," which is used to predict the response to selection for a breeding program cycle, we review methodologies and strategies that have been used to successfully breed crops with improved levels of drought resistance, where the target population of environments (TPEs) is a spatially and temporally heterogeneous mixture of drought-affected and favorable (water-sufficient) environments. Long-term improvement of temperate maize for the US corn belt is used as a case study and compared with progress for other crops and geographies. Integration of trait information across scales, from genomes to ecosystems, is needed to accurately predict yield outcomes for genotypes within the current and future TPEs. This will require transdisciplinary teams to explore, identify, and exploit novel opportunities to accelerate breeding program outcomes; both improved germplasm resources and improved products (cultivars, hybrids, clones, and populations) that outperform and replace the products in use by farmers, in combination with modified agronomic management strategies suited to their local environments.
Collapse
Affiliation(s)
| | - Carlos D Messina
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA
| |
Collapse
|
5
|
Brown KE, Koenig D. On the hidden temporal dynamics of plant adaptation. CURRENT OPINION IN PLANT BIOLOGY 2022; 70:102298. [PMID: 36126489 DOI: 10.1016/j.pbi.2022.102298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 07/28/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Adaptation to a wide range of environments is a major driver of plant diversity. It is now possible to catalog millions of potential adaptive genomic differences segregating between environments within a plant species in a single experiment. Understanding which of these changes contributes to adaptive phenotypic divergence between plant populations is a major goal of evolutionary biologists and crop breeders. In this review, we briefly highlight the approaches frequently used to understand the genetic basis of adaptive phenotypes in plants, and we discuss some of the limitations of these methods. We propose that direct observation of the process of adaptation using multigenerational studies and whole genome sequencing is a crucial missing component of recent studies of plant adaptation because it complements several shortcomings of sampling-based techniques.
Collapse
Affiliation(s)
- Keely E Brown
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| |
Collapse
|
6
|
Mostert‐O'Neill MM, Tate H, Reynolds SM, Mphahlele MM, van den Berg G, Verryn SD, Acosta JJ, Borevitz JO, Myburg AA. Genomic consequences of artificial selection during early domestication of a wood fibre crop. THE NEW PHYTOLOGIST 2022; 235:1944-1956. [PMID: 35657639 PMCID: PMC9541791 DOI: 10.1111/nph.18297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
From its origins in Australia, Eucalyptus grandis has spread to every continent, except Antarctica, as a wood crop. It has been cultivated and bred for over 100 yr in places such as South Africa. Unlike most annual crops and fruit trees, domestication of E. grandis is still in its infancy, representing a unique opportunity to interrogate the genomic consequences of artificial selection early in the domestication process. To determine how a century of artificial selection has changed the genome of E. grandis, we generated single nucleotide polymorphism genotypes for 1080 individuals from three advanced South African breeding programmes using the EUChip60K chip, and investigated population structure and genome-wide differentiation patterns relative to wild progenitors. Breeding and wild populations appeared genetically distinct. We found genomic evidence of evolutionary processes known to have occurred in other plant domesticates, including interspecific introgression and intraspecific infusion from wild material. Furthermore, we found genomic regions with increased linkage disequilibrium and genetic differentiation, putatively representing early soft sweeps of selection. This is, to our knowledge, the first study of genomic signatures of domestication in a timber species looking beyond the first few generations of cultivation. Our findings highlight the importance of intra- and interspecific hybridization during early domestication.
Collapse
Affiliation(s)
- Marja M. Mostert‐O'Neill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
| | - Hannah Tate
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
| | - S. Melissa Reynolds
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
| | - Makobatjatji M. Mphahlele
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
- Mondi Forests, Tree Improvement Technology Programme, Trahar Technology Centre – TTCMountain Home Estate, Off Dennis Shepstone Dr.Hilton3245South Africa
| | - Gert van den Berg
- Sappi Forests Research, Shaw Research CentrePO Box 473Howick3290South Africa
| | - Steve D. Verryn
- Creation Breeding Innovations75 Kafue St.Lynnwood Glen0081South Africa
| | - Juan J. Acosta
- Camcore, Department of Forestry and Environmental ResourcesNorth Carolina State UniversityPO Box 7626RaleighNC27695USA
| | - Justin O. Borevitz
- Research School of Biology and Centre for Biodiversity Analysis, ARC Centre of Excellence in Plant Energy BiologyAustralian National UniversityCanberraACT0200Australia
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPrivate Bag X20Pretoria0028South Africa
| |
Collapse
|
7
|
de Miguel M, Rodríguez-Quilón I, Heuertz M, Hurel A, Grivet D, Jaramillo-Correa JP, Vendramin GG, Plomion C, Majada J, Alía R, Eckert AJ, González-Martínez SC. Polygenic adaptation and negative selection across traits, years and environments in a long-lived plant species (Pinus pinaster Ait., Pinaceae). Mol Ecol 2022; 31:2089-2105. [PMID: 35075727 DOI: 10.1111/mec.16367] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
A decade of genetic association studies in multiple organisms suggests that most complex traits are polygenic, i.e., they have a genetic architecture determined by numerous loci each with small effect-size. Thus, determining the degree of polygenicity and its variation across traits, environments and time is crucial to understand the genetic basis of phenotypic variation. We applied multilocus approaches to estimate the degree of polygenicity of fitness-related traits in a long-lived plant (Pinus pinaster Ait., maritime pine) and to analyze this variation across environments and years. We evaluated five categories of fitness-related traits (survival, height, phenology, functional, and biotic-stress response traits) in a clonal common-garden network, planted in contrasted environments (over 12,500 trees). Most of the analyzed traits showed evidence of local adaptation based on Qst -Fst comparisons. We further observed a remarkably stable degree of polygenicity, averaging 6% (range of 0-27%), across traits, environments and years. We detected evidence of negative selection, which could explain, at least partially, the high degree of polygenicity. Because polygenic adaptation can occur rapidly, our results suggest that current predictions on the capacity of natural forest tree populations to adapt to new environments should be revised, especially in the current context of climate change.
Collapse
Affiliation(s)
- Marina de Miguel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France.,EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Isabel Rodríguez-Quilón
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | | | - Agathe Hurel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Juan-Pablo Jaramillo-Correa
- Department of Evolutionary Ecology, Institute of Ecology, Universidad Nacional Autónoma de México, AP 70-275, México City, CDMX 04510, Mexico
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, Division of Florence, National Research Council, 50019, Sesto Fiorentino (FI), Italy
| | | | - Juan Majada
- Sección Forestal, SERIDA, Finca Experimental ''La Mata'', 33820, Grado, Principado de Asturias, Spain
| | - Ricardo Alía
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | | |
Collapse
|
8
|
Abraham-Juárez MJ, Barnes AC, Aragón-Raygoza A, Tyson D, Kur A, Strable J, Rellán-Álvarez R. The arches and spandrels of maize domestication, adaptation, and improvement. CURRENT OPINION IN PLANT BIOLOGY 2021; 64:102124. [PMID: 34715472 DOI: 10.1016/j.pbi.2021.102124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
People living in the Balsas River basin in southwest México domesticated maize from the bushy grass teosinte. Nine thousand years later, in 2021, Ms. Deb Haaland - a member of the Pueblo of Laguna tribe of New Mexico - wore a dress adorned with a cornstalk when she was sworn in as the Secretary of Interior of the United States of America. This choice of garment highlights the importance of the coevolution of maize and the farmers who, through careful selection over thousands of years, domesticated maize and adapted the physiology and shoot architecture of maize to fit local environments and growth habits. Some traits such as tillering were directly selected on (arches), and others such as tassel size are the by-products (spandrels) of maize evolution. Here, we review current knowledge of the underlying cellular, developmental, physiological, and metabolic processes that were selected by farmers and breeders, which have positioned maize as a top global staple crop.
Collapse
Affiliation(s)
- María Jazmín Abraham-Juárez
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Irapuato, 36821, Mexico
| | - Allison C Barnes
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alejandro Aragón-Raygoza
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA; Unidad de Genómica Avanzada, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, Guanajuato, Mexico
| | - Destiny Tyson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Andi Kur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Josh Strable
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Rubén Rellán-Álvarez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA.
| |
Collapse
|
9
|
McGaugh SE, Lorenz AJ, Flagel LE. The utility of genomic prediction models in evolutionary genetics. Proc Biol Sci 2021; 288:20210693. [PMID: 34344180 PMCID: PMC8334854 DOI: 10.1098/rspb.2021.0693] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/15/2021] [Indexed: 12/25/2022] Open
Abstract
Variation in complex traits is the result of contributions from many loci of small effect. Based on this principle, genomic prediction methods are used to make predictions of breeding value for an individual using genome-wide molecular markers. In breeding, genomic prediction models have been used in plant and animal breeding for almost two decades to increase rates of genetic improvement and reduce the length of artificial selection experiments. However, evolutionary genomics studies have been slow to incorporate this technique to select individuals for breeding in a conservation context or to learn more about the genetic architecture of traits, the genetic value of missing individuals or microevolution of breeding values. Here, we outline the utility of genomic prediction and provide an overview of the methodology. We highlight opportunities to apply genomic prediction in evolutionary genetics of wild populations and the best practices when using these methods on field-collected phenotypes.
Collapse
Affiliation(s)
- Suzanne E. McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Lab, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Aaron J. Lorenz
- Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Lex E. Flagel
- Plant and Microbial Biology, University of Minnesota, 140 Gortner Lab, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
- Bayer Crop Science, 700 W Chesterfield Parkway, Chesterfield, MO 63017, USA
| |
Collapse
|
10
|
Voss-Fels KP, Wei X, Ross EM, Frisch M, Aitken KS, Cooper M, Hayes BJ. Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1493-1511. [PMID: 33587151 DOI: 10.1007/s00122-021-03785-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 01/27/2021] [Indexed: 05/14/2023]
Abstract
Simulations highlight the potential of genomic selection to substantially increase genetic gain for complex traits in sugarcane. The success rate depends on the trait genetic architecture and the implementation strategy. Genomic selection (GS) has the potential to increase the rate of genetic gain in sugarcane beyond the levels achieved by conventional phenotypic selection (PS). To assess different implementation strategies, we simulated two different GS-based breeding strategies and compared genetic gain and genetic variance over five breeding cycles to standard PS. GS scheme 1 followed similar routines like conventional PS but included three rapid recurrent genomic selection (RRGS) steps. GS scheme 2 also included three RRGS steps but did not include a progeny assessment stage and therefore differed more fundamentally from PS. Under an additive trait model, both simulated GS schemes achieved annual genetic gains of 2.6-2.7% which were 1.9 times higher compared to standard phenotypic selection (1.4%). For a complex non-additive trait model, the expected annual rates of genetic gain were lower for all breeding schemes; however, the rates for the GS schemes (1.5-1.6%) were still greater than PS (1.1%). Investigating cost-benefit ratios with regard to numbers of genotyped clones showed that substantial benefits could be achieved when only 1500 clones were genotyped per 10-year breeding cycle for the additive genetic model. Our results show that under a complex non-additive genetic model, the success rate of GS depends on the implementation strategy, the number of genotyped clones and the stage of the breeding program, likely reflecting how changes in QTL allele frequencies change additive genetic variance and therefore the efficiency of selection. These results are encouraging and motivate further work to facilitate the adoption of GS in sugarcane breeding.
Collapse
Affiliation(s)
- Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Xianming Wei
- Sugar Research Australia, Mackay, QLD, 4741, Australia
| | - Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, Giessen, Germany
| | - Karen S Aitken
- Agriculture and Food, CSIRO, QBP, St. Lucia, QLD, 4067, Australia
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| |
Collapse
|
11
|
Reneau JW, Khangura RS, Stager A, Erndwein L, Weldekidan T, Cook DD, Dilkes BP, Sparks EE. Maize brace roots provide stalk anchorage. PLANT DIRECT 2020; 4:e00284. [PMID: 33204937 PMCID: PMC7649601 DOI: 10.1002/pld3.284] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/19/2020] [Accepted: 10/08/2020] [Indexed: 05/16/2023]
Abstract
Mechanical failure, known as lodging, negatively impacts yield and grain quality in crops. Limiting crop loss from lodging requires an understanding of the plant traits that contribute to lodging-resistance. In maize, specialized aerial brace roots are reported to reduce root lodging. However, their direct contribution to plant biomechanics has not been measured. In this manuscript, we use a non-destructive field-based mechanical test on plants before and after the removal of brace roots. This precisely determines the contribution of brace roots to establish a rigid base (i.e. stalk anchorage) that limits plant deflection in maize. These measurements demonstrate that the more brace root whorls that contact the soil, the greater their overall contribution to anchorage, but that the contributions of each whorl to anchorage were not equal. Previous studies demonstrated that the number of nodes that produce brace roots is correlated with flowering time in maize. To determine if flowering time selection alters the brace root contribution to anchorage, a subset of the Hallauer's Tusón tropical population was analyzed. Despite significant variation in flowering time and anchorage, selection neither altered the number of brace root whorls in the soil nor the overall contribution of brace roots to anchorage. These results demonstrate that brace roots provide a rigid base in maize and that the contribution of brace roots to anchorage was not linearly related to flowering time.
Collapse
Affiliation(s)
- Jonathan W. Reneau
- Department of Plant and Soil Sciences and the Delaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
| | | | - Adam Stager
- Department of Plant and Soil Sciences and the Delaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
| | - Lindsay Erndwein
- Department of Plant and Soil Sciences and the Delaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
| | - Teclemariam Weldekidan
- Department of Plant and Soil Sciences and the Delaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
| | - Douglas D. Cook
- Department of Mechanical EngineeringBrigham Young UniversityProvoUTUSA
| | - Brian P. Dilkes
- Department of BiochemistryPurdue UniversityWest LafayetteINUSA
| | - Erin E. Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
| |
Collapse
|
12
|
Genomic insight into the developmental history of southern highbush blueberry populations. Heredity (Edinb) 2020; 126:194-205. [PMID: 32873965 DOI: 10.1038/s41437-020-00362-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/16/2020] [Accepted: 08/18/2020] [Indexed: 11/08/2022] Open
Abstract
Interspecific hybridization is a common breeding approach for introducing novel traits and genetic diversity to breeding populations. Southern highbush blueberry (SHB) is a blueberry cultivar group that has been intensively bred over the last 60 years. Specifically, it was developed by multiple interspecific crosses between northern highbush blueberry [NHB, Vaccinium corymbosum L. (2n = 4x = 48)] and low-chill Vaccinium species to expand the geographic limits of highbush blueberry production. In this study, we genotyped polyploid blueberries, including 105 SHB, 17 NHB, and 10 rabbiteye blueberry (RE) (Vaccinium virgatum Aiton), from the accessions planted at Poplarville, Mississippi, and accessions distributed in Japan, based on the double-digest restriction site-associated DNA sequencing. The genome-wide SNP data clearly indicated that RE cultivars were genetically distinct from SHB and NHB cultivars, whereas NHB and SHB were genetically indistinguishable. The population structure results appeared to reflect the differences in the allele selection strategies that breeders used for developing germplasm adapted to local climates. The genotype data implied that there are no or very few genomic segments that were commonly introgressed from low-chill Vaccinium species to the SHB genome. Principal component analysis-based outlier detection analysis found a few loci associated with a variable that could partially differentiate NHB and SHB. These SNP loci were detected in Mb-scale haplotype blocks and may be close to the functional genes related to SHB development. Collectively, the data generated in this study suggest a polygenic adaptation of SHB to the southern climate, and may be relevant for future population-scale genome-wide analyses of blueberry.
Collapse
|