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Joly-Lopez Z, Flowers JM, Purugganan MD. Developing maps of fitness consequences for plant genomes. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:101-7. [PMID: 26950251 DOI: 10.1016/j.pbi.2016.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/02/2016] [Accepted: 02/17/2016] [Indexed: 05/22/2023]
Abstract
Predicting the fitness consequences of mutations, and their concomitant impacts on molecular and cellular function as well as organismal phenotypes, is an important challenge in biology that has new relevance in an era when genomic data is readily available. The ability to construct genomewide maps of fitness consequences in plant genomes is a recent development that has profound implications for our ability to predict the fitness effects of mutations and discover functional elements. Here we highlight approaches to building fitness consequence maps to infer regions under selection. We emphasize computational methods applied primarily to the study of human disease that translate physical maps of within-species genome variation into maps of fitness effects of individual natural mutations. Maps of fitness consequences in plants, combined with traditional genetic approaches, could accelerate discovery of functional elements such as regulatory sequences in non-coding DNA and genetic polymorphisms associated with key traits, including agronomically-important traits such as yield and environmental stress responses.
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Affiliation(s)
- Zoé Joly-Lopez
- Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place, New York University, New York, NY 10003, United States
| | - Jonathan M Flowers
- Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place, New York University, New York, NY 10003, United States; Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, NYU Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place, New York University, New York, NY 10003, United States; Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, NYU Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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Martinez AK, Soriano JM, Tuberosa R, Koumproglou R, Jahrmann T, Salvi S. Yield QTLome distribution correlates with gene density in maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:300-309. [PMID: 26566847 DOI: 10.1016/j.plantsci.2015.09.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 05/09/2023]
Abstract
The genetic control of yield and related traits in maize has been addressed by many quantitative trait locus (QTL) studies, which have produced a wealth of QTL information, also known as QTLome. In this study, we assembled a yield QTLome database and carried out QTL meta-analysis based on 44 published studies, representing 32 independent mapping populations and 49 parental lines. A total of 808 unique QTLs were condensed to 84 meta-QTLs and were projected on the 10 maize chromosomes. Seventy-four percent of QTLs showed a proportion of phenotypic variance explained (PVE) smaller than 10% confirming the high genetic complexity of grain yield. Yield QTLome projection on the genetic map suggested pericentromeric enrichment of QTLs. Conversely, pericentromeric depletion of QTLs was observed when the physical map was considered, suggesting gene density as the main driver of yield QTL distribution on chromosomes. Dominant and overdominant yield QTLs did not distribute differently from additive effect QTLs.
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Affiliation(s)
- Ana Karine Martinez
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Jose Miguel Soriano
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy; Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | | | | | - Silvio Salvi
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
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Gaut BS, Díez CM, Morrell PL. Genomics and the Contrasting Dynamics of Annual and Perennial Domestication. Trends Genet 2015; 31:709-719. [PMID: 26603610 DOI: 10.1016/j.tig.2015.10.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/08/2015] [Accepted: 10/15/2015] [Indexed: 12/20/2022]
Abstract
Plant domestication modifies a wild species genetically for human use. Among thousands of domesticated plants, a major distinction is the difference between annual and perennial life cycles. The domestication of perennials is expected to follow different processes than annuals, with distinct genetic outcomes. Here we examine domestication from a population genetics perspective, with a focus on three issues: genetic bottlenecks during domestication, introgression as a source of local adaptation, and genetic load. These three issues have been studied nominally in major annual crops but even less extensively in perennials. Here we highlight lessons from annual plants, motivations to study these issues in perennial plants, and new approaches that may lead to further progress.
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Affiliation(s)
- Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA.
| | - Concepción M Díez
- Departamento de Agronomía, Universidad de Córdoba - Campus de Excelencia Internacional Agroalimentario ceiA3, Edificio C4, Campus de Rabanales, 14014 Córdoba, Spain
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
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The Genomic Impacts of Drift and Selection for Hybrid Performance in Maize. Genetics 2015; 201:1201-11. [PMID: 26385980 DOI: 10.1534/genetics.115.182410] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 09/11/2015] [Indexed: 12/29/2022] Open
Abstract
Although maize is naturally an outcrossing organism, modern breeding utilizes highly inbred lines in controlled crosses to produce hybrids. The U.S. Department of Agriculture's reciprocal recurrent selection experiment between the Iowa Stiff Stalk Synthetic (BSSS) and the Iowa Corn Borer Synthetic No. 1 (BSCB1) populations represents one of the longest running experiments to understand the response to selection for hybrid performance. To investigate the genomic impact of this selection program, we genotyped the progenitor lines and >600 individuals across multiple cycles of selection using a genome-wide panel of ∼40,000 SNPs. We confirmed previous results showing a steady temporal decrease in genetic diversity within populations and a corresponding increase in differentiation between populations. Thanks to detailed historical information on experimental design, we were able to perform extensive simulations using founder haplotypes to replicate the experiment in the absence of selection. These simulations demonstrate that while most of the observed reduction in genetic diversity can be attributed to genetic drift, heterozygosity in each population has fallen more than expected. We then took advantage of our high-density genotype data to identify extensive regions of haplotype fixation and trace haplotype ancestry to single founder inbred lines. The vast majority of regions showing such evidence of selection differ between the two populations, providing evidence for the dominance model of heterosis. We discuss how this pattern is likely to occur during selection for hybrid performance and how it poses challenges for dissecting the impacts of modern breeding and selection on the maize genome.
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Renaut S, Rieseberg LH. The Accumulation of Deleterious Mutations as a Consequence of Domestication and Improvement in Sunflowers and Other Compositae Crops. Mol Biol Evol 2015; 32:2273-83. [PMID: 25939650 DOI: 10.1093/molbev/msv106] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism data. Although we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased toward nonsynonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome. Finally, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. Although the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.
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Affiliation(s)
- Sebastien Renaut
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Loren H Rieseberg
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada Department of Biology, Indiana University - Bloomington
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Rodgers-Melnick E, Bradbury PJ, Elshire RJ, Glaubitz JC, Acharya CB, Mitchell SE, Li C, Li Y, Buckler ES. Recombination in diverse maize is stable, predictable, and associated with genetic load. Proc Natl Acad Sci U S A 2015; 112:3823-8. [PMID: 25775595 PMCID: PMC4378432 DOI: 10.1073/pnas.1413864112] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Among the fundamental evolutionary forces, recombination arguably has the largest impact on the practical work of plant breeders. Varying over 1,000-fold across the maize genome, the local meiotic recombination rate limits the resolving power of quantitative trait mapping and the precision of favorable allele introgression. The consequences of low recombination also theoretically extend to the species-wide scale by decreasing the power of selection relative to genetic drift, and thereby hindering the purging of deleterious mutations. In this study, we used genotyping-by-sequencing (GBS) to identify 136,000 recombination breakpoints at high resolution within US and Chinese maize nested association mapping populations. We find that the pattern of cross-overs is highly predictable on the broad scale, following the distribution of gene density and CpG methylation. Several large inversions also suppress recombination in distinct regions of several families. We also identify recombination hotspots ranging in size from 1 kb to 30 kb. We find these hotspots to be historically stable and, compared with similar regions with low recombination, to have strongly differentiated patterns of DNA methylation and GC content. We also provide evidence for the historical action of GC-biased gene conversion in recombination hotspots. Finally, using genomic evolutionary rate profiling (GERP) to identify putative deleterious polymorphisms, we find evidence for reduced genetic load in hotspot regions, a phenomenon that may have considerable practical importance for breeding programs worldwide.
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Affiliation(s)
| | - Peter J Bradbury
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; US Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853; and
| | - Robert J Elshire
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | | | | | - Sharon E Mitchell
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | - Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853; US Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853; and
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