1
|
Zhai J, Gokaslan A, Schiff Y, Berthel A, Liu ZY, Miller ZR, Scheben A, Stitzer MC, Romay MC, Buckler ES, Kuleshov V. Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.596709. [PMID: 38895432 PMCID: PMC11185591 DOI: 10.1101/2024.06.04.596709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Understanding the function and fitness effects of diverse plant genomes requires transferable models. Language models (LMs) pre-trained on large-scale biological sequences can learn evolutionary conservation, thus expected to offer better cross-species prediction through fine-tuning on limited labeled data compared to supervised deep learning models. We introduce PlantCaduceus, a plant DNA LM based on the Caduceus and Mamba architectures, pre-trained on a carefully curated dataset consisting of 16 diverse Angiosperm genomes. Fine-tuning PlantCaduceus on limited labeled Arabidopsis data for four tasks involving transcription and translation modeling demonstrated high transferability to maize that diverged 160 million years ago, outperforming the best baseline model by 1.45-fold to 7.23-fold. PlantCaduceus also enables genome-wide deleterious mutation identification without multiple sequence alignment (MSA). PlantCaduceus demonstrated a threefold enrichment of rare alleles in prioritized deleterious mutations compared to MSA-based methods and matched state-of-the-art protein LMs. PlantCaduceus is a versatile pre-trained DNA LM expected to accelerate plant genomics and crop breeding applications.
Collapse
Affiliation(s)
- Jingjing Zhai
- Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853
| | - Aaron Gokaslan
- Department of Computer Science, Cornell University, Ithaca, NY, USA 14853
| | - Yair Schiff
- Department of Computer Science, Cornell University, Ithaca, NY, USA 14853
| | - Ana Berthel
- Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853
| | - Zong-Yan Liu
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY USA 14853
| | - Zachary R. Miller
- Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY USA 11724
| | | | - M. Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY USA 14853
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY USA 14853
- USDA-ARS; Ithaca, NY, USA 14853
| | - Volodymyr Kuleshov
- Department of Computer Science, Cornell University, Ithaca, NY, USA 14853
| |
Collapse
|
2
|
Fu YB. Patterns of the Predicted Mutation Burden in 19,778 Domesticated Barley Accessions Conserved Ex Situ. Int J Mol Sci 2024; 25:5930. [PMID: 38892116 PMCID: PMC11172543 DOI: 10.3390/ijms25115930] [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: 04/02/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
Long-term conservation of more than 7 million plant germplasm accessions in 1750 genebanks worldwide is a challenging mission. The extent of deleterious mutations present in conserved germplasm and the genetic risk associated with accumulative mutations are largely unknown. This study took advantage of published barley genomic data to predict sample-wise mutation burdens for 19,778 domesticated barley (Hordeum vulgare L.) accessions conserved ex situ. It was found that the conserved germplasm harbored 407 deleterious mutations and 337 (or 82%) identified deleterious alleles were present in 20 (or 0.1%) or fewer barley accessions. Analysis of the predicted mutation burdens revealed significant differences in mutation burden for several groups of barley germplasm (landrace > cultivar (or higher burden estimate in landrace than in cultivar); winter barley > spring barley; six-rowed barley > two-rowed barley; and 1000-accession core collection > non-core germplasm). Significant differences in burden estimate were also found among seven major geographical regions. The sample-wise predicted mutation burdens were positively correlated with the estimates of sample average pairwise genetic difference. These findings are significant for barley germplasm management and utilization and for a better understanding of the genetic risk in conserved plant germplasm.
Collapse
Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| |
Collapse
|
3
|
Fu YB, Peterson GW, Horbach C. Deleterious and Adaptive Mutations in Plant Germplasm Conserved Ex Situ. Mol Biol Evol 2023; 40:msad238. [PMID: 37931158 PMCID: PMC10724023 DOI: 10.1093/molbev/msad238] [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: 08/23/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023] Open
Abstract
Conserving more than 7 million plant germplasm accessions in 1,750 genebanks worldwide raises the hope of securing the food supply for humanity for future generations. However, there is a genetic cost for such long-term germplasm conservation, which has been largely unaccounted for before. We investigated the extent and variation of deleterious and adaptive mutations in 490 individual plants representing barley, wheat, oat, soybean, maize, rapa, and sunflower collections in a seed genebank using RNA-Seq technology. These collections were found to have a range of deleterious mutations detected from 125 (maize) to 83,695 (oat) with a mean of 13,537 and of the averaged sample-wise mutation burden per deleterious locus from 0.069 to 0.357 with a mean of 0.200. Soybean and sunflower collections showed that accessions acquired earlier had increased mutation burdens. The germplasm with more years of storage in several collections carried more deleterious and fewer adaptive mutations. The samples with more cycles of germplasm regeneration revealed fewer deleterious and more adaptive mutations. These findings are significant for understanding mutational dynamics and genetic cost in conserved germplasm and have implications for long-term germplasm management and conservation.
Collapse
Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, Canada
| | - Gregory W Peterson
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, Canada
| | - Carolee Horbach
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK S7N 0X2, Canada
| |
Collapse
|
4
|
Kumar M, Conroy G, Ogbourne S, Cairns K, Borburgh L, Subramanian S. Genomic signatures of bottleneck and founder effects in dingoes. Ecol Evol 2023; 13:e10525. [PMID: 37732287 PMCID: PMC10508967 DOI: 10.1002/ece3.10525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/29/2023] [Accepted: 08/30/2023] [Indexed: 09/22/2023] Open
Abstract
Dingoes arrived in Australia during the mid-Holocene and are the top-order terrestrial predator on the continent. Although dingoes subsequently spread across the continent, the initial founding population(s) could have been small. We investigated this hypothesis by sequencing the whole genomes of three dingoes and also obtaining the genome data from nine additional dingoes and 56 canines, including wolves, village dogs and breed dogs, and examined the signatures of bottlenecks and founder effects. We found that the nucleotide diversity of dingoes was low, 36% less than highly inbred breed dogs and 3.3 times lower than wolves. The number of runs of homozygosity (RoH) segments in dingoes was 1.6-4.7 times higher than in other canines. While examining deleterious mutational load, we observed that dingoes carried elevated ratios of nonsynonymous-to-synonymous diversities, significantly higher numbers of homozygous deleterious Single Nucleotide Variants (SNVs), and increased numbers of loss of function SNVs, compared to breed dogs, village dogs, and wolves. Our findings can be explained by bottlenecks and founder effects during the establishment of dingoes in mainland Australia. These findings highlight the need for conservation-based management of dingoes and the need for wildlife managers to be cognisant of these findings when considering the use of lethal control measures across the landscape.
Collapse
Affiliation(s)
- Manoharan Kumar
- School of Science, Technology, and EngineeringThe University of the Sunshine CoastMoreton BayQueenslandAustralia
| | - Gabriel Conroy
- Centre for BioinnovationThe University of the Sunshine CoastSippy DownsQueenslandAustralia
- School of Science, Technology, and EngineeringThe University of the Sunshine CoastSippy DownsQueenslandAustralia
| | - Steven Ogbourne
- Centre for BioinnovationThe University of the Sunshine CoastSippy DownsQueenslandAustralia
| | - Kylie Cairns
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental SciencesUNSW AustraliaSydneyNew South WalesAustralia
- Centre for Ecosystem Science, School of Biological, Earth and Environmental SciencesUNSW AustraliaSydneyNew South WalesAustralia
| | - Liesbeth Borburgh
- School of Science, Technology, and EngineeringThe University of the Sunshine CoastSippy DownsQueenslandAustralia
| | - Sankar Subramanian
- School of Science, Technology, and EngineeringThe University of the Sunshine CoastMoreton BayQueenslandAustralia
- Centre for BioinnovationThe University of the Sunshine CoastSippy DownsQueenslandAustralia
| |
Collapse
|
5
|
Dwivedi SL, Heslop-Harrison P, Spillane C, McKeown PC, Edwards D, Goldman I, Ortiz R. Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools. TRENDS IN PLANT SCIENCE 2023; 28:685-697. [PMID: 36764870 DOI: 10.1016/j.tplants.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 12/03/2022] [Accepted: 01/18/2023] [Indexed: 05/13/2023]
Abstract
Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex traits. The difficulty of distinguishing favorable from unfavorable variants reduces the power of selection, while favorable trait variation and heterosis may be attributable to deleterious alleles. Here, we review the roles of deleterious mutations in crop breeding and discuss how they can be used as a new avenue for crop improvement with emerging genomic tools, including HapMaps and pangenome analysis, aiding the identification, removal, or exploitation of deleterious mutations.
Collapse
Affiliation(s)
| | - Pat Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Irwin Goldman
- Department of Horticulture, College of Agricultural and Life Sciences, University of Wisconsin Madison, WI 53706, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, SE 23053, Sweden.
| |
Collapse
|
6
|
Ramasamy U, Elizur A, Subramanian S. Deleterious mutation load in the admixed mice population. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1084502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Deleterious mutation loads are known to correlate negatively with effective population size (Ne). Due to this reason, previous studies observed a higher proportion of harmful mutations in small populations than that in large populations. However, the mutational load in an admixed population that derived from introgression between individuals from two populations with vastly different Ne is not known. We investigated this using the whole genome data from two subspecies of the mouse (Mus musculus castaneus and Mus musculus musculus) with significantly different Ne. We used the ratio of diversities at nonsynonymous and synonymous sites (dN/dS) to measure the harmful mutation load. Our results showed that this ratio observed for the admixed population was intermediate between those of the parental populations. The dN/dS ratio of the hybrid population was significantly higher than that of M. m. castaneus but lower than that of M. m. musculus. Our analysis revealed a significant positive correlation between the proportion of M. m. musculus ancestry in admixed individuals and their dN/dS ratio. This suggests that the admixed individuals with high proportions of M. m. musculus ancestry have large dN/dS ratios. We also used the proportion of deleterious nonsynonymous SNVs as a proxy for deleterious mutation load, which also produced similar results. The observed results were in concordance with those expected by theory. We also show a shift in the distribution of fitness effects of nonsynonymous SNVs in the admixed genomes compared to the parental populations. These findings suggest that the deleterious mutation load of the admixed population is determined by the proportion of the ancestries of the subspecies. Therefore, it is important to consider the status and the level of genetic admixture of the populations whilst estimating the mutation loads.
Collapse
|
7
|
Xie J, Wang W, Yang T, Zhang Q, Zhang Z, Zhu X, Li N, Zhi L, Ma X, Zhang S, Liu Y, Wang X, Li F, Zhao Y, Jia X, Zhou J, Jiang N, Li G, Liu M, Liu S, Li L, Zeng A, Du M, Zhang Z, Li J, Zhang Z, Li Z, Zhang H. Large-scale genomic and transcriptomic profiles of rice hybrids reveal a core mechanism underlying heterosis. Genome Biol 2022; 23:264. [PMID: 36550554 PMCID: PMC9773586 DOI: 10.1186/s13059-022-02822-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Heterosis is widely used in agriculture. However, its molecular mechanisms are still unclear in plants. Here, we develop, sequence, and record the phenotypes of 418 hybrids from crosses between two testers and 265 rice varieties from a mini-core collection. RESULTS Phenotypic analysis shows that heterosis is dependent on genetic backgrounds and environments. By genome-wide association study of 418 hybrids and their parents, we find that nonadditive QTLs are the main genetic contributors to heterosis. We show that nonadditive QTLs are more sensitive to the genetic background and environment than additive ones. Further simulations and experimental analysis support a novel mechanism, homo-insufficiency under insufficient background (HoIIB), underlying heterosis. We propose heterosis in most cases is not due to heterozygote advantage but homozygote disadvantage under the insufficient genetic background. CONCLUSION The HoIIB model elucidates that genetic background insufficiency is the intrinsic mechanism of background dependence, and also the core mechanism of nonadditive effects and heterosis. This model can explain most known hypotheses and phenomena about heterosis, and thus provides a novel theory for hybrid rice breeding in future.
Collapse
Affiliation(s)
- Jianyin Xie
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Weiping Wang
- grid.496830.00000 0004 7648 0514State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125 China
| | - Tao Yang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Quan Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhifang Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xiaoyang Zhu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Ni Li
- grid.496830.00000 0004 7648 0514State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125 China
| | - Linran Zhi
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xiaoqian Ma
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Shuyang Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Yan Liu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xueqiang Wang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Fengmei Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,grid.428986.90000 0001 0373 6302Sanya Nanfan Research Institute of Hainan University, Sanya, 572024 China
| | - Yan Zhao
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xuewei Jia
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jieyu Zhou
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Ningjia Jiang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,Sanya Institute of China Agricultural University, Sanya, 572024 China
| | - Gangling Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Miaosong Liu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Shijin Liu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Lin Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - An Zeng
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,grid.428986.90000 0001 0373 6302Sanya Nanfan Research Institute of Hainan University, Sanya, 572024 China ,Sanya Institute of China Agricultural University, Sanya, 572024 China
| | - Mengke Du
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,grid.428986.90000 0001 0373 6302Sanya Nanfan Research Institute of Hainan University, Sanya, 572024 China
| | - Zhanying Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jinjie Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Ziding Zhang
- grid.22935.3f0000 0004 0530 8290State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193 China
| | - Zichao Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,Sanya Institute of China Agricultural University, Sanya, 572024 China ,grid.22935.3f0000 0004 0530 8290State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193 China
| | - Hongliang Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,grid.428986.90000 0001 0373 6302Sanya Nanfan Research Institute of Hainan University, Sanya, 572024 China ,Sanya Institute of China Agricultural University, Sanya, 572024 China
| |
Collapse
|
8
|
Ramstein GP, Buckler ES. Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize. Genome Biol 2022; 23:183. [PMID: 36050782 PMCID: PMC9438327 DOI: 10.1186/s13059-022-02747-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/15/2022] [Indexed: 11/10/2022] Open
Abstract
Background Crop improvement through cross-population genomic prediction and genome editing requires identification of causal variants at high resolution, within fewer than hundreds of base pairs. Most genetic mapping studies have generally lacked such resolution. In contrast, evolutionary approaches can detect genetic effects at high resolution, but they are limited by shifting selection, missing data, and low depth of multiple-sequence alignments. Here we use genomic annotations to accurately predict nucleotide conservation across angiosperms, as a proxy for fitness effect of mutations. Results Using only sequence analysis, we annotate nonsynonymous mutations in 25,824 maize gene models, with information from bioinformatics and deep learning. Our predictions are validated by experimental information: within-species conservation, chromatin accessibility, and gene expression. According to gene ontology and pathway enrichment analyses, predicted nucleotide conservation points to genes in central carbon metabolism. Importantly, it improves genomic prediction for fitness-related traits such as grain yield, in elite maize panels, by stringent prioritization of fewer than 1% of single-site variants. Conclusions Our results suggest that predicting nucleotide conservation across angiosperms may effectively prioritize sites most likely to impact fitness-related traits in crops, without being limited by shifting selection, missing data, and low depth of multiple-sequence alignments. Our approach—Prediction of mutation Impact by Calibrated Nucleotide Conservation (PICNC)—could be useful to select polymorphisms for accurate genomic prediction, and candidate mutations for efficient base editing. The trained PICNC models and predicted nucleotide conservation at protein-coding SNPs in maize are publicly available in CyVerse (10.25739/hybz-2957). Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02747-2.
Collapse
Affiliation(s)
- Guillaume P Ramstein
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark. .,Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.,USDA-ARS, Ithaca, NY, 14853, USA
| |
Collapse
|
9
|
Ochoa A, Onorato DP, Roelke-Parker ME, Culver M, Fitak RR. Give and Take: Effects of Genetic Admixture on Mutation Load in Endangered Florida Panthers. J Hered 2022; 113:491-499. [PMID: 35930593 DOI: 10.1093/jhered/esac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/02/2022] [Indexed: 11/14/2022] Open
Abstract
Genetic admixture is a biological event inherent to genetic rescue programs aimed at the long-term conservation of endangered wildlife. Although the success of such programs can be measured by the increase in genetic diversity and fitness of subsequent admixed individuals, predictions supporting admixture costs to fitness due to the introduction of novel deleterious alleles are necessary. Here, we analyzed nonsynonymous variation from conserved genes to quantify and compare levels of mutation load (i.e., proportion of deleterious alleles and genotypes carrying these alleles) among endangered Florida panthers and non-endangered Texas pumas. Specifically, we used canonical (i.e., non-admixed) Florida panthers, Texas pumas, and F1 (canonical Florida x Texas) panthers dating from a genetic rescue program and Everglades National Park panthers with Central American ancestry resulting from an earlier admixture event. We found neither genetic drift nor selection significantly reduced overall proportions of deleterious alleles in the severely bottlenecked canonical Florida panthers. Nevertheless, the deleterious alleles identified were distributed into a disproportionately high number of homozygous genotypes due to close inbreeding in this group. Conversely, admixed Florida panthers (either with Texas or Central American ancestry) presented reduced levels of homozygous genotypes carrying deleterious alleles but increased levels of heterozygous genotypes carrying these variants relative to canonical Florida panthers. Although admixture is likely to alleviate the load of standing deleterious variation present in homozygous genotypes, our results suggest introduced novel deleterious alleles (temporarily present in heterozygous state) in genetically rescued populations could potentially be expressed in subsequent generations if their effective sizes remain small.
Collapse
Affiliation(s)
- Alexander Ochoa
- Department of Biology and Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL
| | - David P Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL
| | - Melody E Roelke-Parker
- Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD
| | - Melanie Culver
- U.S. Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, and School of Natural Resources and the Environment, University of Arizona, Tucson, AZ
| | - Robert R Fitak
- Department of Biology and Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL
| |
Collapse
|
10
|
Gou X, Feng X, Shi H, Guo T, Xie R, Liu Y, Wang Q, Li H, Yang B, Chen L, Lu Y. PPVED: A machine learning tool for predicting the effect of single amino acid substitution on protein function in plants. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1417-1431. [PMID: 35398963 PMCID: PMC9241370 DOI: 10.1111/pbi.13823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/03/2022] [Indexed: 05/31/2023]
Abstract
Single amino acid substitution (SAAS) produces the most common variant of protein function change under physiological conditions. As the number of SAAS events in plants has increased exponentially, an effective prediction tool is required to help identify and distinguish functional SAASs from the whole genome as either potentially causal traits or as variants. Here, we constructed a plant SAAS database that stores 12 865 SAASs in 6172 proteins and developed a tool called Plant Protein Variation Effect Detector (PPVED) that predicts the effect of SAASs on protein function in plants. PPVED achieved an 87% predictive accuracy when applied to plant SAASs, an accuracy that was much higher than those from six human database software: SIFT, PROVEAN, PANTHER-PSEP, PhD-SNP, PolyPhen-2, and MutPred2. The predictive effect of six SAASs from three proteins in Arabidopsis and maize was validated with wet lab experiments, of which five substitution sites were accurately predicted. PPVED could facilitate the identification and characterization of genetic variants that explain observed phenotype variations in plants, contributing to solutions for challenges in functional genomics and systems biology. PPVED can be accessed under a CC-BY (4.0) license via http://www.ppved.org.cn.
Collapse
Affiliation(s)
- Xiangjian Gou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjiangSichuanChina
- Maize Research InstituteSichuan Agricultural UniversityWenjiangSichuanChina
| | - Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjiangSichuanChina
- Maize Research InstituteSichuan Agricultural UniversityWenjiangSichuanChina
| | - Haoran Shi
- Chengdu Academy of Agricultural and Forestry SciencesWenjiangSichuanChina
| | - Tingting Guo
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Rongqian Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjiangSichuanChina
- Maize Research InstituteSichuan Agricultural UniversityWenjiangSichuanChina
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjiangSichuanChina
- Triticeae Research InstituteSichuan Agricultural UniversityWenjiangSichuanChina
| | - Qi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjiangSichuanChina
| | - Hongxiang Li
- College of Information EngineeringSichuan Agricultural UniversityYa’anSichuanChina
| | - Banglie Yang
- College of Information EngineeringSichuan Agricultural UniversityYa’anSichuanChina
| | - Lixue Chen
- College of Information EngineeringSichuan Agricultural UniversityYa’anSichuanChina
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjiangSichuanChina
- Maize Research InstituteSichuan Agricultural UniversityWenjiangSichuanChina
| |
Collapse
|
11
|
Guerra‐García A, Rojas‐Barrera IC, Ross‐Ibarra J, Papa R, Piñero D. The genomic signature of wild‐to‐crop introgression during the domestication of scarlet runner bean (
Phaseolus coccineus
L.). Evol Lett 2022; 6:295-307. [PMID: 35937471 PMCID: PMC9346085 DOI: 10.1002/evl3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 03/06/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022] Open
Abstract
The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small‐scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open‐pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single‐nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.
Collapse
Affiliation(s)
- Azalea Guerra‐García
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
- Department of Plant Sciences University of Saskatchewan Saskatoon SK S7N 5A2 Canada
| | - Idalia C. Rojas‐Barrera
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
- Environmental Genomics Max Planck Institute for Evolutionary Biology 24306 Plön Germany
| | - Jeffrey Ross‐Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center University of California, Davis Davis California 95616
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali Università Politecnica delle Marche Ancona 60131 Italy
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
| |
Collapse
|
12
|
Rare and population-specific functional variation across pig lines. Genet Sel Evol 2022; 54:39. [PMID: 35659233 PMCID: PMC9164375 DOI: 10.1186/s12711-022-00732-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/17/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND It is expected that functional, mainly missense and loss-of-function (LOF), and regulatory variants are responsible for most phenotypic differences between breeds and genetic lines of livestock species that have undergone diverse selection histories. However, there is still limited knowledge about the existing missense and LOF variation in commercial livestock populations, in particular regarding population-specific variation and how it can affect applications such as across-breed genomic prediction. METHODS We re-sequenced the whole genome of 7848 individuals from nine commercial pig lines (average sequencing coverage: 4.1×) and imputed whole-genome genotypes for 440,610 pedigree-related individuals. The called variants were categorized according to predicted functional annotation (from LOF to intergenic) and prevalence level (number of lines in which the variant segregated; from private to widespread). Variants in each category were examined in terms of their distribution along the genome, alternative allele frequency, per-site Wright's fixation index (FST), individual load, and association to production traits. RESULTS Of the 46 million called variants, 28% were private (called in only one line) and 21% were widespread (called in all nine lines). Genomic regions with a low recombination rate were enriched with private variants. Low-prevalence variants (called in one or a few lines only) were enriched for lower allele frequencies, lower FST, and putatively functional and regulatory roles (including LOF and deleterious missense variants). On average, individuals carried fewer private deleterious missense alleles than expected compared to alleles with other predicted consequences. Only a small subset of the low-prevalence variants had intermediate allele frequencies and explained small fractions of phenotypic variance (up to 3.2%) of production traits. The significant low-prevalence variants had higher per-site FST than the non-significant ones. These associated low-prevalence variants were tagged by other more widespread variants in high linkage disequilibrium, including intergenic variants. CONCLUSIONS Most low-prevalence variants have low minor allele frequencies and only a small subset of low-prevalence variants contributed detectable fractions of phenotypic variance of production traits. Accounting for low-prevalence variants is therefore unlikely to noticeably benefit across-breed analyses, such as the prediction of genomic breeding values in a population using reference populations of a different genetic background.
Collapse
|
13
|
Xiao Y, Jiang S, Cheng Q, Wang X, Yan J, Zhang R, Qiao F, Ma C, Luo J, Li W, Liu H, Yang W, Song W, Meng Y, Warburton ML, Zhao J, Wang X, Yan J. The genetic mechanism of heterosis utilization in maize improvement. Genome Biol 2021; 22:148. [PMID: 33971930 PMCID: PMC8108465 DOI: 10.1186/s13059-021-02370-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In maize hybrid breeding, complementary pools of parental lines with reshuffled genetic variants are established for superior hybrid performance. To comprehensively decipher the genetics of heterosis, we present a new design of multiple linked F1 populations with 42,840 F1 maize hybrids, generated by crossing a synthetic population of 1428 maternal lines with 30 elite testers from diverse genetic backgrounds and phenotyped for agronomic traits. RESULTS We show that, although yield heterosis is correlated with the widespread, minor-effect epistatic QTLs, it may be resulted from a few major-effect additive and dominant QTLs in early developmental stages. Floral transition is probably one critical stage for heterosis formation, in which epistatic QTLs are activated by paternal contributions of alleles that counteract the recessive, deleterious maternal alleles. These deleterious alleles, while rare, epistatically repress other favorable QTLs. We demonstrate this with one example, showing that Brachytic2 represses the Ubiquitin3 locus in the maternal lines; in hybrids, the paternal allele alleviates this repression, which in turn recovers the height of the plant and enhances the weight of the ear. Finally, we propose a molecular design breeding by manipulating key genes underlying the transition from vegetative-to-reproductive growth. CONCLUSION The new population design is used to dissect the genetic basis of heterosis which accelerates maize molecular design breeding by diminishing deleterious epistatic interactions.
Collapse
Affiliation(s)
- Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuqin Jiang
- National Maize Improvement Center, Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qian Cheng
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Shaanxi, China
| | - Xiaqing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agricultural & Forestry Sciences, Beijing, 100097, China
| | - Jun Yan
- National Maize Improvement Center, Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ruyang Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agricultural & Forestry Sciences, Beijing, 100097, China
| | - Feng Qiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuang Ma
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Shaanxi, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenyu Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenhao Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yijiang Meng
- College of Life Science, Hebei Agricultural University, Baoding, 071001, China
| | - Marilyn L Warburton
- United States Department of Agriculture-Agricultural Research Service, Corn Host Plant Resistance Research Unit, Box 9555, MS, 39762, Mississippi State, USA
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agricultural & Forestry Sciences, Beijing, 100097, China.
| | - Xiangfeng Wang
- National Maize Improvement Center, Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
| |
Collapse
|
14
|
Scossa F, Fernie AR. Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants? Comput Struct Biotechnol J 2021; 19:1579-1594. [PMID: 33868595 PMCID: PMC8039532 DOI: 10.1016/j.csbj.2021.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023] Open
Abstract
Whilst substantial research effort has been placed on understanding the interactions of plant proteins with their molecular partners, relatively few studies in plants - by contrast to work in other organisms - address how these interactions evolve. It is thought that ancestral proteins were more promiscuous than modern proteins and that specificity often evolved following gene duplication and subsequent functional refining. However, ancestral protein resurrection studies have found that some modern proteins have evolved de novo from ancestors lacking those functions. Intriguingly, the new interactions evolved as a consequence of just a few mutations and, as such, acquisition of new functions appears to be neither difficult nor rare, however, only a few of them are incorporated into biological processes before they are lost to subsequent mutations. Here, we detail the approach of ancestral sequence reconstruction (ASR), providing a primer to reconstruct the sequence of an ancestral gene. We will present case studies from a range of different eukaryotes before discussing the few instances where ancestral reconstructions have been used in plants. As ASR is used to dig into the remote evolutionary past, we will also present some alternative genetic approaches to investigate molecular evolution on shorter timescales. We argue that the study of plant secondary metabolism is particularly well suited for ancestral reconstruction studies. Indeed, its ancient evolutionary roots and highly diverse landscape provide an ideal context in which to address the focal issue around the emergence of evolutionary novelties and how this affects the chemical diversification of plant metabolism.
Collapse
Key Words
- APR, ancestral protein resurrection
- ASR, ancestral sequence reconstruction
- Ancestral sequence reconstruction
- CDS, coding sequence
- Evolution
- GR, glucocorticoid receptor
- GWAS, genome wide association study
- Genomics
- InDel, insertion/deletion
- MCMC, Markov Chain Monte Carlo
- ML, maximum likelihood
- MP, maximum parsimony
- MR, mineralcorticoid receptor
- MSA, multiple sequence alignment
- Metabolism
- NJ, neighbor-joining
- Phylogenetics
- Plants
- SFS, site frequency spectrum
Collapse
Affiliation(s)
- Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| |
Collapse
|
15
|
Lozano R, Gazave E, Dos Santos JPR, Stetter MG, Valluru R, Bandillo N, Fernandes SB, Brown PJ, Shakoor N, Mockler TC, Cooper EA, Taylor Perkins M, Buckler ES, Ross-Ibarra J, Gore MA. Comparative evolutionary genetics of deleterious load in sorghum and maize. NATURE PLANTS 2021; 7:17-24. [PMID: 33452486 DOI: 10.1038/s41477-020-00834-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Sorghum and maize share a close evolutionary history that can be explored through comparative genomics1,2. To perform a large-scale comparison of the genomic variation between these two species, we analysed ~13 million variants identified from whole-genome resequencing of 499 sorghum lines together with 25 million variants previously identified in 1,218 maize lines. Deleterious mutations in both species were prevalent in pericentromeric regions, enriched in non-syntenic genes and present at low allele frequencies. A comparison of deleterious burden between sorghum and maize revealed that sorghum, in contrast to maize, departed from the domestication-cost hypothesis that predicts a higher deleterious burden among domesticates compared with wild lines. Additionally, sorghum and maize population genetic summary statistics were used to predict a gene deleterious index with an accuracy greater than 0.5. This research represents a key step towards understanding the evolutionary dynamics of deleterious variants in sorghum and provides a comparative genomics framework to start prioritizing these variants for removal through genome editing and breeding.
Collapse
Affiliation(s)
- Roberto Lozano
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Elodie Gazave
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Jhonathan P R Dos Santos
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Markus G Stetter
- Botanical Institute, Biozentrum, University of Cologne, Cologne, Germany
| | - Ravi Valluru
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- University of Lincoln, Lincoln, UK
| | - Nonoy Bandillo
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Samuel B Fernandes
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Patrick J Brown
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Nadia Shakoor
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Elizabeth A Cooper
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - M Taylor Perkins
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Edward S Buckler
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R. W. Holley Center for Agriculture and Health, Ithaca, NY, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA.
- Center for Population Biology and Genome Center, University of California Davis, Davis, CA, USA.
| | - Michael A Gore
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
16
|
Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding. G3-GENES GENOMES GENETICS 2020; 10:4001-4011. [PMID: 32900902 PMCID: PMC7642940 DOI: 10.1534/g3.120.401269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Plant breeding leads to the genetic improvement of target traits by selecting a small number of genotypes from among typically large numbers of candidate genotypes after careful evaluation. In this study, we first investigated how mutations at conserved nucleotide sites normally viewed as deleterious, such as nonsynonymous sites, accumulated in a wheat, Triticum aestivum, breeding lineage. By comparing a 150 year old ancestral and modern cultivar, we found recent nucleotide polymorphisms altered amino acids and occurred within conserved genes at frequencies expected in the absence of purifying selection. Mutations that are deleterious in other contexts likely had very small or no effects on target traits within the breeding lineage. Second, we investigated if breeders selected alleles with favorable effects on some traits and unfavorable effects on others and used different alleles to compensate for the latter. An analysis of a segregating population derived from the ancestral and modern parents provided one example of this phenomenon. The recent cultivar contains the Rht-B1b green revolution semi-dwarfing allele and compensatory alleles that reduce its negative effects. However, improvements in traits other than plant height were due to pleiotropic loci with favorable effects on traits and to favorable loci with no detectable pleiotropic effects. Wheat breeding appears to tolerate mutations at conserved nucleotide sites and to only select for alleles with both favorable and unfavorable effects on traits in exceptional situations.
Collapse
|
17
|
Zeitler L, Ross-Ibarra J, Stetter MG. Selective Loss of Diversity in Doubled-Haploid Lines from European Maize Landraces. G3 (BETHESDA, MD.) 2020; 10:2497-2506. [PMID: 32467127 PMCID: PMC7341142 DOI: 10.1534/g3.120.401196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/28/2019] [Indexed: 11/18/2022]
Abstract
Maize landraces are well adapted to their local environments and present valuable sources of genetic diversity for breeding and conservation. But the maintenance of open-pollinated landraces in ex-situ programs is challenging, as regeneration of seed can often lead to inbreeding depression and the loss of diversity due to genetic drift. Recent reports suggest that the production of doubled-haploid (DH) lines from landraces may serve as a convenient means to preserve genetic diversity in a homozygous form that is immediately useful for modern breeding. The production of doubled-haploid (DH) lines presents an extreme case of inbreeding which results in instantaneous homozygosity genome-wide. Here, we analyzed the effect of DH production on genetic diversity, using genome-wide SNP data from hundreds of individuals of five European landraces and their related DH lines. In contrast to previous findings, we observe a dramatic loss of diversity at both the haplotype level and that of individual SNPs. We identify thousands of SNPs that exhibit allele frequency differences larger than expected under models of neutral genetic drift and document losses of shared haplotypes. We find evidence consistent with selection at functional sites that are potentially involved in the diversity differences between landrace and DH populations. Although we were unable to uncover more details about the mode of selection, we conclude that landrace DH lines may be a valuable tool for the introduction of variation into maize breeding programs but come at the cost of decreased genetic diversity.
Collapse
Affiliation(s)
- Leo Zeitler
- Department of Biology, Institute of Molecular Plant Biology, ETH Zürich, Zürich, Switzerland
- Department of Plant Sciences, University of California, Davis, CA
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, CA,
- Department of Evolution and Ecology, Genome Center, and Center for Population Biology, University of California, Davis, CA, and
| | - Markus G Stetter
- Department of Plant Sciences, University of California, Davis, CA,
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences, University of Cologne, Germany
| |
Collapse
|
18
|
Ramstein GP, Larsson SJ, Cook JP, Edwards JW, Ersoz ES, Flint-Garcia S, Gardner CA, Holland JB, Lorenz AJ, McMullen MD, Millard MJ, Rocheford TR, Tuinstra MR, Bradbury PJ, Buckler ES, Romay MC. Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize. Genetics 2020; 215:215-230. [PMID: 32152047 PMCID: PMC7198274 DOI: 10.1534/genetics.120.303025] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 02/26/2020] [Indexed: 01/04/2023] Open
Abstract
Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize.
Collapse
Affiliation(s)
| | - Sara J Larsson
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853
| | - Jason P Cook
- Division of Plant Science, University of Missouri, Columbia, Missouri 56211
| | - Jode W Edwards
- U.S. Department of Agriculture-Agricultural Research Service, Ames, Iowa 50011
| | | | - Sherry Flint-Garcia
- U.S. Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, Missouri 56211
| | - Candice A Gardner
- U.S. Department of Agriculture-Agricultural Research Service, Ames, Iowa 50011
| | - James B Holland
- U.S. Department of Agriculture-Agricultural Research Service, Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Aaron J Lorenz
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
| | - Michael D McMullen
- U.S. Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, Missouri 56211
| | - Mark J Millard
- U.S. Department of Agriculture-Agricultural Research Service, Ames, Iowa 50011
| | | | | | - Peter J Bradbury
- U.S. Department of Agriculture-Agricultural Research Service, Ithaca, New York 14853
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
- U.S. Department of Agriculture-Agricultural Research Service, Ithaca, New York 14853
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
| |
Collapse
|
19
|
Agriculture and the Disruption of Plant–Microbial Symbiosis. Trends Ecol Evol 2020; 35:426-439. [DOI: 10.1016/j.tree.2020.01.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 12/29/2022]
|
20
|
Joly-Lopez Z, Platts AE, Gulko B, Choi JY, Groen SC, Zhong X, Siepel A, Purugganan MD. An inferred fitness consequence map of the rice genome. NATURE PLANTS 2020; 6:119-130. [PMID: 32042156 PMCID: PMC7446671 DOI: 10.1038/s41477-019-0589-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/20/2019] [Indexed: 05/04/2023]
Abstract
The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa). We inferred fitCons scores (ρ) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae. We found ρ to be multimodal, with ~9% of the rice genome falling into classes where more than half of the bases would probably have a fitness consequence if mutated. Around 2% of the rice genome showed evidence of weak negative selection, frequently at candidate regulatory sites, including a novel set of 1,000 potentially active enhancer elements. This fitCons map provides perspective on the evolutionary forces associated with genome diversity, aids in genome annotation and can guide crop breeding programs.
Collapse
Affiliation(s)
- Zoé Joly-Lopez
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Adrian E Platts
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Brad Gulko
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Simon C Groen
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Xuehua Zhong
- Laboratory of Genetics and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.
- Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, NYU Abu Dhabi, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
21
|
Kono TJY, Liu C, Vonderharr EE, Koenig D, Fay JC, Smith KP, Morrell PL. The Fate of Deleterious Variants in a Barley Genomic Prediction Population. Genetics 2019; 213:1531-1544. [PMID: 31653677 PMCID: PMC6893365 DOI: 10.1534/genetics.119.302733] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023] Open
Abstract
Targeted identification and purging of deleterious genetic variants has been proposed as a novel approach to animal and plant breeding. This strategy is motivated, in part, by the observation that demographic events and strong selection associated with cultivated species pose a "cost of domestication." This includes an increase in the proportion of genetic variants that are likely to reduce fitness. Recent advances in DNA resequencing and sequence constraint-based approaches to predict the functional impact of a mutation permit the identification of putatively deleterious SNPs (dSNPs) on a genome-wide scale. Using exome capture resequencing of 21 barley lines, we identified 3855 dSNPs among 497,754 total SNPs. We generated whole-genome resequencing data of Hordeum murinum ssp. glaucum as a phylogenetic outgroup to polarize SNPs as ancestral vs. derived. We also observed a higher proportion of dSNPs per synonymous SNPs (sSNPs) in low-recombination regions of the genome. Using 5215 progeny from a genomic prediction experiment, we examined the fate of dSNPs over three breeding cycles. Adjusting for initial frequency, derived alleles at dSNPs reduced in frequency or were lost more often than other classes of SNPs. The highest-yielding lines in the experiment, as chosen by standard genomic prediction approaches, carried fewer homozygous dSNPs than randomly sampled lines from the same progeny cycle. In the final cycle of the experiment, progeny selected by genomic prediction had a mean of 5.6% fewer homozygous dSNPs relative to randomly chosen progeny from the same cycle.
Collapse
Affiliation(s)
- Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Emily E Vonderharr
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Justin C Fay
- Department of Biology, University of Rochester, New York 14627
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| |
Collapse
|
22
|
Washburn JD, McElfresh MJ, Birchler JA. Progressive heterosis in genetically defined tetraploid maize. J Genet Genomics 2019; 46:389-396. [PMID: 31444136 DOI: 10.1016/j.jgg.2019.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 01/24/2019] [Accepted: 02/20/2019] [Indexed: 12/30/2022]
Abstract
Progressive heterosis, i.e., the additional hybrid vigor in double-cross tetraploid hybrids not found in their single-cross tetraploid parents, has been documented in a number of species including alfalfa, potato, and maize. In this study, four artificially induced maize tetraploids, directly derived from standard inbred lines, were crossed in pairs to create two single-cross hybrids. These hybrids were then crossed to create double-cross hybrids containing genetic material from all four original lines. Replicated field-based phenotyping of the materials over four years indicated a strong progressive heterosis phenotype in tetraploids but not in their diploid counterparts. In particular, the above ground dry weight phenotype of double-cross tetraploid hybrids was on average 34% and 56% heavier than that of the single-cross tetraploid hybrids and the double-cross diploid counterparts, respectively. Additionally, whole-genome resequencing of the original inbred lines and further analysis of these data did not show the expected spectrum of alleles to explain tetraploid progressive heterosis under the complementation of complete recessive model. These results underscore the reality of the progressive heterosis phenotype, its potential utility for increasing crop biomass production, and the need for exploring alternative hypothesis to explain it at a molecular level.
Collapse
Affiliation(s)
- Jacob D Washburn
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211, USA
| | - Mitchell J McElfresh
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211, USA.
| |
Collapse
|
23
|
Affiliation(s)
- Mirte Bosse
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
- Department of Ecological Science, Animal Ecology Group, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- * E-mail:
| |
Collapse
|
24
|
Dagilis AJ, Kirkpatrick M, Bolnick DI. The evolution of hybrid fitness during speciation. PLoS Genet 2019; 15:e1008125. [PMID: 31059513 PMCID: PMC6502311 DOI: 10.1371/journal.pgen.1008125] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/04/2019] [Indexed: 12/27/2022] Open
Abstract
The evolution of postzygotic reproductive isolation is an important component of speciation. But before isolation is complete there is sometimes a phase of heterosis in which hybrid fitness exceeds that of the two parental species. The genetics and evolution of heterosis and postzygotic isolation have typically been studied in isolation, precluding the development of a unified theory of speciation. Here, we develop a model that incorporates both positive and negative gene interactions, and accounts for the evolution of both heterosis and postzygotic isolation. We parameterize the model with recent data on the fitness effects of 10,000 mutations in yeast, singly and in pairwise epistatic combinations. The model makes novel predictions about the types of interactions that contribute to declining hybrid fitness. We reproduce patterns familiar from earlier models of speciation (e.g. Haldane's Rule and Darwin's Corollary) and identify new mechanisms that may underlie these patterns. Our approach provides a general framework for integrating experimental data from gene interaction networks into speciation theory and makes new predictions about the genetic mechanisms of speciation.
Collapse
Affiliation(s)
- Andrius J. Dagilis
- Integrative Biology Department, University of Texas at Austin, Austin, Texas, United States of America
| | - Mark Kirkpatrick
- Integrative Biology Department, University of Texas at Austin, Austin, Texas, United States of America
| | - Daniel I. Bolnick
- Integrative Biology Department, University of Texas at Austin, Austin, Texas, United States of America
- Department of Ecology and Evolutionary Biology, University of Connecticut, Mansfield, Connecticut, United States of America
| |
Collapse
|
25
|
He F, Pasam R, Shi F, Kant S, Keeble-Gagnere G, Kay P, Forrest K, Fritz A, Hucl P, Wiebe K, Knox R, Cuthbert R, Pozniak C, Akhunova A, Morrell PL, Davies JP, Webb SR, Spangenberg G, Hayes B, Daetwyler H, Tibbits J, Hayden M, Akhunov E. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat Genet 2019; 51:896-904. [PMID: 31043759 DOI: 10.1038/s41588-019-0382-2] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/26/2019] [Indexed: 11/09/2022]
Abstract
Introgression is a potential source of beneficial genetic diversity. The contribution of introgression to adaptive evolution and improvement of wheat as it was disseminated worldwide remains unknown. We used targeted re-sequencing of 890 diverse accessions of hexaploid and tetraploid wheat to identify wild-relative introgression. Introgression, and selection for improvement and environmental adaptation, each reduced deleterious allele burden. Introgression increased diversity genome wide and in regions harboring major agronomic genes, and contributed alleles explaining a substantial proportion of phenotypic variation. These results suggest that historic gene flow from wild relatives made a substantial contribution to the adaptive diversity of modern bread wheat.
Collapse
Affiliation(s)
- Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Raj Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Fan Shi
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Surya Kant
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | | | - Pippa Kay
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Pierre Hucl
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Krystalee Wiebe
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ron Knox
- Swift Current Research and Development Centre, Swift Current, Saskatchewan, Canada
| | - Richard Cuthbert
- Swift Current Research and Development Centre, Swift Current, Saskatchewan, Canada
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, USA
| | - John P Davies
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN, USA
| | - Steve R Webb
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN, USA
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Ben Hayes
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, University of Queensland, St Lucia, Queensland, Australia
| | - Hans Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia.
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
| |
Collapse
|
26
|
Johnsson M, Gaynor RC, Jenko J, Gorjanc G, de Koning DJ, Hickey JM. Removal of alleles by genome editing (RAGE) against deleterious load. Genet Sel Evol 2019; 51:14. [PMID: 30995904 PMCID: PMC6472060 DOI: 10.1186/s12711-019-0456-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 04/01/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND In this paper, we simulate deleterious load in an animal breeding program, and compare the efficiency of genome editing and selection for decreasing it. Deleterious variants can be identified by bioinformatics screening methods that use sequence conservation and biological prior information about protein function. However, once deleterious variants have been identified, how can they be used in breeding? RESULTS We simulated a closed animal breeding population that is subject to both natural selection against deleterious load and artificial selection for a quantitative trait representing the breeding goal. Deleterious load was polygenic and was due to either codominant or recessive variants. We compared strategies for removal of deleterious alleles by genome editing (RAGE) to selection against carriers. When deleterious variants were codominant, the best strategy for prioritizing variants was to prioritize low-frequency variants. When deleterious variants were recessive, the best strategy was to prioritize variants with an intermediate frequency. Selection against carriers was inefficient when variants were codominant, but comparable to editing one variant per sire when variants were recessive. CONCLUSIONS Genome editing of deleterious alleles reduces deleterious load, but requires the simultaneous editing of multiple deleterious variants in the same sire to be effective when deleterious variants are recessive. In the short term, selection against carriers is a possible alternative to genome editing when variants are recessive. Our results suggest that, in the future, there is the potential to use RAGE against deleterious load in animal breeding.
Collapse
Affiliation(s)
- Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland UK
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden
| | - R. Chris Gaynor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland UK
| | - Janez Jenko
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland UK
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland UK
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden
| | - John M. Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland UK
| |
Collapse
|
27
|
Voss-Fels KP, Cooper M, Hayes BJ. Accelerating crop genetic gains with genomic selection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:669-686. [PMID: 30569365 DOI: 10.1007/s00122-018-3270-8] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 12/12/2018] [Indexed: 05/05/2023]
Abstract
Genomic prediction based on additive genetic effects can accelerate genetic gain. There are opportunities for further improvement by including non-additive effects that access untapped sources of genetic diversity. Several studies have reported a worrying gap between the projected global future demand for plant-based products and the current annual rates of production increase, indicating that enhancing the rate of genetic gain might be critical for future food security. Therefore, new breeding technologies and strategies are required to significantly boost genetic improvement of future crop cultivars. Genomic selection (GS) has delivered considerable genetic gain in animal breeding and is becoming an essential component of many modern plant breeding programmes as well. In this paper, we review the lessons learned from implementing GS in livestock and the impact of GS on crop breeding, and discuss important features for the success of GS under different breeding scenarios. We highlight major challenges associated with GS including rapid genotyping, phenotyping, genotype-by-environment interaction and non-additivity and give examples for opportunities to overcome these issues. Finally, the potential of combining GS with other modern technologies in order to maximise the rate of crop genetic improvement is discussed, including the potential of increasing prediction accuracy by integration of crop growth models in GS frameworks.
Collapse
Affiliation(s)
- Kai Peter Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ben John Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
| |
Collapse
|
28
|
Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum ( Sorghum bicolor). Genetics 2019; 211:1075-1087. [PMID: 30622134 PMCID: PMC6404259 DOI: 10.1534/genetics.118.301742] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/22/2018] [Indexed: 11/18/2022] Open
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a major staple food cereal for millions of people worldwide. Valluru et al. identify putative deleterious mutations among ∼5.5M segregating variants of 229 diverse sorghum... Sorghum (Sorghum bicolor L.) is a major food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. The lack of recombination, drift, and the coupling with favorable loci impede the removal of deleterious mutations from the genome by selection. To study how deleterious variants impact phenotypes, we identified putative deleterious mutations among ∼5.5 M segregating variants of 229 diverse biomass sorghum lines. We provide the whole-genome estimate of the deleterious burden in sorghum, showing that ∼33% of nonsynonymous substitutions are putatively deleterious. The pattern of mutation burden varies appreciably among racial groups. Across racial groups, the mutation burden correlated negatively with biomass, plant height, specific leaf area (SLA), and tissue starch content (TSC), suggesting that deleterious burden decreases trait fitness. Putatively deleterious variants explain roughly one-half of the genetic variance. However, there is only moderate improvement in total heritable variance explained for biomass (7.6%) and plant height (average of 3.1% across all stages). There is no advantage in total heritable variance for SLA and TSC. The contribution of putatively deleterious variants to phenotypic diversity therefore appears to be dependent on the genetic architecture of traits. Overall, these results suggest that incorporating putatively deleterious variants into genomic models slightly improves prediction accuracy because of extensive linkage. Knowledge of deleterious variants could be leveraged for sorghum breeding through either genome editing and/or conventional breeding that focuses on the selection of progeny with fewer deleterious alleles.
Collapse
|
29
|
Bosse M, Megens H, Derks MFL, de Cara ÁMR, Groenen MAM. Deleterious alleles in the context of domestication, inbreeding, and selection. Evol Appl 2019; 12:6-17. [PMID: 30622631 PMCID: PMC6304688 DOI: 10.1111/eva.12691] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 05/30/2018] [Accepted: 06/12/2018] [Indexed: 12/21/2022] Open
Abstract
Each individual has a certain number of harmful mutations in its genome. These mutations can lower the fitness of the individual carrying them, dependent on their dominance and selection coefficient. Effective population size, selection, and admixture are known to affect the occurrence of such mutations in a population. The relative roles of demography and selection are a key in understanding the process of adaptation. These are factors that are potentially influenced and confounded in domestic animals. Here, we hypothesize that the series of events of bottlenecks, introgression, and strong artificial selection associated with domestication increased mutational load in domestic species. Yet, mutational load is hard to quantify, so there are very few studies available revealing the relevance of evolutionary processes. The precise role of artificial selection, bottlenecks, and introgression in further increasing the load of deleterious variants in animals in breeding and conservation programmes remains unclear. In this paper, we review the effects of domestication and selection on mutational load in domestic species. Moreover, we test some hypotheses on higher mutational load due to domestication and selective sweeps using sequence data from commercial pig and chicken lines. Overall, we argue that domestication by itself is not a prerequisite for genetic erosion, indicating that fitness potential does not need to decline. Rather, mutational load in domestic species can be influenced by many factors, but consistent or strong trends are not yet clear. However, methods emerging from molecular genetics allow discrimination of hypotheses about the determinants of mutational load, such as effective population size, inbreeding, and selection, in domestic systems. These findings make us rethink the effect of our current breeding schemes on fitness of populations.
Collapse
Affiliation(s)
- Mirte Bosse
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Hendrik‐Jan Megens
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Martijn F. L. Derks
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Ángeles M. R. de Cara
- Centre d’Ecologie Fonctionnelle et EvolutiveCNRSUniversité de MontpellierUniversité Paul Valéry Montpellier 3EPHE, IRDMontpellierFrance
| | - Martien A. M. Groenen
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| |
Collapse
|
30
|
Torkamaneh D, Laroche J, Rajcan I, Belzile F. Identification of candidate domestication-related genes with a systematic survey of loss-of-function mutations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:1218-1227. [PMID: 30246271 DOI: 10.1111/tpj.14104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
Domestication is an important key co-evolutionary process through which humans have extensively altered the genomic make-up and appearance of both plants and animals. The identification of domestication-related genes remains very arduous. In this study, we present a systematic analytical approach that harnesses two recent advances in genomics, whole-genome sequencing (WGS) and prediction of loss-of-function (LOF) mutations, to greatly facilitate the assembly of an enriched catalogue of domestication-related candidate genes. Using WGS data for 296 cultivated (Glycine max) and 64 wild soybean accessions, we identified 8699 LOF variants, and 116 genes that are uniquely fixed for one or more LOF allele(s) in domesticated soybeans. Existing soybean transcriptomic data led us to overcome analytical challenges associated with whole-genome duplications and to identify neo- or subfunctionalized genes. This systematic approach allowed us to identify 110 candidate domestication-related genes in an efficient and rapid way. This catalogue contains previously well characterized domestication genes in soybean, as well as some orthologs from other domesticated crop species. In addition, it comprises many promising candidate domestication genes. Overall, this collection of candidate domestication-related genes in soybean is almost twice as large as the sum of all previously reported candidate genes in all other crops. We believe this systematic approach could readily be used in wide range of species.
Collapse
Affiliation(s)
- Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
- Department of Plant Agriculture, Crop Science Bldg., University of Guelph, Guelph, ON, Canada
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, Crop Science Bldg., University of Guelph, Guelph, ON, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| |
Collapse
|
31
|
Kono TJY, Lei L, Shih CH, Hoffman PJ, Morrell PL, Fay JC. Comparative Genomics Approaches Accurately Predict Deleterious Variants in Plants. G3 (BETHESDA, MD.) 2018; 8:3321-3329. [PMID: 30139765 PMCID: PMC6169392 DOI: 10.1534/g3.118.200563] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 08/10/2018] [Indexed: 12/11/2022]
Abstract
Recent advances in genome resequencing have led to increased interest in prediction of the functional consequences of genetic variants. Variants at phylogenetically conserved sites are of particular interest, because they are more likely than variants at phylogenetically variable sites to have deleterious effects on fitness and contribute to phenotypic variation. Numerous comparative genomic approaches have been developed to predict deleterious variants, but the approaches are nearly always assessed based on their ability to identify known disease-causing mutations in humans. Determining the accuracy of deleterious variant predictions in nonhuman species is important to understanding evolution, domestication, and potentially to improving crop quality and yield. To examine our ability to predict deleterious variants in plants we generated a curated database of 2,910 Arabidopsis thaliana mutants with known phenotypes. We evaluated seven approaches and found that while all performed well, their relative ranking differed from prior benchmarks in humans. We conclude that deleterious mutations can be reliably predicted in A. thaliana and likely other plant species, but that the relative performance of various approaches does not necessarily translate from one species to another.
Collapse
Affiliation(s)
- Thomas J Y Kono
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 551085
| | - Li Lei
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 551085
| | - Ching-Hua Shih
- Department of Genetics, Washington University, St. Louis, MO 63110
| | - Paul J Hoffman
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 551085
| | - Peter L Morrell
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 551085
| | - Justin C Fay
- Department of Genetics, Washington University, St. Louis, MO 63110
| |
Collapse
|
32
|
Jordan KW, Wang S, He F, Chao S, Lun Y, Paux E, Sourdille P, Sherman J, Akhunova A, Blake NK, Pumphrey MO, Glover K, Dubcovsky J, Talbert L, Akhunov ED. The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1039-1054. [PMID: 29952048 PMCID: PMC6174997 DOI: 10.1111/tpj.14009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/21/2018] [Accepted: 06/06/2018] [Indexed: 05/18/2023]
Abstract
Recombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence-based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome-wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans-acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans-acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low-recombining pericentromeric regions of chromosomes.
Collapse
Affiliation(s)
| | - Shichen Wang
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Present address:
TEES‐AgriLife Center for Bioinformatics and Genomic Systems EngineeringTexas A&M University101 Gateway, Suite ACollege StationTX77845USA
| | - Fei He
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Shiaoman Chao
- USDA‐ARS Cereal Crops Research Unit1605 Albrecht Blvd NFargoNDUSA
| | - Yanni Lun
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Present address:
TEES‐AgriLife Center for Bioinformatics and Genomic Systems EngineeringTexas A&M University101 Gateway, Suite ACollege StationTX77845USA
| | - Etienne Paux
- INRA GDEC Auvergne‐Rhône‐AlpesClermont‐FerrandFrance
| | | | | | - Alina Akhunova
- Integrated Genomics FacilityKansas State UniversityManhattanKSUSA
| | | | | | - Karl Glover
- Department of Agronomy, Horticulture and Plant ScienceSouth Dakota State UniversityBrookingsSDUSA
| | - Jorge Dubcovsky
- Department of Plant SciencesUniversity of CaliforniaDavis, DavisCAUSA
- Howard Hughes Medical InstituteChevy ChaseMD20815USA
| | | | | |
Collapse
|
33
|
Chen J, Ni P, Tran Thi TN, Kamaldinov EV, Petukhov VL, Han J, Liu X, Šprem N, Zhao S. Selective constraints in cold-region wild boars may defuse the effects of small effective population size on molecular evolution of mitogenomes. Ecol Evol 2018; 8:8102-8114. [PMID: 30250687 PMCID: PMC6144961 DOI: 10.1002/ece3.4221] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/25/2018] [Accepted: 05/11/2018] [Indexed: 12/15/2022] Open
Abstract
Spatial range expansion during population colonization is characterized by demographic events that may have significant effects on the efficiency of natural selection. Population genetics suggests that genetic drift brought by small effective population size (Ne) may undermine the efficiency of selection, leading to a faster accumulation of nonsynonymous mutations. However, it is still unknown whether this effect might be balanced or even reversed by strong selective constraints. Here, we used wild boars and local domestic pigs from tropical (Vietnam) and subarctic region (Siberia) as animal model to evaluate the effects of functional constraints and genetic drift on shaping molecular evolution. The likelihood-ratio test revealed that Siberian clade evolved significantly different from Vietnamese clades. Different datasets consistently showed that Siberian wild boars had lower Ka/Ks ratios than Vietnamese samples. The potential role of positive selection for branches with higher Ka/Ks was evaluated using branch-site model comparison. No signal of positive selection was found for the higher Ka/Ks in Vietnamese clades, suggesting the interclade difference was mainly due to the reduction in Ka/Ks for Siberian samples. This conclusion was further confirmed by the result from a larger sample size, among which wild boars from northern Asia (subarctic and nearby region) had lower Ka/Ks than those from southern Asia (temperate and tropical region). The lower Ka/Ks might be due to either stronger functional constraints, which prevent nonsynonymous mutations from accumulating in subarctic wild boars, or larger Ne in Siberian wild boars, which can boost the efficacy of purifying selection to remove functional mutations. The latter possibility was further ruled out by the Bayesian skyline plot analysis, which revealed that historical Ne of Siberian wild boars was smaller than that of Vietnamese wild boars. Altogether, these results suggest stronger functional constraints acting on mitogenomes of subarctic wild boars, which may provide new insights into their local adaptation of cold resistance.
Collapse
Affiliation(s)
- Jianhai Chen
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinois
| | - Pan Ni
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
| | - Thuy Nhien Tran Thi
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
- National Institute of Animal SciencesHanoiVietnam
| | - Evgeniy Varisovich Kamaldinov
- Federal State Budgetary Educational Institution of Higher EducationNovosibirsk State Agrarian UniversityNovosibirskRussia
| | - Valeriy Lavrentyevich Petukhov
- Federal State Budgetary Educational Institution of Higher EducationNovosibirsk State Agrarian UniversityNovosibirskRussia
| | - Jianlin Han
- International Livestock Research Institute (ILRI)NairobiKenya
- CAAS‐ILRI Joint Laboratory on Livestock and Forage Genetic ResourcesInstitute of Animal ScienceChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xiangdong Liu
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
| | - Nikica Šprem
- Department of Fisheries, Beekeeping, Game Management and Special ZoologyFaculty of AgricultureUniversity of ZagrebZagrebCroatia
| | - Shuhong Zhao
- Key Lab of Agricultural Animal Genetics and BreedingMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- The Cooperative Innovation Center for Sustainable Pig ProductionHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
34
|
Xie X, Yang Y, Ren Q, Ding X, Bao P, Yan B, Yan X, Han J, Yan P, Qiu Q. Accumulation of deleterious mutations in the domestic yak genome. Anim Genet 2018; 49:384-392. [DOI: 10.1111/age.12703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2018] [Indexed: 12/19/2022]
Affiliation(s)
- X. Xie
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Y. Yang
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Q. Ren
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - X. Ding
- Key Laboratory of Yak Breeding Engineering Gansu Province; Lanzhou Institute of Husbandry and Pharmaceutical Sciences; Chinese Academy of Agricultural Science; Lanzhou 730050 China
| | - P. Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province; Lanzhou Institute of Husbandry and Pharmaceutical Sciences; Chinese Academy of Agricultural Science; Lanzhou 730050 China
| | - B. Yan
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - X. Yan
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - J. Han
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - P. Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province; Lanzhou Institute of Husbandry and Pharmaceutical Sciences; Chinese Academy of Agricultural Science; Lanzhou 730050 China
| | - Q. Qiu
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| |
Collapse
|
35
|
Wang XJ, Hu QJ, Guo XY, Wang K, Ru DF, German DA, Weretilnyk EA, Abbott RJ, Lascoux M, Liu JQ. Demographic expansion and genetic load of the halophyte model plantEutrema salsugineum. Mol Ecol 2018; 27:2943-2955. [DOI: 10.1111/mec.14738] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 05/16/2018] [Accepted: 05/24/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Xiao-Juan Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Quan-Jun Hu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Xin-Yi Guo
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Kun Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Da-Fu Ru
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Dmitry A. German
- Department of Biodiversity and Plant Systematics; Centre for Organismal Studies (COS Heidelberg); Heidelberg University; Heidelberg Germany
- South-Siberian Botanical Garden; Altai State University; Barnaul Russia
| | | | | | - Martin Lascoux
- Department of Ecology and Genetics; Evolutionary Biology Center and Science for Life Laboratory; Uppsala University; Uppsala Sweden
| | - Jian-quan Liu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
- State Key Laboratory of Grassland Agro-Ecosystem; College of Life Science; Lanzhou University; Lanzhou China
| |
Collapse
|
36
|
Fiévet JB, Nidelet T, Dillmann C, de Vienne D. Heterosis Is a Systemic Property Emerging From Non-linear Genotype-Phenotype Relationships: Evidence From in Vitro Genetics and Computer Simulations. Front Genet 2018; 9:159. [PMID: 29868111 PMCID: PMC5968397 DOI: 10.3389/fgene.2018.00159] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/17/2018] [Indexed: 11/13/2022] Open
Abstract
Heterosis, the superiority of hybrids over their parents for quantitative traits, represents a crucial issue in plant and animal breeding as well as evolutionary biology. Heterosis has given rise to countless genetic, genomic and molecular studies, but has rarely been investigated from the point of view of systems biology. We hypothesized that heterosis is an emergent property of living systems resulting from frequent concave relationships between genotypic variables and phenotypes, or between different phenotypic levels. We chose the enzyme-flux relationship as a model of the concave genotype-phenotype (GP) relationship, and showed that heterosis can be easily created in the laboratory. First, we reconstituted in vitro the upper part of glycolysis. We simulated genetic variability of enzyme activity by varying enzyme concentrations in test tubes. Mixing the content of "parental" tubes resulted in "hybrids," whose fluxes were compared to the parental fluxes. Frequent heterotic fluxes were observed, under conditions that were determined analytically and confirmed by computer simulation. Second, to test this model in a more realistic situation, we modeled the glycolysis/fermentation network in yeast by considering one input flux, glucose, and two output fluxes, glycerol and acetaldehyde. We simulated genetic variability by randomly drawing parental enzyme concentrations under various conditions, and computed the parental and hybrid fluxes using a system of differential equations. Again we found that a majority of hybrids exhibited positive heterosis for metabolic fluxes. Cases of negative heterosis were due to local convexity between certain enzyme concentrations and fluxes. In both approaches, heterosis was maximized when the parents were phenotypically close and when the distributions of parental enzyme concentrations were contrasted and constrained. These conclusions are not restricted to metabolic systems: they only depend on the concavity of the GP relationship, which is commonly observed at various levels of the phenotypic hierarchy, and could account for the pervasiveness of heterosis.
Collapse
Affiliation(s)
- Julie B Fiévet
- GQE-Le Moulon, INRA, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Sud, Gif-sur-Yvette, France
| | - Thibault Nidelet
- Sciences Pour l'Œnologie, INRA, Université de Montpellier, Montpellier, France
| | - Christine Dillmann
- GQE-Le Moulon, INRA, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Sud, Gif-sur-Yvette, France
| | - Dominique de Vienne
- GQE-Le Moulon, INRA, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Sud, Gif-sur-Yvette, France
| |
Collapse
|
37
|
Kovalev MS, Igolkina AA, Samsonova MG, Nuzhdin SV. A Pipeline for Classifying Deleterious Coding Mutations in Agricultural Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1734. [PMID: 30546376 PMCID: PMC6279870 DOI: 10.3389/fpls.2018.01734] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/08/2018] [Indexed: 05/18/2023]
Abstract
The impact of deleterious variation on both plant fitness and crop productivity is not completely understood and is a hot topic of debates. The deleterious mutations in plants have been solely predicted using sequence conservation methods rather than function-based classifiers due to lack of well-annotated mutational datasets in these organisms. Here, we developed a machine learning classifier based on a dataset of deleterious and neutral mutations in Arabidopsis thaliana by extracting 18 informative features that discriminate deleterious mutations from neutral, including 9 novel features not used in previous studies. We examined linear SVM, Gaussian SVM, and Random Forest classifiers, with the latter performing best. Random Forest classifiers exhibited a markedly higher accuracy than the popular PolyPhen-2 tool in the Arabidopsis dataset. Additionally, we tested whether the Random Forest, trained on the Arabidopsis dataset, accurately predicts deleterious mutations in Orýza sativa and Pisum sativum and observed satisfactory levels of performance accuracy (87% and 93%, respectively) higher than obtained by the PolyPhen-2. Application of Transfer learning in classifiers did not improve their performance. To additionally test the performance of the Random Forest classifier across different angiosperm species, we applied it to annotate deleterious mutations in Cicer arietinum and validated them using population frequency data. Overall, we devised a classifier with the potential to improve the annotation of putative functional mutations in QTL and GWAS hit regions, as well as for the evolutionary analysis of proliferation of deleterious mutations during plant domestication; thus optimizing breeding improvement and development of new cultivars.
Collapse
Affiliation(s)
- Maxim S. Kovalev
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
| | - Anna A. Igolkina
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
- *Correspondence: Anna A. Igolkina, Maria G. Samsonova,
| | - Maria G. Samsonova
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
- *Correspondence: Anna A. Igolkina, Maria G. Samsonova,
| | - Sergey V. Nuzhdin
- Department of Applied Mathematics, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russia
- Program Molecular & Computational Biology, Dornsife College of Letters Arts and Science, University of Southern California, Los Angeles, CA, United States
| |
Collapse
|
38
|
Conte GL, Hodgins KA, Yeaman S, Degner JC, Aitken SN, Rieseberg LH, Whitlock MC. Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex. BMC Genomics 2017; 18:970. [PMID: 29246191 PMCID: PMC5731209 DOI: 10.1186/s12864-017-4344-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/21/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Mutation load is expected to be reduced in hybrids via complementation of deleterious alleles. While local adaptation of hybrids confounds phenotypic tests for reduced mutation load, it may be possible to assess variation in load by analyzing the distribution of putatively deleterious alleles. Here, we use this approach in the interior spruce (Picea glauca x P. engelmannii) hybrid complex, a group likely to suffer from high mutation load and in which hybrids exhibit local adaptation to intermediate conditions. We used PROVEAN to bioinformatically predict whether non-synonymous alleles are deleterious, based on conservation of the position and abnormality of the amino acid change. RESULTS As expected, we found that predicted deleterious alleles were at lower average allele frequencies than alleles not predicted to be deleterious. We were unable to detect a phenotypic effect on juvenile growth rate of the many rare alleles predicted to be deleterious. Both the proportion of alleles predicted to be deleterious and the proportion of loci homozygous for predicted deleterious alleles were higher in P. engelmannii (Engelmann spruce) than in P. glauca (white spruce), due to higher diversity and frequencies of rare alleles in Engelmann. Relative to parental species, the proportion of alleles predicted to be deleterious was intermediate in hybrids, and the proportion of loci homozygous for predicted deleterious alleles was lowest. CONCLUSION Given that most deleterious alleles are recessive, this suggests that mutation load is reduced in hybrids due to complementation of deleterious alleles. This effect may enhance the fitness of hybrids.
Collapse
Affiliation(s)
- Gina L Conte
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. .,Department of Botany, University of British Columbia, 3200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
| | - Kathryn A Hodgins
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,Present Address: School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
| | - Sam Yeaman
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,Present Address: Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada
| | - Jon C Degner
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, 3200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, 4200-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| |
Collapse
|
39
|
Fitness Costs and Variation in Transmission Distortion Associated with the Abnormal Chromosome 10 Meiotic Drive System in Maize. Genetics 2017; 208:297-305. [PMID: 29122827 DOI: 10.1534/genetics.117.300060] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/02/2017] [Indexed: 01/03/2023] Open
Abstract
Meiotic drive describes a process whereby selfish genetic elements are transmitted at levels greater than Mendelian expectations. Maize abnormal chromosome 10 (Ab10) encodes a meiotic drive system that exhibits strong preferential segregation through female gametes. We performed transmission assays on nine Ab10 chromosomes from landraces and teosinte lines and found a transmission advantage of 62-79% in heterozygotes. Despite this transmission advantage, Ab10 is present at low frequencies in natural populations, suggesting that it carries large negative fitness consequences. We measured pollen transmission, the percentage of live pollen, seed production, and seed size to estimate several of the possible fitness effects of Ab10. We found no evidence that Ab10 affects pollen transmission, i.e., Ab10 and N10 pollen are transmitted equally from heterozygous fathers. However, at the diploid (sporophyte) level, both heterozygous and homozygous Ab10-I-MMR individuals show decreased pollen viability, decreased seed set, and decreased seed weight. The observed fitness costs can nearly but not entirely account for the observed frequencies of Ab10. Sequence analysis shows a surprising amount of molecular variation among Ab10 haplotypes, suggesting that there may be other phenotypic variables that contribute to the low but stable equilibrium frequencies.
Collapse
|
40
|
Kantar MB, Nashoba AR, Anderson JE, Blackman BK, Rieseberg LH. The Genetics and Genomics of Plant Domestication. Bioscience 2017. [DOI: 10.1093/biosci/bix114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
|
41
|
Yang J, Mezmouk S, Baumgarten A, Buckler ES, Guill KE, McMullen MD, Mumm RH, Ross-Ibarra J. Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLoS Genet 2017; 13:e1007019. [PMID: 28953891 PMCID: PMC5633198 DOI: 10.1371/journal.pgen.1007019] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 10/09/2017] [Accepted: 09/13/2017] [Indexed: 12/20/2022] Open
Abstract
Deleterious alleles have long been proposed to play an important role in patterning phenotypic variation and are central to commonly held ideas explaining the hybrid vigor observed in the offspring of a cross between two inbred parents. We test these ideas using evolutionary measures of sequence conservation to ask whether incorporating information about putatively deleterious alleles can inform genomic selection (GS) models and improve phenotypic prediction. We measured a number of agronomic traits in both the inbred parents and hybrids of an elite maize partial diallel population and re-sequenced the parents of the population. Inbred elite maize lines vary for more than 350,000 putatively deleterious sites, but show a lower burden of such sites than a comparable set of traditional landraces. Our modeling reveals widespread evidence for incomplete dominance at these loci, and supports theoretical models that more damaging variants are usually more recessive. We identify haplotype blocks using an identity-by-decent (IBD) analysis and perform genomic prediction analyses in which we weigh blocks on the basis of complementation for segregating putatively deleterious variants. Cross-validation results show that incorporating sequence conservation in genomic selection improves prediction accuracy for grain yield and other fitness-related traits as well as heterosis for those traits. Our results provide empirical support for an important role for incomplete dominance of deleterious alleles in explaining heterosis and demonstrate the utility of incorporating functional annotation in phenotypic prediction and plant breeding.
Collapse
Affiliation(s)
- Jinliang Yang
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Sofiane Mezmouk
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | | | - Edward S. Buckler
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
- Institute for Genomic Diversity, Ithaca, New York, United States of America
- US Department of Agriculture–Agricultural Research Service, Ithaca, New York, United States of America
| | - Katherine E. Guill
- US Department of Agriculture, Agricultural Research Service, Columbia, Missouri, United States of America
| | - Michael D. McMullen
- US Department of Agriculture, Agricultural Research Service, Columbia, Missouri, United States of America
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Rita H. Mumm
- Department of Crop Sciences and the Illinois Plant Breeding Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
- Center for Population Biology and Genome Center, University of California, Davis, California, United States of America
| |
Collapse
|
42
|
Moyers BT, Morrell PL, McKay JK. Genetic Costs of Domestication and Improvement. J Hered 2017; 109:103-116. [DOI: 10.1093/jhered/esx069] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/02/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
- Brook T Moyers
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN (Morrell)
| | - John K McKay
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO
| |
Collapse
|
43
|
Melchinger AE, Schopp P, Müller D, Schrag TA, Bauer E, Unterseer S, Homann L, Schipprack W, Schön CC. Safeguarding Our Genetic Resources with Libraries of Doubled-Haploid Lines. Genetics 2017; 206:1611-1619. [PMID: 28468909 PMCID: PMC5500154 DOI: 10.1534/genetics.115.186205] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/21/2017] [Indexed: 01/02/2023] Open
Abstract
Thousands of landraces are stored in seed banks as "gold reserves" for future use in plant breeding. In many crops, their utilization is hampered because they represent heterogeneous populations of heterozygous genotypes, which harbor a high genetic load. We show, with high-density genotyping in five landraces of maize, that libraries of doubled-haploid (DH) lines capture the allelic diversity of genetic resources in an unbiased way. By comparing allelic differentiation between heterozygous plants from the original landraces and 266 derived DH lines, we find conclusive evidence that, in the DH production process, sampling of alleles is random across the entire allele frequency spectrum, and purging of landraces from their genetic load does not act on specific genomic regions. Based on overall process efficiency, we show that generating DH lines is feasible for genetic material that has never been selected for inbreeding tolerance. We conclude that libraries of DH lines will make genetic resources accessible to crop improvement by linking molecular inventories of seed banks with meaningful phenotypes.
Collapse
Affiliation(s)
- Albrecht E Melchinger
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
| | - Pascal Schopp
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
| | - Dominik Müller
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
| | - Tobias A Schrag
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
| | - Eva Bauer
- School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Sandra Unterseer
- School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Linda Homann
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
| | - Wolfgang Schipprack
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
| | - Chris-Carolin Schön
- School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| |
Collapse
|
44
|
Ramu P, Esuma W, Kawuki R, Rabbi IY, Egesi C, Bredeson JV, Bart RS, Verma J, Buckler ES, Lu F. Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nat Genet 2017; 49:959-963. [DOI: 10.1038/ng.3845] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 03/21/2017] [Indexed: 12/20/2022]
|
45
|
Brandenburg JT, Mary-Huard T, Rigaill G, Hearne SJ, Corti H, Joets J, Vitte C, Charcosset A, Nicolas SD, Tenaillon MI. Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. PLoS Genet 2017; 13:e1006666. [PMID: 28301472 PMCID: PMC5373671 DOI: 10.1371/journal.pgen.1006666] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 03/30/2017] [Accepted: 03/01/2017] [Indexed: 12/27/2022] Open
Abstract
Through the local selection of landraces, humans have guided the adaptation of crops to a vast range of climatic and ecological conditions. This is particularly true of maize, which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges worldwide. Here, we sequenced 67 genomes with an average sequencing depth of 18x to document routes of introduction, admixture and selective history of European maize and its American counterparts. To avoid the confounding effects of recent breeding, we targeted germplasm (lines) directly derived from landraces. Among our lines, we discovered 22,294,769 SNPs and between 0.9% to 4.1% residual heterozygosity. Using a segmentation method, we identified 6,978 segments of unexpectedly high rate of heterozygosity. These segments point to genes potentially involved in inbreeding depression, and to a lesser extent to the presence of structural variants. Genetic structuring and inferences of historical splits revealed 5 genetic groups and two independent European introductions, with modest bottleneck signatures. Our results further revealed admixtures between distinct sources that have contributed to the establishment of 3 groups at intermediate latitudes in North America and Europe. We combined differentiation- and diversity-based statistics to identify both genes and gene networks displaying strong signals of selection. These include genes/gene networks involved in flowering time, drought and cold tolerance, plant defense and starch properties. Overall, our results provide novel insights into the evolutionary history of European maize and highlight a major role of admixture in environmental adaptation, paralleling recent findings in humans.
Collapse
Affiliation(s)
- Jean-Tristan Brandenburg
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| | - Tristan Mary-Huard
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
- UMR 518 AgroParisTech/INRA, France
| | - Guillem Rigaill
- Institute of Plant Sciences Paris-Saclay, UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot, Sorbonne Paris-Cité, France
| | - Sarah J. Hearne
- CIMMYT (International Maize and Wheat Improvement Centre), El Batan, Texcoco, Edo de Mexico, Mexico
| | - Hélène Corti
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| | - Johann Joets
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| | - Clémentine Vitte
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| | - Alain Charcosset
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| | - Stéphane D. Nicolas
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| | - Maud I. Tenaillon
- Génétique Quantitative et Evolution – Le Moulon, Institut National de la Recherche agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, France
| |
Collapse
|
46
|
Bitocchi E, Rau D, Benazzo A, Bellucci E, Goretti D, Biagetti E, Panziera A, Laidò G, Rodriguez M, Gioia T, Attene G, McClean P, Lee RK, Jackson SA, Bertorelle G, Papa R. High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits. FRONTIERS IN PLANT SCIENCE 2017; 7:2005. [PMID: 28111584 PMCID: PMC5216878 DOI: 10.3389/fpls.2016.02005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 12/16/2016] [Indexed: 05/05/2023]
Abstract
Crop species have been deeply affected by the domestication process, and there have been many efforts to identify selection signatures at the genome level. This knowledge will help geneticists to better understand the evolution of organisms, and at the same time, help breeders to implement successful breeding strategies. Here, we focused on domestication in the Mesoamerican gene pool of Phaseolus vulgaris by sequencing 49 gene fragments from a sample of 45 P. vulgaris wild and domesticated accessions, and as controls, two accessions each of the closely related species Phaseolus coccineus and Phaseolus dumosus. An excess of nonsynonymous mutations within the domesticated germplasm was found. Our data suggest that the cost of domestication alone cannot explain fully this finding. Indeed, the significantly higher frequency of polymorphisms in the coding regions observed only in the domesticated plants (compared to noncoding regions), the fact that these mutations were mostly nonsynonymous and appear to be recently derived mutations, and the investigations into the functions of their relative genes (responses to biotic and abiotic stresses), support a scenario that involves new functional mutations selected for adaptation during domestication. Moreover, consistent with this hypothesis, selection analysis and the possibility to compare data obtained for the same genes in different studies of varying sizes, data types, and methodologies allowed us to identify four genes that were strongly selected during domestication. Each selection candidate is involved in plant resistance/tolerance to abiotic stresses, such as heat, drought, and salinity. Overall, our study suggests that domestication acted to increase functional diversity at target loci, which probably controlled traits related to expansion and adaptation to new agro-ecological growing conditions.
Collapse
Affiliation(s)
- Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Domenico Rau
- Department of Agriculture, Università degli Studi di SassariSassari, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, Università degli Studi di FerraraFerrara, Italy
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Daniela Goretti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå UniversityUmeå, Sweden
| | - Eleonora Biagetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Alex Panziera
- Department of Life Sciences and Biotechnology, Università degli Studi di FerraraFerrara, Italy
| | - Giovanni Laidò
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per la CerealicolturaFoggia, Italy
| | - Monica Rodriguez
- Department of Agriculture, Università degli Studi di SassariSassari, Italy
| | - Tania Gioia
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della BasilicataPotenza, Italy
| | - Giovanna Attene
- Department of Agriculture, Università degli Studi di SassariSassari, Italy
| | - Phillip McClean
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - Rian K. Lee
- Department of Plant Sciences, North Dakota State UniversityFargo, ND, USA
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, University of GeorgiaAthens, GA, USA
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, Università degli Studi di FerraraFerrara, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| |
Collapse
|
47
|
Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids. Proc Natl Acad Sci U S A 2016; 113:E7317-E7326. [PMID: 27803326 DOI: 10.1073/pnas.1615268113] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The ubiquity of nonparental hybrid phenotypes, such as hybrid vigor and hybrid inferiority, has interested biologists for over a century and is of considerable agricultural importance. Although examples of both phenomena have been subject to intense investigation, no general model for the molecular basis of nonadditive genetic variance has emerged, and prediction of hybrid phenotypes from parental information continues to be a challenge. Here we explore the genetics of hybrid phenotype in 435 Arabidopsis thaliana individuals derived from intercrosses of 30 parents in a half diallel mating scheme. We find that nonadditive genetic effects are a major component of genetic variation in this population and that the genetic basis of hybrid phenotype can be mapped using genome-wide association (GWA) techniques. Significant loci together can explain as much as 20% of phenotypic variation in the surveyed population and include examples that have both classical dominant and overdominant effects. One candidate region inherited dominantly in the half diallel contains the gene for the MADS-box transcription factor AGAMOUS-LIKE 50 (AGL50), which we show directly to alter flowering time in the predicted manner. Our study not only illustrates the promise of GWA approaches to dissect the genetic architecture underpinning hybrid performance but also demonstrates the contribution of classical dominance to genetic variance.
Collapse
|
48
|
Kono TJY, Fu F, Mohammadi M, Hoffman PJ, Liu C, Stupar RM, Smith KP, Tiffin P, Fay JC, Morrell PL. The Role of Deleterious Substitutions in Crop Genomes. Mol Biol Evol 2016; 33:2307-17. [PMID: 27301592 PMCID: PMC4989107 DOI: 10.1093/molbev/msw102] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Populations continually incur new mutations with fitness effects ranging from lethal to adaptive. While the distribution of fitness effects of new mutations is not directly observable, many mutations likely either have no effect on organismal fitness or are deleterious. Historically, it has been hypothesized that a population may carry many mildly deleterious variants as segregating variation, which reduces the mean absolute fitness of the population. Recent advances in sequencing technology and sequence conservation-based metrics for inferring the functional effect of a variant permit examination of the persistence of deleterious variants in populations. The issue of segregating deleterious variation is particularly important for crop improvement, because the demographic history of domestication and breeding allows deleterious variants to persist and reach moderate frequency, potentially reducing crop productivity. In this study, we use exome resequencing of 15 barley accessions and genome resequencing of 8 soybean accessions to investigate the prevalence of deleterious single nucleotide polymorphisms (SNPs) in the protein-coding regions of the genomes of two crops. We conclude that individual cultivars carry hundreds of deleterious SNPs on average, and that nonsense variants make up a minority of deleterious SNPs. Our approach identifies known phenotype-altering variants as deleterious more frequently than the genome-wide average, suggesting that putatively deleterious variants are likely to affect phenotypic variation. We also report the implementation of a SNP annotation tool BAD_Mutations that makes use of a likelihood ratio test based on alignment of all currently publicly available Angiosperm genomes.
Collapse
Affiliation(s)
- Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Fengli Fu
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Mohsen Mohammadi
- Department of Agronomy and Plant Genetics, University of Minnesota Department of Agronomy, Purdue University
| | - Paul J Hoffman
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Peter Tiffin
- Department of Plant Biology, University of Minnesota
| | | | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota
| |
Collapse
|
49
|
Zhang M, Zhou L, Bawa R, Suren H, Holliday J. Recombination Rate Variation, Hitchhiking, and Demographic History Shape Deleterious Load in Poplar. Mol Biol Evol 2016; 33:2899-2910. [DOI: 10.1093/molbev/msw169] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
|
50
|
Beissinger TM, Wang L, Crosby K, Durvasula A, Hufford MB, Ross-Ibarra J. Recent demography drives changes in linked selection across the maize genome. NATURE PLANTS 2016; 2:16084. [PMID: 27294617 DOI: 10.1038/nplants.2016.84] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/12/2016] [Indexed: 05/14/2023]
Abstract
Genetic diversity is shaped by the interaction of drift and selection, but the details of this interaction are not well understood. The impact of genetic drift in a population is largely determined by its demographic history, typically summarized by its long-term effective population size (Ne). Rapidly changing population demographics complicate this relationship, however. To better understand how changing demography impacts selection, we used whole-genome sequencing data to investigate patterns of linked selection in domesticated and wild maize (teosinte). We produce the first whole-genome estimate of the demography of maize domestication, showing that maize was reduced to approximately 5% the population size of teosinte before it experienced rapid expansion post-domestication to population sizes much larger than its ancestor. Evaluation of patterns of nucleotide diversity in and near genes shows little evidence of selection on beneficial amino acid substitutions, and that the domestication bottleneck led to a decline in the efficiency of purifying selection in maize. Young alleles, however, show evidence of much stronger purifying selection in maize, reflecting the much larger effective size of present day populations. Our results demonstrate that recent demographic change-a hall-mark of many species including both humans and crops-can have immediate and wide-ranging impacts on diversity that conflict with expectations based on long-term Ne alone.
Collapse
Affiliation(s)
- Timothy M Beissinger
- Department of Plant Sciences, University of California, Davis, California 95616, USA
- US Department of Agriculture, Agricultural Research Service, Columbia, Missouri 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Li Wang
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Kate Crosby
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Arun Durvasula
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, California 95616, USA
- Genome Center and Center for Population Biology, University of California, Davis, California 95616, USA
| |
Collapse
|