1
|
Zhang T, Peng W, Xiao H, Cao S, Chen Z, Su X, Luo Y, Liu Z, Peng Y, Yang X, Jiang GF, Xu X, Ma Z, Zhou Y. Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1408-1426. [PMID: 38578160 DOI: 10.1111/jipb.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/04/2024] [Indexed: 04/06/2024]
Abstract
Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.
Collapse
Affiliation(s)
- Tianhao Zhang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenjing Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Hua Xiao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Shuo Cao
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Key Laboratory of Horticultural Plant Biology Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhuyifu Chen
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiangnian Su
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Yuanyuan Luo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Zhongjie Liu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yanling Peng
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xiping Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Guo-Feng Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest Plantation, College of Forestry, Guangxi University, Nanning, 530004, China
| | - Xiaodong Xu
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Zhiyao Ma
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yongfeng Zhou
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| |
Collapse
|
2
|
Ahrens CW, Murray K, Mazanec RA, Ferguson S, Jones A, Tissue DT, Byrne M, Borevitz JO, Rymer PD. Genomic determinants, architecture, and constraints in drought-related traits in Corymbia calophylla. BMC Genomics 2024; 25:640. [PMID: 38937661 PMCID: PMC11209971 DOI: 10.1186/s12864-024-10531-8] [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: 09/15/2023] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Drought adaptation is critical to many tree species persisting under climate change, however our knowledge of the genetic basis for trees to adapt to drought is limited. This knowledge gap impedes our fundamental understanding of drought response and application to forest production and conservation. To improve our understanding of the genomic determinants, architecture, and trait constraints, we assembled a reference genome and detected ~ 6.5 M variants in 432 phenotyped individuals for the foundational tree Corymbia calophylla. RESULTS We found 273 genomic variants determining traits with moderate heritability (h2SNP = 0.26-0.64). Significant variants were predominantly in gene regulatory elements distributed among several haplotype blocks across all chromosomes. Furthermore, traits were constrained by frequent epistatic and pleiotropic interactions. CONCLUSIONS Our results on the genetic basis for drought traits in Corymbia calophylla have several implications for the ability to adapt to climate change: (1) drought related traits are controlled by complex genomic architectures with large haplotypes, epistatic, and pleiotropic interactions; (2) the most significant variants determining drought related traits occurred in regulatory regions; and (3) models incorporating epistatic interactions increase trait predictions. Our findings indicate that despite moderate heritability drought traits are likely constrained by complex genomic architecture potentially limiting trees response to climate change.
Collapse
Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.
- Cesar Australia, Brunswick, VIC, 3058, Australia.
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Richard A Mazanec
- Biodiversity and Conservation Science, Western Australian Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6151, Australia
| | - Scott Ferguson
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Western Australian Department of Biodiversity, Conservation and Attractions, Kensington, WA, 6151, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| |
Collapse
|
3
|
Poikela N, Laetsch DR, Hoikkala V, Lohse K, Kankare M. Chromosomal Inversions and the Demography of Speciation in Drosophila montana and Drosophila flavomontana. Genome Biol Evol 2024; 16:evae024. [PMID: 38482698 PMCID: PMC10972691 DOI: 10.1093/gbe/evae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 04/01/2024] Open
Abstract
Chromosomal inversions may play a central role in speciation given their ability to locally reduce recombination and therefore genetic exchange between diverging populations. We analyzed long- and short-read whole-genome data from sympatric and allopatric populations of 2 Drosophila virilis group species, Drosophila montana and Drosophila flavomontana, to understand if inversions have contributed to their divergence. We identified 3 large alternatively fixed inversions on the X chromosome and one on each of the autosomes 4 and 5. A comparison of demographic models estimated for inverted and noninverted (colinear) chromosomal regions suggests that these inversions arose before the time of the species split. We detected a low rate of interspecific gene flow (introgression) from D. montana to D. flavomontana, which was further reduced inside inversions and was lower in allopatric than in sympatric populations. Together, these results suggest that the inversions were already present in the common ancestral population and that gene exchange between the sister taxa was reduced within inversions both before and after the onset of species divergence. Such ancestrally polymorphic inversions may foster speciation by allowing the accumulation of genetic divergence in loci involved in adaptation and reproductive isolation inside inversions early in the speciation process, while gene exchange at colinear regions continues until the evolving reproductive barriers complete speciation. The overlapping X inversions are particularly good candidates for driving the speciation process of D. montana and D. flavomontana, since they harbor strong genetic incompatibilities that were detected in a recent study of experimental introgression.
Collapse
Affiliation(s)
- Noora Poikela
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ville Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
| |
Collapse
|
4
|
Yang N, Wang Y, Liu X, Jin M, Vallebueno-Estrada M, Calfee E, Chen L, Dilkes BP, Gui S, Fan X, Harper TK, Kennett DJ, Li W, Lu Y, Ding J, Chen Z, Luo J, Mambakkam S, Menon M, Snodgrass S, Veller C, Wu S, Wu S, Zhuo L, Xiao Y, Yang X, Stitzer MC, Runcie D, Yan J, Ross-Ibarra J. Two teosintes made modern maize. Science 2023; 382:eadg8940. [PMID: 38033071 DOI: 10.1126/science.adg8940] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/02/2023] [Indexed: 12/02/2023]
Abstract
The origins of maize were the topic of vigorous debate for nearly a century, but neither the current genetic model nor earlier archaeological models account for the totality of available data, and recent work has highlighted the potential contribution of a wild relative, Zea mays ssp. mexicana. Our population genetic analysis reveals that the origin of modern maize can be traced to an admixture between ancient maize and Zea mays ssp. mexicana in the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas.
Collapse
Affiliation(s)
- Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Miguel Vallebueno-Estrada
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, 36821 Guanajuato, México
| | - Erin Calfee
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Brian P Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650200, China
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Ziqi Chen
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Sowmya Mambakkam
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Mitra Menon
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
| | - Samantha Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Carl Veller
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Shenshen Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Siying Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Zhuo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Michelle C Stitzer
- Institute for Genomic Diversity and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Daniel Runcie
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Yazhouwan National Laboratory, Sanya 572024, China
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Genome Center, University of California, Davis, CA 95616, USA
| |
Collapse
|
5
|
Bock DG, Cai Z, Elphinstone C, González-Segovia E, Hirabayashi K, Huang K, Keais GL, Kim A, Owens GL, Rieseberg LH. Genomics of plant speciation. PLANT COMMUNICATIONS 2023; 4:100599. [PMID: 37050879 PMCID: PMC10504567 DOI: 10.1016/j.xplc.2023.100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form. Now, the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research. Here, we review these recent genome-enabled developments in plant speciation. We discuss complications related to identification of reproductive isolation (RI) loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation, as increasingly revealed by new sequencing technologies. Further, we review how genomics has advanced what we know of some routes to new species formation, like hybridization or whole-genome duplication, while casting doubt on others, like population bottlenecks and genetic drift. While genomics can fast-track identification of genes and mutations that confer RI, we emphasize that follow-up molecular and field experiments remain critical. Nonetheless, genomics has clarified the outsized role of ancient variants rather than new mutations, particularly early during speciation. We conclude by highlighting promising avenues of future study. These include expanding what we know so far about the role of epigenetic and structural changes during speciation, broadening the scope and taxonomic breadth of plant speciation genomics studies, and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.
Collapse
Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Zhe Cai
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Eric González-Segovia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Graeme L Keais
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Amy Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
6
|
Harringmeyer OS, Hoekstra HE. Chromosomal inversion polymorphisms shape the genomic landscape of deer mice. Nat Ecol Evol 2022; 6:1965-1979. [PMID: 36253543 PMCID: PMC9715431 DOI: 10.1038/s41559-022-01890-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/17/2022] [Indexed: 12/15/2022]
Abstract
Chromosomal inversions are an important form of structural variation that can affect recombination, chromosome structure and fitness. However, because inversions can be challenging to detect, the prevalence and hence the significance of inversions segregating within species remains largely unknown, especially in natural populations of mammals. Here, by combining population-genomic and long-read sequencing analyses in a single, widespread species of deer mouse (Peromyscus maniculatus), we identified 21 polymorphic inversions that are large (1.5-43.8 Mb) and cause near-complete suppression of recombination when heterozygous (0-0.03 cM Mb-1). We found that inversion breakpoints frequently occur in centromeric and telomeric regions and are often flanked by long inverted repeats (0.5-50 kb), suggesting that they probably arose via ectopic recombination. By genotyping inversions in populations across the species' range, we found that the inversions are often widespread and do not harbour deleterious mutational loads, and many are likely to be maintained as polymorphisms by divergent selection. Comparisons of forest and prairie ecotypes of deer mice revealed 13 inversions that contribute to differentiation between populations, of which five exhibit significant associations with traits implicated in local adaptation. Taken together, these results show that inversion polymorphisms have a significant impact on recombination, genome structure and genetic diversity in deer mice and likely facilitate local adaptation across the widespread range of this species.
Collapse
Affiliation(s)
- Olivia S Harringmeyer
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| | - Hopi E Hoekstra
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Museum of Comparative Zoology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
7
|
Zhao J, Zheng X, Qiao L, Yang C, Wu B, He Z, Tang Y, Li G, Yang Z, Zheng J, Qi Z. Genome-wide association study reveals structural chromosome variations with phenotypic effects in wheat (Triticum aestivum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1447-1461. [PMID: 36345647 DOI: 10.1111/tpj.16023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Structural chromosome variations (SCVs) are large-scale genomic variations that can be detected by fluorescence in situ hybridization (FISH). SCVs have played important roles in the genome evolution of wheat (Triticum aestivum L.), but little is known about their genetic effects. In this study, a total of 543 wheat accessions from the Chinese wheat mini-core collection and the Shanxi Province wheat collection were used for chromosome analysis using oligonucleotide probe multiplex FISH. A total of 139 SCVs including translocations, pericentric inversions, presence/absence variations (PAVs), and copy number variations (CNVs) in heterochromatin were identified at 230 loci. The distribution frequency of SCVs varied between ecological regions and between landraces and modern cultivars. Structural analysis using SCVs as markers clearly divided the landraces and modern cultivars into different groups. There are very clear instances illustrating alien introgression and wide application of foreign germplasms improved the chromosome diversity of Chinese modern wheat cultivars. A genome-wide association study (GWAS) identified 29 SCVs associated with 12 phenotypic traits, and five (RT4AS•4AL-1DS/1DL•1DS-4AL, Mg2A-3, Mr3B-10, Mr7B-13, and Mr4A-7) of them were further validated using a doubled haploid population and advanced sib-lines, implying the potential value of these SCVs. Importantly, the number of favored SCVs that were associated with agronomic trait improvement was significantly higher in modern cultivars compared to landraces, indicating positive selection in wheat breeding. This study demonstrates the significant effects of SCVs during wheat breeding and provides an efficient method of mining favored SCVs in wheat and other crops.
Collapse
Affiliation(s)
- Jiajia Zhao
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xingwei Zheng
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Ling Qiao
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Chenkang Yang
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Bangbang Wu
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Ziming He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuqing Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, China
| | - Jun Zheng
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Zengjun Qi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
8
|
Chen L, Luo J, Jin M, Yang N, Liu X, Peng Y, Li W, Phillips A, Cameron B, Bernal JS, Rellán-Álvarez R, Sawers RJH, Liu Q, Yin Y, Ye X, Yan J, Zhang Q, Zhang X, Wu S, Gui S, Wei W, Wang Y, Luo Y, Jiang C, Deng M, Jin M, Jian L, Yu Y, Zhang M, Yang X, Hufford MB, Fernie AR, Warburton ML, Ross-Ibarra J, Yan J. Genome sequencing reveals evidence of adaptive variation in the genus Zea. Nat Genet 2022; 54:1736-1745. [PMID: 36266506 DOI: 10.1038/s41588-022-01184-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/10/2022] [Indexed: 11/09/2022]
Abstract
Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in wild relatives of maize. Here, we characterize a high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 70 million single-nucleotide polymorphisms. The variation map reveals evidence of selection within taxa displaying novel adaptations. We focus on adaptive alleles in highland teosinte and temperate maize, highlighting the key role of flowering-time-related pathways in their adaptation. To show the utility of variants in these data, we generate mutant alleles for two flowering-time candidate genes. This work provides an extensive sampling of the genetic diversity of Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.
Collapse
Affiliation(s)
- Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China.
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yong Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Alyssa Phillips
- Center for Population Biology, University of California Davis, Davis, CA, USA.,Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Brenda Cameron
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Julio S Bernal
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Rubén Rellán-Álvarez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Ruairidh J H Sawers
- Department of Plant Science, The Pennsylvania State University, State College, PA, USA
| | - Qing Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yuejia Yin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Xinnan Ye
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jiali Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaoting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Shenshen Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wenjie Wei
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Chenglin Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Min Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Liumei Jian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yanhui Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Maolin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Marilyn L Warburton
- United States Department of Agriculture-Agricultural Research Service: Western Regional Plant Introduction Station, Washington State University, Pullman, WA, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, Center for Population Biology, Genome Center, University of California Davis, Davis, CA, USA.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. .,Hubei Hongshan Laboratory, Wuhan, China.
| |
Collapse
|
9
|
Hollenbeck CM, Portnoy DS, Garcia de la Serrana D, Magnesen T, Matejusova I, Johnston IA. Temperature-associated selection linked to putative chromosomal inversions in king scallop ( Pecten maximus). Proc Biol Sci 2022; 289:20221573. [PMID: 36196545 PMCID: PMC9532988 DOI: 10.1098/rspb.2022.1573] [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] [Indexed: 11/27/2022] Open
Abstract
The genomic landscape of divergence—the distribution of differences among populations or species across the genome—is increasingly characterized to understand the role that microevolutionary forces such as natural selection and recombination play in causing and maintaining genetic divergence. This line of inquiry has also revealed chromosome structure variation to be an important factor shaping the landscape of adaptive genetic variation. Owing to a high prevalence of chromosome structure variation and the strong pressure for local adaptation necessitated by their sessile nature, bivalve molluscs are an ideal taxon for exploring the relationship between chromosome structure variation and local adaptation. Here, we report a population genomic survey of king scallop (Pecten maximus) across its natural range in the northeastern Atlantic Ocean, using a recent chromosome-level genome assembly. We report the presence of at least three large (12–22 Mb), putative chromosomal inversions associated with sea surface temperature and whose frequencies are in contrast to neutral population structure. These results highlight a potentially large role for recombination-suppressing chromosomal inversions in local adaptation and suggest a hypothesis to explain the maintenance of differences in reproductive timing found at relatively small spatial scales across king scallop populations.
Collapse
Affiliation(s)
- Christopher M Hollenbeck
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA.,Texas A&M AgriLife Research, College Station, TX, USA
| | - David S Portnoy
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Daniel Garcia de la Serrana
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Thorolf Magnesen
- Department of Biological Sciences, University of Bergen, Thormøhlensgt 53B, Bergen, Norway
| | - Iveta Matejusova
- Marine Science Scotland, Marine Laboratory, 375 Victoria Road, Aberdeen AB11 9DB, UK
| | - Ian A Johnston
- Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife KY16 8LB, UK.,Xelect Ltd, Horizon House, Abbey Walk, St Andrews KY16 9LB, UK
| |
Collapse
|
10
|
Chen Y, Schreiber M, Bayer MM, Dawson IK, Hedley PE, Lei L, Akhunova A, Liu C, Smith KP, Fay JC, Muehlbauer GJ, Steffenson BJ, Morrell PL, Waugh R, Russell JR. The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1580-1594. [PMID: 35834607 PMCID: PMC9546296 DOI: 10.1111/tpj.15908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/30/2022] [Accepted: 07/13/2022] [Indexed: 05/17/2023]
Abstract
The distribution of recombination events along large cereal chromosomes is uneven and is generally restricted to gene-rich telomeric ends. To understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 Hordeum vulgare (barley) cultivars, landraces and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared with wild barley. We observed a mixture of completely and partially differentiated single-nucleotide polymorphisms (SNPs) between domesticated and wild gene pools, suggesting that domesticated gene pools were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. Although most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated the two-row and six-row types associated with different geographical origins. Within the pericentromeric regions we identified 22 387 non-synonymous SNPs, 92 of which were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be 'highly deleterious'. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools, with different evolutionary processes driving domestication and diversification.
Collapse
Affiliation(s)
- Yun‐Yu Chen
- The James Hutton Institute, InvergowrieDundeeDD2 5DAUK
- Fios GenomicsBioQuarter, 13 Little France RdEdinburghEH16 4UXUK
| | - Miriam Schreiber
- The James Hutton Institute, InvergowrieDundeeDD2 5DAUK
- Division of Plant Sciences, School of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
| | | | - Ian K. Dawson
- The James Hutton Institute, InvergowrieDundeeDD2 5DAUK
- Scotland's Rural College, Kings BuildingsWest Mains RdEdinburghEH9 3JGUK
| | | | - Li Lei
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Alina Akhunova
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
- Department of Plant PathologyKansas State UniversityThrockmorton HallManhattanKS66506USA
| | - Chaochih Liu
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Kevin P. Smith
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Justin C. Fay
- Department of BiologyUniversity of Rochester319 HutchisonRochesterNY14627USA
| | - Gary J. Muehlbauer
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Brian J. Steffenson
- Department of Plant PathologyUniversity of Minnesota495 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Peter L. Morrell
- Department of Agronomy & Plant GeneticsUniversity of Minnesota411 Borlaug Hall, 1991 Buford CircleSt PaulMN55108USA
| | - Robbie Waugh
- The James Hutton Institute, InvergowrieDundeeDD2 5DAUK
- Division of Plant Sciences, School of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
| | | |
Collapse
|
11
|
Hager ER, Harringmeyer OS, Wooldridge TB, Theingi S, Gable JT, McFadden S, Neugeboren B, Turner KM, Jensen JD, Hoekstra HE. A chromosomal inversion contributes to divergence in multiple traits between deer mouse ecotypes. Science 2022; 377:399-405. [PMID: 35862520 DOI: 10.1126/science.abg0718] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
How locally adapted ecotypes are established and maintained within a species is a long-standing question in evolutionary biology. Using forest and prairie ecotypes of deer mice (Peromyscus maniculatus), we characterized the genetic basis of variation in two defining traits-tail length and coat color-and discovered a 41-megabase chromosomal inversion linked to both. The inversion frequency is 90% in the dark, long-tailed forest ecotype; decreases across a habitat transition; and is absent from the light, short-tailed prairie ecotype. We implicate divergent selection in maintaining the inversion at frequencies observed in the wild, despite high levels of gene flow, and explore fitness benefits that arise from suppressed recombination within the inversion. We uncover a key role for a large, previously uncharacterized inversion in the evolution and maintenance of classic mammalian ecotypes.
Collapse
Affiliation(s)
- Emily R Hager
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Olivia S Harringmeyer
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - T Brock Wooldridge
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Shunn Theingi
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jacob T Gable
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Sade McFadden
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Beverly Neugeboren
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kyle M Turner
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Hopi E Hoekstra
- Department of Molecular and Cellular Biology, Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
12
|
Ferrari G, Atmore LM, Jentoft S, Jakobsen KS, Makowiecki D, Barrett JH, Star B. An accurate assignment test for extremely low-coverage whole-genome sequence data. Mol Ecol Resour 2021; 22:1330-1344. [PMID: 34779123 DOI: 10.1111/1755-0998.13551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.
Collapse
Affiliation(s)
- Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M Atmore
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Daniel Makowiecki
- Department of Environmental Archaeology and Human Paleoecology, Institute of Archaeology, Nicolaus Copernicus University, Torun, Poland
| | - James H Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge, UK.,Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
13
|
Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree. Proc Natl Acad Sci U S A 2021; 118:2102914118. [PMID: 34408075 DOI: 10.1073/pnas.2102914118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic structural variants (SVs) can play important roles in adaptation and speciation. Yet the overall fitness effects of SVs are poorly understood, partly because accurate population-level identification of SVs requires multiple high-quality genome assemblies. Here, we use 31 chromosome-scale, haplotype-resolved genome assemblies of Theobroma cacao-an outcrossing, long-lived tree species that is the source of chocolate-to investigate the fitness consequences of SVs in natural populations. Among the 31 accessions, we find over 160,000 SVs, which together cover eight times more of the genome than single-nucleotide polymorphisms and short indels (125 versus 15 Mb). Our results indicate that a vast majority of these SVs are deleterious: they segregate at low frequencies and are depleted from functional regions of the genome. We show that SVs influence gene expression, which likely impairs gene function and contributes to the detrimental effects of SVs. We also provide empirical support for a theoretical prediction that SVs, particularly inversions, increase genetic load through the accumulation of deleterious nucleotide variants as a result of suppressed recombination. Despite the overall detrimental effects, we identify individual SVs bearing signatures of local adaptation, several of which are associated with genes differentially expressed between populations. Genes involved in pathogen resistance are strongly enriched among these candidates, highlighting the contribution of SVs to this important local adaptation trait. Beyond revealing empirical evidence for the evolutionary importance of SVs, these 31 de novo assemblies provide a valuable resource for genetic and breeding studies in T cacao.
Collapse
|
14
|
Ranavat S, Becher H, Newman MF, Gowda V, Twyford AD. A Draft Genome of the Ginger Species Alpinia nigra and New Insights into the Genetic Basis of Flexistyly. Genes (Basel) 2021; 12:1297. [PMID: 34573279 PMCID: PMC8468202 DOI: 10.3390/genes12091297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022] Open
Abstract
Angiosperms possess various strategies to ensure reproductive success, such as stylar polymorphisms that encourage outcrossing. Here, we investigate the genetic basis of one such dimorphism that combines both temporal and spatial separation of sexual function, termed flexistyly. It is a floral strategy characterised by the presence of two morphs that differ in the timing of stylar movement. We performed a de novo assembly of the genome of Alpinia nigra using high-depth genomic sequencing. We then used Pool-seq to identify candidate regions for flexistyly based on allele frequency or coverage differences between pools of anaflexistylous and cataflexistylous morphs. The final genome assembly size was 2 Gb, and showed no evidence of recent polyploidy. The Pool-seq did not reveal large regions with high FST values, suggesting large structural chromosomal polymorphisms are unlikely to underlie differences between morphs. Similarly, no region had a 1:2 mapping depth ratio which would be indicative of hemizygosity. We propose that flexistyly is governed by a small genomic region that might be difficult to detect with Pool-seq, or a complex genomic region that proved difficult to assemble. Our genome will be a valuable resource for future studies of gingers, and provides the first steps towards characterising this complex floral phenotype.
Collapse
Affiliation(s)
- Surabhi Ranavat
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (H.B.); (A.D.T.)
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK;
| | - Hannes Becher
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (H.B.); (A.D.T.)
| | - Mark F. Newman
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK;
| | - Vinita Gowda
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India;
| | - Alex D. Twyford
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (H.B.); (A.D.T.)
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK;
| |
Collapse
|
15
|
Mérot C, Berdan EL, Cayuela H, Djambazian H, Ferchaud AL, Laporte M, Normandeau E, Ragoussis J, Wellenreuther M, Bernatchez L. Locally Adaptive Inversions Modulate Genetic Variation at Different Geographic Scales in a Seaweed Fly. Mol Biol Evol 2021; 38:3953-3971. [PMID: 33963409 PMCID: PMC8382925 DOI: 10.1093/molbev/msab143] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci at a potentially massive scale. In this study, we examined how chromosomal inversions shape genetic variation across a species range and ask how their contribution to adaptation in the face of gene flow varies across geographic scales. We sampled the seaweed fly Coelopa frigida along a bioclimatic gradient stretching across 10° of latitude, a salinity gradient, and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyze 1,446 low-coverage whole genomes collected along those gradients. We found several large nonrecombining genomic regions, including putative inversions. In contrast to the collinear regions, inversions and low-recombining regions differentiated populations more strongly, either along an ecogeographic cline or at a fine-grained scale. These genomic regions were associated with environmental factors and adaptive phenotypes, albeit with contrasting patterns. Altogether, our results highlight the importance of recombination in shaping adaptation to environmental heterogeneity at local and large scales.
Collapse
Affiliation(s)
- Claire Mérot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Emma L Berdan
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Hugo Cayuela
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Anne-Laure Ferchaud
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Martin Laporte
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | | | - Maren Wellenreuther
- Seafood Research Unit, Plant & Food Research, Port Nelson, Nelson, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| |
Collapse
|
16
|
The genomic basis of geographic differentiation and fiber improvement in cultivated cotton. Nat Genet 2021; 53:916-924. [PMID: 33859417 DOI: 10.1038/s41588-021-00844-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/15/2021] [Indexed: 02/02/2023]
Abstract
Large-scale genomic surveys of crop germplasm are important for understanding the genetic architecture of favorable traits. The genomic basis of geographic differentiation and fiber improvement in cultivated cotton is poorly understood. Here, we analyzed 3,248 tetraploid cotton genomes and confirmed that the extensive chromosome inversions on chromosomes A06 and A08 underlies the geographic differentiation in cultivated Gossypium hirsutum. We further revealed that the haplotypic diversity originated from landraces, which might be essential for understanding adaptative evolution in cultivated cotton. Introgression and association analyses identified new fiber quality-related loci and demonstrated that the introgressed alleles from two diploid cottons had a large effect on fiber quality improvement. These loci provided the potential power to overcome the bottleneck in fiber quality improvement. Our study uncovered several critical genomic signatures generated by historical breeding effects in cotton and a wealth of data that enrich genomic resources for the research community.
Collapse
|
17
|
Ngoot-Chin T, Zulkifli MA, van de Weg E, Zaki NM, Serdari NM, Mustaffa S, Zainol Abidin MI, Sanusi NSNM, Smulders MJM, Low ETL, Ithnin M, Singh R. Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers. PLANTA 2021; 253:63. [PMID: 33544231 DOI: 10.1007/s00425-021-03567-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/04/2021] [Indexed: 05/14/2023]
Abstract
Karyotyping using high-density genome-wide SNP markers identified various chromosomal aberrations in oil palm (Elaeis guineensis Jacq.) with supporting evidence from the 2C DNA content measurements (determined using FCM) and chromosome counts. Oil palm produces a quarter of the world's total vegetable oil. In line with its global importance, an initiative to sequence the oil palm genome was carried out successfully, producing huge amounts of sequence information, allowing SNP discovery. High-capacity SNP genotyping platforms have been widely used for marker-trait association studies in oil palm. Besides genotyping, a SNP array is also an attractive tool for understanding aberrations in chromosome inheritance. Exploiting this, the present study utilized chromosome-wide SNP allelic distributions to determine the ploidy composition of over 1,000 oil palms from a commercial F1 family, including 197 derived from twin-embryo seeds. Our method consisted of an inspection of the allelic intensity ratio using SNP markers. For palms with a shifted or abnormal distribution ratio, the SNP allelic frequencies were plotted along the pseudo-chromosomes. This method proved to be efficient in identifying whole genome duplication (triploids) and aneuploidy. We also detected several loss of heterozygosity regions which may indicate small chromosomal deletions and/or inheritance of identical by descent regions from both parents. The SNP analysis was validated by flow cytometry and chromosome counts. The triploids were all derived from twin-embryo seeds. This is the first report on the efficiency and reliability of SNP array data for karyotyping oil palm chromosomes, as an alternative to the conventional cytogenetic technique. Information on the ploidy composition and chromosomal structural variation can help to better understand the genetic makeup of samples and lead to a more robust interpretation of the genomic data in marker-trait association analyses.
Collapse
Affiliation(s)
- Ting Ngoot-Chin
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Muhammad Azwan Zulkifli
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Noorhariza Mohd Zaki
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Norhalida Mohamed Serdari
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Suzana Mustaffa
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mohd Isa Zainol Abidin
- Plant Breeding and Services Department, KULIM Plantations Berhad, 81900, Kota Tinggi, Johor, Malaysia
| | - Nik Shazana Nik Mohd Sanusi
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | | | - Eng Ti Leslie Low
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Maizura Ithnin
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| |
Collapse
|
18
|
Rönspies M, Schindele P, Puchta H. CRISPR/Cas-mediated chromosome engineering: opening up a new avenue for plant breeding. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:177-183. [PMID: 33258473 DOI: 10.1093/jxb/eraa463] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/03/2020] [Indexed: 05/21/2023]
Abstract
The advent of powerful site-specific nucleases, particularly the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system, which enables precise genome manipulation, has revolutionized plant breeding. Until recently, the main focus of researchers has been to simply knock-in or knock-out single genes, or to induce single base changes, but constant improvements of this technology have enabled more ambitious applications that aim to improve plant productivity or other desirable traits. One long-standing aim has been the induction of targeted chromosomal rearrangements (crossovers, inversions, or translocations). The feasibility of this technique has the potential to transform plant breeding, because natural rearrangements, like inversions, for example, typically present obstacles to the breeding process. In this way, genetic linkages between traits could be altered to combine or separate favorable and deleterious genes, respectively. In this review, we discuss recent breakthroughs in the field of chromosome engineering in plants and their potential applications in the field of plant breeding. In the future, these approaches might be applicable in shaping plant chromosomes in a directed manner, based on plant breeding needs.
Collapse
Affiliation(s)
- Michelle Rönspies
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg, Karlsruhe, Germany
| | - Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg, Karlsruhe, Germany
| |
Collapse
|
19
|
Dai P, Sun G, Jia Y, Pan Z, Tian Y, Peng Z, Li H, He S, Du X. Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3273-3285. [PMID: 32844253 DOI: 10.1007/s00122-020-03668-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/08/2020] [Indexed: 05/06/2023]
Abstract
Three extensive eco-haplotypes associated with population differentiation and environmental adaptability in Upland cotton were identified, with A06_85658585, A08_43734499 and A06_113104285 considered the eco-loci for environmental adaptability. Population divergence is suggested to be the primary force driving the evolution of environmental adaptability in various species. Chromosome inversion increases reproductive isolation between subspecies and accelerates population divergence to adapt to new environments. Although modern cultivated Upland cotton (Gossypium hirsutum L.) has spread worldwide, the noticeable phenotypic differences still existed among cultivars grown in different areas. In recent years, the long-distance migration of cotton cultivation areas throughout China has demanded that breeders better understand the genetic basis of environmental adaptability in Upland cotton. Here, we integrated the genotypes of 419 diverse accessions, long-term environment-associated variables (EAVs) and environment-associated traits (EATs) to evaluate subgroup differentiation and identify adaptive loci in Upland cotton. Two highly divergent genomic regions were found on chromosomes A06 and A08, which likely caused by extensive chromosome inversions. The subgroups could be geographically classified based on distinct haplotypes in the divergent regions. A genome-wide association study (GWAS) also confirmed that loci located in these regions were significantly associated with environmental adaptability in Upland cotton. Our study first revealed the cause of population divergence in Upland cotton, as well as the consequences of variation in its environmental adaptability. These findings provide new insights into the genetic basis of environmental adaptability in Upland cotton, which could accelerate the development of molecular markers for adaptation to climate change in future cotton breeding.
Collapse
Affiliation(s)
- Panhong Dai
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Agricultural College, Yangtze University, Jingzhou, 434000, China
| | - Gaofei Sun
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- School of Computer Science & Information Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Yinhua Jia
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhaoe Pan
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yingbing Tian
- Agricultural College, Yangtze University, Jingzhou, 434000, China
| | - Zhen Peng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Hongge Li
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Shoupu He
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
| | - Xiongming Du
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
| |
Collapse
|
20
|
Schmidt C, Fransz P, Rönspies M, Dreissig S, Fuchs J, Heckmann S, Houben A, Puchta H. Changing local recombination patterns in Arabidopsis by CRISPR/Cas mediated chromosome engineering. Nat Commun 2020. [PMID: 32887885 DOI: 10.10382/fs41467-020-18277-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
Chromosomal inversions are recurrent rearrangements that occur between different plant isolates or cultivars. Such inversions may underlie reproductive isolation in evolution and represent a major obstacle for classical breeding as no crossovers can be observed between inverted sequences on homologous chromosomes. The heterochromatic knob (hk4S) on chromosome 4 is the most well-known inversion of Arabidopsis. If a knob carrying accession such as Col-0 is crossed with a knob-less accession such as Ler-1, crossovers cannot be recovered within the inverted region. Our work shows that by egg-cell specific expression of the Cas9 nuclease from Staphylococcus aureus, a targeted reversal of the 1.1 Mb long hk4S-inversion can be achieved. By crossing Col-0 harbouring the rearranged chromosome 4 with Ler-1, meiotic crossovers can be restored into a region with previously no detectable genetic exchange. The strategy of somatic chromosome engineering for breaking genetic linkage has huge potential for application in plant breeding.
Collapse
Affiliation(s)
- Carla Schmidt
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76133, Karlsruhe, Germany
| | - Paul Fransz
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute of Life Sciences, University of Amsterdam, Postbus 1210, 1000 BE, Amsterdam, Netherlands
| | - Michelle Rönspies
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76133, Karlsruhe, Germany
| | - Steven Dreissig
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle Wittenberg, Karl-Freiherr-von-Fritsch-Str. 4, 06120, Halle, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Gatersleben, Germany
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Gatersleben, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstraße 3, 06466, Gatersleben, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76133, Karlsruhe, Germany.
| |
Collapse
|
21
|
Changing local recombination patterns in Arabidopsis by CRISPR/Cas mediated chromosome engineering. Nat Commun 2020; 11:4418. [PMID: 32887885 PMCID: PMC7474074 DOI: 10.1038/s41467-020-18277-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/12/2020] [Indexed: 01/20/2023] Open
Abstract
Chromosomal inversions are recurrent rearrangements that occur between different plant isolates or cultivars. Such inversions may underlie reproductive isolation in evolution and represent a major obstacle for classical breeding as no crossovers can be observed between inverted sequences on homologous chromosomes. The heterochromatic knob (hk4S) on chromosome 4 is the most well-known inversion of Arabidopsis. If a knob carrying accession such as Col-0 is crossed with a knob-less accession such as Ler-1, crossovers cannot be recovered within the inverted region. Our work shows that by egg-cell specific expression of the Cas9 nuclease from Staphylococcus aureus, a targeted reversal of the 1.1 Mb long hk4S-inversion can be achieved. By crossing Col-0 harbouring the rearranged chromosome 4 with Ler-1, meiotic crossovers can be restored into a region with previously no detectable genetic exchange. The strategy of somatic chromosome engineering for breaking genetic linkage has huge potential for application in plant breeding.
Collapse
|
22
|
Wilder AP, Palumbi SR, Conover DO, Therkildsen NO. Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome. Evol Lett 2020; 4:430-443. [PMID: 33014419 PMCID: PMC7523562 DOI: 10.1002/evl3.189] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/09/2020] [Accepted: 07/13/2020] [Indexed: 11/09/2022] Open
Abstract
The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome‐wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity for rapid adaptation from standing genetic variation, but we know little about the patterns of genomic variation across the species range that enable this remarkable adaptability. Here, we use low‐coverage, whole‐transcriptome sequencing of Atlantic silversides sampled along an environmental cline to show marked signatures of divergent selection across a gradient of neutral differentiation. Atlantic silversides sampled across 1371 km of the southern section of its distribution have very low genome‐wide differentiation (median FST = 0.006 across 1.9 million variants), consistent with historical connectivity and observations of recent migrants. Yet almost 14,000 single nucleotide polymorphisms (SNPs) are nearly fixed (FST > 0.95) for alternate alleles. Highly differentiated SNPs cluster into four tight linkage disequilibrium (LD) blocks that span hundreds of genes and several megabases. Variants in these LD blocks are disproportionately nonsynonymous and concentrated in genes enriched for multiple functions related to known adaptations in silversides, including variation in lipid storage, metabolic rate, and spawning behavior. Elevated levels of absolute divergence and demographic modeling suggest selection maintaining divergence across these blocks under gene flow. These findings represent an extreme case of heterogeneity in levels of differentiation across the genome, and highlight how gene flow shapes genomic architecture in continuous populations. Locally adapted alleles may be common features of populations distributed along environmental gradients, and will likely be key to conserving variation to enable future responses to environmental change.
Collapse
Affiliation(s)
- Aryn P Wilder
- Department of Natural Resources Cornell University Ithaca New York 14853.,Current address: San Diego Zoo Institute for Conservation Research Escondido California 92027
| | - Stephen R Palumbi
- Department of Biology, Hopkins Marine Station Stanford University Pacific Grove California 93950
| | - David O Conover
- Department of Biology University of Oregon Eugene Oregon 97403
| | | |
Collapse
|
23
|
Zhou Y, Gaut BS. Large chromosomal variants drive adaptation in sunflowers. NATURE PLANTS 2020; 6:734-735. [PMID: 32665649 DOI: 10.1038/s41477-020-0705-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA.
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA.
| |
Collapse
|
24
|
Pan Y, Wen C, Han Y, Wang Y, Li Y, Li S, Cheng X, Weng Y. QTL for horticulturally important traits associated with pleiotropic andromonoecy and carpel number loci, and a paracentric inversion in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2271-2290. [PMID: 32306094 DOI: 10.1007/s00122-020-03596-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/05/2020] [Indexed: 06/11/2023]
Abstract
The legendary cucumber inbred line WI2757 possesses a rare combination of resistances against nine pathogens, which is an important germplasm for cucumber breeding. However, WI2757 flowers late and does not perform well under field conditions. The genetic basis for horticulturally important traits other than disease resistances in WI2757 is largely unknown. In this study, we conducted QTL mapping using F2 and recombinant inbred line (RIL) populations from the WI2757 × True Lemon cross that were segregating for multiple traits. Phenotypic data were collected in replicated field trials across multiple years for seven traits including fruit carpel number (CN) and sex expression. A high-density SNP-based genetic map was developed with genotyping by sequencing of the RIL population, which revealed a region on chromosome 1 with strong recombination suppression. The reduced recombination in this region was due to a ~ 10-Mbp paracentric inversion in WI2757 that was confirmed with additional segregation and cytological (FISH) analyses. Thirty-six QTL were detected for flowering time, fruit length (FL), fruit diameter (FD), fruit shape (LD), fruit number (FN), CN, and powdery mildew resistance. Five moderate- or major-effect QTL for FL, FD, LD, and FN inside the inversion are likely the pleiotropic effects of the andromonoecy (m), or the cn locus. The major-effect flowering time QTL ft1.1 was also mapped inside the inversion, which seems to be different from the previously assigned delayed flowering in WI2757. Implications of these findings on the use of WI2757 in cucumber breeding are discussed.
Collapse
Affiliation(s)
- Yupeng Pan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Changlong Wen
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Yonghua Han
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Yuhui Wang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sen Li
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Horticulture College, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiaomao Cheng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yiqun Weng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, 1575 Linden Dr., Madison, WI, 53706, USA.
| |
Collapse
|
25
|
Silva JC, Soares FAF, Sattler MC, Clarindo WR. Repetitive sequences and structural chromosome alterations promote intraspecific variations in Zea mays L. karyotype. Sci Rep 2020; 10:8866. [PMID: 32483238 PMCID: PMC7264354 DOI: 10.1038/s41598-020-65779-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/07/2020] [Indexed: 12/02/2022] Open
Abstract
LTR-retrotransposons, knobs and structural chromosome alterations contribute to shape the structure and organization of the Zea mays karyotype. Our initial nuclear DNA content data of Z. mays accessions revealed an intraspecific variation (2 C = 2.00 pg to 2 C = 6.10 pg), suggesting differences in their karyotypes. We aimed to compare the karyotypes of three Z. mays accessions in search of the differences and similarities among them. Karyotype divergences were demonstrated among the accessions, despite their common chromosome number (2n = 20) and ancestral origin. Cytogenomic analyses showed that repetitive sequences and structural chromosome alterations play a significant role in promoting intraspecific nuclear DNA content variation. In addition, heterozygous terminal deletion in chromosome 3 was pointed out as a cause of lower nuclear 2 C value. Besides this, translocation was also observed in the short arm of chromosome 1. Differently, higher 2 C value was associated with the more abundant distribution of LTR-retrotransposons from the family Grande in the karyotype. Moreover, heteromorphism involving the number and position of the 180-bp knob sequence was found among the accessions. Taken together, we provide insights on the pivotal role played by repetitive sequences and structural chromosome alterations in shaping the karyotype of Z. mays.
Collapse
Affiliation(s)
- Jéssica Coutinho Silva
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil.
| | - Fernanda Aparecida Ferrari Soares
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil
| | - Mariana Cansian Sattler
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil
| | - Wellington Ronildo Clarindo
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, ZIP 36570-900, Viçosa, MG, Brazil
| |
Collapse
|
26
|
Chen Q, Samayoa LF, Yang CJ, Bradbury PJ, Olukolu BA, Neumeyer MA, Romay MC, Sun Q, Lorant A, Buckler ES, Ross-Ibarra J, Holland JB, Doebley JF. The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication. PLoS Genet 2020; 16:e1008791. [PMID: 32407310 PMCID: PMC7266358 DOI: 10.1371/journal.pgen.1008791] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/02/2020] [Accepted: 04/22/2020] [Indexed: 11/19/2022] Open
Abstract
The genetics of domestication has been extensively studied ever since the rediscovery of Mendel's law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication. We also observed more dominance in maize than teosinte, likely a consequence of selective removal of additive variants. We observed that large effect QTL have low minor allele frequency (MAF) in both maize and teosinte. Regions of the genome that are strongly differentiated between teosinte and maize (high FST) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. We also observed that genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication. Finally, we observed that about 75% of the additive variance in both teosinte and maize is "missing" in the sense that it cannot be ascribed to detectable QTL and only 25% of variance maps to specific QTL. This latter result suggests that morphological evolution during domestication is largely attributable to very large numbers of QTL of very small effect.
Collapse
Affiliation(s)
- Qiuyue Chen
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Luis Fernando Samayoa
- Department of Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Chin Jian Yang
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Peter J. Bradbury
- US Department of Agriculture–Agricultural Research Service, Cornell University, Ithaca, New York, United States of America
| | - Bode A. Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Michael A. Neumeyer
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Maria Cinta Romay
- Genomic Diversity Facility, Cornell University, Ithaca, New York, United States of America
| | - Qi Sun
- Genomic Diversity Facility, Cornell University, Ithaca, New York, United States of America
| | - Anne Lorant
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Edward S. Buckler
- US Department of Agriculture–Agricultural Research Service, Cornell University, Ithaca, New York, United States of America
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - James B. Holland
- Department of Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America
- US Department of Agriculture–Agricultural Research Service Plant Science Research Unit, North Carolina State University, Raleigh, North Carolina, United States of America
| | - John F. Doebley
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
27
|
A universal chromosome identification system for maize and wild Zea species. Chromosome Res 2020; 28:183-194. [PMID: 32219602 DOI: 10.1007/s10577-020-09630-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/16/2022]
Abstract
Maize was one of the first eukaryotic species in which individual chromosomes can be identified cytologically, which made maize one of the oldest models for genetics and cytogenetics research. Nevertheless, consistent identification of all 10 chromosomes from different maize lines as well as from wild Zea species remains a challenge. We developed a new technique for maize chromosome identification based on fluorescence in situ hybridization (FISH). We developed two oligonucleotide-based probes that hybridize to 24 chromosomal regions. Individual maize chromosomes show distinct FISH signal patterns, which allow universal identification of all chromosomes from different Zea species. We developed karyotypes from three Zea mays subspecies and two additional wild Zea species based on individually identified chromosomes. A paracentric inversion was discovered on the long arm of chromosome 4 in Z. nicaraguensis and Z. luxurians based on modifications of the FISH signal patterns. Chromosomes from these two species also showed distinct distribution patterns of terminal knobs compared with other Zea species. These results support that Z. nicaraguensis and Z. luxurians are closely related species.
Collapse
|
28
|
Huang K, Rieseberg LH. Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:296. [PMID: 32256515 DOI: 10.3389/fpls.2020.00296/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/27/2020] [Indexed: 05/24/2023]
Abstract
Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.
Collapse
Affiliation(s)
- Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
29
|
Huang K, Rieseberg LH. Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:296. [PMID: 32256515 PMCID: PMC7093584 DOI: 10.3389/fpls.2020.00296] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/27/2020] [Indexed: 05/11/2023]
Abstract
Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.
Collapse
Affiliation(s)
- Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
30
|
Schmidt C, Schindele P, Puchta H. From gene editing to genome engineering: restructuring plant chromosomes via CRISPR/Cas. ABIOTECH 2020; 1:21-31. [PMID: 36305002 PMCID: PMC9584095 DOI: 10.1007/s42994-019-00002-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/03/2019] [Indexed: 01/16/2023]
Abstract
In the last years, tremendous progress has been achieved in the field of gene editing in plants. By the induction of single site-specific double-strand breaks (DSBs), the knockout of genes by non-homologous end joining has become routine in many plant species. Recently, the efficiency of inducing pre-planned mutations by homologous recombination has also been improved considerably. However, very little effort has been undertaken until now to achieve more complex changes in plant genomes by the simultaneous induction of several DSBs. Several reports have been published on the efficient induction of deletions. However, the induction of intrachromosomal inversions and interchromosomal recombination by the use of CRISPR/Cas has only recently been reported. In this review, we want to sum up these results and put them into context with regards to what is known about natural chromosome rearrangements in plants. Moreover, we review the recent progress in CRISPR/Cas-based mammalian chromosomal rearrangements, which might be inspiring for plant biologists. In the long run, the controlled restructuring of plant genomes should enable us to link or break linkage of traits at will, thus defining a new area of plant breeding.
Collapse
Affiliation(s)
- Carla Schmidt
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76133 Karlsruhe, Germany
| | - Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76133 Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76133 Karlsruhe, Germany
| |
Collapse
|
31
|
Abstract
Maize is an excellent model for the study of plant adaptation. Indeed, post domestication maize quickly adapted to a host of new environments across the globe. And work over the last decade has begun to highlight the role of the wild relatives of maize-the teosintes Zea mays ssp. parviglumis and ssp. mexicana-as excellent models for dissecting long-term local adaptation.Although human-driven selection associated with maize domestication has been extensively studied, the genetic basis of natural variation is still poorly understood. Here we review studies on the genetic basis of adaptation and plasticity in maize and its wild relatives. We highlight a range of different processes that contribute to adaptation and discuss evidence from natural, cultivated, and experimental populations. From an applied perspective, understanding the genetic bases of adaptation and the contribution of plasticity will provide us with new tools to both better understand and mitigate the effect of climate changes on natural and cultivated populations.
Collapse
|
32
|
Fustier MA, Martínez-Ainsworth NE, Aguirre-Liguori JA, Venon A, Corti H, Rousselet A, Dumas F, Dittberner H, Camarena MG, Grimanelli D, Ovaskainen O, Falque M, Moreau L, de Meaux J, Montes-Hernández S, Eguiarte LE, Vigouroux Y, Manicacci D, Tenaillon MI. Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude. PLoS Genet 2019; 15:e1008512. [PMID: 31860672 PMCID: PMC6944379 DOI: 10.1371/journal.pgen.1008512] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 01/06/2020] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
In plants, local adaptation across species range is frequent. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Genome scans are popular to uncover outlier loci potentially involved in the genetic architecture of local adaptation, however links between outliers and phenotypic variation are rarely addressed. Here we focused on adaptation of teosinte populations along two elevation gradients in Mexico that display continuous environmental changes at a short geographical scale. We used two common gardens, and phenotyped 18 traits in 1664 plants from 11 populations of annual teosintes. In parallel, we genotyped these plants for 38 microsatellite markers as well as for 171 outlier single nucleotide polymorphisms (SNPs) that displayed excess of allele differentiation between pairs of lowland and highland populations and/or correlation with environmental variables. Our results revealed that phenotypic differentiation at 10 out of the 18 traits was driven by local selection. Trait covariation along the elevation gradient indicated that adaptation to altitude results from the assembly of multiple co-adapted traits into a complex syndrome: as elevation increases, plants flower earlier, produce less tillers, display lower stomata density and carry larger, longer and heavier grains. The proportion of outlier SNPs associating with phenotypic variation, however, largely depended on whether we considered a neutral structure with 5 genetic groups (73.7%) or 11 populations (13.5%), indicating that population stratification greatly affected our results. Finally, chromosomal inversions were enriched for both SNPs whose allele frequencies shifted along elevation as well as phenotypically-associated SNPs. Altogether, our results are consistent with the establishment of an altitudinal syndrome promoted by local selective forces in teosinte populations in spite of detectable gene flow. Because elevation mimics climate change through space, SNPs that we found underlying phenotypic variation at adaptive traits may be relevant for future maize breeding.
Collapse
Affiliation(s)
- Margaux-Alison Fustier
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Natalia E. Martínez-Ainsworth
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Jonás A. Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Anthony Venon
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Hélène Corti
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Agnès Rousselet
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Fabrice Dumas
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Hannes Dittberner
- Institute of Botany, University of Cologne Biocenter, Cologne, Germany
| | - María G. Camarena
- Campo Experimental Bajío, InstitutoNacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Mexico
| | - Daniel Grimanelli
- UMR Diversité, Adaptation et Développement des plantes, Université de Montpellier, Institut de Recherche pour le développement, Montpellier, France
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Matthieu Falque
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Laurence Moreau
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Juliette de Meaux
- Institute of Botany, University of Cologne Biocenter, Cologne, Germany
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, InstitutoNacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Yves Vigouroux
- UMR Diversité, Adaptation et Développement des plantes, Université de Montpellier, Institut de Recherche pour le développement, Montpellier, France
| | - Domenica Manicacci
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Maud I. Tenaillon
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| |
Collapse
|
33
|
Rowan BA, Heavens D, Feuerborn TR, Tock AJ, Henderson IR, Weigel D. An Ultra High-Density Arabidopsis thaliana Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features. Genetics 2019; 213:771-787. [PMID: 31527048 PMCID: PMC6827372 DOI: 10.1534/genetics.119.302406] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/28/2019] [Indexed: 11/18/2022] Open
Abstract
Many environmental, genetic, and epigenetic factors are known to affect the frequency and positioning of meiotic crossovers (COs). Suppression of COs by large, cytologically visible inversions and translocations has long been recognized, but relatively little is known about how smaller structural variants (SVs) affect COs. To examine fine-scale determinants of the CO landscape, including SVs, we used a rapid, cost-effective method for high-throughput sequencing to generate a precise map of >17,000 COs between the Col-0 and Ler-0 accessions of Arabidopsis thaliana COs were generally suppressed in regions with SVs, but this effect did not depend on the size of the variant region, and was only marginally affected by the variant type. CO suppression did not extend far beyond the SV borders and CO rates were slightly elevated in the flanking regions. Disease resistance gene clusters, which often exist as SVs, exhibited high CO rates at some loci, but there was a tendency toward depressed CO rates at loci where large structural differences exist between the two parents. Our high-density map also revealed in fine detail how CO positioning relates to genetic (DNA motifs) and epigenetic (chromatin structure) features of the genome. We conclude that suppression of COs occurs over a narrow region spanning large- and small-scale SVs, representing an influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.
Collapse
Affiliation(s)
- Beth A Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | | | - Tatiana R Feuerborn
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Andrew J Tock
- Department of Plant Sciences, University of Cambridge, CB2 3EA, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, CB2 3EA, United Kingdom
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| |
Collapse
|
34
|
Lei L, Poets AM, Liu C, Wyant SR, Hoffman PJ, Carter CK, Shaw BG, Li X, Muehlbauer GJ, Katagiri F, Morrell PL. Environmental Association Identifies Candidates for Tolerance to Low Temperature and Drought. G3 (BETHESDA, MD.) 2019; 9:3423-3438. [PMID: 31439717 PMCID: PMC6778781 DOI: 10.1534/g3.119.400401] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/17/2019] [Indexed: 11/24/2022]
Abstract
Barley (Hordeum vulgare ssp. vulgare) is cultivated from the equator to the Arctic Circle. The wild progenitor species, Hordeum vulgare ssp. spontaneum, occupies a relatively narrow latitudinal range (∼30 - 40° N) primarily at low elevation (< 1,500 m). Adaptation to the range of cultivation has occurred over ∼8,000 years. The genetic basis of adaptation is amenable to study through environmental association. An advantage of environmental association in a well-characterized crop is that many loci that contribute to climatic adaptation and abiotic stress tolerance have already been identified. This provides the opportunity to determine if environmental association approaches effectively identify these loci of large effect. Using published genotyping from 7,864 SNPs in 803 barley landraces, we examined allele frequency differentiation across multiple partitions of the data and mixed model associations relative to bioclimatic variables. Using newly generated resequencing data from a subset of these landraces, we tested for linkage disequilibrium (LD) between SNPs queried in genotyping and SNPs in neighboring loci. Six loci previously reported to contribute to adaptive differences in flowering time and abiotic stress in barley and six loci previously identified in other plant species were identified in our analyses. In many cases, patterns of LD are consistent with the causative variant occurring in the immediate vicinity of the queried SNP. The identification of barley orthologs to well-characterized genes may provide a new understanding of the nature of adaptive variation and could permit a more targeted use of potentially adaptive variants in barley breeding and germplasm improvement.
Collapse
Affiliation(s)
- Li Lei
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Ana M Poets
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Skylar R Wyant
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Paul J Hoffman
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Corey K Carter
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Brian G Shaw
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Xin Li
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota 55108
| | - Fumiaki Katagiri
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| |
Collapse
|
35
|
MacQueen A, Tian D, Chang W, Holub E, Kreitman M, Bergelson J. Population Genetics of the Highly Polymorphic RPP8 Gene Family. Genes (Basel) 2019; 10:genes10090691. [PMID: 31500388 PMCID: PMC6771003 DOI: 10.3390/genes10090691] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/31/2019] [Accepted: 09/03/2019] [Indexed: 02/06/2023] Open
Abstract
Plant nucleotide-binding domain and leucine-rich repeat containing (NLR) genes provide some of the most extreme examples of polymorphism in eukaryotic genomes, rivalling even the vertebrate major histocompatibility complex. Surprisingly, this is also true in Arabidopsis thaliana, a predominantly selfing species with low heterozygosity. Here, we investigate how gene duplication and intergenic exchange contribute to this extraordinary variation. RPP8 is a three-locus system that is configured chromosomally as either a direct-repeat tandem duplication or as a single copy locus, plus a locus 2 Mb distant. We sequenced 48 RPP8 alleles from 37 accessions of A. thaliana and 12 RPP8 alleles from Arabidopsis lyrata to investigate the patterns of interlocus shared variation. The tandem duplicates display fixed differences and share less variation with each other than either shares with the distant paralog. A high level of shared polymorphism among alleles at one of the tandem duplicates, the single-copy locus and the distal locus, must involve both classical crossing over and intergenic gene conversion. Despite these polymorphism-enhancing mechanisms, the observed nucleotide diversity could not be replicated under neutral forward-in-time simulations. Only by adding balancing selection to the simulations do they approach the level of polymorphism observed at RPP8. In this NLR gene triad, genetic architecture, gene function and selection all combine to generate diversity.
Collapse
Affiliation(s)
- Alice MacQueen
- Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210008, China.
| | - Wenhan Chang
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA.
| | - Eric Holub
- School of Life Sciences, Wellesbourne Innovation Campus, University of Warwick, Wellesbourne CV359EF, UK.
| | - Martin Kreitman
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA.
| | - Joy Bergelson
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
36
|
Xue W, Anderson SN, Wang X, Yang L, Crisp PA, Li Q, Noshay J, Albert PS, Birchler JA, Bilinski P, Stitzer MC, Ross-Ibarra J, Flint-Garcia S, Chen X, Springer NM, Doebley JF. Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize. Genetics 2019; 213:143-160. [PMID: 31320409 PMCID: PMC6727801 DOI: 10.1534/genetics.119.302378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/03/2019] [Indexed: 11/18/2022] Open
Abstract
In the course of generating populations of maize with teosinte chromosomal introgressions, an unusual sickly plant phenotype was noted in individuals from crosses with two teosinte accessions collected near Valle de Bravo, Mexico. The plants of these Bravo teosinte accessions appear phenotypically normal themselves and the F1 plants appear similar to typical maize × teosinte F1s. However, upon backcrossing to maize, the BC1 and subsequent generations display a number of detrimental characteristics including shorter stature, reduced seed set, and abnormal floral structures. This phenomenon is observed in all BC individuals and there is no chromosomal segment linked to the sickly plant phenotype in advanced backcross generations. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Whole-genome shotgun sequencing reveals a small number of genomic sequences, some with homology to transposable elements, that have increased in copy number in the backcross populations. Transcriptome analysis of seedlings, which do not have striking phenotypic abnormalities, identified segments of 18 maize genes that exhibit increased expression in sickly plants. A de novo assembly of transcripts present in plants exhibiting the sickly phenotype identified a set of 59 upregulated novel transcripts. These transcripts include some examples with sequence similarity to transposable elements and other sequences present in the recurrent maize parent (W22) genome as well as novel sequences not present in the W22 genome. Genome-wide profiles of gene expression, DNA methylation, and small RNAs are similar between sickly plants and normal controls, although a few upregulated transcripts and transposable elements are associated with altered small RNA or methylation profiles. This study documents hybrid incompatibility and genome instability triggered by the backcrossing of Bravo teosinte with maize. We name this phenomenon "hybrid decay" and present ideas on the mechanism that may underlie it.
Collapse
Affiliation(s)
- Wei Xue
- College of Agronomy, Shenyang Agricultural University, 110866 Liaoning Province, China
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Sarah N Anderson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Xufeng Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, 518060 Guangdong Province, China
| | - Liyan Yang
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
- Life Science College, Shanxi Normal University, 041004 Shanxi Province, China
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Qing Li
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Jaclyn Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Patrice S Albert
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Paul Bilinski
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Michelle C Stitzer
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Sherry Flint-Garcia
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
- Agricultural Research Service, United States Department of Agriculture, Columbia, Missouri 65211
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen University, 518060 Guangdong Province, China
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - John F Doebley
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| |
Collapse
|
37
|
Li K, Wen W, Alseekh S, Yang X, Guo H, Li W, Wang L, Pan Q, Zhan W, Liu J, Li Y, Wu X, Brotman Y, Willmitzer L, Li J, Fernie AR, Yan J. Large-scale metabolite quantitative trait locus analysis provides new insights for high-quality maize improvement. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:216-230. [PMID: 30888713 DOI: 10.1111/tpj.14317] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/27/2019] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
It is generally recognized that many favorable genes which were lost during domestication, including those related to both nutritional value and stress resistance, remain hidden in wild relatives. To uncover such genes in teosinte, an ancestor of maize, we conducted metabolite profiling in a BC2 F7 population generated from a cross between the maize wild relative (Zea mays ssp. mexicana) and maize inbred line Mo17. In total, 65 primary metabolites were quantified in four tissues (seedling-stage leaf, grouting-stage leaf, young kernel and mature kernel) with clear tissue-specific patterns emerging. Three hundred and fifty quantitative trait loci (QTLs) for these metabolites were obtained, which were distributed unevenly across the genome and included two QTL hotspots. Metabolite concentrations frequently increased in the presence of alleles from the teosinte genome while the opposite was observed for grain yield and shape trait QTLs. Combination of the multi-tissue transcriptome and metabolome data provided considerable insight into the metabolic variations between maize and its wild relatives. This study thus identifies favorable genes hidden in the wild relative which should allow us to balance high yield and quality in future modern crop breeding programs.
Collapse
Affiliation(s)
- Kun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Centre of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Xiaohong Yang
- Beijing Key Laboratory of Crop Genetic Improvement, National Maize Improvement Center of China, China Agricultural University, West Yuanmingyuan Lu 2, 100193, Haidian, Beijing, China
| | - Huan Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Luxi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Wei Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Yanhua Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Xiao Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Lothar Willmitzer
- Centre of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Jiansheng Li
- Beijing Key Laboratory of Crop Genetic Improvement, National Maize Improvement Center of China, China Agricultural University, West Yuanmingyuan Lu 2, 100193, Haidian, Beijing, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Centre of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| |
Collapse
|
38
|
Aguirre-Liguori JA, Gaut BS, Jaramillo-Correa JP, Tenaillon MI, Montes-Hernández S, García-Oliva F, Hearne SJ, Eguiarte LE. Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana). Mol Ecol 2019; 28:2814-2830. [PMID: 30980686 DOI: 10.1111/mec.15098] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 03/27/2019] [Accepted: 04/08/2019] [Indexed: 01/03/2023]
Abstract
Patterns of genomic divergence between hybridizing taxa can be heterogeneous along the genome. Both differential introgression and local adaptation may contribute to this pattern. Here, we analysed two teosinte subspecies, Zea mays ssp. parviglumis and ssp. mexicana, to test whether their divergence has occurred in the face of gene flow and to infer which environmental variables have been important drivers of their ecological differentiation. We generated 9,780 DArTseqTM SNPs for 47 populations, and used an additional data set containing 33,454 MaizeSNP50 SNPs for 49 populations. With these data, we inferred features of demographic history and performed genome wide scans to determine the number of outlier SNPs associated with climate and soil variables. The two data sets indicate that divergence has occurred or been maintained despite continuous gene flow and/or secondary contact. Most of the significant SNP associations were to temperature and to phosphorus concentration in the soil. A large proportion of these candidate SNPs were located in regions of high differentiation that had been identified previously as putative inversions. We therefore propose that genomic differentiation in teosintes has occurred by a process of adaptive divergence, with putative inversions contributing to reduced gene flow between locally adapted populations.
Collapse
Affiliation(s)
- Jonás A Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California
| | - Juan Pablo Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maud I Tenaillon
- Génétique Quantitative et Evolution- Le Moulon, INRA, Gif-sur-Yvette, France
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, México
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, México
| | - Sarah J Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| |
Collapse
|
39
|
Schmidt C, Pacher M, Puchta H. Efficient induction of heritable inversions in plant genomes using the CRISPR/Cas system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:577-589. [PMID: 30900787 DOI: 10.1111/tpj.14322] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/11/2019] [Accepted: 03/15/2019] [Indexed: 05/02/2023]
Abstract
During the evolution of plant genomes, sequence inversions occurred repeatedly making the respective regions inaccessible for meiotic recombination and thus for breeding. Therefore, it is important to develop technologies that allow the induction of inversions within chromosomes in a directed and efficient manner. Using the Cas9 nuclease from Staphylococcus aureus (SaCas9), we were able to obtain scarless heritable inversions with high efficiency in the model plant Arabidopsis thaliana. Via deep sequencing, we defined the patterns of junction formation in wild-type and in the non-homologous end-joining (NHEJ) mutant ku70-1. Surprisingly, in plants deficient of KU70, inversion induction is enhanced, indicating that KU70 is required for tethering the local broken ends together during repair. However, in contrast to wild-type, most junctions are formed by microhomology-mediated NHEJ and thus are imperfect with mainly deletions, making this approach unsuitable for practical applications. Using egg-cell-specific expression of Cas9, we were able to induce heritable inversions at different genomic loci and at intervals between 3 and 18 kb, in the percentage range, in the T1 generation. By screening individual lines, inversion frequencies of up to the 10% range were found in T2. Most of these inversions had scarless junctions and were without any sequence change within the inverted region, making the technology attractive for use in crop plants. Applying our approach, it should be possible to reverse natural inversions and induce artificial ones to break or fix linkages between traits at will.
Collapse
Affiliation(s)
- Carla Schmidt
- Botanical Institute, Fritz-Haber-Weg 4, 76133, Karlsruhe, Germany
| | - Michael Pacher
- Botanical Institute, Fritz-Haber-Weg 4, 76133, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Fritz-Haber-Weg 4, 76133, Karlsruhe, Germany
| |
Collapse
|
40
|
Flagel LE, Blackman BK, Fishman L, Monnahan PJ, Sweigart A, Kelly JK. GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity. PLoS Comput Biol 2019; 15:e1006949. [PMID: 30986215 PMCID: PMC6483263 DOI: 10.1371/journal.pcbi.1006949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 04/25/2019] [Accepted: 03/15/2019] [Indexed: 11/18/2022] Open
Abstract
Understanding genomic structural variation such as inversions and translocations is a key challenge in evolutionary genetics. We develop a novel statistical approach to comparative genetic mapping to detect large-scale structural mutations from low-level sequencing data. The procedure, called Genome Order Optimization by Genetic Algorithm (GOOGA), couples a Hidden Markov Model with a Genetic Algorithm to analyze data from genetic mapping populations. We demonstrate the method using both simulated data (calibrated from experiments on Drosophila melanogaster) and real data from five distinct crosses within the flowering plant genus Mimulus. Application of GOOGA to the Mimulus data corrects numerous errors (misplaced sequences) in the M. guttatus reference genome and confirms or detects eight large inversions polymorphic within the species complex. Finally, we show how this method can be applied in genomic scans to improve the accuracy and resolution of Quantitative Trait Locus (QTL) mapping.
Collapse
Affiliation(s)
- Lex E. Flagel
- Bayer Crop Science, Chesterfield, MO, United States of America
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, United States of America
- * E-mail: (LEF); (JKK)
| | - Benjamin K. Blackman
- Department of Plant and Microbial Biology, University of California—Berkeley, Berkeley, CA, United States of America
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, MT, United States of America
| | - Patrick J. Monnahan
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, United States of America
| | - Andrea Sweigart
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - John K. Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America
- * E-mail: (LEF); (JKK)
| |
Collapse
|
41
|
Interhomolog polymorphism shapes meiotic crossover within the Arabidopsis RAC1 and RPP13 disease resistance genes. PLoS Genet 2018; 14:e1007843. [PMID: 30543623 PMCID: PMC6307820 DOI: 10.1371/journal.pgen.1007843] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/27/2018] [Accepted: 11/20/2018] [Indexed: 12/11/2022] Open
Abstract
During meiosis, chromosomes undergo DNA double-strand breaks (DSBs), which can be repaired using a homologous chromosome to produce crossovers. Meiotic recombination frequency is variable along chromosomes and tends to concentrate in narrow hotspots. We mapped crossover hotspots located in the Arabidopsis thaliana RAC1 and RPP13 disease resistance genes, using varying haplotypic combinations. We observed a negative non-linear relationship between interhomolog divergence and crossover frequency within the hotspots, consistent with polymorphism locally suppressing crossover repair of DSBs. The fancm, recq4a recq4b, figl1 and msh2 mutants, or lines with increased HEI10 dosage, are known to show increased crossovers throughout the genome. Surprisingly, RAC1 crossovers were either unchanged or decreased in these genetic backgrounds, showing that chromosome location and local chromatin environment are important for regulation of crossover activity. We employed deep sequencing of crossovers to examine recombination topology within RAC1, in wild type, fancm, recq4a recq4b and fancm recq4a recq4b backgrounds. The RAC1 recombination landscape was broadly conserved in the anti-crossover mutants and showed a negative relationship with interhomolog divergence. However, crossovers at the RAC1 5'-end were relatively suppressed in recq4a recq4b backgrounds, further indicating that local context may influence recombination outcomes. Our results demonstrate the importance of interhomolog divergence in shaping recombination within plant disease resistance genes and crossover hotspots.
Collapse
|
42
|
Eco-Evolutionary Genomics of Chromosomal Inversions. Trends Ecol Evol 2018; 33:427-440. [DOI: 10.1016/j.tree.2018.04.002] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 01/17/2023]
|
43
|
Manchanda N, Snodgrass SJ, Ross-Ibarra J, Hufford MB. Evolution and Adaptation in the Maize Genome. COMPENDIUM OF PLANT GENOMES 2018. [DOI: 10.1007/978-3-319-97427-9_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
|
44
|
Lawrence EJ, Griffin CH, Henderson IR. Modification of meiotic recombination by natural variation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5471-5483. [PMID: 28992351 DOI: 10.1093/jxb/erx306] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Meiosis is a specialized cell division that produces haploid gametes required for sexual reproduction. During the first meiotic division, homologous chromosomes pair and undergo reciprocal crossing over, which recombines linked sequence variation. Meiotic recombination frequency varies extensively both within and between species. In this review, we will examine the molecular basis of meiotic recombination rate variation, with an emphasis on plant genomes. We first consider cis modification caused by polymorphisms at the site of recombination, or elsewhere on the same chromosome. We review cis effects caused by mismatches within recombining joint molecules, the effect of structural hemizygosity, and the role of specific DNA sequence motifs. In contrast, trans modification of recombination is exerted by polymorphic loci encoding diffusible molecules, which are able to modulate recombination on the same and/or other chromosomes. We consider trans modifiers that act to change total recombination levels, hotspot locations, or interactions between homologous and homeologous chromosomes in polyploid species. Finally, we consider the significance of genetic variation that modifies meiotic recombination for adaptation and evolution of plant species.
Collapse
Affiliation(s)
- Emma J Lawrence
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Catherine H Griffin
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| |
Collapse
|
45
|
Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population. G3-GENES GENOMES GENETICS 2017; 7:2259-2270. [PMID: 28546385 PMCID: PMC5499133 DOI: 10.1534/g3.117.043000] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Brassica rapa is a model species for agronomic, ecological, evolutionary, and translational studies. Here, we describe high-density SNP discovery and genetic map construction for a B. rapa recombinant inbred line (RIL) population derived from field collected RNA sequencing (RNA-Seq) data. This high-density genotype data enables the detection and correction of putative genome misassemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1-8.0% of the annotated B. rapa genome. We demonstrate how using this new resource leads to a significant improvement for QTL analysis over the current low-density genetic map. Improvements are achieved by the increased mapping resolution and by having known genomic coordinates to anchor the markers for candidate gene discovery. These new molecular resources and improvements in the genome annotation will benefit the Brassicaceae genomics community and may help guide other communities in fine-tuning genome annotations.
Collapse
|
46
|
Aguirre-Liguori JA, Tenaillon MI, Vázquez-Lobo A, Gaut BS, Jaramillo-Correa JP, Montes-Hernandez S, Souza V, Eguiarte LE. Connecting genomic patterns of local adaptation and niche suitability in teosintes. Mol Ecol 2017; 26:4226-4240. [PMID: 28612956 DOI: 10.1111/mec.14203] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 04/14/2017] [Accepted: 06/01/2017] [Indexed: 01/04/2023]
Abstract
The central abundance hypothesis predicts that local adaptation is a function of the distance to the centre of a species' geographic range. To test this hypothesis, we gathered genomic diversity data from 49 populations, 646 individuals and 33,464 SNPs of two wild relatives of maize, the teosintes Zea mays ssp. parviglumis and Zea. mays. ssp. mexicana. We examined the association between the distance to their climatic and geographic centroids and the enrichment of SNPs bearing signals of adaptation. We identified candidate adaptive SNPs in each population by combining neutrality tests and cline analyses. By applying linear regression models, we found that the number of candidate SNPs is positively associated with niche suitability, while genetic diversity is reduced at the limits of the geographic distribution. Our results suggest that overall, populations located at the limit of the species' niches are adapting locally. We argue that local adaptation to this limit could initiate ecological speciation processes and facilitate adaptation to global change.
Collapse
Affiliation(s)
- J A Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - M I Tenaillon
- Génétique Quantitative et Evolution - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - A Vázquez-Lobo
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - B S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - J P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - S Montes-Hernandez
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Guanajuato, Mexico
| | - V Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - L E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
47
|
Lu X, Yang L, Yu M, Lai J, Wang C, McNeil D, Zhou M, Yang C. A novel Zea mays ssp. mexicana L. MYC-type ICE-like transcription factor gene ZmmICE1, enhances freezing tolerance in transgenic Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 113:78-88. [PMID: 28189052 DOI: 10.1016/j.plaphy.2017.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/26/2017] [Accepted: 02/01/2017] [Indexed: 05/02/2023]
Abstract
The annual Zea mays ssp. mexicana L., a member of the teosinte group, is a close wild relative of maize and thus can be effectively used in maize improvement. In this study, an ICE-like gene, ZmmICE1, was isolated from a cDNA library of RNA-Seq from cold-treated seedling tissues of Zea mays ssp. mexicana L. The deduced protein of ZmmICE1 contains a highly conserved basic helix-loop-helix (bHLH) domain and C-terminal region of ICE-like proteins. The ZmmICE1 protein localizes to the nucleus and shows sumoylation when expressed in an Escherichia coli reconstitution system. In addition, yeast one hybrid assays indicated that ZmmICE1 has transactivation activities. Moreover, ectopic expression of ZmmICE1 in the Arabidopsis ice1-2 mutant increased freezing tolerance. The ZmmICE1 overexpressed plants showed lower electrolyte leakage (EL), reduced contents of malondialdehyde (MDA). The expression of downstream cold related genes of Arabidopsis C-repeat-binding factors (AtCBF1, AtCBF2 and AtCBF3), cold-responsive genes (AtCOR15A and AtCOR47), kinesin-1 member gene (AtKIN1) and responsive to desiccation gene (AtRD29A) was significantly induced when compared with wild type under low temperature treatment. Taken together, these results indicated that ZmmICE1 is the homolog of Arabidopsis inducer of CBF expression genes (AtICE1/2) and plays an important role in the regulation of freezing stress response.
Collapse
Affiliation(s)
- Xiang Lu
- Tasmanian Institute of Agriculture, University of Tasmania, PO Box 46, Kings Meadows, TAS 7249, Australia; Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China; College of Pratacultural Science, Gansu Agriculture University, Lanzhou 730070, China.
| | - Lei Yang
- College of Life Science, Anhui Normal University, Wuhu 241000, China.
| | - Mengyuan Yu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Chao Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - David McNeil
- Tasmanian Institute of Agriculture, University of Tasmania, PO Box 46, Kings Meadows, TAS 7249, Australia.
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, PO Box 46, Kings Meadows, TAS 7249, Australia.
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China; Dongli Planting and Farming Industrial Co., LTD, Lianzhou 513400, China.
| |
Collapse
|
48
|
Fustier MA, Brandenburg JT, Boitard S, Lapeyronnie J, Eguiarte LE, Vigouroux Y, Manicacci D, Tenaillon MI. Signatures of local adaptation in lowland and highland teosintes from whole-genome sequencing of pooled samples. Mol Ecol 2017; 26:2738-2756. [DOI: 10.1111/mec.14082] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 02/21/2017] [Indexed: 01/01/2023]
Affiliation(s)
- M.-A. Fustier
- Génétique Quantitative et Evolution - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; Ferme du Moulon F-91190 Gif-sur-Yvette France
| | - J.-T. Brandenburg
- Génétique Quantitative et Evolution - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; Ferme du Moulon F-91190 Gif-sur-Yvette France
| | - S. Boitard
- GenPhySe; Université de Toulouse, INRA, INPT, INP-ENVT; 24 chemin de Borde-Rouge - Auzeville Tolosane; F-31326 Castanet Tolosan France
| | - J. Lapeyronnie
- GenPhySe; Université de Toulouse, INRA, INPT, INP-ENVT; 24 chemin de Borde-Rouge - Auzeville Tolosane; F-31326 Castanet Tolosan France
| | - L. E. Eguiarte
- Departamento de Ecología Evolutiva; Instituto de Ecología; Universidad Nacional Autónoma de México; Apartado Postal 70-275 Coyoacán 04510 México D.F. Mexico
| | - Y. Vigouroux
- Institut de Recherche pour le développement (IRD); UMR Diversité, Adaptation et Développement des plantes (DIADE); Université de Montpellier; 911 avenue Agropolis, F-34394 Montpellier Cedex 5 France
| | - D. Manicacci
- Génétique Quantitative et Evolution - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; Ferme du Moulon F-91190 Gif-sur-Yvette France
| | - M. I. Tenaillon
- Génétique Quantitative et Evolution - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; Ferme du Moulon F-91190 Gif-sur-Yvette France
| |
Collapse
|
49
|
Puzey JR, Willis JH, Kelly JK. Population structure and local selection yield high genomic variation in Mimulus guttatus. Mol Ecol 2017; 26:519-535. [PMID: 27859786 PMCID: PMC5274581 DOI: 10.1111/mec.13922] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 09/30/2016] [Accepted: 11/07/2016] [Indexed: 12/30/2022]
Abstract
Across western North America, Mimulus guttatus exists as many local populations adapted to site-specific environmental challenges. Gene flow between locally adapted populations will affect genetic diversity both within demes and across the larger metapopulation. Here, we analyse 34 whole-genome sequences from the intensively studied Iron Mountain population (IM) in conjunction with sequences from 22 Mimulus individuals sampled from across western North America. Three striking features of these data address hypotheses about migration and selection in a locally adapted population. First, we find very high levels of intrapopulation polymorphism (synonymous π = 0.033). Variation outside of genes is likely even higher but difficult to estimate because excessive divergence reduces the efficiency of read mapping. Second, IM exhibits a significantly positive genomewide average for Tajima's D. This indicates allele frequencies are typically more intermediate than expected from neutrality, opposite the pattern observed in many other species. Third, IM exhibits a distinctive haplotype structure with a genomewide excess of positive associations between rarer alleles at linked loci. This suggests an important effect of gene flow from other Mimulus populations, although a residual effect of population founding might also contribute. The combination of multiple analyses, including a novel tree-based analytic method, illustrates how the balance of local selection, limited dispersal and metapopulation dynamics manifests across the genome. The overall genomic pattern of sequence diversity suggests successful gene flow of divergent immigrant genotypes into IM. However, many loci show patterns indicative of local adaptation, particularly at SNPs associated with chromosomal inversions.
Collapse
Affiliation(s)
- Joshua R. Puzey
- Department of Biology, College of William and Mary, Williamsburg, Virginia, 23187
- Department of Biology, Duke University, Durham, North Carolina, 27708
| | - John H. Willis
- Department of Biology, Duke University, Durham, North Carolina, 27708
| | - John K. Kelly
- Department of Ecology and Evolution, University of Kansas, Lawrence, Kansas, 27708
| |
Collapse
|
50
|
Fransz P, Linc G, Lee C, Aflitos SA, Lasky JR, Toomajian C, Ali H, Peters J, van Dam P, Ji X, Kuzak M, Gerats T, Schubert I, Schneeberger K, Colot V, Martienssen R, Koornneef M, Nordborg M, Juenger TE, de Jong H, Schranz ME. Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:159-178. [PMID: 27436134 PMCID: PMC5113708 DOI: 10.1111/tpj.13262] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/29/2016] [Accepted: 07/01/2016] [Indexed: 05/02/2023]
Abstract
Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17-Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F-box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium between the inverted region and the early flowering Col-FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South-Eastern Europe approximately 5000 years ago and the FRI-Col allele to North-West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The 'American haplotype' was identified from several European localities, potentially due to return migration.
Collapse
Affiliation(s)
- Paul Fransz
- Department of Plant Development and (Epi)GeneticsSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
| | - Gabriella Linc
- Department of Plant Development and (Epi)GeneticsSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
- Present address: Centre for Agricultural ResearchHungarian Academy of SciencesAgricultural InstituteMartonvásárHungary
| | - Cheng‐Ruei Lee
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 3Vienna1030Austria
| | | | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
| | | | - Hoda Ali
- Department of Cytogenetics and Genome AnalysisThe Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
- Present address: Department of Genetics and CytologyNational Research CenterCairoEgypt
| | - Janny Peters
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
| | - Peter van Dam
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
- Present address: Department of Molecular Plant PathologyUniversity of AmsterdamAmsterdamThe Netherlands
| | - Xianwen Ji
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
| | - Mateusz Kuzak
- MAD, Dutch Genomics Service & Support ProviderSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
- Present address: Netherlands eScience CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Tom Gerats
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
| | - Ingo Schubert
- Department of Cytogenetics and Genome AnalysisThe Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | | | - Vincent Colot
- Unité de Recherche en Génomique Végétale (URGV)INRA/CNRS/UEVE 2 Rue Gaston CrémieuxEvry Cedex91057France
- Present address: Institut de Biologie de l'Ecole Normale Supérieure (IBENS)ParisFrance
| | - Rob Martienssen
- Cold Spring Harbor LaboratoryCold Spring HarborNew YorkNY11724USA
| | - Maarten Koornneef
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
- Max Planck Institute for Plant Breeding ResearchKöln50829Germany
| | - Magnus Nordborg
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 3Vienna1030Austria
| | | | - Hans de Jong
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
| | | |
Collapse
|