51
|
|
52
|
Adavoudi R, Pilot M. Consequences of Hybridization in Mammals: A Systematic Review. Genes (Basel) 2021; 13:50. [PMID: 35052393 PMCID: PMC8774782 DOI: 10.3390/genes13010050] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010-2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.
Collapse
Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, ul. Nadwiślańska 108, 80-680 Gdańsk, Poland;
| |
Collapse
|
53
|
Chen S, Milne R, Zhou R, Meng K, Yin Q, Guo W, Ma Y, Mao K, Xu K, Kim YD, Do TV, Liao W, Fan Q. When tropical and subtropical congeners met: Multiple ancient hybridization events within Eriobotrya in the Yunnan-Guizhou Plateau, a tropical-subtropical transition area in China. Mol Ecol 2021; 31:1543-1561. [PMID: 34910340 DOI: 10.1111/mec.16325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 01/09/2023]
Abstract
Global climate changes during the Miocene may have created ample opportunities for hybridization between members of tropical and subtropical biomes at the boundary between these zones. Yet, very few studies have explored this possibility. The Yunnan-Guizhou Plateau (YGP) in Southwest China is a biodiversity hotspot for vascular plants, located in a transitional area between the floristic regions of tropical Southeast Asia and subtropical East Asia. The genus Eriobotrya (Rosaceae) comprises both tropical and subtropical taxa, with 12 species recorded in the YGP, making it a suitable basis for testing the hypothesis of between-biome hybridization. Therefore, we surveyed the evolutionary history of Eriobotrya by examining three chloroplast regions and five nuclear genes for 817 individuals (47 populations) of 23 Eriobotrya species (including 19 populations of 12 species in the YGP), plus genome re-sequencing of 33 representative samples. We concluded that: (1) phylogenetic positions for 16 species exhibited strong cytonuclear conflicts, most probably due to ancient hybridization; (2) the YGP is a hotspot for hybridization, with 11 species showing clear evidence of chloroplast capture; and (3) Eriobotrya probably originated in tropical Asia during the Eocene. From the Miocene onwards, the intensification of the Eastern Asia monsoon and global cooling may have shifted the tropical-subtropical boundary and caused secondary contact between species, thus providing ample opportunity for hybridization and diversification of Eriobotrya, especially in the YGP. Our study highlights the significant role that paleoclimate changes probably played in driving hybridization and generating rich species diversity in climate transition zones.
Collapse
Affiliation(s)
- Sufang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Richard Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Kaikai Meng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qianyi Yin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Guo
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongpeng Ma
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Kewang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Young-Dong Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon City, South Korea
| | - Truong Van Do
- Vietnam National Museum of Nature, Vietnam Academy of Science & Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science & Technology, Hanoi, Vietnam
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| |
Collapse
|
54
|
Martins FB, Moraes ACL, Aono AH, Ferreira RCU, Chiari L, Simeão RM, Barrios SCL, Santos MF, Jank L, do Valle CB, Vigna BBZ, de Souza AP. A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses. FRONTIERS IN PLANT SCIENCE 2021; 12:737919. [PMID: 34745171 PMCID: PMC8569613 DOI: 10.3389/fpls.2021.737919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Artificial hybridization plays a fundamental role in plant breeding programs since it generates new genotypic combinations that can result in desirable phenotypes. Depending on the species and mode of reproduction, controlled crosses may be challenging, and contaminating individuals can be introduced accidentally. In this context, the identification of such contaminants is important to avoid compromising further selection cycles, as well as genetic and genomic studies. The main objective of this work was to propose an automated multivariate methodology for the detection and classification of putative contaminants, including apomictic clones (ACs), self-fertilized individuals, half-siblings (HSs), and full contaminants (FCs), in biparental polyploid progenies of tropical forage grasses. We established a pipeline to identify contaminants in genotyping-by-sequencing (GBS) data encoded as allele dosages of single nucleotide polymorphism (SNP) markers by integrating principal component analysis (PCA), genotypic analysis (GA) measures based on Mendelian segregation, and clustering analysis (CA). The combination of these methods allowed for the correct identification of all contaminants in all simulated progenies and the detection of putative contaminants in three real progenies of tropical forage grasses, providing an easy and promising methodology for the identification of contaminants in biparental progenies of tetraploid and hexaploid species. The proposed pipeline was made available through the polyCID Shiny app and can be easily coupled with traditional genetic approaches, such as linkage map construction, thereby increasing the efficiency of breeding programs.
Collapse
Affiliation(s)
- Felipe Bitencourt Martins
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | - Aline Costa Lima Moraes
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | - Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | | | - Lucimara Chiari
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | - Rosangela Maria Simeão
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | | | - Liana Jank
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), São Paulo, Brazil
| |
Collapse
|
55
|
Lyu R, He J, Luo Y, Lin L, Yao M, Cheng J, Xie L, Pei L, Yan S, Li L. Natural Hybrid Origin of the Controversial "Species" Clematis × pinnata (Ranunculaceae) Based on Multidisciplinary Evidence. FRONTIERS IN PLANT SCIENCE 2021; 12:745988. [PMID: 34712260 PMCID: PMC8545901 DOI: 10.3389/fpls.2021.745988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/22/2021] [Indexed: 05/23/2023]
Abstract
Interspecific hybridization is common and has often been viewed as a driving force of plant diversity. However, it raises taxonomic problems and thus impacts biodiversity estimation and biological conservation. Although previous molecular phylogenetic studies suggested that interspecific hybridization may be rather common in Clematis, and artificial hybridization has been widely applied to produce new Clematis cultivars for nearly two centuries, the issue of natural hybridization of Clematis has never been addressed in detail. In this study, we tested the hybrid origin of a mesophytic and cold-adapted vine species, Clematis pinnata, which is a rare and taxonomically controversial taxon endemic to northern China. Using field investigations, flow cytometry (FCM), phylogenomic analysis, morphological statistics, and niche modeling, we tested hybrid origin and species status of C. pinnata. The FCM results showed that all the tested species were homoploid (2n = 16). Phylonet and HyDe analyses based on transcriptome data showed the hybrid origins of C. × pinnata from either C. brevicaudata × C. heracleifolia or C. brevicaudata × C. tubulosa. The plastome phylogeny depicted that C. × pinnata in different sampling sites originated by different hybridization events. Morphological analysis showed intermediacy of C. × pinnata between its putative parental species in many qualitative and quantitative characters. Niche modeling results suggested that C. × pinnata had not been adapted to a novel ecological niche independent of its putative parents. These findings demonstrated that plants of C. × pinnata did not formed a self-evolved clade and should not be treated as a species. The present study also suggests that interspecific hybridization is a common mechanism in Clematis to generate diversity and variation, and it may play an important role in the evolution and diversification of this genus. Our study implies that morphological diversity caused by natural hybridization may overstate the real species diversity in Clematis.
Collapse
Affiliation(s)
- Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Lele Lin
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Min Yao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Linying Pei
- Beijing Engineering Research Center for Landscape Plant, Beijing Forestry University Forest Science Co. Ltd., Beijing, China
| | - Shuangxi Yan
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Liangqian Li
- Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
56
|
Triguero-Piñero P, de Vega C, Aparicio A, Albaladejo RG. Isolation of microsatellite markers for the endemic Phlomis lychnitis (Lamiaceae). Mol Biol Rep 2021; 48:8233-8238. [PMID: 34617241 DOI: 10.1007/s11033-021-06730-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/28/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Phlomis lychnitis is a mostly endemic species of the Iberian Peninsula that frequently hybridizes with the narrow endemic P. crinita subsp. malacitana in southern Spain. Whenever they coexist they form homoploid hybrid zones. Unlike hybridization at the polyploid level, the process of hybridization at the homoploid level is much less well known. METHODS AND RESULTS In this study we report the development of 22 microsatellite markers through next-generation sequencing technologies for P. lychnitis. We characterize the genetic diversity for two populations of this species for the 10 markers that resulted to be polymorphic. Further, we check the transferability of these polymorphic markers to one population of P. crinita subsp. malacitana to verify the potential use of these markers for hybridization studies. The values of expected heterozygosity for P. lychnitis were higher than in P. crinita subsp. malacitana, and the three analyzed populations displayed negative values for the inbreeding coefficient which is compatible with the frequent instances of hybridization and introgression between species. CONCLUSIONS This set of polymorphic markers are useful for further studies aiming at a deeper understanding of the homoploid hybrid process between these species. Additionally, this is the first panel of microsatellite markers developed for the genus Phlomis, a genus very rich in endemic species and with medicinal properties that could benefit from the use of these new markers.
Collapse
Affiliation(s)
- Paloma Triguero-Piñero
- Departamento de Biología Vegetal y Ecología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González no 2, 41012, Seville, Spain
| | - Clara de Vega
- Departamento de Biología Vegetal y Ecología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González no 2, 41012, Seville, Spain
| | - Abelardo Aparicio
- Departamento de Biología Vegetal y Ecología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González no 2, 41012, Seville, Spain
| | - Rafael G Albaladejo
- Departamento de Biología Vegetal y Ecología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González no 2, 41012, Seville, Spain.
| |
Collapse
|
57
|
Abstract
The world’s food and agricultural programs have gradually declined into an unsustainable situation due to challenges such as increase in world population, varied agro-climatic regions, increase temperature, extreme sole-culture growing techniques, and water shortage. A considerable emphasis has been put on few staple food crops coupled with repeated dieting, food scarcity, and essential mineral deficits, frequently inducing dietary disorders. Because relying on staple crops may lead to serious food shortages in the future, we must adjust our dietary habits to include a diverse range of non-staple foods and maximize their use in order to achieve food security and reduce the nutritional gap. To assure healthy meals around the world, an authentic and reasonable strategy is presented to draw additional awareness towards variations in agricultural production techniques and dietary preferences. The EAT-Lancet declaration highlighted the importance of increasing agri-based foods to achieve sustainable health. Expanding overlooked crops with abundant genetic stocks and possibly beneficial characteristics is an approach that might meet food and nutritional security challenges. Although undervalued, pumpkin is a valuable vegetable herbaceous plant that contributes to global food and nutritional security. This crop has already been identified as a revolutionary age crop, balanced food, and more adapted to low soil and atmospheric circumstances than other major crops. This review paper focuses on the potential uses of pumpkin as an underutilized crop; diversification and development of hybrids, particularly hybridization breeding through diallel mating design; and how implementation of this “modern” technology would contribute to the breeding of the neglected pumpkin vegetable and stimulate productivity and nourish the world’s largest malnourished, deprived, and starved populations.
Collapse
|
58
|
Köhler M, Oakley LJ, Font F, Peñas MLL, Majure LC. On the continuum of evolution: a putative new hybrid speciation event in Opuntia (Cactaceae) between a native and an introduced species in southern South America. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1967510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Matias Köhler
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
| | - Luis J. Oakley
- Cátedra de Botánica, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Santa Fe, Argentina
- Red List Authority Coordinator for the Temperate South American Plant Specialist Groups – International Union for Conservation of Nature (IUCN), Gland, Switzerland
| | - Fabián Font
- Herbario Museo de Farmacobotánica “Juan A. Domínguez” (BAF), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. Laura Las Peñas
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Facultas de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba – CONICET, Córdoba, Argentina
| | - Lucas C. Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
| |
Collapse
|
59
|
Savadi S, Mangalassery S, Sandesh MS. Advances in genomics and genome editing for breeding next generation of fruit and nut crops. Genomics 2021; 113:3718-3734. [PMID: 34517092 DOI: 10.1016/j.ygeno.2021.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/21/2021] [Accepted: 09/02/2021] [Indexed: 12/18/2022]
Abstract
Fruit tree crops are an essential part of the food production systems and are key to achieve food and nutrition security. Genetic improvement of fruit trees by conventional breeding has been slow due to the long juvenile phase. Advancements in genomics and molecular biology have paved the way for devising novel genetic improvement tools like genome editing, which can accelerate the breeding of these perennial crops to a great extent. In this article, advancements in genomics of fruit trees covering genome sequencing, transcriptome sequencing, genome editing technologies (GET), CRISPR-Cas system based genome editing, potential applications of CRISPR-Cas9 in fruit tree crops improvement, the factors influencing the CRISPR-Cas editing efficiency and the challenges for CRISPR-Cas9 applications in fruit tree crops improvement are reviewed. Besides, base editing, a recently emerging more precise editing system, and the future perspectives of genome editing in the improvement of fruit and nut crops are covered.
Collapse
Affiliation(s)
- Siddanna Savadi
- ICAR- Directorate of Cashew Research (DCR), Puttur 574 202, Dakshina Kannada, Karnataka, India.
| | | | - M S Sandesh
- ICAR- Directorate of Cashew Research (DCR), Puttur 574 202, Dakshina Kannada, Karnataka, India
| |
Collapse
|
60
|
Feng JW, Lu Y, Shao L, Zhang J, Li H, Chen LL. Phasing analysis of the transcriptome and epigenome in a rice hybrid reveals the inheritance and difference in DNA methylation and allelic transcription regulation. PLANT COMMUNICATIONS 2021; 2:100185. [PMID: 34327321 PMCID: PMC8299081 DOI: 10.1016/j.xplc.2021.100185] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 03/14/2021] [Accepted: 04/13/2021] [Indexed: 05/16/2023]
Abstract
Hybrids are always a focus of botanical research and have a high practical value in agricultural production. To better understand allele regulation and differences in DNA methylation in hybrids, we developed a phasing pipeline for hybrid rice based on two parental genomes (PP2PG), which is applicable for Iso-Seq, RNA-Seq, and Bisulfite sequencing (BS-Seq). Using PP2PG, we analyzed differences in gene transcription, alternative splicing, and DNA methylation in an allele-specific manner between parents and progeny or different progeny alleles. The phasing of Iso-Seq data provided a great advantage in separating the whole gene structure and producing a significantly higher separation ratio than RNA-Seq. The interaction of hybrid alleles was studied by constructing an allele co-expression network that revealed the dominant allele effect in the network. The expression variation between parents and the parental alleles in progeny showed tissue- or environment-specific patterns, which implied a preference for trans-acting regulation under different conditions. In addition, by comparing allele-specific DNA methylation, we found that CG methylation was more likely to be inherited than CHG and CHH methylation, and its enrichment in genic regions was connected to gene structure. In addition to an effective phasing pipeline, we also identified differentiation in OsWAK38 gene structure that may have led to the expansion of allele functions in hybrids. In summary, we developed a phasing pipeline and provided valuable insights into alternative splicing, interaction networks, trans-acting regulation, and the inheritance of DNA methylation in hybrid rice.
Collapse
Affiliation(s)
- Jia-Wu Feng
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yue Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Lin Shao
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Huan Li
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
- Corresponding author
| |
Collapse
|
61
|
Graham AM, Peters JL, Wilson RE, Muñoz-Fuentes V, Green AJ, Dorfsman DA, Valqui TH, Winker K, McCracken KG. Adaptive introgression of the beta-globin cluster in two Andean waterfowl. Heredity (Edinb) 2021; 127:107-123. [PMID: 33903741 PMCID: PMC8249413 DOI: 10.1038/s41437-021-00437-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/04/2021] [Accepted: 04/08/2021] [Indexed: 11/09/2022] Open
Abstract
Introgression of beneficial alleles has emerged as an important avenue for genetic adaptation in both plant and animal populations. In vertebrates, adaptation to hypoxic high-altitude environments involves the coordination of multiple molecular and cellular mechanisms, including selection on the hypoxia-inducible factor (HIF) pathway and the blood-O2 transport protein hemoglobin (Hb). In two Andean duck species, a striking DNA sequence similarity reflecting identity by descent is present across the ~20 kb β-globin cluster including both embryonic (HBE) and adult (HBB) paralogs, though it was yet untested whether this is due to independent parallel evolution or adaptive introgression. In this study, we find that identical amino acid substitutions in the β-globin cluster that increase Hb-O2 affinity have likely resulted from historical interbreeding between high-altitude populations of two different distantly-related species. We examined the direction of introgression and discovered that the species with a deeper mtDNA divergence that colonized high altitude earlier in history (Anas flavirostris) transferred adaptive genetic variation to the species with a shallower divergence (A. georgica) that likely colonized high altitude more recently possibly following a range shift into a novel environment. As a consequence, the species that received these β-globin variants through hybridization might have adapted to hypoxic conditions in the high-altitude environment more quickly through acquiring beneficial alleles from the standing, hybrid-origin variation, leading to faster evolution.
Collapse
Affiliation(s)
- Allie M Graham
- Eccles Institute for Human Genetics, University of Utah, Salt Lake City, UT, USA.
| | - Jeffrey L Peters
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Robert E Wilson
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Andy J Green
- Department of Wetland Ecology, Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Daniel A Dorfsman
- Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Thomas H Valqui
- Centro de Ornitología y Biodiversidad (CORBIDI), Surco, Lima, Perú
- Universidad Nacional Agraria, La Molina, Perú
| | - Kevin Winker
- University of Alaska Museum and Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Kevin G McCracken
- Human Genetics and Genomics, Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
- Centro de Ornitología y Biodiversidad (CORBIDI), Surco, Lima, Perú.
- University of Alaska Museum and Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, USA.
- Department of Biology, University of Miami, Coral Gables, FL, USA.
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL, USA.
| |
Collapse
|
62
|
Doyle JJ. Defining coalescent genes: Theory meets practice in organelle phylogenomics. Syst Biol 2021; 71:476-489. [PMID: 34191012 DOI: 10.1093/sysbio/syab053] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
The species tree paradigm that dominates current molecular systematic practice infers species trees from collections of sequences under assumptions of the multispecies coalescent (MSC), i.e., that there is free recombination between the sequences and no (or very low) recombination within them. These coalescent genes (c-genes) are thus defined in an historical rather than molecular sense, and can in theory be as large as an entire genome or as small as a single nucleotide. A debate about how to define c-genes centers on the contention that nuclear gene sequences used in many coalescent analyses undergo too much recombination, such that their introns comprise multiple c-genes, violating a key assumption of the MSC. Recently a similar argument has been made for the genes of plastid (e.g., chloroplast) and mitochondrial genomes, which for the last 30 or more years have been considered to represent a single c-gene for the purposes of phylogeny reconstruction because they are non-recombining in a historical sense. Consequently, it has been suggested that these genomes should be analyzed using coalescent methods that treat their genes-over 70 protein-coding genes in the case of most plastid genomes (plastomes)-as independent estimates of species phylogeny, in contrast to the usual practice of concatenation, which is appropriate for generating gene trees. However, although recombination certainly occurs in the plastome, as has been recognized since the 1970's, it is unlikely to be phylogenetically relevant. This is because such historically effective recombination can only occur when plastomes with incongruent histories are brought together in the same plastid. However, plastids sort rapidly into different cell lineages and rarely fuse. Thus, because of plastid biology, the plastome is a more canonical c-gene than is the average multi-intron mammalian nuclear gene. The plastome should thus continue to be treated as a single estimate of the underlying species phylogeny, as should the mitochondrial genome. The implications of this long-held insight of molecular systematics for studies in the phylogenomic era are explored.
Collapse
Affiliation(s)
- Jeff J Doyle
- Plant Biology Section, Plant Breeding & Genetics Section, and L. H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| |
Collapse
|
63
|
Goulet-Scott BE, Garner AG, Hopkins R. Genomic analyses overturn two long-standing homoploid hybrid speciation hypotheses. Evolution 2021; 75:1699-1710. [PMID: 34101168 DOI: 10.1111/evo.14279] [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: 02/09/2021] [Revised: 04/27/2021] [Accepted: 05/11/2021] [Indexed: 01/21/2023]
Abstract
The importance of hybridization in generating biological diversity has been historically controversial. Previously, inference about hybridization was limited by dependence on morphological data; with the advent of the next-generation sequencing tools for nonmodel organisms, the evolutionary significance of hybridization is more evident. Here, we test classic hypotheses of hybrid origins of two species in the Phlox pilosa complex. Morphological intermediacy motivated the hypotheses that Phlox amoena lighthipei and Phlox pilosa deamii were independent homoploid hybrid lineages derived from P. amoena amoena and P. pilosa pilosa. We use double-digest restriction site-associated DNA sequencing of individuals from throughout the range of these taxa to conduct the most thorough analysis of evolutionary history in this system to date. Surprisingly, we find no support for the hybrid origin of P. pilosa deamii or P. amoena lighthipei. Our data do identify a history of admixture in individuals collected at a contemporary hybrid zone between the putative parent lineages. We show that three very different evolutionary histories, only one of which involves hybrid origin, have produced intermediate or recombinant morphological traits between P. amoena amoena and P. pilosa pilosa. Although morphological data are still an efficient means of generating hypotheses about past gene flow, genomic data are now the standard of evidence for elucidating evolutionary history.
Collapse
Affiliation(s)
- Benjamin E Goulet-Scott
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Austin G Garner
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138.,Arnold Arboretum of Harvard University, Boston, Massachusetts, 02131
| |
Collapse
|
64
|
Li
X, Wei G, El-Kassaby YA, Fang Y. Hybridization and introgression in sympatric and allopatric populations of four oak species. BMC PLANT BIOLOGY 2021; 21:266. [PMID: 34107871 PMCID: PMC8188795 DOI: 10.1186/s12870-021-03007-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 05/05/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Hybridization and introgression are vital sources of novel genetic variation driving diversification during reticulated evolution. Quercus is an important model clade, having extraordinary diverse and abundant members in the Northern hemisphere, that are used to studying the introgression of species boundaries and adaptive processes. China is the second-largest distribution center of Quercus, but there are limited studies on introgressive hybridization. RESULTS Here, we screened 17 co-dominant nuclear microsatellite markers to investigate the hybridization and introgression of four oaks (Quercus acutissima, Quercus variabilis, Quercus fabri, and Quercus serrata) in 10 populations. We identified 361 alleles in the four-oak species across 17 loci, and all loci were characterized by high genetic variability (HE = 0.844-0.944) and moderate differentiation (FST = 0.037-0.156) levels. A population differentiation analysis revealed the following: allopatric homologous (FST = 0.064) < sympatric heterogeneous (FST = 0.071) < allopatric heterogeneous (FST = 0.084). A Bayesian admixture analysis determined four types of hybrids (Q. acutissima × Q. variabilis, Q. fabri × Q. serrata, Q. acutissima × Q. fabri, and Q. acutissima × Q. variabilis × Q. fabri) and their asymmetric introgression. Our results revealed that interspecific hybridization is commonly observed within the section Quercus, with members having tendency to hybridize. CONCLUSIONS Our study determined the basic hybridization and introgression states among the studied four oak species and extended our understanding of the evolutionary role of hybridization. The results provide useful theoretical data for formulating conservation strategies.
Collapse
Affiliation(s)
- Xuan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 PR China
- Department of Forest and Conservation Sciences Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4 Canada
| | - Gaoming Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 PR China
- School of Physics and Electronics Henan University, Jinming Avenue, Jinming District, Kaifeng, 475001 PR China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4 Canada
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037 PR China
| |
Collapse
|
65
|
Abstract
In keeping with the directive in Executive Order 13874 (Modernizing the Regulatory Framework for Agricultural Biotechnology Products) to adopt regulatory approaches that are proportionate to risk and avoid arbitrary distinctions across like products, the US Department of Agriculture (USDA) revised its biotechnology regulations by promulgating the Sustainable, Ecological, Consistent, Uniform, Responsible, and Efficient (SECURE) rule. Specifically, the SECURE rule 1) establishes exemptions for plants modified by genetic engineering where the modification could otherwise have been made through conventional breeding, 2) uses risk posed by the introduced trait to determine whether an organism is regulated, rather than relying on whether the organism was developed using a plant pest, and 3) provides a mechanism for a rapid initial review to efficiently distinguish plants developed using genetic engineering that do not pose plausible pathways to increased plant pest risk from those that do. As a result of the focused oversight on potentially riskier crops developed using genetic engineering, USDA is expected to improve the efficiency and effectiveness of its oversight program. The reduced regulatory burden is expected to promote innovation by expanding the number and diversity of developers to include smaller businesses and academics and to increase the number and variety of traits being developed through biotechnology.
Collapse
Affiliation(s)
- Neil E Hoffman
- Biotechnology Regulatory Services, Animal Plant Health Inspection Services, US Department of Agriculture, Riverdale, MD 20737
| |
Collapse
|
66
|
|
67
|
Fetter KC, Nelson DM, Keller SR. Growth-defense trade-offs masked in unadmixed populations are revealed by hybridization. Evolution 2021; 75:1450-1465. [PMID: 33914360 DOI: 10.1111/evo.14227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/15/2021] [Indexed: 12/20/2022]
Abstract
Organisms are constantly challenged by pathogens and pests, which can drive the evolution of growth-defense strategies. Plant stomata are essential for gas exchange during photosynthesis and conceptually lie at the intersection of the physiological demands of growth and exposure to foliar fungal pathogens. Generations of natural selection for locally adapted growth-defense strategies can eliminate variation between traits, potentially masking trade-offs and selection conflicts that may have existed in the past. Hybrid populations offer a unique opportunity to reset the clock on selection and to study potentially maladaptive trait variation before selection removes it. We study the interactions of growth, stomatal, ecopysiological, and disease resistance traits in poplars (Populus) after infection by the leaf rust Melampsora medusae. Phenotypes were measured in a common garden and genotyped at 227K SNPs. We isolate the effects of hybridization on trait variance, discover correlations between stomatal, ecophysiology, and disease resistance, examine trade-offs and selection conflicts, and explore the evolution of growth-defense strategies potentially mediated by selection for stomatal traits on the upper leaf surface. These results suggest an important role for stomata in determining growth-defense strategies in organisms susceptible to foliar pathogens, and reinforces the contribution of hybridization studies toward our understanding of trait evolution.
Collapse
Affiliation(s)
- Karl C Fetter
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA.,Department of Plant Biology, University of Vermont, Burlington, Vermont, 05405, USA
| | - David M Nelson
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, Maryland, 21532, USA
| | - Stephen R Keller
- Department of Plant Biology, University of Vermont, Burlington, Vermont, 05405, USA
| |
Collapse
|
68
|
Rosli MAF, Mediani A, Azizan KA, Baharum SN, Goh HH. UPLC-TOF-MS/MS-Based Metabolomics Analysis Reveals Species-Specific Metabolite Compositions in Pitchers of Nepenthes ampullaria, Nepenthes rafflesiana, and Their Hybrid Nepenthes × hookeriana. FRONTIERS IN PLANT SCIENCE 2021; 12:655004. [PMID: 33968110 PMCID: PMC8096924 DOI: 10.3389/fpls.2021.655004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/15/2021] [Indexed: 05/14/2023]
Abstract
Hybridization is key to the evolution and diversity of plants in nature. Nepenthaceae comprises a family of diverse tropical carnivorous pitcher plant species with extensive hybridization. However, there is no study to date on the metabolite expression of hybrids in this family. We performed a non-targeted metabolomics analysis of the pitchers of two Nepenthes species with different dietary habits, namely, the semi-detritivorous N. ampullaria and carnivorous N. rafflesiana with their hybrid (N. × hookeriana) for a comparative study. The whole-pitcher samples were extracted in methanol:chloroform:water (3:1:1) via sonication-assisted extraction and analyzed using ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) followed by data analysis to profile chemical compositions. A total of 1,441 metabolite features were profiled from the three species in which 43.3% of features in the hybrid samples were not found in either of its parents. The partial least squares discriminant analysis (PLS-DA) found 324 metabolite features with variable in projection (VIP) values greater than one in which 55 features were statistically significant. This showed that the hybrid is closer to N. rafflesiana, which is consistent to the previous study on gene and protein expressions. A total of 105 metabolites were putatively identified with manual searches using public metabolite databases. Phenols were detected to be the most abundant secondary metabolites due to a high flavonoid content, especially in N. rafflesiana. The most abundant feature 476.3s:449.102 was found to be the most significant VIP for distinguishing between the three species as a chemical marker. This is the first study comparing metabolites in the carnivory organs of different Nepenthes species with comprehensive profiling and putative identification. The differential metabolite compositions in the pitchers of different species might have ecological implications with the hybrid showing intermediate phenotype between the parents as well as manifesting unique metabolites. However, there is no clear evidence of metabolites related to the differences in dietary habits between the hybrid and the two parent species.
Collapse
Affiliation(s)
| | | | | | | | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| |
Collapse
|
69
|
Tian L, Wang E, Lin X, Ji L, Chang J, Chen H, Wang J, Chen D, Tran LSP, Tian C. Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding. BMC Genomics 2021; 22:278. [PMID: 33865333 PMCID: PMC8052703 DOI: 10.1186/s12864-021-07587-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 04/07/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Rice, which serves as a staple food for more than half of the world's population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined. RESULTS In the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together. CONCLUSIONS This study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.
Collapse
Affiliation(s)
- Lei Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Enze Wang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Xiaolong Lin
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Ji
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingjing Chang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongping Chen
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Jilin Wang
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Dazhou Chen
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam.
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Chunjie Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China.
- Key Laboratory of Straw Biology and Utilization of the Ministry of Education, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
| |
Collapse
|
70
|
Shukla K, Laursen AE, Benavides J, Ejbari N, Campbell LG. Growth and fecundity of colonizing hybrid Raphanus populations are environmentally dependent. AMERICAN JOURNAL OF BOTANY 2021; 108:580-597. [PMID: 33855711 DOI: 10.1002/ajb2.1640] [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: 05/14/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Hybrid gene pools harbor more genetic variation than progenitor populations. Thus, we expect hybrid populations to exhibit more dynamic evolutionary responses to environmental variation. We ask how environmental variation experienced by adapted and transplanted populations influence the success of late-generation hybrid populations during invasion. METHODS For four generations, 20 wild (Raphanus raphanistrum) and 20 hybrid radish (R. sativus × R. raphanistrum) plant populations evolved under experimentally manipulated moisture conditions (dry, wet, control-sheltered, or control-unsheltered plots; i.e., evolutionary environment) in old fields near Toronto, Canada. We planted advanced-generation wild and hybrid radishes in sheltered plots and exposed them to either an evolutionary or a novel watering environment. To determine how soil moisture would influence invasion success, we compared the phenotype and fecundity of plants grown in these various environments. RESULTS Hybridization produced larger plants. In wet environments, hybrid seedlings emerged more frequently and expressed higher photosynthetic activity. Low-moisture, novel conditions delayed and reduced seedling emergence frequency. Hybrid plants and those that evolved under relatively wet environments exhibited higher aboveground biomass. Hybrid plants from control-sheltered plots colonizing novel moisture environments were more fecund than comparable wild plants. CONCLUSIONS Dry environments are less likely than other evolutionary environments to contribute colonists. However, relatively wet locations support the evolution of relatively fecund plants, especially crop-wild hybrid populations. Thus, our results provide a strong mechanistic explanation for variation in the relative success of crop-wild hybrids among study locations and a new standard for studies that assess the risk of crop-wild hybridization events.
Collapse
Affiliation(s)
- Kruti Shukla
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
| | - Andrew E Laursen
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
| | - Jessica Benavides
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
| | - Neda Ejbari
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
| | - Lesley G Campbell
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
| |
Collapse
|
71
|
Pfennig KS. Biased Hybridization and Its Impact on Adaptive Introgression. Trends Ecol Evol 2021; 36:488-497. [PMID: 33752896 DOI: 10.1016/j.tree.2021.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Gene exchange between species can influence ecological and evolutionary processes ranging from population rescue to adaptive radiation. Genomic tools have provided new insights into the prevalence and nature of gene exchange between species. However, much remains unknown of how ecological, behavioral, and evolutionary factors determine what genetic variation moves between species in the first place. In particular, more research is needed that evaluates whether such factors bias gene flow from one species to another, and whether any such biases affect how genetic variation from another species is ultimately retained in the genome of a given species. Addressing this issue is crucial in a changing world where hybridization and introgression might determine which species succeed and which become extinct.
Collapse
Affiliation(s)
- Karin S Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
| |
Collapse
|
72
|
Wollenweber TE, van Deenen N, Roelfs KU, Prüfer D, Gronover CS. Microscopic and Transcriptomic Analysis of Pollination Processes in Self-Incompatible Taraxacum koksaghyz. PLANTS 2021; 10:plants10030555. [PMID: 33809548 PMCID: PMC7998978 DOI: 10.3390/plants10030555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/23/2022]
Abstract
The transition of the Russian dandelion Taraxacum koksaghyz (Asteraceae) to a profitable, alternative crop producing natural rubber and inulin requires the optimization of several agronomic traits, cultivation conditions and harvesting procedures to improve the yield. However, efficient breeding is hindered by the obligatory sexual outcrossing of this species. Several other asters have been investigated to determine the mechanism of self-incompatibility, but the underlying molecular basis remains unclear. We therefore investigated the self-pollination and cross-pollination of two compatible T. koksaghyz varieties (TkMS2 and TkMS3) by microscopy and transcriptomic analysis to shed light on the pollination process. Self-pollination showed typical sporophytic self-incompatibility characteristics, with the rare pollen swelling at the pollen tube apex. In contrast, cross-pollination was characterized by pollen germination and penetration of the stigma by the growing pollen tubes. RNA-Seq was used to profile gene expression in the floret tissue during self-pollination and cross-pollination, and the differentially expressed genes were identified. This revealed three candidates for the early regulation of pollination in T. koksaghyz, which can be used to examine self-incompatibility mechanisms in more detail and to facilitate breeding programs.
Collapse
Affiliation(s)
- Tassilo Erik Wollenweber
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, 48143 Muenster, Germany; (T.E.W.); (N.v.D.); (D.P.)
| | - Nicole van Deenen
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, 48143 Muenster, Germany; (T.E.W.); (N.v.D.); (D.P.)
| | - Kai-Uwe Roelfs
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Muenster, Germany;
| | - Dirk Prüfer
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, 48143 Muenster, Germany; (T.E.W.); (N.v.D.); (D.P.)
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Muenster, Germany;
| | - Christian Schulze Gronover
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Muenster, Germany;
- Correspondence: ; Tel.: +49(0)251-83-24998
| |
Collapse
|
73
|
|
74
|
Garcia-Lor A, Bermejo A, Morales J, Hernández M, Medina A, Cuenca J, Navarro L, Aleza P. Strategies to Produce Grapefruit-Like Citrus Varieties With a Low Furanocoumarin Content and Distinctive Flavonoid Profiles. FRONTIERS IN PLANT SCIENCE 2021; 12:640512. [PMID: 33719319 PMCID: PMC7943927 DOI: 10.3389/fpls.2021.640512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Pummelos and hybrids, such as grapefruits, have high furanocoumarin and low flavonoid contents. Furanocoumarins interact negatively with certain drugs, while flavonoids are antioxidant compounds with health benefits. To obtain new grapefruit-like varieties with low furanocoumarin and high flavonoid contents, diploid and triploid hybrid populations from crosses between diploid and tetraploid "Clemenules" clementine and diploid "Pink" pummelo were recovered and analyzed. With regard to furanocoumarins, triploids produce less bergapten, bergamottin and 6,7-DHB than diploids. Regarding flavonoids, triploids yielded more eriocitrin, narirutin, hesperidin and neohesperidin than diploids, whereas no differences were observed in neoeriocitrin and naringin. These results indicate that, the strategy to recover triploid hybrids by 4x × 2x crosses is more appropriate than the recovery of diploid hybrids by 2x × 2x crosses for obtaining grapefruit-like varieties of citrus with lower furanocoumarin and higher flavonoid contents.
Collapse
|
75
|
Priest SJ, Coelho MA, Mixão V, Clancey SA, Xu Y, Sun S, Gabaldón T, Heitman J. Factors enforcing the species boundary between the human pathogens Cryptococcus neoformans and Cryptococcus deneoformans. PLoS Genet 2021; 17:e1008871. [PMID: 33465111 PMCID: PMC7846113 DOI: 10.1371/journal.pgen.1008871] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 01/29/2021] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
Hybridization has resulted in the origin and variation in extant species, and hybrids continue to arise despite pre- and post-zygotic barriers that limit their formation and evolutionary success. One important system that maintains species boundaries in prokaryotes and eukaryotes is the mismatch repair pathway, which blocks recombination between divergent DNA sequences. Previous studies illuminated the role of the mismatch repair component Msh2 in blocking genetic recombination between divergent DNA during meiosis. Loss of Msh2 results in increased interspecific genetic recombination in bacterial and yeast models, and increased viability of progeny derived from yeast hybrid crosses. Hybrid isolates of two pathogenic fungal Cryptococcus species, Cryptococcus neoformans and Cryptococcus deneoformans, are isolated regularly from both clinical and environmental sources. In the present study, we sought to determine if loss of Msh2 would relax the species boundary between C. neoformans and C. deneoformans. We found that crosses between these two species in which both parents lack Msh2 produced hybrid progeny with increased viability and high levels of aneuploidy. Whole-genome sequencing revealed few instances of recombination among hybrid progeny and did not identify increased levels of recombination in progeny derived from parents lacking Msh2. Several hybrid progeny produced structures associated with sexual reproduction when incubated alone on nutrient-rich medium in light, a novel phenotype in Cryptococcus. These findings represent a unique, unexpected case where rendering the mismatch repair system defective did not result in increased meiotic recombination across a species boundary. This suggests that alternative pathways or other mismatch repair components limit meiotic recombination between homeologous DNA and enforce species boundaries in the basidiomycete Cryptococcus species. Several mechanisms enforce species boundaries by either preventing the formation of hybrid zygotes, known as pre-zygotic barriers, or preventing the viability and fecundity of hybrids, known as post-zygotic barriers. Despite these barriers, interspecific hybrids form at an appreciable frequency, such as hybrid isolates of the human fungal pathogenic species, Cryptococcus neoformans and Cryptococcus deneoformans, which are regularly isolated from both clinical and environmental sources. C. neoformans x C. deneoformans hybrids are typically highly aneuploid, sterile, and display phenotypes intermediate to those of either parent, although self-fertile isolates and transgressive phenotypes have been observed. One important mechanism known to enforce species boundaries or lead to incipient speciation is the DNA mismatch repair system, which blocks recombination between divergent DNA sequences during meiosis. The aim of this study was to determine if genetically deleting the DNA mismatch repair component Msh2 would relax the species boundary between C. neoformans and C. deneoformans. Progeny derived from C. neoformans x C. deneoformans crosses in which both parental strains lacked Msh2 had higher viability, and unlike previous studies in Saccharomyces, these Cryptococcus hybrid progeny had higher levels of aneuploidy and no observable increase in meiotic recombination at the whole-genome level.
Collapse
Affiliation(s)
- Shelby J. Priest
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Marco A. Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Verónica Mixão
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Shelly Applen Clancey
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Yitong Xu
- Program in Cell and Molecular Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
76
|
Undin M, Lockhart PJ, Hills SFK, Castro I. Genetic Rescue and the Plight of Ponui Hybrids. FRONTIERS IN CONSERVATION SCIENCE 2021. [DOI: 10.3389/fcosc.2020.622191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Long-term sustainable and resilient populations is a key goal of conservation. How to best achieve this is controversial. There are, for instance, polarized views concerning the fitness and conservation value of hybrid populations founded through multi-origin translocations. A classic example concerns Apteryx (kiwi) in New Zealand. The A. mantelli of Ponui Island constitute a hybrid population where the birds are highly successful in their island habitat. A key dilemma for managers is understanding the reason for this success. Are the hybrid birds of Ponui Island of “no future conservation value” as recently asserted, or do they represent an outstanding example of genetic rescue and an important resource for future translocations? There has been a paradigm shift in scientific thinking concerning hybrids, but the ecological significance of admixed genomes remains difficult to assess. This limits what we can currently predict in conservation science. New understanding from genome science challenges the sufficiency of population genetic models to inform decision making and suggests instead that the contrasting outcomes of hybridization, “outbreeding depression” and “heterosis,” require understanding additional factors that modulate gene and protein expression and how these factors are influenced by the environment. We discuss these findings and the investigations that might help us to better understand the birds of Ponui, inform conservation management of kiwi and provide insight relevant for the future survival of Apteryx.
Collapse
|
77
|
Kong S, Kubatko LS. Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data. Syst Biol 2021; 70:891-907. [PMID: 33404632 DOI: 10.1093/sysbio/syaa092] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 11/13/2020] [Indexed: 11/13/2022] Open
Abstract
Interspecific hybridization is an important evolutionary phenomenon that generates genetic variability in a population and fosters species diversity in nature. The availability of large genome scale datasets has revolutionized hybridization studies to shift from the observation of the presence or absence of hybrids to the investigation of the genomic constitution of hybrids and their genome-specific evolutionary dynamics. Although a handful of methods have been proposed in an attempt to identify hybrids, accurate detection of hybridization from genomic data remains a challenging task. In addition to methods that infer phylogenetic networks or that utilize pairwise divergence, site pattern frequency based and population genetic clustering approaches are popularly used in practice, though the performance of these methods under different hybridization scenarios has not been extensively examined. Here, we use simulated data to comparatively evaluate the performance of four tools that are commonly used to infer hybridization events: the site pattern frequency based methods HyDe and the D-statistic (i.e., the ABBA-BABA test) and the population clustering approaches structure and ADMIXTURE. We consider single hybridization scenarios that vary in the time of hybridization and the amount of incomplete lineage sorting (ILS) for different proportions of parental contributions (γ); introgressive hybridization; multiple hybridization scenarios; and a mixture of ancestral and recent hybridization scenarios. We focus on the statistical power to detect hybridization and the false discovery rate (FDR) for comparisons of the D-statistic and HyDe, and the accuracy of the estimates of γ as measured by the mean squared error for HyDe, structure, and ADMIXTURE. Both HyDe and the D-statistic are powerful for detecting hybridization in all scenarios except those with high ILS, although the D-statistic often has an unacceptably high FDR. The estimates of γ in HyDe are impressively robust and accurate whereas structure and ADMIXTURE sometimes fail to identify hybrids, particularly when the proportional parental contributions are asymmetric (i.e., when γ is close to 0). Moreover, the posterior distribution estimated using structure exhibits multimodality in many scenarios, making interpretation difficult. Our results provide guidance in selecting appropriate methods for identifying hybrid populations from genomic data.
Collapse
Affiliation(s)
- Sungsik Kong
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Laura S Kubatko
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Department of Statistics, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
78
|
Bhattacharya A, Parkhi V, Char B. Genome editing for crop improvement: A perspective from India. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY. PLANT : JOURNAL OF THE TISSUE CULTURE ASSOCIATION 2021; 57:565-573. [PMID: 34075289 PMCID: PMC8152710 DOI: 10.1007/s11627-021-10184-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/12/2021] [Indexed: 05/11/2023]
Abstract
Human population is expected to reach to about 10 billion by 2050. Climate change affects crop production, thus posing food security challenges. Conventional breeding alone will not bridge the gap between current level of crop production and expected levels in the decades to come in the food production systems. Rate of genetic gain with time has remained narrow considerably. Biotechnology-enabled crops developed through genome editing will have a part to play in improving crop productivity, meeting food, nutrition security besides catering to regional preferences and fetching valuable foreign exchange. Political, social, economical proposition, scientific will, retailer and consumer acceptance are a must for genome editing (GE) to succeed and add value in the food value chain. This will also help to make agriculture a lucrative profession and attract youth. Therefore, the present review looks into existing regulations governing crops developed using biotechnology in India, institutes involved in genome editing, prospects of new tools developed in this sphere such as DNA-free editing systems, nanotechnology, their applicability in crop improvement efforts, social and future prospects taking cue from recent global developments. This will make GE more appealing to stakeholders and defray any safety concerns.
Collapse
Affiliation(s)
- Anjanabha Bhattacharya
- Mahyco Research Centre, Mahyco Private Limited, Jalna-Aurangabad Road, Dawalwadi, Jalna, Maharashtra 431203 India
| | - Vilas Parkhi
- Mahyco Research Centre, Mahyco Private Limited, Jalna-Aurangabad Road, Dawalwadi, Jalna, Maharashtra 431203 India
| | - Bharat Char
- Mahyco Research Centre, Mahyco Private Limited, Jalna-Aurangabad Road, Dawalwadi, Jalna, Maharashtra 431203 India
| |
Collapse
|
79
|
Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae. G3-GENES GENOMES GENETICS 2020; 10:4387-4398. [PMID: 32988994 PMCID: PMC7718754 DOI: 10.1534/g3.120.401596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the Zea-Tripsacum clade to investigate TE activity and accumulation after a shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and Tripsacum species, in addition to two closely related diploid species, Urelytrum digitatum and Sorghum bicolor, revealed variation in repeat content among all taxa included in the study. The repeat composition of Urelytrum is more similar to that of Zea and Tripsacum compared to Sorghum, despite the similarity in genome size with the latter. Although LTR-retrotransposons were abundant in all species, we observed an expansion of the copia superfamily, specifically in Z. mays and T. dactyloides, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of these retroelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. Specifically, copia insertions in Zea and T. dactyloides were significantly enriched near genes involved in abiotic stress response, suggesting independent evolution post Zea-Tripsacum divergence. The lack of copia insertions near the orthologous genes in S. bicolor suggests that duplicate gene copies generated during polyploidization may offer novel neutral sites for TEs to insert, thereby providing an avenue for subfunctionalization via TE insertional mutagenesis.
Collapse
|
80
|
Folk RA, Siniscalchi CM, Soltis DE. Angiosperms at the edge: Extremity, diversity, and phylogeny. PLANT, CELL & ENVIRONMENT 2020; 43:2871-2893. [PMID: 32926444 DOI: 10.1111/pce.13887] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/21/2020] [Accepted: 08/13/2020] [Indexed: 05/26/2023]
Abstract
A hallmark of flowering plants is their ability to invade some of the most extreme and dynamic habitats, including cold and dry biomes, to a far greater extent than other land plants. Recent work has provided insight to the phylogenetic distribution and evolutionary mechanisms which have enabled this success, yet needed is a synthesis of evolutionary perspectives with plant physiological traits, morphology, and genomic diversity. Linking these disparate components will not only lead to better understand the evolutionary parallelism and diversification of plants with these two strategies, but also to provide the framework needed for directing future research. We summarize the primary physiological and structural traits involved in response to cold- and drought stress, outline the phylogenetic distribution of these adaptations, and describe the recurring association of these changes with rapid diversification events that occurred in multiple lineages over the past 15 million years. Across these threefold facets of dry-cold correlation (traits, phylogeny, and time) we stress the contrast between (a) the amazing diversity of solutions flowering plants have developed in the face of extreme environments and (b) a broad correlation between cold and dry adaptations that in some cases may hint at deep common origins.
Collapse
Affiliation(s)
- Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Carolina M Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
81
|
Farhat P, Siljak-Yakovlev S, Valentin N, Fabregat C, Lopez-Udias S, Salazar-Mendias C, Altarejos J, Adams RP. Gene flow between diploid and tetraploid junipers - two contrasting evolutionary pathways in two Juniperus populations. BMC Evol Biol 2020; 20:148. [PMID: 33167862 PMCID: PMC7650182 DOI: 10.1186/s12862-020-01688-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene flow and polyploidy have been found to be important in Juniperus evolution. However, little evidence has been published elucidating the association of both phenomena in juniper taxa in the wild. Two main areas were studied in Spain (Eastern Iberian Range and Sierra de Baza) with both diploid and tetraploid taxa present in sympatry. Gene flow and ploidy level were assessed for these taxa and the resulted offspring. RESULTS Twenty-two allo-triploid hybrids between J. sabina var. sabina and J. thurifera were found in the Eastern Iberian Range population. However, in the Sierra de Baza population no triploids were found. Instead, 18 allo-tetraploid hybrids between two tetraploid taxa: J. sabina var. balkanensis and J. thurifera were discovered. High genetic diversity was exhibited among the tetraploid hybrids at Sierra de Baza, in contrast to the genetically identical triploid hybrids at the Eastern Iberian Range; this suggests meiotic difficulties within the triploid hybrids. In addition, unidirectional gene flow was observed in both studied areas. CONCLUSION Polyploidy and hybridization can be complementary partners in the evolution of Juniperus taxa in sympatric occurrences. Juniperus was shown to be an ideal coniferous model to study these two phenomena, independently or in concert.
Collapse
Affiliation(s)
- Perla Farhat
- Biology Department, Baylor University, Waco, TX, 76798, USA.
- Present address: Key Laboratory of Bio-resources and Eco-environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China.
| | - Sonja Siljak-Yakovlev
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, 91405, Orsay, France
| | - Nicolas Valentin
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Carlos Fabregat
- Jardí Botànic de la Universitat de València, 46008, València, Spain
| | | | - Carlos Salazar-Mendias
- Departamento de Biología Animal, Biología Vegetal y Ecología. Universidad de Jaén, 23071, Jaén, Spain
| | - Joaquín Altarejos
- Departamento de Química Inorgánica y Orgánica, Universidad de Jaén, 23071, Jaén, Spain
| | - Robert P Adams
- Biology Department, Baylor University, Waco, TX, 76798, USA
| |
Collapse
|
82
|
Lukhtanov VA, Dincă V, Friberg M, Vila R, Wiklund C. Incomplete Sterility of Chromosomal Hybrids: Implications for Karyotype Evolution and Homoploid Hybrid Speciation. Front Genet 2020; 11:583827. [PMID: 33193715 PMCID: PMC7594530 DOI: 10.3389/fgene.2020.583827] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/14/2020] [Indexed: 11/17/2022] Open
Abstract
Heterozygotes for major chromosomal rearrangements such as fusions and fissions are expected to display a high level of sterility due to problems during meiosis. However, some species, especially plants and animals with holocentric chromosomes, are known to tolerate chromosomal heterozygosity even for multiple rearrangements. Here, we studied male meiotic chromosome behavior in four hybrid generations (F1–F4) between two chromosomal races of the Wood White butterfly Leptidea sinapis differentiated by at least 24 chromosomal fusions/fissions. Previous work showed that these hybrids were fertile, although their fertility was reduced as compared to crosses within chromosomal races. We demonstrate that (i) F1 hybrids are highly heterozygous with nearly all chromosomes participating in the formation of trivalents at the first meiotic division, and (ii) that from F1 to F4 the number of trivalents decreases and the number of bivalents increases. We argue that the observed process of chromosome sorting would, if continued, result in a new homozygous chromosomal race, i.e., in a new karyotype with intermediate chromosome number and, possibly, in a new incipient homoploid hybrid species. We also discuss the segregational model of karyotype evolution and the chromosomal model of homoploid hybrid speciation.
Collapse
Affiliation(s)
- Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Saint Petersburg, Russia
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Magne Friberg
- Biodiversity Unit, Department of Biology, Lund University, Lund, Sweden
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | |
Collapse
|
83
|
Citrus Flavonoids as Promising Phytochemicals Targeting Diabetes and Related Complications: A Systematic Review of In Vitro and In Vivo Studies. Nutrients 2020; 12:nu12102907. [PMID: 32977511 PMCID: PMC7598193 DOI: 10.3390/nu12102907] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/17/2020] [Accepted: 09/19/2020] [Indexed: 01/04/2023] Open
Abstract
The consumption of plant-based food is important for health promotion, especially concerning the prevention and management of chronic diseases. Flavonoids are the main bioactive compounds in citrus fruits, with multiple beneficial effects, especially antidiabetic effects. We systematically review the potential antidiabetic action and molecular mechanisms of citrus flavonoids based on in vitro and in vivo studies. A search of the PubMed, EMBASE, Scopus, and Web of Science Core Collection databases for articles published since 2010 was carried out using the keywords citrus, flavonoid, and diabetes. All articles identified were analyzed, and data were extracted using a standardized form. The search identified 38 articles, which reported that 19 citrus flavonoids, including 8-prenylnaringenin, cosmosiin, didymin, diosmin, hesperetin, hesperidin, isosiennsetin, naringenin, naringin, neohesperidin, nobiletin, poncirin, quercetin, rhoifolin, rutin, sineesytin, sudachitin, tangeretin, and xanthohumol, have antidiabetic potential. These flavonoids regulated biomarkers of glycemic control, lipid profiles, renal function, hepatic enzymes, and antioxidant enzymes, and modulated signaling pathways related to glucose uptake and insulin sensitivity that are involved in the pathogenesis of diabetes and its related complications. Citrus flavonoids, therefore, are promising antidiabetic candidates, while their antidiabetic effects remain to be verified in forthcoming human studies.
Collapse
|
84
|
Courtier‐Orgogozo V, Danchin A, Gouyon P, Boëte C. Evaluating the probability of CRISPR-based gene drive contaminating another species. Evol Appl 2020; 13:1888-1905. [PMID: 32908593 PMCID: PMC7463340 DOI: 10.1111/eva.12939] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
The probability D that a given clustered regularly interspaced short palindromic repeats (CRISPR)-based gene drive element contaminates another, nontarget species can be estimated by the following Drive Risk Assessment Quantitative Estimate (DRAQUE) Equation: D = h y b + t r a n s f × e x p r e s s × c u t × f l a n k × i m m u n e × n o n e x t i n c t with hyb = probability of hybridization between the target species and a nontarget species; transf = probability of horizontal transfer of a piece of DNA containing the gene drive cassette from the target species to a nontarget species (with no hybridization); express = probability that the Cas9 and guide RNA genes are expressed; cut = probability that the CRISPR-guide RNA recognizes and cuts at a DNA site in the new host; flank = probability that the gene drive cassette inserts at the cut site; immune = probability that the immune system does not reject Cas9-expressing cells; nonextinct = probability of invasion of the drive within the population. We discuss and estimate each of the seven parameters of the equation, with particular emphasis on possible transfers within insects, and between rodents and humans. We conclude from current data that the probability of a gene drive cassette to contaminate another species is not insignificant. We propose strategies to reduce this risk and call for more work on estimating all the parameters of the formula.
Collapse
Affiliation(s)
| | - Antoine Danchin
- Institut Cochin INSERM U1016 – CNRS UMR8104 – Université Paris DescartesParisFrance
| | - Pierre‐Henri Gouyon
- Institut de Systématique, Évolution, BiodiversitéMuséum National d'Histoire NaturelleCNRSSorbonne UniversitéEPHEUAParisFrance
| | | |
Collapse
|
85
|
Gabaldón T. Patterns and impacts of nonvertical evolution in eukaryotes: a paradigm shift. Ann N Y Acad Sci 2020; 1476:78-92. [PMID: 32860228 PMCID: PMC7589212 DOI: 10.1111/nyas.14471] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/19/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022]
Abstract
Evolution of eukaryotic species and their genomes has been traditionally understood as a vertical process in which genetic material is transmitted from parents to offspring along a lineage, and in which genetic exchange is restricted within species boundaries. However, mounting evidence from comparative genomics indicates that this paradigm is often violated. Horizontal gene transfer and mating between diverged lineages blur species boundaries and challenge the reconstruction of evolutionary histories of species and their genomes. Nonvertical evolution might be more restricted in eukaryotes than in prokaryotes, yet it is not negligible and can be common in certain groups. Recognition of such processes brings about the need to incorporate this complexity into our models, as well as to conceptually reframe eukaryotic diversity and evolution. Here, I review the recent work from genomics studies that supports the effects of nonvertical modes of evolution including introgression, hybridization, and horizontal gene transfer in different eukaryotic groups. I then discuss emerging patterns and effects, illustrated by specific examples, that support the conclusion that nonvertical processes are often at the root of important evolutionary transitions and adaptations. I will argue that a paradigm shift is needed to naturally accommodate nonvertical processes in eukaryotic evolution.
Collapse
Affiliation(s)
- Toni Gabaldón
- Barcelona Supercomputing Centre (BCS-CNS), Barcelona, Spain.,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| |
Collapse
|
86
|
Baiakhmetov E, Nowak A, Gudkova PD, Nobis M. Morphological and genome-wide evidence for natural hybridisation within the genus Stipa (Poaceae). Sci Rep 2020; 10:13803. [PMID: 32796878 PMCID: PMC7427808 DOI: 10.1038/s41598-020-70582-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022] Open
Abstract
Hybridisation in the wild between closely related species is a common mechanism of speciation in the plant kingdom and, in particular, in the grass family. Here we explore the potential for natural hybridisation in Stipa (one of the largest genera in Poaceae) between genetically distant species at their distribution edges in Mountains of Central Asia using integrative taxonomy. Our research highlights the applicability of classical morphological and genome reduction approaches in studies on wild plant species. The obtained results revealed a new nothospecies, Stipa × lazkovii, which exhibits intermediate characters to S. krylovii and S. bungeana. A high-density DArTseq assay disclosed that S. × lazkovii is an F1 hybrid, and established that the plastid and mitochondrial DNA was inherited from S. bungeana. In addition, molecular markers detected a hybridisation event between morphologically and genetically distant species S. bungeana and probably S. glareosa. Moreover, our findings demonstrated an uncertainty on the taxonomic status of S. bungeana that currently belongs to the section Leiostipa, but it is genetically closer to S. breviflora from the section Barbatae. Finally, we noticed a discrepancy between the current molecular data with the previous findings on S. capillata and S. sareptana.
Collapse
Affiliation(s)
- Evgenii Baiakhmetov
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland. .,Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave, 634050, Tomsk, Russia.
| | - Arkadiusz Nowak
- Botanical Garden-Centre for Biological Diversity Conservation, Polish Academy of Sciences, Prawdziwka 2, 02-973, Warszawa, Poland.,Institute of Biology, Opole University, Oleska 22, 45-052, Opole, Poland
| | - Polina D Gudkova
- Research Laboratory 'Herbarium', National Research Tomsk State University, Lenin 36 Ave, 634050, Tomsk, Russia.,Department of Biology, Altai State University, Lenin 61 Ave, 656049, Barnaul, Russia
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland.
| |
Collapse
|
87
|
Harpur BA, Kadri SM, Orsi RO, Whitfield CW, Zayed A. Defense Response in Brazilian Honey Bees (Apis mellifera scutellata × spp.) Is Underpinned by Complex Patterns of Admixture. Genome Biol Evol 2020; 12:1367-1377. [PMID: 32597950 PMCID: PMC7487160 DOI: 10.1093/gbe/evaa128] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2020] [Indexed: 12/30/2022] Open
Abstract
In 1957, an invasive and highly defensive honey bee began to spread across Brazil. In the previous year, Brazilian researchers hoped to produce a subtropical-adapted honey bee by crossing local commercial honey bees (of European origin) with a South African honey bee subspecies (Apis mellifera scutellata; an A-lineage honey bee subspecies). The resulting cross-African hybrid honey bees (AHBs)-escaped from their enclosure and spread through the Americas. Today, AHB is the most common honey bee from Northern Argentina to the Southern United States. AHBs are much more likely to sting nest intruders than managed European-derived honey bee colonies. Previous studies have explored how genetic variation contributes to differences in defense response between European-derived honey bee and AHB. Although this work demonstrated very strong genetic effects on defense response, they have yet to pinpoint which genes influence variation in defense response within AHBs, specifically. We quantified defense response for 116 colonies in Brazil and performed pooled sequencing on the most phenotypically divergent samples. We identified 65 loci containing 322 genes that were significantly associated with defense response. Loci were strongly associated with metabolic function, consistent with previous functional genomic analyses of this phenotype. Additionally, defense-associated loci had nonrandom and unexpected patterns of admixture. Defense response was not simply the product of more A-lineage honey bee ancestry as previously assumed, but rather an interaction between A-lineage and European alleles. Our results suggest that a combination of A-lineage and European alleles play roles in defensive behavior in AHBs.
Collapse
Affiliation(s)
| | - Samir M Kadri
- Departamento de Produção Animal, Faculdade de Medicina Veterinária e Zootecnia de Botucatu, Univervidade Estadual Paulista, UNESP, Botucatu, São Paulo, Brazil
| | - Ricardo O Orsi
- Departamento de Produção Animal, Faculdade de Medicina Veterinária e Zootecnia de Botucatu, Univervidade Estadual Paulista, UNESP, Botucatu, São Paulo, Brazil
| | | | - Amro Zayed
- Department of Biology, Faculty of Sciences, York University, Toronto, Canada
| |
Collapse
|
88
|
Quilodrán CS, Montoya-Burgos JI, Currat M. Harmonizing hybridization dissonance in conservation. Commun Biol 2020; 3:391. [PMID: 32694629 PMCID: PMC7374702 DOI: 10.1038/s42003-020-1116-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/25/2020] [Indexed: 12/24/2022] Open
Abstract
A dramatic increase in the hybridization between historically allopatric species has been induced by human activities. However, the notion of hybridization seems to lack consistency in two respects. On the one hand, it is inconsistent with the biological species concept, which does not allow for interbreeding between species, and on the other hand, it is considered either as an evolutionary process leading to the emergence of new biodiversity or as a cause of biodiversity loss, with conservation implications. In the first case, we argue that conservation biology should avoid the discussion around the species concept and delimit priorities of conservation units based on the impact on biodiversity if taxa are lost. In the second case, we show that this is not a paradox but an intrinsic property of hybridization, which should be considered in conservation programmes. We propose a novel view of conservation guidelines, in which human-induced hybridization may also be a tool to enhance the likelihood of adaptation to changing environmental conditions or to increase the genetic diversity of taxa affected by inbreeding depression. The conservation guidelines presented here represent a guide for the development of programmes aimed at protecting biodiversity as a dynamic evolutionary system.
Collapse
Affiliation(s)
- Claudio S Quilodrán
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
- Laboratory of Anthropology, Genetics and Peopling History, Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.
| | - Juan I Montoya-Burgos
- Laboratory of Vertebrate Evolution, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| |
Collapse
|
89
|
Yi G, Shin H, Park HR, Park JE, Ahn JH, Lim S, Lee JG, Lee EJ, Huh JH. Revealing biomass heterosis in the allodiploid xBrassicoraphanus, a hybrid between Brassica rapa and Raphanus sativus, through integrated transcriptome and metabolites analysis. BMC PLANT BIOLOGY 2020; 20:252. [PMID: 32493222 PMCID: PMC7268423 DOI: 10.1186/s12870-020-02470-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/26/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Heterosis is biologically important but the molecular basis of the phenomenon is poorly understood. We characterized intergeneric hybrids between B. rapa cv. Chiifu and R. sativus cv. WK10039 as an extreme example of heterosis. Taking advantage of clear heterosis phenotypes and the genetic distance between parents, we performed transcriptome and metabolite analysis to decipher the molecular basis of heterosis. RESULTS The heterosis was expressed as fresh weight in the field and as inflorescence stem length in the glass house. Flowering time, distributed as a normal segregating population, ranged from the early flowering of one parent to the late flowering of the other, in contrast to the homogeneous flowering time in a typical F1 population, indicating unstable allelic interactions. The transcriptome and metabolome both indicated that sugar metabolism was altered, suggesting that the change in metabolism was linked to the heterosis. Because alleles were not shared between the hybridized genomes, classic models only partly explain this heterosis, indicating that other mechanisms are involved. CONCLUSION The differential expression of genes for primary and secondary metabolism, along with the altered metabolite profiles, suggests that heterosis could involve a change in balance between primary and secondary metabolism.
Collapse
Affiliation(s)
- Gibum Yi
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
- Department of Central Area Crop Science, National Institute of Crop Science, RDA, Suwon, 16429 Republic of Korea
| | - Hosub Shin
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Hye Rang Park
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Jeong Eun Park
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Jong Hwa Ahn
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Illumina Korea, Yeongdeungpo-gu, Seoul, 07325 South Korea
| | - Sooyeon Lim
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
- National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jeollabuk-do 55365 South Korea
| | - Jeong Gu Lee
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
| | - Eun Jin Lee
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Gwanak-gu, Seoul, 08826 South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
| |
Collapse
|
90
|
Schnitzler CK, Turchetto C, Teixeira MC, Freitas LB. What could be the fate of secondary contact zones between closely related plant species? Genet Mol Biol 2020; 43:e20190271. [PMID: 32556035 PMCID: PMC7299303 DOI: 10.1590/1678-4685-gmb-2019-0271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/24/2020] [Indexed: 11/26/2022] Open
Abstract
Interspecific hybridization has been fundamental in plant evolution.
Nevertheless, the fate of hybrid zones throughout the generations remains poorly
addressed. We analyzed a pair of recently diverged, interfertile, and sympatric
Petunia species to ask what fate the interspecific hybrid
population has met over time. We analyzed the genetic diversity in two
generations from two contact sites and evaluated the effect of introgression. To
do this, we collected all adult plants from the contact zones, including
canonicals and intermediary colored individuals, and compared them with purebred
representatives of both species based on seven highly informative microsatellite
loci. We compared the genetic diversity observed in the contact zones with what
is seen in isolated populations of each species, considering two generations of
these annual species. Our results have confirmed the genetic differentiation
between the species and the hybrid origin of the majority of the intermediary
colored individuals. We also observed a differentiation related to genetic
variability and inbreeding levels among the populations. Over time, there were
no significant differences per site related to genetic diversity or phenotype
composition. We found two stable populations kept by high inbreeding and
backcross rates that influence the genetic diversity of their parental species
through introgression.
Collapse
Affiliation(s)
- Carolina K Schnitzler
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Caroline Turchetto
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Marcelo C Teixeira
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Loreta B Freitas
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| |
Collapse
|
91
|
Pieper S, Dorken M, Freeland J. Genetic structure in hybrids and progenitors provides insight into processes underlying an invasive cattail (Typha × glauca) hybrid zone. Heredity (Edinb) 2020; 124:714-725. [PMID: 32203248 PMCID: PMC7239851 DOI: 10.1038/s41437-020-0307-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 11/09/2022] Open
Abstract
Traditional models of hybrid zones have assumed relatively low hybrid fitness, and thus focussed more on interspecific gene flow than on hybrid dispersal. Therefore, when hybrids have high fitness and the potential for autonomous dispersal, we have limited understanding of whether hybrid dispersal or repeated local hybrid formation is more important for maintaining hybrid zones. The invasive hybrid cattail Typha × glauca occupies an extensive hybrid zone in northeastern North America where it is sympatric with its progenitors T. latifolia and T. angustifolia. We characterized genetic diversity and genetic structure of the three taxa across a broad spatial scale where the maternal parent is relatively rare, and tested the hypothesis that the hybrid shows stronger evidence of gene flow than its progenitor species, particularly among disturbed sites (ditches) compared with established wetlands. Support for this hypothesis would suggest that dispersal, rather than repeated local formation, is more important for maintaining hybrid zones. Within each taxon, genetic differentiation among ditches was comparable to that among wetlands, although clonal richness was consistently greater in ditches, suggesting more frequent seed establishment. Genetic structure across sites was more pronounced in the hybrid compared with either progenitor species. Overall, our data reflect relatively low gene flow in hybrids, and suggest that hybrids are more likely to be created in situ than to be introduced from other sites. Despite the high fitness of invasive T. × glauca and its potential for autonomy, local processes appear more important than dispersal in maintaining this hybrid zone.
Collapse
Affiliation(s)
- Sara Pieper
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Marcel Dorken
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
- Department of Biology, Trent University, Peterborough, ON, Canada
| | - Joanna Freeland
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada.
- Department of Biology, Trent University, Peterborough, ON, Canada.
| |
Collapse
|
92
|
Nagamitsu T, Uchiyama K, Izuno A, Shimizu H, Nakanishi A. Environment-dependent introgression from Quercus dentata to a coastal ecotype of Quercus mongolica var. crispula in northern Japan. THE NEW PHYTOLOGIST 2020; 226:1018-1028. [PMID: 31424559 PMCID: PMC7216917 DOI: 10.1111/nph.16131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/09/2019] [Indexed: 05/25/2023]
Abstract
Introgression from one species in a specific environment to another may facilitate colonization of the environment by the recipient species. However, such environment-dependent introgression has been clarified in limited plant taxa. In northern Japan, there are two interfertile oak species: Quercus dentata (Qd) in coastal areas and Q. mongolica var. crispula (Qc) in inland areas. However, at higher latitudes where Qd is rare, a coastal Qc ecotype with Qd-like traits is distributed in the coastal areas. We distinguished inland Qc, coastal Qc, and coastal Qd populations based on genome-wide genotypes and multitrait phenotypes and verified introgression from coastal Qd to coastal Qc using reduced library sequencing. Genotypes and phenotypes differed among the populations, and coastal Qc was intermediate between inland Qc and coastal Qd. The ABBA-BABA test showed introgression from coastal Qd to coastal Qc. In coastal Qc, we found various stages of introgression after the first generation of backcross but detected no genomic regions where introgression was enhanced. Overall, we show evidence for introgression from a coastal species to an ecotype of an inland species, which has colonized the coastal environment. It remains unclear whether introgressed alleles are selected in the coastal environment.
Collapse
Affiliation(s)
- Teruyoshi Nagamitsu
- Hokkaido Research Center, Forestry and Forest Products Research InstituteForest Research and Management OrganizationSapporo062‐8516Japan
| | - Kentaro Uchiyama
- Department of Forest Molecular Genetics and BiotechnologyForestry and Forest Products Research InstituteForest Research and Management OrganizationTsukuba305‐8687Japan
| | - Ayako Izuno
- Department of Forest Molecular Genetics and BiotechnologyForestry and Forest Products Research InstituteForest Research and Management OrganizationTsukuba305‐8687Japan
| | - Hajime Shimizu
- Greenery Research and Information CenterForestry Research InstituteHokkaido Research OrganizationBibai079‐0198Japan
| | - Atsushi Nakanishi
- Hokkaido Research Center, Forestry and Forest Products Research InstituteForest Research and Management OrganizationSapporo062‐8516Japan
| |
Collapse
|
93
|
Mérot C, Debat V, Le Poul Y, Merrill RM, Naisbit RE, Tholance A, Jiggins CD, Joron M. Hybridization and transgressive exploration of colour pattern and wing morphology in Heliconius butterflies. J Evol Biol 2020; 33:942-956. [PMID: 32255231 DOI: 10.1111/jeb.13626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/19/2022]
Abstract
Hybridization can generate novel phenotypes distinct from those of parental lineages, a phenomenon known as transgressive trait variation. Transgressive phenotypes might negatively or positively affect hybrid fitness, and increase available variation. Closely related species of Heliconius butterflies regularly produce hybrids in nature, and hybridization is thought to play a role in the diversification of novel wing colour patterns despite strong stabilizing selection due to interspecific mimicry. Here, we studied wing phenotypes in first- and second-generation hybrids produced by controlled crosses between either two co-mimetic species of Heliconius or between two nonmimetic species. We quantified wing size, shape and colour pattern variation and asked whether hybrids displayed transgressive wing phenotypes. Discrete traits underlain by major-effect loci, such as the presence or absence of colour patches, generate novel phenotypes. For quantitative traits, such as wing shape or subtle colour pattern characters, hybrids only exceed the parental range in specific dimensions of the morphological space. Overall, our study addresses some of the challenges in defining and measuring phenotypic transgression for multivariate traits and our data suggest that the extent to which transgressive trait variation in hybrids contributes to phenotypic diversity depends on the complexity and the genetic architecture of the traits.
Collapse
Affiliation(s)
- Claire Mérot
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,IBIS, Université Laval, Québec, QC, Canada
| | - Vincent Debat
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Yann Le Poul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Division of Evolutionary Biology, Ludwig-Maximilians-Universität, München, Germany
| | - Richard M Merrill
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität, München, Germany.,Department of Zoology, University of Cambridge, Cambridge, UK.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Russell E Naisbit
- Smithsonian Tropical Research Institute, Panama City, Panama.,Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Adélie Tholance
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Mathieu Joron
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,UMR 5175, CNRS-Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France
| |
Collapse
|
94
|
Dunning LT, Christin PA. Reticulate evolution, lateral gene transfer, and innovation in plants. AMERICAN JOURNAL OF BOTANY 2020; 107:541-544. [PMID: 32198762 DOI: 10.1002/ajb2.1452] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Affiliation(s)
- Luke T Dunning
- Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | | |
Collapse
|
95
|
Li J, Milne RI, Ru D, Miao J, Tao W, Zhang L, Xu J, Liu J, Mao K. Allopatric divergence and hybridization withinCupressus chengiana(Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China. Mol Ecol 2020; 29:1250-1266. [DOI: 10.1111/mec.15407] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Jialiang Li
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Richard I. Milne
- Institute of Molecular Plant Sciences The University of Edinburgh Edinburgh UK
| | - Dafu Ru
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
| | - Jibin Miao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Wenjing Tao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Lei Zhang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Jingjing Xu
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Jianquan Liu
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| | - Kangshan Mao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education College of Life Sciences State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan University Chengdu China
| |
Collapse
|
96
|
Reutimann O, Gugerli F, Rellstab C. A species-discriminatory single-nucleotide polymorphism set reveals maintenance of species integrity in hybridizing European white oaks (Quercus spp.) despite high levels of admixture. ANNALS OF BOTANY 2020; 125:663-676. [PMID: 31912148 PMCID: PMC7102958 DOI: 10.1093/aob/mcaa001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/04/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND AIMS Hybridization and introgression play an important role in the evolution and diversification of plants. To assess the degree of past and current hybridization, the level of genetic admixture in populations needs to be investigated. Ongoing hybridization and blurred species separation have made it challenging to assign European white oak taxa based on leaf morphology and/or genetic markers and to assess the level of admixture. Therefore, there is a need for powerful markers that differentiate between taxa. Here, we established a condensed set of single-nucleotide polymorphism (SNP) markers to reliably differentiate between the three most common oak species in temperate European forests (Quercus robur, Q. petraea, Q. pubescens) and to assess the degree of admixture in a large set of selected Swiss populations. METHODS A training set of 194 presumably pure reference samples from Switzerland and Europe was used to assign 633 test individuals with two different approaches (population genetic-based/Bayesian vs. assumption-free/discriminative classifier) using 58 selected SNPs from coding regions. Admixture was calculated at the individual and population level with the Shannon diversity index based on individual assignment probabilities. KEY RESULTS Depending on the approach, 97.5-100 % of training individuals were assigned correctly, and additional analyses showed that the established SNP set could be further reduced while maintaining its discriminatory power. The two assignment approaches showed high overlap (99 %) in assigning training individuals and slightly less overlap in test individuals (84 %). Levels of admixture varied widely among populations. Mixed stands of Q. petraea and Q. pubescens revealed much higher degrees of admixture than mixed stands of the other two taxon pairs, accentuating high levels of gene flow between these two taxa in Switzerland. CONCLUSIONS Our set of SNPs warrants reliable taxon discrimination with great potential for further applications. We show that the three European white oak taxa have largely retained their species integrity in Switzerland despite high levels of admixture.
Collapse
Affiliation(s)
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | | |
Collapse
|
97
|
Morard M, Benavent-Gil Y, Ortiz-Tovar G, Pérez-Través L, Querol A, Toft C, Barrio E. Genome structure reveals the diversity of mating mechanisms in Saccharomyces cerevisiae x Saccharomyces kudriavzevii hybrids, and the genomic instability that promotes phenotypic diversity. Microb Genom 2020; 6:e000333. [PMID: 32065577 PMCID: PMC7200066 DOI: 10.1099/mgen.0.000333] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/15/2020] [Indexed: 01/03/2023] Open
Abstract
Interspecific hybridization has played an important role in the evolution of eukaryotic organisms by favouring genetic interchange between divergent lineages to generate new phenotypic diversity involved in the adaptation to new environments. This way, hybridization between Saccharomyces species, involving the fusion between their metabolic capabilities, is a recurrent adaptive strategy in industrial environments. In the present study, whole-genome sequences of natural hybrids between Saccharomyces cerevisiae and Saccharomyces kudriavzevii were obtained to unveil the mechanisms involved in the origin and evolution of hybrids, as well as the ecological and geographic contexts in which spontaneous hybridization and hybrid persistence take place. Although Saccharomyces species can mate using different mechanisms, we concluded that rare-mating is the most commonly used, but other mechanisms were also observed in specific hybrids. The preponderance of rare-mating was confirmed by performing artificial hybridization experiments. The mechanism used to mate determines the genomic structure of the hybrid and its final evolutionary outcome. The evolution and adaptability of the hybrids are triggered by genomic instability, resulting in a wide diversity of genomic rearrangements. Some of these rearrangements could be adaptive under the stressful conditions of the industrial environment.
Collapse
Affiliation(s)
- Miguel Morard
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Yaiza Benavent-Gil
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Guadalupe Ortiz-Tovar
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
- Present address: Centro de Estudios Vitivinícolas de Baja California, México, CETYS Universidad, Ensenada, Baja California, Mexico
| | - Laura Pérez-Través
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| | - Christina Toft
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
- Present address: Institute for Integrative and Systems Biology, Universitat de València and CSIC, Paterna, Valencia, Spain
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (IATA), CSIC, Paterna, Valencia, Spain
| |
Collapse
|
98
|
Ball JW, Robinson TP, Wardell-Johnson GW, Bovill J, Byrne M, Nevill PG. Fine-scale species distribution modelling and genotyping by sequencing to examine hybridisation between two narrow endemic plant species. Sci Rep 2020; 10:1562. [PMID: 32005887 PMCID: PMC6994521 DOI: 10.1038/s41598-020-58525-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 01/14/2020] [Indexed: 01/11/2023] Open
Abstract
Hybridization has an important and often positive role in plant evolution. However, it can also have negative consequences for species. Two closely related species of Ornduffia are endemic to the Porongurup Range in the South West Australian Global Biodiversity Hotspot. The rare Ornduffia calthifolia is found exclusively on the summits, while O. marchantii is more widely dispersed across a greater range of elevation and is not considered threatened. Hybridisation in suitable overlapping habitat has been suspected between them for decades. Here we combine genotyping by sequencing to verify hybridisation genetically, and fine scale (2 m resolution) species distribution modelling (SDM) to test if hybrids occur in suitable intersecting habitat. From a study area of c. 4700 ha, SDM identified c. 275 ha and c. 322 ha of suitable habitat for O. calthifolia and O. marchantii, respectively. We identified range overlap between species of c. 59 ha), which enveloped 32 individuals confirmed to be hybrids. While the hybrids were at the margin of suitable habitat for O. marchantii, their preference for elevated habitat was closer to the more narrowly distributed O. calthifolia. The combination of genetic data and fine scale spatial modelling approaches enabled a better understanding of hybridisation among taxa of conservation significance. However, the level to which hybrid proliferation and competition for habitat presents as a threat to O. calthifolia is currently unknown and requires priority in conservation management given the threats from global warming and disturbance by tourism.
Collapse
Affiliation(s)
- J W Ball
- School of Earth and Planetary Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia.,ARC Centre for Mine Site Restoration and School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - T P Robinson
- School of Earth and Planetary Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - G W Wardell-Johnson
- ARC Centre for Mine Site Restoration and School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - J Bovill
- Centre for Australian National Biodiversity Research, National Research Collections Australia, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - M Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Perth, WA, 6983, Australia.,School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - P G Nevill
- ARC Centre for Mine Site Restoration and School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia.
| |
Collapse
|
99
|
Zhou S, Ni S, Dai J, Zhou Q, Zhou R, Liu Y. Natural hybridization between Phyllagathis and Sporoxeia species produces a hybrid without reproductive organs. PLoS One 2020; 15:e0227625. [PMID: 31914145 PMCID: PMC6949006 DOI: 10.1371/journal.pone.0227625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/22/2019] [Indexed: 01/05/2023] Open
Abstract
Natural hybridization plays important roles in plant evolution and speciation. In this study, we sequenced ribosomal internal transcribed spacer (nrITS), four low-copy nuclear genes (Dbr1, SOS4a, SOS4b and PCRF1) and the chloroplast intergenic spacer trnV-trnM to test the hypothesis of hybridization between two species of Phyllagathis and Sporoxeia (Sonerileae/Dissochaeteae, Melastomataceae). Our results provided compelling evidence for the hybridization hypothesis. All hybrid individuals sampled were first-generation hybrids. The failure of flower production in the F1 hybrid individuals may work as the barrier preventing later-generation hybridization or backcross. Analysis of the chloroplast trnV-trnM sequences showed that the hybridization is bidirectional with S. petelotii as the major maternal parent. Several factors, such as sympatry, similar habitat preference, overlapping flowering season and shared pollinators, might have contributed to this hybridization event. The "intergeneric" hybridization reported in this study suggests close relationship between P. longicalcarata and S. petelotii.
Collapse
Affiliation(s)
- Shuaixi Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuheng Ni
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jinhong Dai
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qiujie Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (RZ); (YL)
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (RZ); (YL)
| |
Collapse
|
100
|
Gemenet DC, da Silva Pereira G, De Boeck B, Wood JC, Mollinari M, Olukolu BA, Diaz F, Mosquera V, Ssali RT, David M, Kitavi MN, Burgos G, Felde TZ, Ghislain M, Carey E, Swanckaert J, Coin LJM, Fei Z, Hamilton JP, Yada B, Yencho GC, Zeng ZB, Mwanga ROM, Khan A, Gruneberg WJ, Buell CR. Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:23-36. [PMID: 31595335 PMCID: PMC6952332 DOI: 10.1007/s00122-019-03437-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/17/2019] [Indexed: 05/10/2023]
Abstract
KEY MESSAGE β-Carotene content in sweetpotato is associated with the Orange and phytoene synthase genes; due to physical linkage of phytoene synthase with sucrose synthase, β-carotene and starch content are negatively correlated. In populations depending on sweetpotato for food security, starch is an important source of calories, while β-carotene is an important source of provitamin A. The negative association between the two traits contributes to the low nutritional quality of sweetpotato consumed, especially in sub-Saharan Africa. Using a biparental mapping population of 315 F1 progeny generated from a cross between an orange-fleshed and a non-orange-fleshed sweetpotato variety, we identified two major quantitative trait loci (QTL) on linkage group (LG) three (LG3) and twelve (LG12) affecting starch, β-carotene, and their correlated traits, dry matter and flesh color. Analysis of parental haplotypes indicated that these two regions acted pleiotropically to reduce starch content and increase β-carotene in genotypes carrying the orange-fleshed parental haplotype at the LG3 locus. Phytoene synthase and sucrose synthase, the rate-limiting and linked genes located within the QTL on LG3 involved in the carotenoid and starch biosynthesis, respectively, were differentially expressed in Beauregard versus Tanzania storage roots. The Orange gene, the molecular switch for chromoplast biogenesis, located within the QTL on LG12 while not differentially expressed was expressed in developing roots of the parental genotypes. We conclude that these two QTL regions act together in a cis and trans manner to inhibit starch biosynthesis in amyloplasts and enhance chromoplast biogenesis, carotenoid biosynthesis, and accumulation in orange-fleshed sweetpotato. Understanding the genetic basis of this negative association between starch and β-carotene will inform future sweetpotato breeding strategies targeting sweetpotato for food and nutritional security.
Collapse
Affiliation(s)
- Dorcus C Gemenet
- International Potato Center, ILRI Campus, Old Naivasha Road, P.O. Box 25171-00603, Nairobi, Kenya.
| | | | - Bert De Boeck
- International Potato Center, Av. La Molina 1895, Lima, Peru
| | - Joshua C Wood
- Michigan State University, East Lansing, MI, 48824, USA
| | | | - Bode A Olukolu
- North Carolina State University, Raleigh, NC, 27695, USA
- University of Tennessee, Knoxville, TN, 37996, USA
| | - Federico Diaz
- International Potato Center, Av. La Molina 1895, Lima, Peru
| | | | | | - Maria David
- International Potato Center, Av. La Molina 1895, Lima, Peru
| | - Mercy N Kitavi
- International Potato Center, ILRI Campus, Old Naivasha Road, P.O. Box 25171-00603, Nairobi, Kenya
| | | | | | - Marc Ghislain
- International Potato Center, ILRI Campus, Old Naivasha Road, P.O. Box 25171-00603, Nairobi, Kenya
| | | | | | - Lachlan J M Coin
- University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | | | - Benard Yada
- National Crops Resources Research Institute (NaCCRI), Namulonge, P.O. Box 7084, Kampala, Uganda
| | - G Craig Yencho
- North Carolina State University, Raleigh, NC, 27695, USA
| | - Zhao-Bang Zeng
- North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Awais Khan
- International Potato Center, Av. La Molina 1895, Lima, Peru
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
| | | | - C Robin Buell
- Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|