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Roberts MD, Davis O, Josephs EB, Williamson RJ. K-mer-based Approaches to Bridging Pangenomics and Population Genetics. Mol Biol Evol 2025; 42:msaf047. [PMID: 40111256 PMCID: PMC11925024 DOI: 10.1093/molbev/msaf047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Revised: 01/10/2025] [Accepted: 02/04/2025] [Indexed: 03/12/2025] Open
Abstract
Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously missed by approaches that map short reads to a single reference. However, many species still lack multiple reference genomes and correctly aligning references to build pangenomes can be challenging for many species, limiting our ability to study this missing genomic variation in population genetics. Here, we argue that k-mers are a very useful but underutilized tool for bridging the reference-focused paradigms of population genetics with the reference-free paradigms of pangenomics. We review current literature on the uses of k-mers for performing three core components of most population genetics analyses: identifying, measuring, and explaining patterns of genetic variation. We also demonstrate how different k-mer-based measures of genetic variation behave in population genetic simulations according to the choice of k, depth of sequencing coverage, and degree of data compression. Overall, we find that k-mer-based measures of genetic diversity scale consistently with pairwise nucleotide diversity (π) up to values of about π=0.025 (R2=0.97) for neutrally evolving populations. For populations with even more variation, using shorter k-mers will maintain the scalability up to at least π=0.1. Furthermore, in our simulated populations, k-mer dissimilarity values can be reliably approximated from counting bloom filters, highlighting a potential avenue to decreasing the memory burden of k-mer-based genomic dissimilarity analyses. For future studies, there is a great opportunity to further develop methods to identifying selected loci using k-mers.
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Affiliation(s)
- Miles D Roberts
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI 48824, USA
| | - Olivia Davis
- Department of Computer Science and Software Engineering, Rose-Hulman Institute of Technology, Terre Haute, IN 47803, USA
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Robert J Williamson
- Department of Computer Science and Software Engineering, Rose-Hulman Institute of Technology, Terre Haute, IN 47803, USA
- Department of Biology and Biomedical Engineering, Rose-Hulman Institute of Technology, Terre Haute, IN 47803, USA
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Wang Z, Zhou J, Zou J, Yang J, Chen W. Characterization of PYL gene family and identification of HaPYL genes response to drought and salt stress in sunflower. PeerJ 2024; 12:e16831. [PMID: 38464756 PMCID: PMC10924776 DOI: 10.7717/peerj.16831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/04/2024] [Indexed: 03/12/2024] Open
Abstract
In the context of global climate change, drought and soil salinity are some of the most devastating abiotic stresses affecting agriculture today. PYL proteins are essential components of abscisic acid (ABA) signaling and play critical roles in responding to abiotic stressors, including drought and salt stress. Although PYL genes have been studied in many species, their roles in responding to abiotic stress are still unclear in the sunflower. In this study, 19 HaPYL genes, distributed on 15 of 17 chromosomes, were identified in the sunflower. Fragment duplication is the main cause of the expansion of PYL genes in the sunflower genome. Based on phylogenetic analysis, HaPYL genes were divided into three subfamilies. Members in the same subfamily share similar protein motifs and gene exon-intron structures, except for the second subfamily. Tissue expression patterns suggested that HaPYLs serve different functions when responding to developmental and environmental signals in the sunflower. Exogenous ABA treatment showed that most HaPYLs respond to an increase in the ABA level. Among these HaPYLs, HaPYL2a, HaPYL4d, HaPYL4g, HaPYL8a, HaPYL8b, HaPYL8c, HaPYL9b, and HaPYL9c were up-regulated with PEG6000 treatment and NaCl treatment. This indicates that they may play a role in resisting drought and salt stress in the sunflower by mediating ABA signaling. Our findings provide some clues to further explore the functions of PYL genes in the sunflower, especially with regards to drought and salt stress resistance.
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Affiliation(s)
- Zhaoping Wang
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
| | - Jiayan Zhou
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
| | - Jian Zou
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
| | - Jun Yang
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
| | - Weiying Chen
- China West Normal University, College of Life Sciences, Nanchong, Sichuan, China
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Ranathunge C, Chimahusky ME, Welch ME. A comparative study of population genetic structure reveals patterns consistent with selection at functional microsatellites in common sunflower. Mol Genet Genomics 2022; 297:1329-1342. [PMID: 35786764 DOI: 10.1007/s00438-022-01920-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 06/16/2022] [Indexed: 10/17/2022]
Abstract
Microsatellites, also known as short tandem repeats (STRs), have long been considered non-functional, neutrally evolving regions of the genome. Recent findings suggest that they can function as drivers of rapid adaptive evolution. Previous work on the common sunflower identified 479 transcribed microsatellites where allele length significantly correlates with gene expression (eSTRs) in a stepwise manner. Here, a population genetic approach is used to test whether eSTR allele length variation is under selection. Genotypic variation among and within populations at 13 eSTRs was compared with that at 19 anonymous microsatellites in 672 individuals from 17 natural populations of sunflower from across a cline running from Saskatchewan to Oklahoma (distance of approximately 1600 km). Expected heterozygosity, allelic richness, and allelic diversity were significantly lower at eSTRs, a pattern consistent with higher relative rates of purifying selection. Further, an analysis of variation in microsatellite allele lengths (lnRV), and heterozygosities (lnRH), indicate recent selective sweeps at the eSTRs. Mean microsatellite allele lengths at four eSTRs within populations are significantly correlated with latitude consistent with the predictions of the tuning-knob model which predicts stepwise relationships between microsatellite allele length and phenotypes. This finding suggests that shorter or longer alleles at eSTRs may be favored in climatic extremes. Collectively, our results imply that eSTRs are likely under selection and that they may be playing a role in facilitating local adaptation across a well-defined cline in the common sunflower.
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Affiliation(s)
- Chathurani Ranathunge
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA.
- School of Health Professions, Eastern Virginia Medical School, Norfolk, VA, 23507, USA.
| | - Melody E Chimahusky
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA
| | - Mark E Welch
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA
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Song JM, Zhang Y, Zhou ZW, Lu S, Ma W, Lu C, Chen LL, Guo L. Oil plant genomes: current state of the science. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2859-2874. [PMID: 35560205 DOI: 10.1093/jxb/erab472] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/22/2021] [Indexed: 05/25/2023]
Abstract
Vegetable oils are an indispensable nutritional component of the human diet as well as important raw materials for a variety of industrial applications such as pharmaceuticals, cosmetics, oleochemicals, and biofuels. Oil plant genomes are highly diverse, and their genetic variation leads to a diversity in oil biosynthesis and accumulation along with agronomic traits. This review discusses plant oil biosynthetic pathways, current state of genome assembly, polyploidy and asymmetric evolution of genomes of oil plants and their wild relatives, and research progress of pan-genomics in oil plants. The availability of complete high-resolution genomes and pan-genomes has enabled the identification of structural variations in the genomes that are associated with the diversity of agronomic and environment fitness traits. These and future genomes also provide powerful tools to understand crop evolution and to harvest the rich natural variations to improve oil crops for enhanced productivity, oil quality, and adaptability to changing environments.
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Affiliation(s)
- Jia-Ming Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhi-Wei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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5
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Scossa F, Fernie AR. The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Comput Struct Biotechnol J 2020; 18:482-500. [PMID: 32180906 PMCID: PMC7063335 DOI: 10.1016/j.csbj.2020.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of novel compounds. Here we present the current hypotheses made on the origin of life and ancestral metabolism and present the theories and mechanisms by which the large chemical diversity of plants might have emerged along evolution. In particular, we provide a survey of statistical methods that can be used to detect signatures of selection at the gene and population level, and discuss potential and limits of these methods for investigating patterns of molecular adaptation in plant metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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6
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Neupane S, Schweitzer SE, Neupane A, Andersen EJ, Fennell A, Zhou R, Nepal MP. Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower ( Helianthus annuus L.). PLANTS (BASEL, SWITZERLAND) 2019; 8:E28. [PMID: 30678298 PMCID: PMC6409774 DOI: 10.3390/plants8020028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/07/2019] [Accepted: 01/16/2019] [Indexed: 12/12/2022]
Abstract
Mitogen-Activated Protein Kinase (MAPK) genes encode proteins that regulate biotic and abiotic stresses in plants through signaling cascades comprised of three major subfamilies: MAP Kinase (MPK), MAPK Kinase (MKK), and MAPKK Kinase (MKKK). The main objectives of this research were to conduct genome-wide identification of MAPK genes in Helianthus annuus and examine functional divergence of these genes in relation to those in nine other plant species (Amborella trichopoda, Aquilegia coerulea, Arabidopsis thaliana, Daucus carota, Glycine max, Oryza sativa, Solanum lycopersicum, Sphagnum fallax, and Vitis vinifera), representing diverse taxonomic groups of the Plant Kingdom. A Hidden Markov Model (HMM) profile of the MAPK genes utilized reference sequences from A. thaliana and G. max, yielding a total of 96 MPKs and 37 MKKs in the genomes of A. trichopoda, A. coerulea, C. reinhardtii, D. carota, H. annuus, S. lycopersicum, and S. fallax. Among them, 28 MPKs and eight MKKs were confirmed in H. annuus. Phylogenetic analyses revealed four clades within each subfamily. Transcriptomic analyses showed that at least 19 HaMPK and seven HaMKK genes were induced in response to salicylic acid (SA), sodium chloride (NaCl), and polyethylene glycol (Peg) in leaves and roots. Of the seven published sunflower microRNAs, five microRNA families are involved in targeting eight MPKs. Additionally, we discussed the need for using MAP Kinase nomenclature guidelines across plant species. Our identification and characterization of MAP Kinase genes would have implications in sunflower crop improvement, and in advancing our knowledge of the diversity and evolution of MAPK genes in the Plant Kingdom.
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Affiliation(s)
- Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Sarah E Schweitzer
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Achal Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Anne Fennell
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA.
| | - Ruanbao Zhou
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
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7
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Neupane S, Andersen EJ, Neupane A, Nepal MP. Genome-Wide Identification of NBS-Encoding Resistance Genes in Sunflower (Helianthus annuus L.). Genes (Basel) 2018; 9:genes9080384. [PMID: 30061549 PMCID: PMC6115920 DOI: 10.3390/genes9080384] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 01/08/2023] Open
Abstract
Nucleotide Binding Site—Leucine-Rich Repeat (NBS-LRR) genes encode disease resistance proteins involved in plants’ defense against their pathogens. Although sunflower is affected by many diseases, only a few molecular details have been uncovered regarding pathogenesis and resistance mechanisms. Recent availability of sunflower whole genome sequences in publicly accessible databases allowed us to accomplish a genome-wide identification of Toll-interleukin-1 receptor-like Nucleotide-binding site Leucine-rich repeat (TNL), Coiled Coil (CC)-NBS-LRR (CNL), Resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) and NBS-LRR (NL) protein encoding genes. Hidden Markov Model (HMM) profiling of 52,243 putative protein sequences from sunflower resulted in 352 NBS-encoding genes, among which 100 genes belong to CNL group including 64 genes with RX_CC like domain, 77 to TNL, 13 to RNL, and 162 belong to NL group. We also identified signal peptides and nuclear localization signals present in the identified genes and their homologs. We found that NBS genes were located on all chromosomes and formed 75 gene clusters, one-third of which were located on chromosome 13. Phylogenetic analyses between sunflower and Arabidopsis NBS genes revealed a clade-specific nesting pattern in CNLs, with RNLs nested in the CNL-A clade, and species-specific nesting pattern for TNLs. Surprisingly, we found a moderate bootstrap support (BS = 50%) for CNL-A clade being nested within TNL clade making both the CNL and TNL clades paraphyletic. Arabidopsis and sunflower showed 87 syntenic blocks with 1049 high synteny hits between chromosome 5 of Arabidopsis and chromosome 6 of sunflower. Expression data revealed functional divergence of the NBS genes with basal level tissue-specific expression. This study represents the first genome-wide identification of NBS genes in sunflower paving avenues for functional characterization and potential crop improvement.
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Affiliation(s)
- Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Achal Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
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Liang C, Wang W, Wang J, Ma J, Li C, Zhou F, Zhang S, Yu Y, Zhang L, Li W, Huang X. Identification of differentially expressed genes in sunflower (Helianthus annuus) leaves and roots under drought stress by RNA sequencing. BOTANICAL STUDIES 2017; 58:42. [PMID: 29071432 PMCID: PMC5656504 DOI: 10.1186/s40529-017-0197-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/02/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sunflower is recognized as one of the most important oil plants with strong tolerance to drought in the world. In order to study the response mechanisms of sunflower plants to drought stress, gene expression profiling using high throughput sequencing was performed for seedling leaves and roots (sunflower inbred line R5) after 24 h of drought stress (15% PEG 6000). The transcriptome assembled using sequences of 12 samples was used as a reference. RESULTS 805 and 198 genes were identified that were differentially expressed in leaves and roots, respectively. Another 71 genes were differentially expressed in both organs, in which more genes were up-regulated than down-regulated. In agreement with results obtained for other crops or from previous sunflower studies, we also observed that nine genes may be associated with the response of sunflower to drought. CONCLUSIONS The results of this study may provide new information regarding the sunflower drought response, as well as add to the number of known genes associated with drought tolerance.
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Affiliation(s)
- Chunbo Liang
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Xuefu Road 368, Harbin, 150086 People’s Republic of China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Wenjun Wang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Jing Wang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Jun Ma
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Cen Li
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Fei Zhou
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Shuquan Zhang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Ying Yu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Liguo Zhang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
| | - Weizhong Li
- Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, 150036 People’s Republic of China
| | - Xutang Huang
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Xuefu Road 368, Harbin, 150086 People’s Republic of China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086 People’s Republic of China
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Ranwez V, Serra A, Pot D, Chantret N. Domestication reduces alternative splicing expression variations in sorghum. PLoS One 2017; 12:e0183454. [PMID: 28886042 PMCID: PMC5590825 DOI: 10.1371/journal.pone.0183454] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/06/2017] [Indexed: 01/09/2023] Open
Abstract
Domestication is known to strongly reduce genomic diversity through population bottlenecks. The resulting loss of polymorphism has been thoroughly documented in numerous cultivated species. Here we investigate the impact of domestication on the diversity of alternative transcript expressions using RNAseq data obtained on cultivated and wild sorghum accessions (ten accessions for each pool). In that aim, we focus on genes expressing two isoforms in sorghum and estimate the ratio between expression levels of those isoforms in each accession. Noticeably, for a given gene, one isoform can either be overexpressed or underexpressed in some wild accessions, whereas in the cultivated accessions, the balance between the two isoforms of the same gene appears to be much more homogenous. Indeed, we observe in sorghum significantly more variation in isoform expression balance among wild accessions than among domesticated accessions. The possibility exists that the loss of nucleotide diversity due to domestication could affect regulatory elements, controlling transcription or degradation of these isoforms. Impact on the isoform expression balance is discussed. As far as we know, this is the first time that the impact of domestication on transcript isoform balance has been studied at the genomic scale. This could pave the way towards the identification of key domestication genes with finely tuned isoform expressions in domesticated accessions while being highly variable in their wild relatives.
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Affiliation(s)
| | - Audrey Serra
- Montpellier SupAgro, UMR AGAP, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Montpellier, France
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Nie G, Tang L, Zhang Y, Huang L, Ma X, Cao X, Pan L, Zhang X, Zhang X. Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial Grass Miscanthus from China. FRONTIERS IN PLANT SCIENCE 2017; 8:801. [PMID: 28559912 PMCID: PMC5432562 DOI: 10.3389/fpls.2017.00801] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 04/28/2017] [Indexed: 05/02/2023]
Abstract
Drought has become a critical environmental stress affecting on plant in temperate area. As one of the promising bio-energy crops to sustainable biomass production, the genus Miscanthus has been widely studied around the world. However, the most widely used hybrid cultivar among this genus, Miscanthus × giganteus is proved poor drought tolerance compared to some parental species. Here we mainly focused on Miscanthus sinensis, which is one of the progenitors of M. × giganteus providing a comparable yield and well abiotic stress tolerance in some places. The main objectives were to characterize the physiological and photosynthetic respond to drought stress and to develop simple sequence repeats (SSRs) markers associated with drought tolerance by transcriptome sequencing within an originally collection of 44 Miscanthus genotypes from southwest China. Significant phenotypic differences were observed among genotypes, and the average of leaf relative water content (RWC) were severely affected by drought stress decreasing from 88.27 to 43.21%, which could well contribute to separating the drought resistant and drought sensitive genotype of Miscanthus. Furthermore, a total of 16,566 gene-associated SSRs markers were identified based on Illumina RNA sequencing under drought conditions, and 93 of them were randomly selected to validate. In total, 70 (75.3%) SSRs were successfully amplified and the generated loci from 30 polymorphic SSRs were used to estimate the genetic differentiation and population structure. Finally, two optimum subgroups of the population were determined by structure analysis and based on association analysis, seven significant associations were identified including two markers with leaf RWC and five markers with photosynthetic traits. With the rich sequencing resources annotation, such associations would serve an efficient tool for Miscanthus drought response mechanism study and facilitate genetic improvement of drought resistant for this species.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural UniversitySichuan, China
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11
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Wu Y, Meng K, Liang X. Distinct patterns of natural selection in Na +/H + antiporter genes in Populus euphratica and Populus pruinosa. Ecol Evol 2016; 7:82-91. [PMID: 28070277 PMCID: PMC5214168 DOI: 10.1002/ece3.2639] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/17/2016] [Accepted: 10/19/2016] [Indexed: 01/28/2023] Open
Abstract
Salt tolerance genes constitute an important class of loci in plant genomes. Little is known about the extent to which natural selection in saline environments has acted upon these loci, and what types of nucleotide diversity such selection has given rise to. Here, we surveyed genetic diversity in three types of Na+/H+ antiporter gene (SOS, NhaD, and NHX, belonging to the cation/proton antiporter 1 family), which have well‐characterized essential roles in plant salt tolerance. Ten Na+/H+ antiporter genes and 16 neutral loci randomly selected as controls were sequenced from 17 accessions of two closely related members of the genus Populus, Populus euphratica and Populus pruinosa, section Turanga, which are native to northwest China. The results show that salt tolerance genes are common targets of natural selection in P. euphratica and P. pruinosa. Moreover, the patterns of nucleotide variation across the three types of Na+/H+ antiporter gene are distinctly different in these two closely related Populus species, and gene flow from P. pruinosa to P. euphratica is highly restricted. Our results suggest that natural selection played an important role in shaping the current distinct patterns of Na+/H+ antiporter genes, resulting in adaptive evolution in P. euphratica and P. pruinosa.
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Affiliation(s)
- Yuxia Wu
- State Key Laboratory of Grassland Agro-Ecosystem School of Life Sciences Lanzhou University Lanzhou Gansu China
| | - Kuibin Meng
- State Key Laboratory of Grassland Agro-Ecosystem School of Life Sciences Lanzhou University Lanzhou Gansu China
| | - Xiaohui Liang
- State Key Laboratory of Grassland Agro-Ecosystem School of Life Sciences Lanzhou University Lanzhou Gansu China
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12
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Zhong X, Feng D, Yu H, Kong L, Li Q. Genetic Variation and Breeding Signature in Mass Selection Lines of the Pacific Oyster (Crassostrea gigas) Assessed by SNP Markers. PLoS One 2016; 11:e0150868. [PMID: 26954577 PMCID: PMC4783100 DOI: 10.1371/journal.pone.0150868] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/05/2016] [Indexed: 11/18/2022] Open
Abstract
In breeding industries, a challenging problem is how to keep genetic diversity over generations. To investigate genetic variation and identify breeding signatures in mass selected lines of Pacific oyster (Crassostrea gigas), three sixth-generation selected lines and four wild populations were assessed using 103 single nucleotide polymorphism (SNP) markers. The genetic diversity data indicated that the selected lines exhibited a significant reduction in the observed heterozygosity and observed number of alleles per locus compared with the wild populations (P≤0.05), indicating the selected lines tended to lose genetic diversity contrasted with the wild populations. The unweighted pair-group method with arithmetic mean (UPGMA) analysis showed that the wild populations and selected lines were not separated into two groups. Using four outlier tests, a total of 17 loci were found under selection at two levels. The global outlier detection suggested that 4 common outlier loci were subject to selection using both the hierarchical island model and Bayesian likelihood approaches. At regional level, 3 SNPs were detected as outlier using at least two outlier tests and one outlier SNP (CgSNP309) was overlapped in the two wild-selected population comparisons. The candidate outlier SNPs provide valuable resources for future association studies in C. gigas.
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Affiliation(s)
- Xiaoxiao Zhong
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Dandan Feng
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Hong Yu
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, China
- * E-mail:
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13
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Haasl RJ, Payseur BA. Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication. Mol Ecol 2015. [PMID: 26224644 DOI: 10.1111/mec.13339] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genomewide scans for natural selection (GWSS) have become increasingly common over the last 15 years due to increased availability of genome-scale genetic data. Here, we report a representative survey of GWSS from 1999 to present and find that (i) between 1999 and 2009, 35 of 49 (71%) GWSS focused on human, while from 2010 to present, only 38 of 83 (46%) of GWSS focused on human, indicating increased focus on nonmodel organisms; (ii) the large majority of GWSS incorporate interpopulation or interspecific comparisons using, for example F(ST), cross-population extended haplotype homozygosity or the ratio of nonsynonymous to synonymous substitutions; (iii) most GWSS focus on detection of directional selection rather than other modes such as balancing selection; and (iv) in human GWSS, there is a clear shift after 2004 from microsatellite markers to dense SNP data. A survey of GWSS meant to identify loci positively selected in response to severe hypoxic conditions support an approach to GWSS in which a list of a priori candidate genes based on potential selective pressures are used to filter the list of significant hits a posteriori. We also discuss four frequently ignored determinants of genomic heterogeneity that complicate GWSS: mutation, recombination, selection and the genetic architecture of adaptive traits. We recommend that GWSS methodology should better incorporate aspects of genomewide heterogeneity using empirical estimates of relevant parameters and/or realistic, whole-chromosome simulations to improve interpretation of GWSS results. Finally, we argue that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach.
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Affiliation(s)
- Ryan J Haasl
- Department of Biology, University of Wisconsin-Platteville, 1 University Plaza, Platteville, WI, 53818, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI, 53706, USA
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14
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Smadja CM, Loire E, Caminade P, Thoma M, Latour Y, Roux C, Thoss M, Penn DJ, Ganem G, Boursot P. Seeking signatures of reinforcement at the genetic level: a hitchhiking mapping and candidate gene approach in the house mouse. Mol Ecol 2015; 24:4222-4237. [PMID: 26132782 DOI: 10.1111/mec.13301] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/12/2015] [Accepted: 06/17/2015] [Indexed: 12/11/2022]
Abstract
Reinforcement is the process by which prezygotic isolation is strengthened as a response to selection against hybridization. Most empirical support for reinforcement comes from the observation of its possible phenotypic signature: an accentuated degree of prezygotic isolation in the hybrid zone as compared to allopatry. Here, we implemented a novel approach to this question by seeking for the signature of reinforcement at the genetic level. In the house mouse, selection against hybrids and enhanced olfactory-based assortative mate preferences are observed in a hybrid zone between the two European subspecies Mus musculus musculus and M. m. domesticus, suggesting a possible recent reinforcement event. To test for the genetic signature of reinforcing selection and identify genes involved in sexual isolation, we adopted a hitchhiking mapping approach targeting genomic regions containing candidate genes for assortative mating in mice. We densely scanned these genomic regions in hybrid zone and allopatric samples using a large number of fast evolving microsatellite loci that allow the detection of recent selection events. We found a handful of loci showing the expected pattern of significant reduction in variability in populations close to the hybrid zone, showing assortative odour preference in mate choice experiments as compared to populations further away and displaying no such preference. These loci lie close to genes that we pinpoint as testable candidates for further investigation.
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Affiliation(s)
- Carole M Smadja
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Etienne Loire
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Pierre Caminade
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Marios Thoma
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Yasmin Latour
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Camille Roux
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Michaela Thoss
- University of Veterinary Medicine Vienna, Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, Vienna, Austria
| | - Dustin J Penn
- University of Veterinary Medicine Vienna, Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, Vienna, Austria
| | - Guila Ganem
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
| | - Pierre Boursot
- Institut des Sciences de l'Evolution UMR 5554 (Centre National de la Recherche Scientifique CNRS, Institut pour la Recherche et le Développement IRD, Université de Montpellier), cc065 Université de Montpellier, Campus Triolet, 34095 Montpellier, France
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15
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Burrell AM, Pepper AE, Hodnett G, Goolsby JA, Overholt WA, Racelis AE, Diaz R, Klein PE. Exploring origins, invasion history and genetic diversity ofImperata cylindrica(L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing. Mol Ecol 2015; 24:2177-93. [DOI: 10.1111/mec.13167] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 12/31/2022]
Affiliation(s)
- A. Millie Burrell
- Institute for Plant Genomics and Biotechnology; Department of Horticultural Sciences; Texas A&M University; College Station TX 77843-2123 USA
| | - Alan E. Pepper
- Department of Biology; Texas A&M University; College Station TX 77843-3258 USA
| | - George Hodnett
- Department of Soil and Crop Sciences; Texas A&M University; College Station TX 77843-2474 USA
| | - John A. Goolsby
- Cattle Fever Tick Research Laboratory; USDA-ARS; Moore Air Base Building 6419 Edinburg TX 78541 USA
| | - William A. Overholt
- Biological Control and Containment Laboratory; University of Florida; 2199 South Rock Road Fort Pierce FL 34945-3138 USA
| | - Alexis E. Racelis
- Department of Biology; University of Texas Pan American; 1201 West University Drive Edinburg TX 78539 USA
| | - Rodrigo Diaz
- Biological Control and Containment Laboratory; University of Florida; 2199 South Rock Road Fort Pierce FL 34945-3138 USA
| | - Patricia E. Klein
- Institute for Plant Genomics and Biotechnology; Department of Horticultural Sciences; Texas A&M University; College Station TX 77843-2123 USA
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16
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Pramod S, Perkins AD, Welch ME. Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome. J Genet 2015; 93:431-42. [PMID: 25189238 DOI: 10.1007/s12041-014-0402-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly 5'UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli.
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Affiliation(s)
- Sreepriya Pramod
- Department of Biological Sciences, Mississippi State University, 219 Harned Hall, 295 Lee Boulevard, MS 39762, USA.
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Li YH, Reif JC, Jackson SA, Ma YS, Chang RZ, Qiu LJ. Detecting SNPs underlying domestication-related traits in soybean. BMC PLANT BIOLOGY 2014; 14:251. [PMID: 25258093 PMCID: PMC4180965 DOI: 10.1186/s12870-014-0251-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 09/18/2014] [Indexed: 05/26/2023]
Abstract
BACKGROUND Cultivated soybean (Glycine max) experienced a severe genetic bottleneck during its domestication and a further loss in diversity during its subsequent selection. Here, a panel of 65 wild (G. soja) and 353 cultivated accessions was genotyped at 552 single-nucleotide polymorphism loci to search for signals of selection during and after domestication. RESULTS The wild and cultivated populations were well differentiated from one another. Application of the Fst outlier test revealed 64 loci showing evidence for selection. Of these, 35 related to selection during domestication, while the other 29 likely gradually became monomorphic as a result of prolonged selection during post domestication. Two of the SNP locus outliers were associated with testa color. CONCLUSIONS Identifying genes controlling domestication-related traits is important for maintaining the diversity of crops. SNP locus outliers detected by a combined forward genetics and population genetics approach can provide markers with utility for the conservation of wild accessions and for trait improvement in the cultivated genepool.
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Affiliation(s)
- Ying-Hui Li
- />The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, P.R. China
| | - Jochen C Reif
- />Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Scott A Jackson
- />Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 USA
| | - Yan-Song Ma
- />The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, P.R. China
- />Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, 150086 Harbin, China
| | - Ru-Zhen Chang
- />The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, P.R. China
| | - Li-Juan Qiu
- />The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081 Beijing, P.R. China
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18
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Quintela M, Johansson MP, Kristjánsson BK, Barreiro R, Laurila A. AFLPs and mitochondrial haplotypes reveal local adaptation to extreme thermal environments in a freshwater gastropod. PLoS One 2014; 9:e101821. [PMID: 25007329 PMCID: PMC4090234 DOI: 10.1371/journal.pone.0101821] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/11/2014] [Indexed: 01/06/2023] Open
Abstract
The way environmental variation shapes neutral and adaptive genetic variation in natural populations is a key issue in evolutionary biology. Genome scans allow the identification of the genetic basis of local adaptation without previous knowledge of genetic variation or traits under selection. Candidate loci for divergent adaptation are expected to show higher FST than neutral loci influenced solely by random genetic drift, migration and mutation. The comparison of spatial patterns of neutral markers and loci under selection may help disentangle the effects of gene flow, genetic drift and selection among populations living in contrasting environments. Using the gastropod Radix balthica as a system, we analyzed 376 AFLP markers and 25 mtDNA COI haplotypes for candidate loci and associations with local adaptation among contrasting thermal environments in Lake Mývatn, a volcanic lake in northern Iceland. We found that 2% of the analysed AFLP markers were under directional selection and 12% of the mitochondrial haplotypes correlated with differing thermal habitats. The genetic networks were concordant for AFLP markers and mitochondrial haplotypes, depicting distinct topologies at neutral and candidate loci. Neutral topologies were characterized by intense gene flow revealed by dense nets with edges connecting contrasting thermal habitats, whereas the connections at candidate loci were mostly restricted to populations within each thermal habitat and the number of edges decreased with temperature. Our results suggest microgeographic adaptation within Lake Mývatn and highlight the utility of genome scans in detecting adaptive divergence.
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Affiliation(s)
- María Quintela
- Dept of Animal Biology, Plant Biology and Ecology, Faculty of Science, University of A Coruña, A Coruña, Spain
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Magnus P. Johansson
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Bjarni K. Kristjánsson
- Hólar University College, Department of Aquaculture and Fish Biology, Sauðarkrokur, Iceland
| | - Rodolfo Barreiro
- Dept of Animal Biology, Plant Biology and Ecology, Faculty of Science, University of A Coruña, A Coruña, Spain
| | - Anssi Laurila
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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19
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Fine-mapping and selective sweep analysis of QTL for cold tolerance in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2014; 4:1635-45. [PMID: 24970882 PMCID: PMC4169155 DOI: 10.1534/g3.114.012757] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
There is a growing interest in investigating the relationship between genes with signatures of natural selection and genes identified in QTL mapping studies using combined population and quantitative genetics approaches. We dissected an X-linked interval of 6.2 Mb, which contains two QTL underlying variation in chill coma recovery time (CCRT) in Drosophila melanogaster from temperate (European) and tropical (African) regions. This resulted in two relatively small regions of 131 kb and 124 kb. The latter one co-localizes with a very strong selective sweep in the European population. We examined the genes within and near the sweep region individually using gene expression analysis and P-element insertion lines. Of the genes overlapping with the sweep, none appears to be related to CCRT. However, we have identified a new candidate gene of CCRT, brinker, which is located just outside the sweep region and is inducible by cold stress. We discuss these results in light of recent population genetics theories on quantitative traits.
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20
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Kawakami T, Darby BJ, Ungerer MC. Transcriptome resources for the perennial sunflowerHelianthus maximilianiobtained from ecologically divergent populations. Mol Ecol Resour 2014; 14:812-9. [DOI: 10.1111/1755-0998.12227] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/07/2014] [Accepted: 01/08/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Takeshi Kawakami
- Division of Biology; Kansas State University; Manhattan KS 66506 USA
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Brian J. Darby
- Department of Biology; University of North Dakota; Grand Forks ND 58202 USA
| | - Mark C. Ungerer
- Division of Biology; Kansas State University; Manhattan KS 66506 USA
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21
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Kantar MB, Baute GJ, Bock DG, Rieseberg LH. Genomic variation in Helianthus: learning from the past and looking to the future. Brief Funct Genomics 2014; 13:328-40. [DOI: 10.1093/bfgp/elu004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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22
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Toivainen T, Pyhäjärvi T, Niittyvuopio A, Savolainen O. A recent local sweep at the PHYA locus in the Northern European Spiterstulen population of Arabidopsis lyrata. Mol Ecol 2014; 23:1040-52. [PMID: 24471518 DOI: 10.1111/mec.12682] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 12/14/2013] [Accepted: 01/08/2014] [Indexed: 11/29/2022]
Abstract
Northern and central European Arabidopsis lyrata ssp. petraea populations are locally adapted to prevailing climatic conditions through differences in timing of life history events. The timing of flowering and, in perennials, the timing of growth cessation influence fitness. Phytochrome A may have an important role in regulating these life history traits as it perceives changes in daylength. We asked whether PHYA has contributed to local adaptation to the northern conditions in A. l. petraea. To search for signals of directional selection at the PHYA locus, we resequenced PHYA and 9 short fragments around PHYA from a 57-kb region from a German (Plech) and a Norwegian (Spiterstulen) population and compared patterns of differentiation and diversity to a set of 19 reference loci around the genome. First, we found that the populations were highly differentiated: there were three nonsynonymous fixed differences at the PHYA locus, which was in stark contrast with the total four fixed differences in the 19 reference loci. Compatible with a sweep hypothesis, variation was almost completely removed from the 9.4-kb region around PHYA in the northern Spiterstulen population. The overall level of linkage disequilibrium (LD) was higher in Spiterstulen, but there was no LD across the PHYA locus in the population, which is also a known consequence of a selective sweep. The sweep has likely occurred after the last glacial maximum, which suggests that it has contributed to adaptation to the northern conditions.
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Affiliation(s)
- Tuomas Toivainen
- Department of Biology, University of Oulu, Oulu, 90014, Finland; Biocenter Oulu, University of Oulu, Oulu, 90014, Finland
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Rieseberg L, Vines T, Gow J, Kane N. Molecular Ecology continues to perform well according to the major publication metrics. Introduction. Mol Ecol 2014; 23:1-15. [PMID: 24372750 DOI: 10.1111/mec.12586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/06/2013] [Indexed: 11/28/2022]
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Corrado G, Piffanelli P, Caramante M, Coppola M, Rao R. SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato. BMC Genomics 2013; 14:835. [PMID: 24279304 PMCID: PMC4046682 DOI: 10.1186/1471-2164-14-835] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/20/2013] [Indexed: 11/10/2022] Open
Abstract
Background The tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes. Results With the aim to examine patterns of polymorphism, characterize population structure and identify putative loci under positive selection, we genotyped 214 tomato accessions (which include cultivated landraces, commercial varieties and wild relatives) using a custom-made Illumina SNP-panel. Most of the 175 successfully scored SNP loci were found to be polymorphic. Population structure analysis and estimates of genetic differentiation indicated that landraces constitute distinct sub-populations. Furthermore, contemporary varieties could be separated in groups (processing, fresh and cherry) that are consistent with the recent breeding aimed at market-class specialization. In addition, at the 95% confidence level, we identified 30, 34 and 37 loci under positive selection between landraces and each of the groups of commercial variety (cherry, processing and fresh market, respectively). Their number and genomic locations imply the presence of some extended regions with high genetic variation between landraces and contemporary varieties. Conclusions Our work provides knowledge concerning the level and distribution of genetic variation within cultivated tomato landraces and increases our understanding of the genetic subdivision of contemporary varieties. The data indicate that adaptation and selection have led to a genomic signature in cultivated landraces and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. The genomic characterization presented here is an essential step towards a future exploitation of the available tomato genetic resources in research and breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-835) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giandomenico Corrado
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, via Università 100, 80055 Portici, NA, Italy.
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Fischer I, Steige KA, Stephan W, Mboup M. Sequence evolution and expression regulation of stress-responsive genes in natural populations of wild tomato. PLoS One 2013; 8:e78182. [PMID: 24205149 PMCID: PMC3799731 DOI: 10.1371/journal.pone.0078182] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 09/09/2013] [Indexed: 11/19/2022] Open
Abstract
The wild tomato species Solanum chilense and S. peruvianum are a valuable non-model system for studying plant adaptation since they grow in diverse environments facing many abiotic constraints. Here we investigate the sequence evolution of regulatory regions of drought and cold responsive genes and their expression regulation. The coding regions of these genes were previously shown to exhibit signatures of positive selection. Expression profiles and sequence evolution of regulatory regions of members of the Asr (ABA/water stress/ripening induced) gene family and the dehydrin gene pLC30-15 were analyzed in wild tomato populations from contrasting environments. For S. chilense, we found that Asr4 and pLC30-15 appear to respond much faster to drought conditions in accessions from very dry environments than accessions from more mesic locations. Sequence analysis suggests that the promoter of Asr2 and the downstream region of pLC30-15 are under positive selection in some local populations of S. chilense. By investigating gene expression differences at the population level we provide further support of our previous conclusions that Asr2, Asr4, and pLC30-15 are promising candidates for functional studies of adaptation. Our analysis also demonstrates the power of the candidate gene approach in evolutionary biology research and highlights the importance of wild Solanum species as a genetic resource for their cultivated relatives.
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Affiliation(s)
- Iris Fischer
- Section of Evolutionary Biology, Department of Biology II, University of Munich, Planegg-Martinsried, Germany
- * E-mail:
| | - Kim A. Steige
- Section of Evolutionary Biology, Department of Biology II, University of Munich, Planegg-Martinsried, Germany
| | - Wolfgang Stephan
- Section of Evolutionary Biology, Department of Biology II, University of Munich, Planegg-Martinsried, Germany
| | - Mamadou Mboup
- Section of Evolutionary Biology, Department of Biology II, University of Munich, Planegg-Martinsried, Germany
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26
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Gandolfi B, Liu H, Griffioen L, Pedersen NC. Simple recessive mutation inENAMis associated with amelogenesis imperfecta in Italian Greyhounds. Anim Genet 2013; 44:569-78. [DOI: 10.1111/age.12043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Barbara Gandolfi
- Center for Companion Animal Health; Koret Center for Veterinary Genetics; School of Veterinary Medicine; University of California; One Shields Avenue; Davis; CA; 95616; USA
| | - Hongwei Liu
- Center for Companion Animal Health; Koret Center for Veterinary Genetics; School of Veterinary Medicine; University of California; One Shields Avenue; Davis; CA; 95616; USA
| | - Layle Griffioen
- Center for Companion Animal Health; Koret Center for Veterinary Genetics; School of Veterinary Medicine; University of California; One Shields Avenue; Davis; CA; 95616; USA
| | - Niels C. Pedersen
- Center for Companion Animal Health; Koret Center for Veterinary Genetics; School of Veterinary Medicine; University of California; One Shields Avenue; Davis; CA; 95616; USA
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27
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Andrew RL, Bernatchez L, Bonin A, Buerkle CA, Carstens BC, Emerson BC, Garant D, Giraud T, Kane NC, Rogers SM, Slate J, Smith H, Sork VL, Stone GN, Vines TH, Waits L, Widmer A, Rieseberg LH. A road map for molecular ecology. Mol Ecol 2013; 22:2605-26. [DOI: 10.1111/mec.12319] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Louis Bernatchez
- DInstitut de Biologie Intégrative et des Systémes; Département de Biologie; 1030, Avenue de la Médecine Université Laval; Québec QC G1V 0A6 Canada
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 Université Joseph Fourier; BP 53, 38041 Grenoble Cedex 9 France
| | - C. Alex. Buerkle
- Department of Botany; University of Wyoming; 1000 E. University Ave. Laramie WY 82071 USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology; 318 W. 12th Ave. The Ohio State University; Columbus OH 43210 USA
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife; Canary Islands 38206 Spain
| | - Dany Garant
- Département de Biologie; Université de Sherbrooke; Sherbrooke QC J1K 2R1 Canada
| | - Tatiana Giraud
- Laboratoire Ecologie, Systématique et Evolution; UMR 8079 CNRS-UPS-AgroParisTech, Bâtiment 360 Univ. Paris Sud; 91405 Orsay cedex France
| | - Nolan C. Kane
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive N.W., Calgary AB T2N 1N4 Canada
| | - Jon Slate
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - Harry Smith
- 79 Melton Road Burton-on-the-Wolds Loughborough LE12 5TQ UK
| | - Victoria L. Sork
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; 4139 Terasaki Life Sciences Building, 610 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road, Edinburgh EH9 3JT UK
| | - Timothy H. Vines
- Molecular Ecology Editorial Office; 6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Lisette Waits
- Department of Fish and Wildlife Sciences; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - Alex Widmer
- ETH Zurich; Institute of Integrative Biology; Universitätstrasse 16 Zurich 8092 Switzerland
| | - Loren H. Rieseberg
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
- Department of Biology; Indiana University; 1001 E. 3 St., Bloomington IN 47405 USA
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Andrew RL, Rieseberg LH. DIVERGENCE IS FOCUSED ON FEW GENOMIC REGIONS EARLY IN SPECIATION: INCIPIENT SPECIATION OF SUNFLOWER ECOTYPES. Evolution 2013; 67:2468-82. [DOI: 10.1111/evo.12106] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 02/20/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany, University of British Columbia, 3529-6270 University Blvd; Vancouver; British Columbia; V6T 1Z4; Canada
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Ohtani M, Kondo T, Tani N, Ueno S, Lee LS, Ng KKS, Muhammad N, Finkeldey R, Na'iem M, Indrioko S, Kamiya K, Harada K, Diway B, Khoo E, Kawamura K, Tsumura Y. Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in South-East Asia. Mol Ecol 2013; 22:2264-79. [PMID: 23432376 DOI: 10.1111/mec.12243] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/26/2012] [Accepted: 01/05/2013] [Indexed: 11/29/2022]
Abstract
Tropical rainforests in South-East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south-western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28-0.09 million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.
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Affiliation(s)
- Masato Ohtani
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
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Schoville SD, Bonin A, François O, Lobreaux S, Melodelima C, Manel S. Adaptive Genetic Variation on the Landscape: Methods and Cases. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2012. [DOI: 10.1146/annurev-ecolsys-110411-160248] [Citation(s) in RCA: 217] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sean D. Schoville
- Laboratoire TIMC-IMAG, UMR-CNRS 5525, Université Joseph Fourier, 38041 Grenoble, France; ,
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
| | - Olivier François
- Laboratoire TIMC-IMAG, UMR-CNRS 5525, Université Joseph Fourier, 38041 Grenoble, France; ,
| | - Stéphane Lobreaux
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
| | - Christelle Melodelima
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
| | - Stéphanie Manel
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Université Joseph Fourier, 38041 Grenoble, France; , , ,
- Laboratoire Population Environnement et Développement, UMR-IRD 151, Université Aix-Marseille, 13331 Marseille, France
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31
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Andrew RL, Kane NC, Baute GJ, Grassa CJ, Rieseberg LH. Recent nonhybrid origin of sunflower ecotypes in a novel habitat. Mol Ecol 2012; 22:799-813. [DOI: 10.1111/mec.12038] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 02/04/2023]
Affiliation(s)
- Rose L. Andrew
- Department of Botany; University of British Columbia; 3529-6270 University Blvd; Vancouver; BC; Canada; V6T 1Z4
| | - Nolan C. Kane
- Department of Botany; University of British Columbia; 3529-6270 University Blvd; Vancouver; BC; Canada; V6T 1Z4
| | - Greg J. Baute
- Department of Botany; University of British Columbia; 3529-6270 University Blvd; Vancouver; BC; Canada; V6T 1Z4
| | - Christopher J. Grassa
- Department of Botany; University of British Columbia; 3529-6270 University Blvd; Vancouver; BC; Canada; V6T 1Z4
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32
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Alheit KV, Maurer HP, Reif JC, Tucker MR, Hahn V, Weissmann EA, Würschum T. Genome-wide evaluation of genetic diversity and linkage disequilibrium in winter and spring triticale (x Triticosecale Wittmack). BMC Genomics 2012; 13:235. [PMID: 22691168 PMCID: PMC3464613 DOI: 10.1186/1471-2164-13-235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 05/24/2012] [Indexed: 11/10/2022] Open
Abstract
Background Recent advances in genotyping with high-density markers nowadays enable genome-wide genomic analyses in crops. A detailed characterisation of the population structure and linkage disequilibrium (LD) is essential for the application of genomic approaches and consequently for knowledge-based breeding. In this study we used the triticale-specific DArT array to analyze population structure, genetic diversity, and LD in a worldwide set of 161 winter and spring triticale lines. Results The principal coordinate analysis revealed that the first principal coordinate divides the triticale population into two clusters according to their growth habit. The density distributions of the first ten principal coordinates revealed that several show a distribution indicative of population structure. In addition, we observed relatedness within growth habits which was higher among the spring types than among the winter types. The genome-wide analysis of polymorphic information content (PIC) showed that the PIC is variable among and along chromosomes and that especially the R genome of spring types possesses a reduced genetic diversity. We also found that several chromosomes showed regions of high genetic distance between the two growth habits, indicative of divergent selection. Regarding linkage disequilibrium, the A and B genomes showed a similar LD of 0.24 for closely linked markers and a decay within approximately 12 cM. LD in the R genome was lower with 0.19 and decayed within a shorter map distance of approximately 5 cM. The extent of LD was generally higher for the spring types compared to the winter types. In addition, we observed strong variability of LD along the chromosomes. Conclusions Our results confirm winter and spring growth habit are the major contributors to population structure in triticale, and a family structure exists in both growth types. The specific patterns of genetic diversity observed within these types, such as the low diversity on some rye chromosomes of spring habits, provide a basis for targeted broadening of the available breeding germplasm. In addition, the genome-wide analysis of the extent and the pattern of LD will assist scientists and breeders alike in the implementation and the interpretation of association mapping in triticale.
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Affiliation(s)
- Katharina V Alheit
- State Plant Breeding Institute, University of Hohenheim, Stuttgart 70593, Germany
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ANDREW ROSEL, OSTEVIK KATHERINEL, EBERT DANIELP, RIESEBERG LORENH. Adaptation with gene flow across the landscape in a dune sunflower. Mol Ecol 2012; 21:2078-91. [DOI: 10.1111/j.1365-294x.2012.05454.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hohenlohe PA, Catchen J, Cresko WA. Population genomic analysis of model and nonmodel organisms using sequenced RAD tags. Methods Mol Biol 2012; 888:235-260. [PMID: 22665285 DOI: 10.1007/978-1-61779-870-2_14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The evolutionary processes of mutation, migration, genetic drift, and natural selection shape patterns of genetic variation among individuals, populations, and species, and they can do so differentially across genomes. The field of population genomics provides a comprehensive genome-scale view of these processes, even beyond traditional model organisms. Until recently, genome-wide studies of genetic variation have been prohibitively expensive. However, next-generation sequencing (NGS) technologies are revolutionizing the field of population genomics, allowing for genetic analysis at scales not previously possible even in organisms for which few genomic resources presently exist. To speed this revolution in evolutionary genetics, we and colleagues developed Restriction site Associated DNA (RAD) sequencing, a method that uses Illumina NGS to simultaneously type and score tens to hundreds of thousands of single nucleotide polymorphism (SNP) markers in hundreds of individuals for minimal investment of resources. The core molecular protocol is described elsewhere in this volume, which can be modified to suit a diversity of evolutionary genetic questions. In this chapter, we outline the conceptual framework of population genomics, relate genomic patterns of variation to evolutionary processes, and discuss how RAD sequencing can be used to study population genomics. In addition, we discuss bioinformatic considerations that arise from unique aspects of NGS data as compared to traditional marker based approaches, and we outline some general analytical approaches for RAD-seq and similar data, including a computational pipeline that we developed called Stacks. This software can be used for the analysis of RAD-seq data in organisms with and without a reference genome. Nonetheless, the development of analytical tools remains in its infancy, and further work is needed to fully quantify sampling variance and biases in these data types. As data-gathering technology continues to advance, our ability to understand genomic evolution in natural populations will be limited more by conceptual and analytical weaknesses than by the amount of molecular data.
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Affiliation(s)
- Paul A Hohenlohe
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR, USA
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MAYROSE MAYA, KANE NOLANC, MAYROSE ITAY, DLUGOSCH KATRINAM, RIESEBERG LORENH. Increased growth in sunflower correlates with reduced defences and altered gene expression in response to biotic and abiotic stress. Mol Ecol 2011; 20:4683-94. [DOI: 10.1111/j.1365-294x.2011.05301.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Fulda S, Mikkat S, Stegmann H, Horn R. Physiology and proteomics of drought stress acclimation in sunflower (Helianthus annuus L.). PLANT BIOLOGY (STUTTGART, GERMANY) 2011; 13:632-42. [PMID: 21668604 DOI: 10.1111/j.1438-8677.2010.00426.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
An easy and manageable in vitro screening system for drought tolerance of sunflower seedlings based on MS media supplemented with polyethylene glycol 6000 was evaluated. Morphological and physiological parameters were compared between control (-0.05 MPa) and drought-stressed (-0.6 MPa) seedlings of Helianthus annuus L. cv. Peredovick. There was a significant growth deficit in drought-stressed plants compared to control plants in terms of hypocotyl length, and shoot and root fresh mass. Shoot growth was more restricted than root growth, resulting in an increased root/shoot ratio of drought-stressed plants. Accumulation of osmolytes such as inositol (65-fold), glucose (58-fold), proline (55-fold), fructose (11-fold) and sucrose (eightfold), in leaves of drought-stressed plants could be demonstrated by gas-liquid chromatography. Soluble protein patterns of leaves were analysed with two-dimensional gel electrophoresis (2D-PAGE) and MALDI-TOF mass spectrometry. A set of 46 protein spots allowed identification of 19 marker proteins. Quantitative changes in protein expression of drought-stressed versus control plants were detected. In leaves of drought-stressed sunflower seedlings six proteins were significantly up-regulated more than twofold: a putative caffeoyl-CoA 3-O-methyltransferase (4.5-fold), a fructokinase 3 (3.3-fold), a vegetative storage protein (2.5-fold), a glycine-rich RNA binding protein (2.2-fold), a CuZn-superoxide dismutase (2.1-fold) and an unknown low molecular weight protein (2.3-fold). These proteins represent general stress proteins induced under drought conditions or proteins contributing to basic carbon metabolism. The up-regulated proteins are interesting candidates for further physiological and molecular investigations regarding drought tolerance in sunflower.
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Affiliation(s)
- S Fulda
- Institut für Biowissenschaften, Pflanzengenetik, Universität Rostock, Albert-Einstein-Strasse 3, Rostock, Germany
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Kane NC, Barker MS, Zhan SH, Rieseberg LH. Molecular Evolution across the Asteraceae: Micro- and Macroevolutionary Processes. Mol Biol Evol 2011; 28:3225-35. [DOI: 10.1093/molbev/msr166] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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38
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Palma-Silva C, Wendt T, Pinheiro F, Barbará T, Fay MF, Cozzolino S, Lexer C. Sympatric bromeliad species (Pitcairnia spp.) facilitate tests of mechanisms involved in species cohesion and reproductive isolation in Neotropical inselbergs. Mol Ecol 2011; 20:3185-201. [PMID: 21672064 DOI: 10.1111/j.1365-294x.2011.05143.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The roles of intra- and interspecific gene flow in speciation and species evolution are topics of great current interest in molecular ecology and evolutionary biology. Recent modelling studies call for new empirical data to test hypotheses arising from the recent shift from a 'whole-genome reproductive isolation' view to a 'genic' view of species and speciation. Particularly scarce (and thus of particular interest) are molecular genetic data on recently radiated, naturally hybridizing species in strongly structured and species-rich environments. Here, we studied four sympatric plant species (Pitcairnia spp.; Bromeliaceae) adapted to Neotropical inselbergs (isolated outcrops resembling habitat 'islands' in tropical rainforests) using nuclear and plastid DNA. Patterns of plastid DNA haplotype sharing and nuclear genomic admixture suggest the presence of both, incomplete lineage sorting and interspecific gene flow over extended periods of time. Integrity and cohesion of inselberg species of Pitcairnia are maintained despite introgression and in the face of extremely low within-species migration rates (N(e)m < 1 migrant per generation). Cross-evaluation of our genetic data against published pollination experiments indicate that species integrity is maintained by the simultaneous action of multiple prezygotic barriers, including flowering phenology, pollinator isolation and divergent mating systems. Postzygotic Bateson-Dobzhansky-Muller incompatibilities appear to contribute to isolation, as suggested by asymmetric introgression rates of single loci. Our results suggest that incomplete lineage sorting, hybridization and introgression form integral aspects of adaptive radiation in Neotropical inselberg 'archipelagos'. Inselbergs with multiple closely related co-occurring species should be of special interest to students of speciation in mountain systems, and to ongoing conservation programmes in the Atlantic Rainforest biodiversity hotspot.
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Affiliation(s)
- C Palma-Silva
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK.
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Fischer I, Camus-Kulandaivelu L, Allal F, Stephan W. Adaptation to drought in two wild tomato species: the evolution of the Asr gene family. THE NEW PHYTOLOGIST 2011; 190:1032-1044. [PMID: 21323928 DOI: 10.1111/j.1469-8137.2011.03648.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Wild tomato species are a valuable system in which to study local adaptation to drought: they grow in diverse environments ranging from mesic to extremely arid conditions. Here, we investigate the evolution of members of the Asr (ABA/water stress/ripening induced) gene family, which have been reported to be involved in the water stress response. We analysed molecular variation in the Asr gene family in populations of two closely related species, Solanum chilense and Solanum peruvianum. We concluded that Asr1 has evolved under strong purifying selection. In contrast to previous reports, we did not detect evidence for positive selection at Asr2. However, Asr4 shows patterns consistent with local adaptation in an S. chilense population that lives in an extremely dry environment. We also discovered a new member of the gene family, Asr5. Our results show that the Asr genes constitute a dynamic gene family and provide an excellent example of tandemly arrayed genes that are of importance in adaptation. Taking the potential distribution of the species into account, it appears that S. peruvianum can cope with a great variety of environmental conditions without undergoing local adaptation, whereas S. chilense undergoes local adaptation more frequently.
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Affiliation(s)
- Iris Fischer
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Létizia Camus-Kulandaivelu
- CIRAD, Biological System Department - Research Unit 39 'Genetic Diversity and Breeding of Forest Tree Species', Campus international de Baillarguet TA A-39/C, 34398 Montpellier Cedex 5, France
| | - François Allal
- CIRAD, Biological System Department - Research Unit 39 'Genetic Diversity and Breeding of Forest Tree Species', Campus international de Baillarguet TA A-39/C, 34398 Montpellier Cedex 5, France
| | - Wolfgang Stephan
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
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Rouse MN, Saleh AA, Seck A, Keeler KH, Travers SE, Hulbert SH, Garrett KA. Genomic and resistance gene homolog diversity of the dominant tallgrass prairie species across the U.S. Great Plains precipitation gradient. PLoS One 2011; 6:e17641. [PMID: 21532756 PMCID: PMC3075248 DOI: 10.1371/journal.pone.0017641] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 02/08/2011] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Environmental variables such as moisture availability are often important in determining species prevalence and intraspecific diversity. The population genetic structure of dominant plant species in response to a cline of these variables has rarely been addressed. We evaluated the spatial genetic structure and diversity of Andropogon gerardii populations across the U.S. Great Plains precipitation gradient, ranging from approximately 48 cm/year to 105 cm/year. METHODOLOGY/PRINCIPAL FINDINGS Genomic diversity was evaluated with AFLP markers and diversity of a disease resistance gene homolog was evaluated by PCR-amplification and digestion with restriction enzymes. We determined the degree of spatial genetic structure using Mantel tests. Genomic and resistance gene homolog diversity were evaluated across prairies using Shannon's index and by averaging haplotype dissimilarity. Trends in diversity across prairies were determined using linear regression of diversity on average precipitation for each prairie. We identified significant spatial genetic structure, with genomic similarity decreasing as a function of distance between samples. However, our data indicated that genome-wide diversity did not vary consistently across the precipitation gradient. In contrast, we found that disease resistance gene homolog diversity was positively correlated with precipitation. SIGNIFICANCE Prairie remnants differ in the genetic resources they maintain. Selection and evolution in this disease resistance homolog is environmentally dependent. Overall, we found that, though this environmental gradient may not predict genomic diversity, individual traits such as disease resistance genes may vary significantly.
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Affiliation(s)
- Matthew N. Rouse
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Amgad A. Saleh
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Amadou Seck
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Kathleen H. Keeler
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Steven E. Travers
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Scot H. Hulbert
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Karen A. Garrett
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
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Coyer JA, Hoarau G, Pearson G, Mota C, Jüterbock A, Alpermann T, John U, Olsen JL. Genomic scans detect signatures of selection along a salinity gradient in populations of the intertidal seaweed Fucus serratus on a 12 km scale. Mar Genomics 2011; 4:41-9. [PMID: 21429464 DOI: 10.1016/j.margen.2010.12.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2010] [Revised: 12/07/2010] [Accepted: 12/13/2010] [Indexed: 01/13/2023]
Abstract
Detecting natural selection in wild populations is a central challenge in evolutionary biology and genomic scans are an important means of detecting allele frequencies that deviate from neutral expectations among marker loci. We used nine anonymous and 15 EST-linked microsatellites, 362 AFLP loci, and several neutrality tests, to identify outlier loci when comparing four populations of the seaweed Fucus serratus spaced along a 12km intertidal shore with a steep salinity gradient. Under criteria of at least two significant tests in at least two population pairs, three EST-derived and three anonymous loci revealed putative signatures of selection. Anonymous locus FsB113 was a consistent outlier when comparing least saline to fully marine sites. Locus F37 was an outlier when comparing the least saline to more saline areas, and was annotated as a polyol transporter/putative mannitol transporter - an important sugar-alcohol associated with osmoregulation by brown algae. The remaining loci could not be annotated using six different data bases. Exclusion of microsatellite outlier loci did not change either the degree or direction of differentiation among populations. In one outlier test, the number of AFLP outlier loci increased as the salinity differences between population pairs increased (up to 14); only four outliers were detected with the second test and only one was consistent with both tests. Consistency may be improved with a much more rigorous approach to replication and/or may be dependent upon the class of marker used.
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Affiliation(s)
- J A Coyer
- Department of Marine Benthic Ecology and Evolution, Center for Ecological and Evolutionary Studies, University of Groningen, Center for Life Sciences, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
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RICHTER-BOIX ALEX, QUINTELA MARÍA, SEGELBACHER GERNOT, LAURILA ANSSI. Genetic analysis of differentiation among breeding ponds reveals a candidate gene for local adaptation in Rana arvalis. Mol Ecol 2011; 20:1582-600. [DOI: 10.1111/j.1365-294x.2011.05025.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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An assessment of the spatial scale of local adaptation in brown trout (Salmo trutta L.): footprints of selection at microsatellite DNA loci. Heredity (Edinb) 2011; 106:488-99. [PMID: 21224872 DOI: 10.1038/hdy.2010.164] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Local adaptation is considered a paradigm in studies of salmonid fish populations. Yet, little is known about the geographical scale of local adaptation. Is adaptive divergence primarily evident at the scale of regions or individual populations? Also, many salmonid populations are subject to spawning intrusion by farmed conspecifics that experience selection regimes fundamentally different from wild populations. This prompts the question if adaptive differences between wild populations and hatchery strains are more pronounced than between different wild populations? We addressed these issues by analyzing variation at 74 microsatellite loci (including anonymous and expressed sequence tag- and quantitative trait locus-linked markers) in 15 anadromous wild brown trout (Salmo trutta L.) populations, representing five geographical regions, along with two lake populations and two hatchery strains used for stocking some of the populations. F(ST)-based outlier tests revealed more outlier loci between different geographical regions separated by 522 ± 228 km (mean ± s.d.) than between populations within regions separated by 117 ± 79 km (mean ± s.d.). A significant association between geographical distance and number of outliers between regions was evident. There was no evidence for more outliers in comparisons involving hatchery trout, but the loci under putative selection generally were not the same as those found to be outliers between wild populations. Our study supports the notion of local adaption being increasingly important at the scale of regions as compared with individual populations, and suggests that loci involved in adaptation to captive environments are not necessarily the same as those involved in adaptive divergence among wild populations.
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Chao S, Dubcovsky J, Dvorak J, Luo MC, Baenziger SP, Matnyazov R, Clark DR, Talbert LE, Anderson JA, Dreisigacker S, Glover K, Chen J, Campbell K, Bruckner PL, Rudd JC, Haley S, Carver BF, Perry S, Sorrells ME, Akhunov ED. Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.). BMC Genomics 2010; 11:727. [PMID: 21190581 PMCID: PMC3020227 DOI: 10.1186/1471-2164-11-727] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 12/29/2010] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico. RESULTS Most of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the pre-defined populations shared significant proportion of genetic ancestry. Estimates of population structure (F(ST)) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated F(ST) were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM). CONCLUSIONS Genome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The higher extent of LD in the wheat D-genome versus the A- and B-genomes likely reflects the episodes of recent introgression and population bottleneck accompanying the origin of hexaploid wheat. The assessment of LD and population structure in this assembled panel of diverse lines provides critical information for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.
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Affiliation(s)
- Shiaoman Chao
- USDA ARS Genotyping Laboratory, Biosciences Research Laboratory, Fargo, ND, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Rustam Matnyazov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
- Institute of Biochemistry and Genetics, RAS, Ufa Russia
| | | | - Luther E Talbert
- Department of Plant Sciences, Montana State University, Bozeman, MT, USA
| | - James A Anderson
- Dept. of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | | | - Karl Glover
- Plant Science Department, South Dakota State University, Brookings, SD, USA
| | - Jianli Chen
- University of Idaho Aberdeen Research & Extension Center, Aberdeen ID, USA
| | - Kim Campbell
- USDA-ARS Wheat Genetics, Quality, Physiology & Disease Research Unit, Washington State University, Pullman WA, USA
| | | | - Jackie C Rudd
- Texas AgriLife Research and Extension Center, Amarillo, TX, USA
| | - Scott Haley
- Soil and Crop Sciences Department, Colorado State University, Fort Collins, CO, USA
| | - Brett F Carver
- Oklahoma State University, Department of Plant and Soil Sciences, Stillwater, OK, USA
| | | | - Mark E Sorrells
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Eduard D Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
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Chao S, Dubcovsky J, Dvorak J, Luo MC, Baenziger SP, Matnyazov R, Clark DR, Talbert LE, Anderson JA, Dreisigacker S, Glover K, Chen J, Campbell K, Bruckner PL, Rudd JC, Haley S, Carver BF, Perry S, Sorrells ME, Akhunov ED. Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.). BMC Genomics 2010. [PMID: 21190581 DOI: 10.1186/1471‐2164‐11‐727] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico. RESULTS Most of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the pre-defined populations shared significant proportion of genetic ancestry. Estimates of population structure (F(ST)) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated F(ST) were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM). CONCLUSIONS Genome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The higher extent of LD in the wheat D-genome versus the A- and B-genomes likely reflects the episodes of recent introgression and population bottleneck accompanying the origin of hexaploid wheat. The assessment of LD and population structure in this assembled panel of diverse lines provides critical information for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.
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Affiliation(s)
- Shiaoman Chao
- USDA ARS Genotyping Laboratory, Biosciences Research Laboratory, Fargo, ND, USA
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Chao S, Dubcovsky J, Dvorak J, Luo MC, Baenziger SP, Matnyazov R, Clark DR, Talbert LE, Anderson JA, Dreisigacker S, Glover K, Chen J, Campbell K, Bruckner PL, Rudd JC, Haley S, Carver BF, Perry S, Sorrells ME, Akhunov ED. Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.). BMC Genomics 2010. [PMID: 21190581 DOI: 10.1186/s12870-015-0628-727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico. RESULTS Most of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the pre-defined populations shared significant proportion of genetic ancestry. Estimates of population structure (F(ST)) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated F(ST) were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM). CONCLUSIONS Genome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The higher extent of LD in the wheat D-genome versus the A- and B-genomes likely reflects the episodes of recent introgression and population bottleneck accompanying the origin of hexaploid wheat. The assessment of LD and population structure in this assembled panel of diverse lines provides critical information for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.
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Affiliation(s)
- Shiaoman Chao
- USDA ARS Genotyping Laboratory, Biosciences Research Laboratory, Fargo, ND, USA
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Turmelle AS, Kunz TH, Sorenson MD. A tale of two genomes: contrasting patterns of phylogeographic structure in a widely distributed bat. Mol Ecol 2010; 20:357-75. [PMID: 21143331 DOI: 10.1111/j.1365-294x.2010.04947.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
One of the most widely distributed bats in the New World, the big brown bat (Eptesicus fuscus) exhibits well-documented geographic variation in morphology and life history traits, suggesting the potential for significant phylogeographic structure as well as adaptive differentiation among populations. In a pattern broadly consistent with morphologically defined subspecies, we found deeply divergent mitochondrial lineages restricted to different geographic regions. In contrast, sequence data from two nuclear loci suggest a general lack of regional genetic structure except for peripheral populations in the Caribbean and Mexico/South America. Coalescent analyses suggest that the striking difference in population structure between genomes cannot be attributed solely to different rates of lineage sorting, but is likely due to male-mediated gene flow homogenizing nuclear genetic diversity across most of the continental range. Despite this ongoing gene flow, selection has apparently been effective in producing and maintaining adaptive differentiation among populations, while strong female site fidelity, maintained over the course of millions of years, has produced remarkably deep divergence among geographically isolated matrilines. Our results highlight the importance of evaluating multiple genetic markers for a more complete understanding of population structure and history.
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Affiliation(s)
- Amy S Turmelle
- Department of Biology, Boston University, Boston, MA 02215, USA.
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Hohenlohe PA, Phillips PC, Cresko WA. USING POPULATION GENOMICS TO DETECT SELECTION IN NATURAL POPULATIONS: KEY CONCEPTS AND METHODOLOGICAL CONSIDERATIONS. INTERNATIONAL JOURNAL OF PLANT SCIENCES 2010; 171:1059-1071. [PMID: 21218185 PMCID: PMC3016716 DOI: 10.1086/656306] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Natural selection shapes patterns of genetic variation among individuals, populations, and species, and it does so differentially across genomes. The field of population genomics provides a comprehensive genome-scale view of the action of selection, even beyond traditional model organisms. However, even with nearly complete genomic sequence information, our ability to detect the signature of selection on specific genomic regions depends on choosing experimental and analytical tools appropriate to the biological situation. For example, processes that occur at different timescales, such as sorting of standing genetic variation, mutation-selection balance, or fixed interspecific divergence, have different consequences for genomic patterns of variation. Inappropriate experimental or analytical approaches may fail to detect even strong selection or falsely identify a signature of selection. Here we outline the conceptual framework of population genomics, relate genomic patterns of variation to evolutionary processes, and identify major biological factors to be considered in studies of selection. As data-gathering technology continues to advance, our ability to understand selection in natural populations will be limited more by conceptual and analytical weaknesses than by the amount of molecular data. Our aim is to bring critical biological considerations to the fore in population genomics research and to spur the development and application of analytical tools appropriate to diverse biological systems.
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Affiliation(s)
- Paul A. Hohenlohe
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon 97403, U.S.A
- Department of Zoology, Oregon State University, Corvallis, Oregon 97331, U.S.A
- Author for correspondence;
| | - Patrick C. Phillips
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon 97403, U.S.A
| | - William A. Cresko
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon 97403, U.S.A
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Barker MS, Dlugosch KM, Dinh L, Challa RS, Kane NC, King MG, Rieseberg LH. EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics. Evol Bioinform Online 2010; 6:143-9. [PMID: 21079755 PMCID: PMC2978936 DOI: 10.4137/ebo.s5861] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent increases in the production of genomic data are yielding new opportunities and challenges for biologists. Among the chief problems posed by next-generation sequencing are assembly and analyses of these large data sets. Here we present an online server, http://EvoPipes.net, that provides access to a wide range of tools for bioinformatic analyses of genomic data oriented for ecological and evolutionary biologists. The EvoPipes.net server includes a basic tool kit for analyses of genomic data including a next-generation sequence cleaning pipeline (SnoWhite), scaffolded assembly software (SCARF), a reciprocal best-blast hit ortholog pipeline (RBH Orthologs), a pipeline for reference protein-based translation and identification of reading frame in transcriptome and genomic DNA (TransPipe), a pipeline to identify gene families and summarize the history of gene duplications (DupPipe), and a tool for developing SSRs or microsatellites from a transcriptome or genomic coding sequence collection (findSSR). EvoPipes.net also provides links to other software developed for evolutionary and ecological genomics, including chromEvol and NU-IN, as well as a forum for discussions of issues relating to genomic analyses and interpretation of results. Overall, these applications provide a basic bioinformatic tool kit that will enable ecologists and evolutionary biologists with relatively little experience and computational resources to take advantage of the opportunities provided by next-generation sequencing in their systems.
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Affiliation(s)
- Michael S Barker
- The Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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PÉREZ-FIGUEROA A, GARCÍA-PEREIRA MJ, SAURA M, ROLÁN-ALVAREZ E, CABALLERO A. Comparing three different methods to detect selective loci using dominant markers. J Evol Biol 2010; 23:2267-2276. [DOI: 10.1111/j.1420-9101.2010.02093.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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