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Kumar Pal A, Vaishnav V, Meena B, Pandey N, Singh Rana T. Adaptive fitness of Sapindus emarginatus Vahl populations towards future climatic regimes and the limiting factors of its distribution. Sci Rep 2020; 10:3803. [PMID: 32123202 PMCID: PMC7052160 DOI: 10.1038/s41598-020-60219-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/30/2020] [Indexed: 11/20/2022] Open
Abstract
Sapindus emarginatus Vahl (Sapindaceae) also known as ‘Indian Soap nut’ is significantly important for saponin content in its fruits. However, its current population in India is heavily fragmented due to a lack of sustainable harvesting practices. Moreover, changing climatic regimes may further limit its distribution and possibly compromise the survival of the species in nature. The aim of the present study was to: predict the future distribution range of S. emarginatus; identify the bioclimatic variables limiting this distribution and to evaluate its adaptive fitness and genomic resilience towards these variables. To determine future species distribution range and identify limiting bioclimatic variables, we applied two different ecological niche models (ENMs; BioClim and MaxEnt) on real occurrence data (n = 88 locations). The adaptive fitness of the species was evaluated by quantifying the genetic variability with AFLP markers and marker-environmental associations, using AFLP-associated Bayesian statistics. We found 77% overlap between the baseline (2030) and predicted (2100) species distribution ranges, which were primarily determined by maximum temperature (TMAX) and mean annual precipitation (MAP). The TMAX and MAP contributed 43.1% and 27.1%, respectively to ENM model prediction. Furthermore, AFLP loci significantly associated with bioclimatic variables, and TMAX and MAP represent the lowest proportion (6.15%), confirming to the severe response of the species genome towards these variables. Nevertheless, the very low Linkage disequilibrium (LD) in these loci (4.54%) suggests that the current sensitivity to TMAX and MAP is subject to change during recombination. Moreover, a combination of high heterozygosity (0.40–0.43) and high within-population variability (91.63 ± 0.31%) confirmed high adaptive fitness to maintain reproductive success. Therefore, the current populations of S. emarginatus have substantial genomic resilience towards future climate change, albeit significant conservation efforts (including mass multiplication) are warranted to avoid future deleterious impacts of inbreeding depression on the fragmented populations.
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Affiliation(s)
- Ashish Kumar Pal
- Plant Diversity, Systematics and Herbarium Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.,Plant Nutrition and Stress Physiology Laboratory, Department of Botany, University of Lucknow, Lucknow, 226007, India
| | - Vivek Vaishnav
- Plant Diversity, Systematics and Herbarium Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Baleshwar Meena
- Plant Diversity, Systematics and Herbarium Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Nalini Pandey
- Plant Nutrition and Stress Physiology Laboratory, Department of Botany, University of Lucknow, Lucknow, 226007, India
| | - Tikam Singh Rana
- Plant Diversity, Systematics and Herbarium Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
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Herrera CM, Alonso C, Medrano M, Pérez R, Bazaga P. Transgenerational epigenetics: Inheritance of global cytosine methylation and methylation-related epigenetic markers in the shrub Lavandula latifolia. AMERICAN JOURNAL OF BOTANY 2018; 105:741-748. [PMID: 29727470 DOI: 10.1002/ajb2.1074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/22/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The ecological and evolutionary significance of natural epigenetic variation (i.e., not based on DNA sequence variants) variation will depend critically on whether epigenetic states are transmitted from parents to offspring, but little is known on epigenetic inheritance in nonmodel plants. METHODS We present a quantitative analysis of transgenerational transmission of global DNA cytosine methylation (= proportion of all genomic cytosines that are methylated) and individual epigenetic markers (= methylation status of anonymous MSAP markers) in the shrub Lavandula latifolia. Methods based on parent-offspring correlations and parental variance component estimation were applied to epigenetic features of field-growing plants ('maternal parents') and greenhouse-grown progenies. Transmission of genetic markers (AFLP) was also assessed for reference. KEY RESULTS Maternal parents differed significantly in global DNA cytosine methylation (range = 21.7-36.7%). Greenhouse-grown maternal families differed significantly in global methylation, and their differences were significantly related to maternal origin. Methylation-sensitive amplified polymorphism (MSAP) markers exhibited significant transgenerational transmission, as denoted by significant maternal variance component of marker scores in greenhouse families and significant mother-offspring correlations of marker scores. CONCLUSIONS Although transmission-related measurements for global methylation and MSAP markers were quantitatively lower than those for AFLP markers taken as reference, this study has revealed extensive transgenerational transmission of genome-wide global cytosine methylation and anonymous epigenetic markers in L. latifolia. Similarity of results for global cytosine methylation and epigenetic markers lends robustness to this conclusion, and stresses the value of considering both types of information in epigenetic studies of nonmodel plants.
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Affiliation(s)
- Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 26, 41092, Sevilla, Spain
| | - Conchita Alonso
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 26, 41092, Sevilla, Spain
| | - Mónica Medrano
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 26, 41092, Sevilla, Spain
| | - Ricardo Pérez
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de La Cartuja, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de, Sevilla, Sevilla, Spain
| | - Pilar Bazaga
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida Américo Vespucio 26, 41092, Sevilla, Spain
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Veselá P, Volařík D, Mráček J. Optimization of AFLP for extremely large genomes over 70 Gb. Mol Ecol Resour 2016; 16:933-45. [PMID: 26849414 DOI: 10.1111/1755-0998.12506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 01/23/2016] [Indexed: 11/29/2022]
Abstract
Here, we present an improved amplified fragment length polymorphism (AFLP) protocol using restriction enzymes (AscI and SbfI) that recognize 8-base pair sequences to provide alternative optimization suitable for species with a genome size over 70 Gb. This cost-effective optimization massively reduces the number of amplified fragments using only +3 selective bases per primer during selective amplification. We demonstrate the effects of the number of fragments and genome size on the appearance of nonidentical comigrating fragments (size homoplasy), which has a negative impact on the informative value of AFLP genotypes. We also present various reaction conditions and their effects on reproducibility and the band intensity of the extremely large genome of Viscum album. The reproducibility of this octo-cutter protocol was calculated using several species with genome sizes ranging from 1 Gb (Carex panicea) to 76 Gb (V. album). The improved protocol also succeeded in detecting high intraspecific variability in species with large genomes (V. album, Galanthus nivalis and Pinus pumila).
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Affiliation(s)
- Petra Veselá
- Department of Forest Botany Dendrology and Geobiocenology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
| | - Daniel Volařík
- Department of Forest Botany Dendrology and Geobiocenology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
| | - Jaroslav Mráček
- Department of Forest Botany Dendrology and Geobiocenology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
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Determination of epigenetic inheritance, genetic inheritance, and estimation of genome DNA methylation in a full-sib family of Cupressus sempervirens L. Gene 2015; 562:180-7. [DOI: 10.1016/j.gene.2015.02.068] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 02/01/2023]
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Genetic diversity and population structure of the red stingray, Dasyatis akajei inferred by AFLP marker. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Zhang H, Yu H, Gao T, Zhang Y, Han Z, Xiao Y. Analysis of genetic diversity and population structure of Pleuronectes yokohamae indicated by AFLP markers. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.04.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abstract
Although most living organisms reproduce sexually, some have developed a uniparental reproduction where the embryo usually derives from the female parent. A unique case of paternal apomixis in plants has been recently reported in Cupressus dupreziana, an endangered Mediterranean conifer. This species produces unreduced pollen that develop into all-paternal embryos within the seed tissues. We analyzed seedlings produced by open-pollinated C. dupreziana seed trees using morphological descriptors, ploidy levels assessed through flow cytometry, and AFLP genetic diversity. In situ C. dupreziana seed trees (from Algeria) produced only diploid C. dupreziana progeny. In contrast, only one-third of the progeny produced by ex situ C. dupreziana seed trees planted in French collections were similar to C. dupreziana seedlings; the other progeny were haploid or diploid C. sempervirens seedlings. These results demonstrate that C. dupreziana ovules allow for the development of all-paternal embryos from pollen produced by another species, C. sempervirens. Thus, the in planta androgenesis is achieved through the combination of the embryogenic behavior of pollen grains and the ability of seed tree ovules to act as a surrogate mother. This phenomenon offers a unique opportunity to produce, by natural means, highly valuable material for genetic studies and selection of sterile cultivars.
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López-Fernández H, Bolnick DI. What causes partial F1 hybrid viability? Incomplete penetrance versus genetic variation. PLoS One 2007; 2:e1294. [PMID: 18074018 PMCID: PMC2121587 DOI: 10.1371/journal.pone.0001294] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 11/16/2007] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Interspecific hybrid crosses often produce offspring with reduced but non-zero survivorship. In this paper we ask why such partial inviability occurs. This partial inviability could arise from incomplete penetrance of lethal Dobzhansky-Muller incompatibilities (DMIs) shared by all members of a hybrid cross. Alternatively, siblings may differ with respect to the presence or number of DMIs, leading to genotype-dependent variation in viability and hence non-Mendelian segregation of parental alleles in surviving F1 hybrids. METHODOLOGY/PRINCIPAL FINDINGS We used amplified fragment length polymorphisms (AFLPs) to test for segregation distortion in one hybrid cross between green and longear sunfish (Lepomis cyanellus and L. megalotis). Hybrids showed partial viability, and twice as much segregation distortion (36.8%) of AFLPs as an intraspecific control cross (18.8%). Incomplete penetrance of DMIs, which should cause genotype-independent mortality, is insufficient to explain the observed segregation distortion. CONCLUSIONS/SIGNIFICANCE We conclude that F1 hybrid sunfish are polymorphic for DMIs, either due to sex-linked DMI loci (causing Haldane's Rule), or polymorphic autosomal DMI loci. Because few AFLP markers were sex-linked (2%), the most parsimonious conclusion is that parents may have been heterozygous for loci causing hybrid inviability.
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Affiliation(s)
- Hernán López-Fernández
- Section of Ecology, Evolutionary Biology and Systematics, Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Daniel I. Bolnick
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
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Yu Q, Alvarez AM, Moore PH, Zee F, Kim MS, de Silva A, Hepperly PR, Ming R. Molecular Diversity of Ralstonia solanacearum Isolated from Ginger in Hawaii. PHYTOPATHOLOGY 2003; 93:1124-1130. [PMID: 18944096 DOI: 10.1094/phyto.2003.93.9.1124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT The genetic diversity of Ralstonia solanacearum strains isolated from ginger (Zingiber officinale) growing on the island of Hawaii was determined by analysis of amplified fragment length polymorphisms (AFLPs). Initially 28 strains of R. solanacearum collected from five host plant species worldwide were analyzed by AFLP. A second analysis was conducted on 55 R. solanacearum strains collected from three ginger farms along the Hamakua Coast of Hawaii, the principle area of ginger cultivation in the state. From the initial analysis, R. solanacearum strains from ginger in Hawaii showed a high degree of similarity at 0.853. In contrast, the average genetic similarity between R. solanacearum strains from heliconia and ginger was only 0.165, and strains from ginger showed little similarity with strains from all other hosts. The second analysis of 55 strains from ginger on different Hawaiian farms confirmed that they were distinct from race 1 strains from tomato. Strains from ginger also showed greater diversity among themselves in the second analysis, and the greatest diversity occurred among strains from a farm where ginger is frequently imported and maintained. Our results provide evidence that R. solanacearum strains from ginger in Hawaii are genetically distinct from local strains from tomato (race 1) and heliconia (race 2).
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Yin TM, Wang XR, Andersson B, Lerceteau-Köhler E. Nearly complete genetic maps of Pinus sylvestris L. (Scots pine) constructed by AFLP marker analysis in a full-sib family. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 106:1075-1083. [PMID: 12671756 DOI: 10.1007/s00122-003-1194-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2001] [Accepted: 10/16/2002] [Indexed: 05/24/2023]
Abstract
We have constructed nearly complete linkage maps of Pinus sylvestris (L.) using AFLP markers based on a two-way pseudo-testcross strategy in a full-sib family founded in an advanced breeding program. With 39 primer combinations, a total of 737 markers (320 from the mother and 417 from the father) segregated in a 1:1 ratio, corresponding to DNA polymorphism: heterozygous in one parent and null in the other. In the maternal parent, 188 framework markers were mapped in 12 linkage groups, equivalent to the Pinus haploid chromosome number, with a total coverage of 1,695.5 cM. In the paternal parent, 245 framework markers established a map with 15 linkage groups, spanning a genome length of 1,718.5 cM. The estimated total map length was L(F) = 1,681 cM for the female and L(M) = 1,645 cM for the male using a modified method-of-moment estimator. Combining these values with those estimated from the observed map lengths in both parents, we estimated the genome length in Scots pine to be between 1,600 and 2,100 cM. Our genome coverage was estimated to be more than 98% with a framework marker interval of 20 cM for both parents. Most of the female and male linkage groups were associated through the analysis of the intercross markers.
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Affiliation(s)
- T-M Yin
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, S-901 83 Umeå, Sweden
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Ribeiro MM, Mariette S, Vendramin GG, Szmidt AE, Plomion C, Kremer A. Comparison of genetic diversity estimates within and among populations of maritime pine using chloroplast simple-sequence repeat and amplified fragment length polymorphism data. Mol Ecol 2002; 11:869-77. [PMID: 11975703 DOI: 10.1046/j.1365-294x.2002.01490.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We compared the genetic variation of Pinus pinaster populations using amplified fragment length polymorphism (AFLP) and chloroplast simple-sequence repeat (cpSSR) loci. Populations' levels of diversity within groups were found to be similar with AFLPs, but not with cpSSRs. The high interlocus variance associated with the AFLP loci could account for the lack of differences in the former. Although AFLPs revealed much lower genetic diversity than cpSSRs, the levels of among-population differentiation found with the two types of marker were similar, provided that loci showing fewer than four null-homozygotes, in any population, were pruned from the AFLP data. Moreover, the French and Portuguese populations were clearly differentiated from each other, with both markers. The Mantel test showed that the genetic distance matrix calculated using the AFLP data was correlated with the matrix derived from the cpSSRs. Because of the concordance found between markers we conclude that gene flow was indeed the predominant force shaping nuclear and chloroplastic genetic variation of the populations within regions, at the geographical scale studied.
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Affiliation(s)
- M M Ribeiro
- Unidade Departamental de Silvicultura e Recursos Naturais, Escola Superior Agrária, 6001-909 Castelo Branco, Portugal.
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Schneider MV, Beukeboom LW, Driessen G, Lapchin L, Bernstein C, Van Alphen JJM. Geographical distribution and genetic relatedness of sympatrical thelytokous and arrhenotokous populations of the parasitoid Venturia canescens (Hymenoptera). J Evol Biol 2002. [DOI: 10.1046/j.1420-9101.2002.00394.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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