scholarly journals Genetic analysis and population structure of wild and cultivated wishbone flower (Torenia fournieri Lind.) lines related to specific floral color

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11702
Author(s):  
Shikai Guan ◽  
Qian Song ◽  
Jinye Zhou ◽  
Haixia Yan ◽  
Yuxiang Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Wild Population ◽  
Wild Populations ◽  
Torenia Fournieri ◽  
Similar Reduction ◽  
Floral Color ◽  
Hybrid Lines

Background The wishbone flower or Torenia fournieri Lind., an annual from tropical Indochina and southern China, is a popular ornamental plant, and many interspecific (T. fournieri × T. concolor) hybrid lines have been bred for the international market. The cultivated lines show a pattern of genetic similarity that correlates with floral color which informs on future breeding strategies. This study aimed to perform genetic analysis and population structure of cultivated hybrid lines comparing with closely related T. concolor wild populations. Methods We applied the retrotransposon based iPBS marker system for genotyping of a total of 136 accessions from 17 lines/populations of Torenia. These included 15 cultivated lines of three series: Duchess (A, B, C); Kauai (D, E, F, G, H, I, J); Little Kiss (K, L, M, N, P) and two wild T. concolor populations (Q and R). PCR products from each individual were applied to estimate the genetic diversity and differentiation between lines/populations. Results Genotyping results showed a pattern of genetic variation differentiating the 17 lines/populations characterized by their specific floral colors. The final PCoA analysis, phylogenetic tree construction, and Bayesian population structural bar plot all showed a clear subdivision of lines/populations analysed. The 15 cultivated hybrid lines and the wild population Q that collected from a small area showed the lowest genetic variability while the other wild population R which sampled from a larger area had the highest genetic variability. Discussion The extremely low genetic variability of 15 cultivated lines indicated that individual line has similar reduction in diversity/heterozygosity from a bottleneck event, and each retained a similar (but different from each other) content of the wild genetic diversity. The genetic variance for the two wild T. concolor populations could be due to our varied sampling methods. The two wild populations (Q, R) and the cultivated hybrid lines (I, K, M, N, P) are genetically more closely related, but strong positive correlations presented in cultivated lines A, C, E, M, and N. These results could be used to guide future Torenia breeding. Conclusions The genetic variation and population structure found in our study showed that cultivated hybrid lines had similar reduction in diversity/heterozygosity from a bottleneck event and each line retained a similar (but different from each other) content of the wild genetic diversity, especially when strong phenotypic selection of floral color overlaps. Generally, environmental factors could induce transposon activation and generate genetic variability which enabled the acceleration of the evolutionary process of wild Torenia species. Our study revealed that wild Torenia populations sampled from broad geographic region represent stronger species strength with outstanding genetic diversity, but selective breeding targeting a specific floral color decreased such genetic variability.

scholarly journals How diverse can rare species be on the margins of genera distribution?

AoB Plants ◽  
2019 ◽  
Vol 11 (4) ◽  
Author(s):  
Alice Backes ◽  
Geraldo Mäder ◽  
Caroline Turchetto ◽  
Ana Lúcia Segatto ◽  
Jeferson N Fregonezi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Habitat Loss ◽  
Evolutionary History ◽  
Founder Effects ◽  
Geographical Isolation ◽  
Genetic Diversity And Structure ◽  
Genetic Patterns

Abstract Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.

Reproductive system and population structure in two Hedysarum subspecies. I. Genetic variation within and between populations

Genome ◽  
1991 ◽  
Vol 34 (3) ◽  
pp. 396-406 ◽  
Author(s):  
Hedi Baatout ◽  
Daniel Combes ◽  
Mohamed Marrakchi
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Population Genetic ◽  
Allozyme Variation ◽  
Wild Populations ◽  
Population Means ◽  
Quantitative Characters ◽  
Different Populations ◽  
Population Genetic Variation

Several samples of wild populations of two subspecies of the genus Hedysarum (H. spinosissimum subspecies capitatum, an outcrosser, and H. spinosissimum subspecies euspinosissimum, a selfer) were examined with respect to variability of 25 quantitative characters and allozyme variation at 13 loci. The amount of phenotypic and genetic variation within and among populations was documented. For most of the 25 quantitative characters, the differences between population means and between the total variances of the populations were higher in the selfer than in the outbreeder. Significant among-population genetic variation was found for nearly all characters in the two subspecies, but the outbreeder had higher within-population variability than the selfer with heterogeneity among characters. However, allozyme variation at 13 loci in about the same number of populations showed higher levels of genetic variability in the outcrossing subspecies capitatum compared with the selfing subspecies euspinosissimum, based on measures of mean number of alleles per locus, mean proportion of polymorphic loci, and mean heterozygosity. Therefore, H. spinosissimum subsp. capitatum appeared to be highly polymorphic in contrast to the greater monomorphism within populations of H. spinosissimum subsp. euspinosissimum. The genetic affinities of different populations of a subspecies are uniformly high, with Nei's genetic identity ranging from 0.983 to 0.997 in the selfing subspecies euspinosissimum and from 0.922 to 1.000 in the outcrossing subspecies capitatum.Key words: Hedysarum, genetic variation, populations, electrophoresis.

scholarly journals Genetic diversity and population structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River

2020 ◽  
Author(s):  
Rong Tang ◽  
Erxi Liu ◽  
Yazhou Zhang ◽  
Johann Schinnerl ◽  
Weibang Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Plant Species ◽  
Ex Situ ◽  
Small Populations ◽  
Wild Populations ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Cultivated Populations

Abstract Background: Amorphophallus albus P. Y. Liu & J. F. Chen (Araceae) is a plant species with extremely small populations (PSESP) and an important economic crop endemic to dry-hot valleys along the Jinsha River. In order to gain information for sustaining the development and conservation of A. albus, we studied the genetic diversity and population structure of this species using microsatellite markers (SSR). In this study, we analysed 364 individuals belonging to 24 populations, including four wild populations and three ex-situ cultivated populations, collected in the provinces Yunnan, Sichuan and Hubei. Results: The population genetic analyses indicated that A. albus possesses moderate genetic diversity with the percentage of polymorphic loci (PPL) from 69.23% to 100%, an expected heterozygosity (He) of 0.504 and an average Shannon's Information Index (I) 0.912. Analysis of molecular variance (AMOVA) indicated that most of the variance (71%) resided within populations and the estimated gene flow (Nm) was 0.61. The results of UPGMA cluster tree, STRUCTURE analyses together with the Mantel test (R2 = 0.352, P < 0.01) indicated that geographically closely located populations are clustered together with some exceptions. Conclusions: Our results showed that A. albus still possesses moderate genetic variation in most of the studied populations, and for now, most cultivated populations were naturally distributed but still some reintroduction exists. For sustaining the present genetic variation, some protections measures are necessary for the wild populations and also for the cultivated ones with high genetic diversity.

scholarly journals Genetic diversity and population structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River

2019 ◽  
Author(s):  
Rong Tang ◽  
Erxi Liu ◽  
Yazhou Zhang ◽  
Johann Schinnerl ◽  
Weibang Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Plant Species ◽  
Ex Situ ◽  
Small Populations ◽  
Wild Populations ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Cultivated Populations

Abstract Background Amorphophallus albus P. Y. Liu & J. F. Chen (Araceae) is a plant species with extremely small populations (PSESP) and important economic crop endemic to dry-hot valleys along the Jinsha River. In order to gain information for sustaining the development and conservation of A. albus , we studied the genetic diversity and population structure of this species using microsatellite markers (SSR). In this study, we analyzed 364 individuals belonging to 24 populations, including four wild populations and three ex-situ cultivated populations, collected in the provinces Yunnan, Sichuan and Hubei.Results The population genetic analyses indicated that A. albus possesses moderate genetic diversity with the percentage of polymorphic loci ( PPL ) from 69.23% to 100%, an expected heterozygosity ( He ) of 0.504 and an average Shannon's Information Index ( I ) 0.912. Analysis of molecular variance (AMOVA) indicated that most of the variance (71%) resided within populations and the estimated gene flow ( Nm ) was 0.61. The results of UPGMA cluster tree, STRUCTURE analyses together with the Mantel test (R 2 = 0.352, P < 0.01) indicated that geographically closely located populations are cluster together with some exceptions.Conclusions Our results showed that A. albus still possesses moderate genetic variation in most of the studied populations, and for now, most cultivated populations were naturally distributed but still some reintroduction exists. For sustaining the present genetic variation, some protections measures are necessary for the wild populations and also for the cultivated ones with high genetic diversity.

scholarly journals Genetic diversity and population structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Rong Tang ◽  
Erxi Liu ◽  
Yazhou Zhang ◽  
Johann Schinnerl ◽  
Weibang Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Plant Species ◽  
Ex Situ ◽  
Small Populations ◽  
Wild Populations ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Cultivated Populations

Abstract Background Amorphophallus albus P. Y. Liu & J. F. Chen (Araceae) is a plant species with extremely small populations (PSESP) and an important economic crop endemic to dry-hot valleys along the Jinsha River. In order to gain information for sustaining the development and conservation of A. albus, we studied the genetic diversity and population structure of this species using microsatellite markers (SSR). In this study, we analysed 364 individuals belonging to 24 populations, including four wild populations and three ex-situ cultivated populations, collected in the provinces Yunnan, Sichuan and Hubei. Results The population genetic analyses indicated that A. albus possesses moderate genetic diversity with the percentage of polymorphic loci (PPL) from 69.23 to 100%, an expected heterozygosity (He) of 0.504 and an average Shannon’s Information Index (I) 0.912. Analysis of molecular variance (AMOVA) indicated that most of the variance (71%) resided within populations and the estimated gene flow (Nm) was 0.61. The results of UPGMA cluster tree, STRUCTURE analyses together with the Mantel test (R2 = 0.352, P < 0.01) indicated that geographically closely located populations are clustered together with some exceptions. Conclusions Our results showed that A. albus still possesses moderate genetic variation in most of the studied populations, and for now, most cultivated populations were naturally distributed but still some reintroduction exists. For sustaining the present genetic variation, some protections measures are necessary for the wild populations and also for the cultivated ones with high genetic diversity.

scholarly journals Genetic diversity and population structure of Cynara cardunculus L. in southern Portugal

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252792
Author(s):  
Maria Miguel Castro ◽  
Daniela Rosa ◽  
Ana M. Ferro ◽  
Ana Faustino ◽  
Ana Paulino ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Wild Population ◽  
Cynara Cardunculus ◽  
Wild Populations ◽  
Significant Genetic Differentiation ◽  
Southern Portugal ◽  
High Level ◽  
Geographic Group ◽  
Future Management

Cynara cardunculus L. is a cardoon species native to the Mediterranean region, which is composed of three botanical taxa, each having distinct biological characteristics. The aim of this study was to examine wild populations of C. cardunculus established in Portugal, in order to determine their genetic diversity, geographic distribution, and population structure. Based on SSR markers, 121 individuals of C. cardunculus from 17 wild populations of the Portuguese Alentejo region were identified and analysed. Ten SSRs were found to be efficient markers in the genetic diversity analysis. The total number of alleles ranged from 9 to 17 per locus. The expected and observed means in heterozygosity, by population analysed, were 0.591 and 0.577, respectively. The wild population exhibited a high level of genetic diversity at the species level. The highest proportion of genetic variation was identified within a geographic group, while variation was lower among groups. Geographic areas having highest genetic diversity were identified in Alvito, Herdade da Abóboda, Herdade da Revilheira and Herdade de São Romão populations. Moreover, significant genetic differentiation existed between wild populations from North-Alentejo geographic locations (Arraiolos, Évora, Monte da Chaminé) and Centro Hortofrutícola, compared with other populations. This study reports genetic diversity among a representative number of wild populations and genotypes of C. cardunculus from Portugal. These results will provide valuable information towards future management of C. cardunculus germplasm.

scholarly journals Genetic variation in native and farmed populations of Tambaqui (Colossoma macropomum) in the Brazilian Amazon: regional discrepancies in farming systems

2013 ◽  
Vol 85 (4) ◽  
pp. 1439-1447 ◽  
Author(s):  
Jonas Aguiar ◽  
Horacio Schneider ◽  
Fatima Gomes ◽  
Jeferson Carneiro ◽  
Simoni Santos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Dna Sequences ◽  
Amazon Basin ◽  
Farming Systems ◽  
Wild Populations ◽  
The West ◽  
Colossoma Macropomum ◽  
Breeding Stock ◽  
History Of

The tambaqui, Colossoma macropomum, is the most popular fish species used for aquaculture in Brazil but there is no study comparing genetic variation among native and farmed populations of this species. In the present study, we analyzed DNA sequences of the mitochondrial DNA to evaluate the genetic diversity among two wild populations, a fry-producing breeding stock, and a sample of fish farm stocks, all from the region of Santarém, in the west of the Brazilian state of Pará. Similar levels of genetic diversity were found in all the samples and surprisingly the breeding stock showed expressive representation of the genetic diversity registered on wild populations. These results contrast considerably with those of the previous study of farmed stocks in the states of Amapá, Pará, Piauí, and Rondônia, which recorded only two haplotypes, indicating a long history of endogamy in the breeding stocks used to produce fry. The results of the two studies show two distinct scenarios of tambaqui farming in the Amazon basin, which must be better evaluated in order to guarantee the successful expansion of this activity in the region, and the rest of Brazil, given that the tambaqui and its hybrids are now farmed throughout the country.

scholarly journals Genome-wide genetic diversity, population structure and admixture analysis in Eritrean Indigenous Cattle

2020 ◽  
Vol 49 (6) ◽  
pp. 1083-1092
Author(s):  
S Goitom ◽  
M.G. Gicheha ◽  
F.K. Njonge ◽  
N Kiplangat
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Population Differentiation ◽  
Principal Component ◽  
Vital Role ◽  
Group Method ◽  
Indigenous Cattle ◽  
Ecological Zones ◽  
Genome Wide

Indigenous cattle play a vital role in subsistence and livelihood of pastoral producers in Eritrea. In order to optimally utilize and conserve these valuable indigenous cattle genetic resources, the need to carry out an inventory of their genetic diversity was recognized. This study assessed the genetic variability, population structure and admixture of the indigenous cattle populations (ICPs) of Eritrea using a genotype by sequencing (GBS) approach. The authors genotyped 188 animals, which were sampled from 27 cattle populations in three diverse agro-ecological zones (western lowlands, highlands and eastern lowlands). The genome-wide analysis results from this study revealed genetic diversity, population structure and admixture among the ICPs. Averages of the minor allele frequency (AF), observed heterozygosity (HO), expected heterozygosity (HE), and inbreeding coefficient (FIS) were 0.157, 0.255, 0.218, and -0.089, respectively. Nei’s genetic distance (Ds) between populations ranged from 0.24 to 0.27. Mean population differentiation (FST) ranged from 0.01 to 0.30. Analysis of molecular variance revealed high genetic variation between the populations. Principal component analysis and the distance-based unweighted pair group method and arithmetic mean analyses revealed weak substructure among the populations, separating them into three genetic clusters. However, multi-locus clustering had the lowest cross-validation error when two genetically distinct groups were modelled. This information about genetic diversity and population structure of Eritrean ICPs provided a basis for establishing their conservation and genetic improvement programmes. Keywords: genetic variability, molecular characterization, population differentiation

scholarly journals The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10274 ◽  
Author(s):  
Mirella Pupo Santos ◽  
João V.S. Rabelo Araujo ◽  
Arthur V. Sant’anna Lopes ◽  
Julio Cesar Fiorio Vettorazzi ◽  
Marcela Santana Bastos Boechat ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Geographical Location ◽  
Inter Simple Sequence Repeat ◽  
Shannon Index ◽  
Conservation Strategies ◽  
Amazon Forest ◽  
Mass Extinctions ◽  
Effective Conservation

Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.

Genetic diversity and population structure of the rice false smut pathogen Ustilaginoidea virens in Sichuan-Chongqing region

Plant Disease ◽  
2021 ◽  
Author(s):  
Anfei Fang ◽  
Zhuangyuan Fu ◽  
Zexiong Wang ◽  
Yuhang Fu ◽  
Yubao Qin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Recombination ◽  
Resistance Breeding ◽  
Ustilaginoidea Virens ◽  
Breeding Lines ◽  
Rice False Smut ◽  
Geographical Populations ◽  
False Smut

Rice false smut caused by Ustilaginoidea virens is currently one of the most devastating fungal diseases of rice panicles worldwide. In this study, two novel molecular markers derived from SNP-rich genomic DNA fragments and a previously reported molecular marker were used for analyzing the genetic diversity and population structure of 167 U. virens isolates collected from nine areas in Sichuan-Chongqing region, China. A total of 62 haplotypes were identified, and a few haplotypes with high frequency were found and distributed in two to three areas, suggesting gene flow among different geographical populations. All isolates were divided into six genetic groups. The groups Ⅰ and Ⅵ were the largest including 61 and 48 isolates, respectively. The pairwise FST values showed significant genetic differentiation among all compared geographical populations. AMOVA showed that intergroup genetic variation accounted for 40.17% of the total genetic variation, while 59.83% of genetic variation came from intragroup. The UPGMA dendrogram and population structure revealed that the genetic composition of isolates collected from ST (Santai), NC (Nanchong), YC (Yongchuan), and WS (Wansheng) dominated by the same genetic subgroup was different from those collected from other areas. In addition, genetic recombination was found in a few isolates. These findings will help to improve the strategies for rice false smut management and resistance breeding, such as evaluating breeding lines with different isolates or haplotypes at different elevations and landforms.

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