Genetic variation at microsatellite loci in the tropical herb <i>Aphelandra aurantiaca</i> (Acanthaceae)

Suárez-Montes, Pilar; Tapia‐López, Rosalinda; Núñez‐Farfán, Juan

doi:10.3732/apps.1500058

Cited by 3 publications

(3 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Similarly, Geng et al [ 45 ] calculated the observed and expected heterozygosity in Acanthus ilicifolius using SSR markers, which ranged from 0.200 to 0.875 and 0.227 to 0.798, respectively. Furthermore, Suárez-Montes et al [ 46 ] also calculated the observed and expected heterozygosity values among the Aphelandra aurantiaca genotypes, ranging from 0.22 to 0.96 and 0.20 to 0.87, respectively, which is higher than the present study. The present investigation also deciphered large differences between the observed and expected heterozygosity, which indicates that the selected population of A. paniculata deviates from Hardy Weinberg’s equilibrium, which might be due to inbreeding, population bottleneck, or random genetic drift [ 17 , 45 ].…”

Section: Resultscontrasting

confidence: 77%

Development of Novel Genomic Simple Sequence Repeat (g-SSR) Markers and Their Validation for Genetic Diversity Analyses in Kalmegh [Andrographis paniculata (Burm. F.) Nees]

Kumar

Paliwal

et al. 2020

Plants

View full text Add to dashboard Cite

Kalmegh (Andrographis paniculata (Burm. F.) Nees) is one of the most important medicinal plants and has been widely explored as traditional medicine. To exploit its natural genetic diversity and initiations of molecular breeding to develop novel cultivars or varieties, developments of genomic resources are essential. Four microsatellite-enriched genomic libraries—(CT)14, (GT)12, (AG)15 and (AAC)8—were constructed using the genomic DNA of A. paniculata. Initially, 183 recombinant colonies were screened for the presence of CT, GT, AG, and AAC microsatellite repeats, out of which 47 clones found positive for the desired simple sequence repeats (SSRs). It was found that few colonies had more than one desirable SSR. Thus, a sum of 67 SSRs were designed and synthesized for their validation among 42 A. paniculata accessions. Out of the 67 SSRs used for genotyping, only 41 were found to be polymorphic. The developed set of g-SSR markers showed substantial genetic variability among the selected A. paniculata accessions, with an average polymorphic information content (PIC) value of 0.32. Neighbor-joining tree analysis, population structure analysis, analysis of molecular variance (AMOVA), and principal coordinate analysis (PCoA) illustrated the considerable genetic diversity among them. The novel g-SSR markers developed in the present study could be important genomic resources for future applications in A. paniculata.

show abstract

Section: Resultscontrasting

confidence: 77%

Development of Novel Genomic Simple Sequence Repeat (g-SSR) Markers and Their Validation for Genetic Diversity Analyses in Kalmegh [Andrographis paniculata (Burm. F.) Nees]

Kumar

Paliwal

et al. 2020

Plants

View full text Add to dashboard Cite

show abstract

“…DNA extraction, amplification, and laboratory setup are detailed in Suárez-Montes, Tapia-López & Núñez-Farfán (2015). We genotyped all sampled individuals and scored alleles using the software GeneMarker V.2.4.0 (SoftGenetics, State College, PA, USA).…”

Section: Microsatellites Analysis and Pcr Amplificationmentioning

confidence: 99%

“…Manuscript to be reviewed individual plants (Table 3). To estimate the outcrossing rate (t) and pollen pool structure ) (ф we used six highly polymorphic unlinked microsatellite loci (0432, 5409, 1233, 4536, 4483, and 1808) (Table S2) (Suárez-Montes, Tapia-López & Núñez-Farfán, 2015) and analyzed the members of the maternal families (6 to 10 families per population).…”

Section: Mating System and Contemporary Gene Flowmentioning

confidence: 99%

Peer Review #1 of "Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest (v0.1)"

2016

View full text Add to dashboard Cite

Introduction. Forest fragmentation reduces population size and increases isolation among remnant populations in fragments, affecting genetic structure. The hummingbirdpollinated herb, Aphelandra aurantiaca, is a key element of regeneration in the understory of tropical rainforests. We examine the effects of rainforest fragmentation on genetic diversity, population structure, demographic history, outcrossing rate, and pollen dynamics. Methods. To study the genetic structure, we sampled forest fragments populations of different size at the Los Tuxtlas region, the northernmost limit of humid tropical rainforest in the Americas. We assessed population demographic change, genetic diversity, population structure, recent gene flow and connectivity among populations across the landscape by analyzing variation at microsatellite loci. We also estimated the mating system and pollen pool structure in four fragments. Results. Despite prevailing habitat fragmentation, populations of A. aurantiaca possess high genetic variation (H e = 0.61), weak genetic structure (R st = 0.037), and slight inbreeding in small fragments. In general, effective population size (N e) is large, but there is a tendency to decrease with fragment size. The highest rate of migrants and first-generation migrants derive mostly from large and medium size fragments. Although events of long distance gene dispersal were detected, most gene dispersal is restricted. Interestingly, populations within the largest fragment are not totally connected. Past demographic fluctuations may have affected the present population genetic structure. Bayesian coalescent analysis revealed the signature of past population expansion, possibly during warmer conditions after the last glacial maximum. Aphelandra aurantiaca shows a mixed mating system (t m = 0.81); outcrossing rate and pollen dynamics have not been affected by habitat fragmentation. A strong pollen pool structure was detected due to few effective pollen donors (N ep) and low distance pollen movement, pointing that most plants received pollen from close neighbors. Discussion. The predicted negative effects of rainforest fragmentation on genetic diversity and population structure of A. aurantiaca seem to have been buffered, as yet,

show abstract

Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest

Suárez-Montes

Chávez‐Pesqueira

Núñez‐Farfán

2016

PeerJ

View full text Add to dashboard Cite

IntroductionTheory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plants, pollen dynamics, mating system, reproductive success. The detection of the effects of contemporary habitat fragmentation on the genetic structure of populations are conditioned by the magnitude of change, given the few number of generations since the onset of fragmentation, especially for long-lived organisms. However, the present-day genetic structure of populations may bear the signature of past demography events. Here, we examine the effects of rainforest fragmentation on the genetic diversity, population structure, mating system (outcrossing rate), indirect gene flow and contemporary pollen dynamics in the understory herb Aphelandra aurantiaca. Also, we assessed its present-day genetic structure under different past demographic scenarios.MethodsTwelve populations of A. aurantiaca were sampled in large (4), medium (3), and small (5) forest fragments in the lowland tropical rainforest at Los Tuxtlas region. Variation at 11 microsatellite loci was assessed in 28–30 reproductive plants per population. In two medium- and two large-size fragments we estimated the density of reproductive plants, and the mating system by analyzing the progeny of different mother plants per population.ResultsDespite prevailing habitat fragmentation, populations of A. aurantiaca possess high genetic variation (He = 0.61), weak genetic structure (Rst = 0.037), and slight inbreeding in small fragments. Effective population sizes (Ne) were large, but slightly lower in small fragments. Migrants derive mostly from large and medium size fragments. Gene dispersal is highly restricted but long distance gene dispersal events were detected. Aphelandra aurantiaca shows a mixed mating system (tm = 0.81) and the outcrossing rate have not been affected by habitat fragmentation. A strong pollen pool structure was detected due to few effective pollen donors (Nep) and low distance pollen movement, pointing that most plants received pollen from close neighbors. Past demographic fluctuations may have affected the present population genetic structure as Bayesian coalescent analysis revealed the signature of past population expansion, possibly during warmer conditions after the last glacial maximum.DiscussionHabitat fragmentation has not increased genetic differentiation or reduced genetic diversity of A. aurantiaca despite dozens of generations since the onset of fragmentation in the region of Los Tuxtlas. Instead, past population expansion is compatible with the lack of observed genetic structure. The predicted negative effects of rainforest fragmentation on genetic diversity and population structure of A. aurantiaca seem to have been buffered owing to its large effective populations and long-distance disper...

show abstract

Genetic variation at microsatellite loci in the tropical herb Aphelandra aurantiaca (Acanthaceae)

Cited by 3 publications

References 13 publications

Development of Novel Genomic Simple Sequence Repeat (g-SSR) Markers and Their Validation for Genetic Diversity Analyses in Kalmegh [Andrographis paniculata (Burm. F.) Nees]

Development of Novel Genomic Simple Sequence Repeat (g-SSR) Markers and Their Validation for Genetic Diversity Analyses in Kalmegh [Andrographis paniculata (Burm. F.) Nees]

Peer Review #1 of "Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest (v0.1)"

Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest

Contact Info

Product

Resources

About