Towards an optimal sampling strategy for assessing genetic variation within and among white clover (Trifolium repens L.) cultivars using AFLP

Khanlou, Khosro Mehdi; Vandepitte, Katrien; Asl, Leila Kheibarshekan; Bockstaele, Erik Van

doi:10.1590/s1415-47572011000200015

Cited by 21 publications

(13 citation statements)

References 45 publications

(56 reference statements)

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“…Although resampling suggested that uneven sampling sizes did not bias our genetic estimates, we would expect if bias was present, sampling too few plants would have underestimated diversity. Although we sampled fewer plants in 1995, compared to 2004 and 2009, 20 individuals were determined to be adequate to assess genetic variation in T. repens , also an insect-pollinated outcrossing perennial species [69]. Our results were also consistent with field observations.…”

Section: Discussionsupporting

confidence: 75%

Conserving Plants in Gene Banks and Nature: Investigating Complementarity with Trifolium thompsonii Morton

Greene

Kisha

et al. 2014

PLoS ONE

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A standard conservation strategy for plant genetic resources integrates in situ (on-farm or wild) and ex situ (gene or field bank) approaches. Gene bank managers collect ex situ accessions that represent a comprehensive snap shot of the genetic diversity of in situ populations at a given time and place. Although simple in theory, achieving complementary in situ and ex situ holdings is challenging. Using Trifolium thompsonii as a model insect-pollinated herbaceous perennial species, we used AFLP markers to compare genetic diversity and structure of ex situ accessions collected at two time periods (1995, 2004) from four locations, with their corresponding in situ populations sampled in 2009. Our goal was to assess the complementarity of the two approaches. We examined how gene flow, selection and genetic drift contributed to population change. Across locations, we found no difference in diversity between ex situ and in situ samples. One population showed a decline in genetic diversity over the 15 years studied. Population genetic differentiation among the four locations was significant, but weak. Association tests suggested infrequent, long distance gene flow. Selection and drift occurred, but differences due to spatial effects were three times as strong as differences attributed to temporal effects, and suggested recollection efforts could occur at intervals greater than fifteen years. An effective collecting strategy for insect pollinated herbaceous perennial species was to sample >150 plants, equalize maternal contribution, and sample along random transects with sufficient space between plants to minimize intrafamilial sampling. Quantifying genetic change between ex situ and in situ accessions allows genetic resource managers to validate ex situ collecting and maintenance protocols, develop appropriate recollection intervals, and provide an early detection mechanism for identifying problematic conditions that can be addressed to prevent further decline in vulnerable in situ populations.

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Section: Discussionsupporting

confidence: 75%

Conserving Plants in Gene Banks and Nature: Investigating Complementarity with Trifolium thompsonii Morton

Greene

Kisha

et al. 2014

PLoS ONE

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“…The differences of average gene diversity between central and peripheral populations were not significant for any of the drought-induced genes used as probes. Khanlou et al (2011) using AFLP markers in three cultivars of T. repens measured genetic diversity values of 0.319, 0.289 and 0.272 for different cultivars, which are similar to the ones found in this study.…”

Section: Resultssupporting

confidence: 87%

DIVERSITY OF DROUGHT-RESPONSIVE GENES IN CENTRAL AND PERIPHERAL POPULATIONS OF Trifolium purpureum Loisel

et al. 2016

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Drought-responsive genes may differ in structure and complexity in native populations of a species established in different ecosystems. Peripheral populations may be a source of genetic variability for breeding cultivated plants for abiotic stresses tolerance and the target for core collections in germplasm preservation programs. Genetic studies including both peripheral and central populations are still limited. This research evaluated genetic diversity of drought-responsive genes in peripheral and central populations of Trifolium purpureum Loisel. Genomic DNA isolated from leaves of three northern and three southern populations of Israel was digested with restriction enzymes and hybridized with four drought-induced and four drought-repressed gene fragments. RFLPs were analyzed for gene diversity, molecular variation and fixation indexes (FST). Gene diversity of drought-induced genes ranged from 0.1 to 0.42 but differences of individual or pooled genes between central and peripheral populations were nonsignificant. Gene diversity for drought-repressed genes ranged from 0.08 to 0.348. Even though there were no differences for individual genes, a joint analysis showed a significantly larger (P ≤ 0.05) gene diversity in peripheral populations of T. Purpureum than in central ones. Variation within populations for both drought-induced and drought-repressed genes was the main component of molecular variance. Fixation index (FST) for drought-induced genes was between 0.029 and 0.214 while for drought repressed genes it was between 0.04 and 0.33. Results of this study show that peripheral population might be a reservoir for drought-responsive genes.

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“…Nei's diversity index is often used in population genetic studies, though it is based exclusively on allele frequency and relies on Hardy-Weinberg Equilibrium (HWE). On the other hand, Shannon index is calculated based on allele richness considering both the number and frequency of the alleles, consequently not assuming HWE [17]. Both indexes were calculated for comparison with other studies.…”

Section: Methodsmentioning

confidence: 99%

Analysis of Genetic Diversity of Two Mangrove Species with Morphological Alterations in a Natural Environment

et al. 2015

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Mangrove is an ecosystem subjected to tide, salinity and nutrient variations. These conditions are stressful to most plants, except to mangrove plants that are well-adapted. However, many mangrove areas have extremely stressful conditions, such as salt marshes, and the plants nearby usually present morphological alterations. In Sepetiba Bay, two species of mangrove plants, Avicennia schaueriana and Laguncularia racemosa, have poor development near a salt marsh (SM) compared to plants at the riverside (RS), which is considered a favorable habitat in mangroves. The level of genetic diversity and its possible correlation with the morphological divergence of SM and RS plants of both species were assessed by AFLP molecular markers. We found moderate genetic differentiation between A. schaueriana plants from SM and RS areas and depleted genetic diversity on SM plants. On the other hand, Laguncularia racemosa plants had no genetic differentiation between areas. It is possible that a limited gene flow among the studied areas might be acting more intensely on A. schaueriana plants, resulting in the observed genetic differentiation. The populations of Laguncularia racemosa appear to be well connected, as genetic differentiation was not significant between the SM and RS populations. Gene flow and genetic drift are acting on neutral genetic diversity of these two mangrove species in the studied areas, and the observed

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Towards an optimal sampling strategy for assessing genetic variation within and among white clover (Trifolium repens L.) cultivars using AFLP

Cited by 21 publications

References 45 publications

Conserving Plants in Gene Banks and Nature: Investigating Complementarity with Trifolium thompsonii Morton

Conserving Plants in Gene Banks and Nature: Investigating Complementarity with Trifolium thompsonii Morton

DIVERSITY OF DROUGHT-RESPONSIVE GENES IN CENTRAL AND PERIPHERAL POPULATIONS OF Trifolium purpureum Loisel

Analysis of Genetic Diversity of Two Mangrove Species with Morphological Alterations in a Natural Environment

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