Genetic diversity of the Andean tuber-bearing species, oca (Oxalis tuberosa Mol.), investigated by inter-simple sequence repeats.

The Andean tuber-bearing species, Oxalis tuberosa Mol., is a vegetatively propagated crop cultivated in the uplands of the Andes. Its genetic diversity was investigated in the present study using the inter-simple sequence repeat (ISSR) technique. Thirty-two accessions originating from South America (Argentina, Bolivia, Chile, and Peru) and maintained in vitro were chosen to represent the ecogeographic diversity of its cultivation area. Twenty-two primers were tested and 9 were selected according to fingerprinting quality and reproducibility. Genetic diversity analysis was performed with 90 markers. Jaccard's genetic distance between accessions ranged from 0 to 0.49 with an average of 0.28 +/- 0.08 (mean +/- SD). Dendrogram (UPGMA (unweighted pair-group method with arithmetic averaging)) and factorial correspondence analysis (FCA) showed that the genetic structure was influenced by the collection site. The two most distant clusters contained all of the Peruvian accessions, one from Bolivia, none from Argentina or Chile. Analysis by country revealed that Peru presented the greatest genetic distances from the other countries and possessed the highest intra-country genetic distance (0.30 +/- 0.08). This suggests that the Peruvian oca accessions form a distinct genetic group. The relatively low level of genetic diversity in the oca species may be related to its predominating reproduction strategy, i.e., vegetative propagation. The extent and structure of the genetic diversity of the species detailed here should help the establishment of conservation strategies.     

Traditional agroecosystems as conservatories and incubators of cultivated plant varietal diversity: the case of fig (<Emphasis Type="Italic">Ficus carica</Emphasis>L.) in Morocco

Background

Traditional agroecosystems are known to host both large crop species diversity and high within crop genetic diversity. In a context of global change, this diversity may be needed to feed the world. Are these agroecosystems museums (i.e. large core collections) or cradles of diversity? We investigated this question for a clonally propagated plant, fig (Ficus carica), within its native range, in Morocco, but as far away as possible from supposed centers of domestication.

Results

Fig varieties were locally numerous. They were found to be mainly highly local and corresponded to clones propagated vegetatively. Nevertheless these clones were often sufficiently old to have accumulated somatic mutations for selected traits (fig skin color) and at neutral loci (microsatellite markers). Further the pattern of spatial genetic structure was similar to the pattern expected in natural population for a mutation/drift/migration model at equilibrium, with homogeneous levels of local genetic diversity throughout Moroccan traditional agroecosystems.

Conclusions

We conclude that traditional agroecosystems constitue active incubators of varietal diversity even for clonally propagated crop species, and even when varieties correspond to clones that are often old. As only female fig is cultivated, wild fig and cultivated fig probably constitute a single evolutionary unit within these traditional agroecosystems. Core collections, however useful, are museums and hence cannot serve the same functions as traditional agroecosystems.

     

Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system

Occurrence of intervarietal or interspecific natural crosses has been reported for many crop plants in traditional farming systems, underlining the potential importance of this source of genetic exchange for the dynamics of genetic diversity of crop plants. In this study, we use microsatellite loci to investigate the role of volunteer seedlings (plants originating from unmanaged sexual reproduction) in the dynamics of genetic diversity of cassava (Manihot esculenta Crantz), a vegetatively propagated crop, in a traditional farming system in Guyana. A previous field study showed that farmers incorporate such plants into the germplasm for vegetative propagation, and that many of them are likely to be assigned by farmers to recognized varieties. Under strict vegetative propagation clonality of varieties is expected. The high proportion of polyclonal varieties observed suggests that incorporation of seedlings into the germplasm for propagation is a frequent event. The molecular variability assessed with microsatellite markers shows that there is high differentiation among heterozygous varieties, whereas populations of seedlings do not depart from the proportions expected under Hardy-Weinberg assumptions. Assignment of seedlings to a recognized variety on the basis of morphological similarity greatly increases genetic diversity within the variety. We argue that recombination and gene flow play a major role in the dynamics of genetic diversity of cassava in traditional farming systems. Documenting unmanaged sexual reproduction and its genetic consequences is a prerequisite for defining strategies of in situ conservation of crop plant genetic resources.     

Structured diversity using EST-PCR and EST-SSR markers in a set of wild blueberry clones and cultivars

Blueberries are perennial, vegetatively propagated out-crossing shrubs with great potential of health benefits. In tetraploid blueberry (Vaccinium spp.), genetic analyses have focused more on diversity, whereas genetic structure has been studied less extensively. This study investigated the genetic structure and diversity in 28 wild clones, six cultivars and two selections of lowbush, half-high and highbush blueberries. Summary statistics, structure estimation and clustering by neighbour-joining (NJ), principal coordinate analysis (PCoA) and by the analysis of molecular variance (AMOVA), using 10 expressed sequence tag-polymerase chain reaction (EST-PCR) and two EST-simple sequence repeat (SSR) primer pairs, were performed to characterize and discriminate the genotypes. A total of 213 markers were detected. Wide genetic diversity was evident from high values of expected heterozygosities, Shannon's index and polymorphism information content, and from AMOVA. Structure analysis subdivided the lowbush blueberries into three distinct groups leaving the half-high and highbush blueberries into one cluster which was in agreement with the NJ clustering and PCoA. Twelve EST-primer pairs efficiently differentiated wild and cultivated blueberries, making this technology valuable for genome mapping and for long-term conservation of blueberry resources for the benefit of germplasm conservation and breeding purposes.     

Thai elite cassava genetic diversity was fortuitously conserved through farming with different sets of varieties

Many in situ conservation programs have been developed to preserve plant landrace diversity and to promote its sustainable utilization, but little is known about the effectiveness of the developed programs in conserving plant genetic diversity. We investigated the effectiveness of an unregulated (i.e., unplanned or open) conservation system maintained by Thai farmers in conserving Thai elite cassava (Manihot esculenta Crantz) varieties. Specifically, we compared genetic diversity of 266 cassava clones that were collected from 80 farms in eight provinces with 16 cassava landraces and varieties released since the 1970s through genotyping with 35 informative simple sequence repeat (SSR) markers. The SSR analysis revealed a large regional heterogeneity in cassava diversity, with a strong genetic differentiation of the assayed clones among the 80 farms (19.8 %) and across the eight provinces (11.8 %). Significant associations were also found between SSR variation and farm agro-ecological factors or some farming practices. However, there was no significant genetic differentiation (0.9 %) between the 266 farm clones and 16 reference varieties. These findings suggest that the Thai elite cassava genetic diversity was fortuitously conserved by the farmers through farming with different sets of varieties. Implications of these findings are discussed with respect to on-farm conservation of plant genetic resources.     

Comparative Evaluation of RAPD, ISSR and Anchored-SSR Markers in the Assessment of Genetic Diversity and Fingerprinting of Oilseed Brassica Genotypes

Forty-two genotypes representing oilseed Brassica species were analyzed for the level of genetic diversity and molecular identity using Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat (ISSR) and 5'-Anchored Simple Sequence Repeat (ASSR) markers. DNA profiles revealed high degree of interspecific polymorphism, while the level was considerably low within a species, particularly in B. juncea. The UPGMA clusters clearly delineated genotypes of the respective Brassica species. Comparison of cophenetic matrices indicated a high degree of correspondence between dendrograms generated by different marker systems. A minimum of 10 random primers (approximately 105 bands) were required for the RAPD profiles to generate the expected cluster. Comparatively less number of primers was required to do the same in case of ISSR (4 primers) and ASSR (3 primers). The principal component analysis revealed similar genetic relationship among the genotypes as in cluster analysis. Although none of the DNA profiles could individually identify all the B. juncea genotypes, a combined DNA profile consisting 125 markers from the informative primers of all the three DNA marker systems could do the same. A positive correlation was found among the marker utility parameters (calculated for individual primers of different marker systems) such as marker index (MI), resolving power (Rp) and discrimination coefficient (D) with the number of genotypes identified by each primer with a few exceptions. Single plant analysis for a set of five B. juncea varieties revealed absence of intra-varietal heterogeneity in case of ASSR profiles, thereby suggesting its utility in varietal identification and differentiation.     

Epigenetic Variability in the Genetically Uniform Forest Tree Species Pinus pinea L

There is an increasing interest in understanding the role of epigenetic variability in forest species and how it may contribute to their rapid adaptation to changing environments. In this study we have conducted a genome-wide analysis of cytosine methylation pattern in Pinus pinea, a species characterized by very low levels of genetic variation and a remarkable degree of phenotypic plasticity. DNA methylation profiles of different vegetatively propagated trees from representative natural Spanish populations of P. pinea were analyzed with the Methylation Sensitive Amplified Polymorphism (MSAP) technique. A high degree of cytosine methylation was detected (64.36% of all scored DNA fragments). Furthermore, high levels of epigenetic variation were observed among the studied individuals. This high epigenetic variation found in P. pinea contrasted with the lack of genetic variation based on Amplified Fragment Length Polymorphism (AFLP) data. In this manner, variable epigenetic markers clearly discriminate individuals and differentiates two well represented populations while the lack of genetic variation revealed with the AFLP markers fail to differentiate at both, individual or population levels. In addition, the use of different replicated trees allowed identifying common polymorphic methylation sensitive MSAP markers among replicates of a given propagated tree. This set of MSAPs allowed discrimination of the 70% of the analyzed trees.     

Influence of ethnic traditional cultures on genetic diversity of rice landraces under on-farm conservation in southwest China

Background

Crop genetic resources are important components of biodiversity. However, with the large-scale promotion of mono-cropping, genetic diversity has largely been lost. Ex-situ conservation approaches were widely used to protect traditional crop varieties worldwide. However, this method fails to maintain the dynamic evolutionary processes of crop genetic resources in their original habitats, leading to genetic diversity reduction and even loss of the capacity of resistance to new diseases and pests. Therefore, on-farm conservation has been considered a crucial complement to ex-situ conservation. This study aimed at clarifying the genetic diversity differences between ex-situ conservation and on-farm conservation and to exploring the influence of traditional cultures on genetic diversity of rice landraces under on-farm conservation.

Methods

The conservation status of rice landrace varieties, including Indica and Japonica, non-glutinous rice (Oryza sativa) and glutinous rice (Oryza sativa var. glutinosa Matsum), was obtained through ethno-biology investigation method in 12 villages of ethnic groups from Guizhou, Yunnan and Guangxi provinces of China. The genetic diversity between 24 pairs of the same rice landraces from different times were compared using simple sequence repeat (SSR) molecular markers technology. The landrace paris studied were collected in 1980 and maintained ex-situ, while 2014 samples were collected on-farm in southwest of China.

Results

The results showed that many varieties of rice landraces have been preserved on-farm by local farmers for hundreds or thousands of years. The number of alleles (Na), effective number of alleles (Ne), Nei genetic diversity index (He) and Shannon information index (I) of rice landraces were significantly higher by 12.3–30.4 % under on-farm conservation than under ex-situ conservation. Compared with the ex-situ conservation approach, rice landraces under on-farm conservation programs had more alleles and higher genetic diversity. In every site we investigated, ethnic traditional cultures play a positive influence on rice landrace variety diversity and genetic diversity.

Conclusion

Most China’s rice landraces were conserved in the ethnic areas of southwest China. On-farm conservation can effectively promote the allelic variation and increase the genetic diversity of rice landraces over the past 35 years. Moreover, ethnic traditional culture practices are a crucial foundation to increase genetic diversity of rice landraces and implement on-farm conservation.

     

Genetic Diversity in Old Portuguese Durum Wheat Cultivars Assessed by Retrotransposon-Based Markers

Retrotransposon-based markers, such as the inter-retrotransposon-amplified polymorphism (IRAP) and the retrotransposon microsatellite-amplified polymorphism (REMAP) are highly informative, multilocus, and reveal insertional polymorphisms among plant individuals. These markers have been used for evolutionary studies, genetic diversity assessment, DNA fingerprinting, genetic mapping linkage, and for the detection of genetic rearrangements induced by polyploidization. In this study, we used IRAP and REMAP markers to assess the genetic diversity among 51 old Portuguese durum wheat cultivars belonging to 27 botanical varieties and to define their genetic relationships. Five IRAP and four REMAP primer combinations were used. IRAP markers revealed 66.3% of polymorphism and an average of 18.4 bands per primer combination which ranged in size from 450 to 3,100?bp. The REMAP technique allowed the detection of 86.36% of inter-cultivar polymorphism and an average of 11 bands per primer combination. The molecular weight of the REMAP bands ranged from 250 to 2,750?bp. The durum wheat cultivars analyzed here belong to 27 botanical varieties of the subspecies Triticum turgidum subsp. turgidum L. [syn. T. turgidum] and Triticum turgidum L. subsp. durum [syn. T. durum] (Desf.) Husn.. Our results showed that the genetic variability assessed by both the IRAP and REMAP markers did not allow the clustering of the durum wheat cultivars according to their taxonomical criteria (subspecies or botanical variety) or homonymy. Nonetheless, these markers were useful for the assessment of genetic diversity at the individual level, for the definition of genetic relationships among cultivars, and for estimation of the genetic structure of the Old collection under analysis. The achieved data could be valuable for future experiments of DNA fingerprinting, genetic improvement, and germplasm conservation in wheat.     

Congruence between morphological and molecular markers inferred from the analysis of the intra-morphotype genetic diversity and the spatial structure of Oxalis tuberosa Mol.

Oxalis tuberosa is an important crop cultivated in the highest Andean zones. A germplasm collection is maintained ex situ by CIP, which has developed a morphological markers system to classify the accessions into morphotypes, i.e. groups of morphologically identical accessions. However, their genetic uniformity is currently unknown. The ISSR technique was used in two experiments to determine the relationships between both morphological and molecular markers systems. The intra-morphotype genetic diversity, the spatial structures of the diversity and the congruence between both markers systems were determined. In the first experience, 44 accessions representing five morphotypes, clearly distinct from each other, were analyzed. At the molecular level, the accessions exactly clustered according to their morphotypes. However, a genetic variability was observed inside each morphotype. In the second experiment, 34 accessions gradually differing from each other on morphological base were analyzed. The morphological clustering showed no geographical structure. On the opposite, the molecular analysis showed that the genetic structure was slightly related to the collection site. The correlation between both markers systems was weak but significant. The lack of perfect congruence between morphological and molecular data suggests that the morphological system may be useful for the morphotypes management but is not appropriate to study the genetic structure of the oca. The spatial structure of the genetic diversity can be related to the evolution of the species and the discordance between the morphological and molecular structures may result from similar selection pressures at different places leading to similar forms with a different genetic background.     

元阳3个长期连续栽培水稻地方品种内部遗传异质性分析

水稻地方品种是稻种资源的重要组成部分,遗传多样性十分丰富,具有推广改良品种所缺少或没有的优质种质,是水稻育种和稻种起源、进化研究不可缺少的过渡材料。目前,对水稻地方品种间遗传多样性研究较多,而对其内部异质性研究甚微。本研究用24对微卫星(SSR)引物对云南元阳梯田3个栽种历史悠久的水稻地方品种的内部遗传异质性进行了分析。共检测出117个等位基因,香农指数为红脚老粳居群(0.5911)>白脚老粳A居群(0.4875)>月亮谷居群(0.3070)。结果显示:3个地方品种的内部遗传异质性丰富,且遗传异质性主要得益于个体间,而非居群间。     

Genetic diversity of endangered Manglietia patungensis assessed by inter simple sequence repeat and sequence-related amplified polymorphism markers

Manglietia patungensis Hu is an endangered plant native to China. Knowledge of its genetic diversity and structure would aid its conservation. This study assessed nine natural populations of M. patungensis using two methods: inter simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. Using 10 ISSR primer pairs, 334 bands were generated, and 10 SRAP primer pairs generated 276 bands. The percent of polymorphic bands (91.32% and 93.48%), Nei's genetic diversity (0.3448 and 0.3323), and Shannon's information index (0.5075 and 0.4935) revealed a high level of genetic diversity at the species level. Total heterozygosity was 0.3439 by ISSR and 0.3281 by SRAP. The mean heterozygosity was 0.2323 by ISSR and 0.2521 by SRAP. The coefficient of genetic differentiation among natural populations was 0.3245 by ISSR and 0.2316 by SRAP. These data indicated higher levels of genetic diversity of M. patungensis within, rather than among, populations. Estimates of gene flow among natural populations were 1.0411 and 1.0589, which implied a certain amount of gene exchange among populations. A Mantel test revealed no significant correlation between genetic and geographic distance. ISSR and SRAP markers are both effective for genetic diversity research in M. Patungensis. Based on these results, conservation of M. patungensis should be performed both in situ and ex situ.     

Genetic structure in two meadow varieties ofEuphrasia stricta on the Baltic island of Gotland (Sweden) and implications for conservation

The annual hemiparasiteEuphrasia stricta occurs on Gotland in two early-flowering meadow varieties.E. stricta var.suecica is on the Swedish red-list as endangered, occurring in Sweden only on the Baltic island of Gotland. It probably has near relatives east of the Baltic proper. The other variety,E. stricta var.tenuis, has a wider distribution occurring almost all over Sweden, but is declining in abundance. Both varieties have close morphological similarities and habitat preferences, raising questions about which level conservation efforts should be focused on, varieties or populations. In this study we describe the genetic structure between and within these two varieties using amplified fragment length polymorphism, AFLP.F _ST between varieties is 0.14, and between populations within the varietiesE. stricta var.suecica and var.tenuis F _ST is 0.60 and 0.26 respectively. The partitioning of gene diversity to different levels shows that 14% of the genetic diversity occurs between varieties, 42% between populations within varieties, and 44% within populations. Significant genetic differentiation was detected between varieties, populations and subpopulations within populations using a constrained principal coordinate analysis. We suggest that all of the existing populations of these two varieties on Gotland should be preserved, since they are few (6E. stricta var.suecica and 5E. stricta var.tenuis) and much of the genetic diversity is partitioned between populations.     

Genetic characterization of Bhutanese native chickens based on an analysis of Red Junglefowl (Gallus gallus gallus and Gallus gallus spadecieus), domestic Southeast Asian and commercial chicken lines (Gallus gallus domesticus)

The genetic diversity of Bhutanese chickens needs to be understood in order to develop a suitable conservation strategy for these birds in Bhutan. In this, work, we used microsatellite markers to examine the genetic diversity of Bhutanese chickens. Four Bhutanese chicken varieties (Black plumage, Frizzle, Naked neck and Red Junglefowl-like, corresponding to Yuebjha Narp, Phulom, Khuilay and Seim, respectively), two subspecies of Red Junglefowl (Gallus gallus gallus and Gallus gallus spadecieus), two varieties of Thai native chickens (Pradhu Hang Dam and Chee; Gallus gallus domesticus) representing the Southeast Asian domestic chicken, and two commercial lines (Broiler and Single Comb White Leghorn) were genotyped with 18 microsatellites that included 16 loci recommended by the FAO/ISAG for investigations of genetic variability in chickens. All loci were polymorphic, with the number of alleles ranging from six (MCW0111) to 23 (MCW0183). Substantial genetic variation was observed in all populations, with the Bhutanese native chicken Yuebjha Narp (Black plumage chicken) showing the lowest genetic variability. Despite extensive intrapopulation variation, the genetic differentiation among 10 populations was moderate. A neighbor-joining tree revealed the genetic relationships involved while principal component analysis showed that Bhutanese native chickens should be given priority in conservation efforts because of their genetic distinctiveness. Chee chickens are especially valuable as a reservoir of predomestic diversity, as indicated by their greater genetic variation and their position in the phylogenetic tree.     

Farmers' use of wild relative and sexual reproduction in a vegetatively propagated crop. The case of yam in Benin

The impact of traditional farmers' management on genetic diversity of vegetatively propagated crops is poorly documented. In this study, we analysed the impact of ennoblement of spontaneous yams, an original traditional farmers' practice, on the genetic diversity of yam (Dioscorea sp.) in Benin. We used 11 microsatellite markers on yam tubers from a small village in northern Benin and demonstrated that wild x cultivated hybrids are spontaneously formed. Many of the spontaneous yams collected by farmers from surrounding savannah areas for ennoblement were shown to be of wild and hybrid genotypes. Moreover, we demonstrated that some yam varieties have a wild or hybrid signature. Lastly, we performed a broader ranging genetic analysis on yam material from throughout Benin and showed that this practice is used in different ecological and ethno-linguistic regions. Through this practice, farmers create new varieties with new genetic combinations via sexual reproduction of wild and cultivated yams. This system, whereby a sexual cycle and asexual propagation are mixed, ensures potential large-scale cultivation of the best genotypes while preserving the potential for future adaptation.     

Cryopreserved storage of clonal germplasm in the USDA National Plant Germplasm System

The US Department of Agriculture-Agricultural Research Service (USDA-ARS), National Plant Germplasm System (NPGS) plant collections are a critical source of genetic diversity for breeding and selection of improved crops, including vegetatively propagated plants. Information on these collections is readily accessible to breeders and researchers on the internet from the Germplasm Resources Information Network (GRIN). The clonal collections are at risk for loss due in part to their genetic diversity that makes growing them in one location a challenge, but also because it is difficult to have duplicate collections without incurring great expense. The development of cryopreservation techniques during the last two decades provides a low maintenance form of security backup for these collections. National plant collections for vegetatively propagated crop plants and their wild relatives are maintained by the USDA-ARS, NPGS at 15 sites across the country. These sites include various combinations of field, greenhouse, screenhouse, and in vitro collections. Cryopreserved backup collections in liquid nitrogen storage were instituted in the 1990s, increased greatly in the 2000s with the advent of new techniques, and are continuing today. Collections of dormant buds of temperate trees, shoot tips of in vitro cultures of many crops, and embryonic axes of some large seeded or recalcitrant seeded plants are all part of the clonal backup storage system.     

Mining and characterization of EST-SSR markers for <Emphasis Type="Italic">Zingiber officinale</Emphasis> Roscoe with transferability to other species of Zingiberaceae

Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons. SSRs were searched in the unigenes and 515 SSR-containing ESTs were identified with a frequency of 1 SSR per 25.21 kb of the genome. These ESTs were also annotated using BLAST2GO. Primers were designed for 349 EST-SSRs and 25 primer pairs were randomly picked for EST SSR study. Out of these, 16 primer pairs could be optimized for amplification in different accessions of Z. officinale as well as other species belonging to Zingiberaceae. GES454, GES466, GES480 and GES486 markers were found to exhibit 100% cross-transferability among different members of Zingiberaceae.     

东北三省2021年水稻审定品种的核心亲本遗传多样性与籼粳分化北大核心CSCD

为了阐明东北三省近年育成水稻品种的遗传基础,该研究通过对2021年育成的256个水稻新品种的系谱进行分析,确定了20个材料为育种核心亲本,并利用44对多态性SSR分子标记和34对InDel籼粳特异性分子标记分析了它们的遗传多样性和籼粳分化程度。结果表明:(1)SSR标记能够高效评价参试材料的多样性水平,共检测到130个等位基因,每个位点检测等位基因(Na)变异为2~5个,平均为2.95个;基因多样性指数(H)变异为0.10~0.75,平均为0.41;多态性信息含量(PIC)变异为0.09~0.70,平均为0.36。(2)遗传多样性分析表明,东北三省20份水稻核心亲本的整体多样性水平较低,黑龙江省核心亲本多样性略高于辽宁省和吉林省。(3)NJ聚类分析表明,20份核心亲本可以划分为3个类群,分别为辽宁类群、吉林类群和黑龙江类群。(4)遗传结构分析表明,20份核心亲本可划分为2个稳定的类群,其中辽宁省核心亲本均处于A类群,黑龙江省核心亲本均处于B类群。(5)籼粳分化分析表明,20份核心亲本遗传背景均为粳稻类型,但都含有少数籼型位点,其籼型基因频率F在0.01~0.19范围内。研究认为,东北三省水稻育种核心亲本遗传基础狭窄、使用频率较高是导致育成品种遗传多样性水平较低的可能原因,在育种中亟待挖掘新种质、引入新资源,丰富遗传背景。     

Population genetics of the Federally Threatened Miccosukee gooseberry (Ribes echinellum), an endemic North American species

Ribes echinellum (Coville) Rehder (Miccosukee gooseberry; Grossulariaceae) is a Federally Threatened species known from only two localities: Jefferson County (Florida, FL) and McCormick County (South Carolina, SC). This perennial shrub, ca. 1 m tall, is deciduous, and reproduces both vegetatively (clonal growth) and sexually (seed production). Recent surveys of the FL population revealed a dramatic decline in plant numbers. To assist in conservation and management of this species in FL and SC populations, microsatellite genetic markers were used to identify genotypes and assess the genetic structure of R. echinellum. We genotyped seven microsatellite loci in 102 individuals: 74 collected in FL and 28 in SC. Unbiased heterozygosity was between 0.28 and 0.53. All seven loci were polymorphic, showing a range of 1.52–2.13 effective number of alleles per locus (mean = 1.75). The two populations of R. echinellum show low genetic diversity, especially in SC. Clonality was not widespread, but was higher in the SC population. Both populations show signatures of bottlenecks but isolation by distance was not evident. We found significant deviation from HW equilibrium, with higher number of heterozygotes than expected. However when HW test was done for the combined populations as two separate groups, only FL showed a significant HW test and for SC the test was non-significant. Bayesian analysis and F_ST values suggest high genetic divergence between the populations. These results are important for developing a recovery plan and an ex situ and reintroduction conservation programs.