Knowledge Of Genetic Diversity Research Articles

Genetic Structure ofNotholithocarpus densiflorus(Fagaceae) from the Species to the Local Scale: A Review of Our Knowledge for Conservation and Replanting

Tanoak, Notholithocarpus densiflorus (Hook. & Arn.) Manos, Cannon & S. H. Oh (Fagaceae), is an important component of mixed-evergreen forests and woodlands in coastal California and Oregon, with incursions into the Sierra Nevada and the Klamath Ranges. Sudden Oak Death (SOD) is causing severe dieback and mortality in tanoak and could transform these ecosystems in areas where the pathogen Phytophthora ramorum S. Werres, A.W.A.M. de Cock can become established. Knowledge of genetic diversity within the species is important for both disease resistance screening, conservation and replanting in sites with high mortality. Here we review what has been learned about the genetic structure within tanoak since SOD has caused disease epidemics in the species. We review published work on genetic structure at the species level and provide some re-analyses of these data that show divergence across the geographic range. We also review recently published data on genetic structure at a fine spatial scale that provides some guidelines for the selection of trees as seed sources. Finally, we interpret a range of seed provenancing strategies in the light of our knowledge of tanoak genetic diversity.

Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar

We performed a population genomics study of the aye-aye, a highly specialized nocturnal lemur from Madagascar. Aye-ayes have low population densities and extensive range requirements that could make this flagship species particularly susceptible to extinction. Therefore, knowledge of genetic diversity and differentiation among aye-aye populations is critical for conservation planning. Such information may also advance our general understanding of Malagasy biogeography, as aye-ayes have the largest species distribution of any lemur. We generated and analyzed whole-genome sequence data for 12 aye-ayes from three regions of Madagascar (North, West, and East). We found that the North population is genetically distinct, with strong differentiation from other aye-ayes over relatively short geographic distances. For comparison, the average FST value between the North and East aye-aye populations--separated by only 248 km--is over 2.1-times greater than that observed between human Africans and Europeans. This finding is consistent with prior watershed- and climate-based hypotheses of a center of endemism in northern Madagascar. Taken together, these results suggest a strong and long-term biogeographical barrier to gene flow. Thus, the specific attention that should be directed toward preserving large, contiguous aye-aye habitats in northern Madagascar may also benefit the conservation of other distinct taxonomic units. To help facilitate future ecological- and conservation-motivated population genomic analyses by noncomputational biologists, the analytical toolkit used in this study is available on the Galaxy Web site.

Use of AFLP Markers to Assess Genetic Diversity in Palmer Amaranth (Amaranthus palmeri) Populations from North Carolina and Georgia

Glyphosate-resistant Palmer amaranth is a serious problem in southern cropping systems. Much phenotypic variation is observed in Palmer amaranth populations with respect to plant growth and development and susceptibility to herbicides. This may be related to levels of genetic diversity existing in populations. Knowledge of genetic diversity in populations of Palmer amaranth may be useful in understanding distribution and development of herbicide resistance. Research was conducted to assess genetic diversity among and within eight Palmer amaranth populations collected from North Carolina and Georgia using amplified fragment length polymorphism (AFLP) markers. Pair-wise genetic similarity (GS) values were found to be relatively low, averaging 0.34. The highest and the lowest GS between populations were 0.49 and 0.24, respectively, while the highest and the lowest GS within populations were 0.56 and 0.36, respectively. Cluster and principal coordinate (PCO) analyses grouped individuals mostly by population (localized geographic region) irrespective of response to glyphosate or gender of individuals. Analysis of molecular variance (AMOVA) results when populations were nested within states revealed significant variation among and within populations within states while variation among states was not significant. Variation among and within populations within state accounted for 19 and 77% of the total variation, respectively, while variation among states accounted for only 3% of the total variation. The within population contribution towards total variation was always higher than among states and among populations within states irrespective of response to glyphosate or gender of individuals. These results are significant in terms of efficacy of similar management approaches both in terms of chemical and biological control in different areas infested with Palmer amaranth.

Genetic diversity and fine-scale spatial genetic structure of different life- history stages in a small, isolated population of <I>Sinojackia huangmeiensis</I> (Styracaceae)

Knowledge of genetic diversity and fine-scale spatial genetic structure (SGS) at different age stages of small isolated populations is important for understanding population dynamics and developing effective conservation measures for fragmented populations. In this study, we used a small, isolated population of Sinojackia huangmeiensi as a case study to investigate the change in the levels of genetic diversity and SGS at different age stages. We mapped and genotyped 60 adults,175 saplings, 198 seedlings using eight microsatellite markers to detect the genetic diversity, SGS and pollen and seed dispersal patterns in a 80 m × 160 m transect located in an original secondary forest surrounded by farmlands. No significant differences in genetic diversity were found among the three life stages, and a significant heterozygote deficiency in the population may result from substantial biparental inbreeding. We found significant fine-scale spatial structure at different age stages within 10 m, suggesting that seed dispersal mainly occurred near a mother tree. Seed dispersal distance and pollen dispersal distance were 9.07±13.38 and 23.81±23.60 m, respectively, and ‘L’ 第 4期 阮咏梅等: 黄梅秤锤树孤立居群的遗传多样性及其小尺度空间遗传结构 461 shaped curves were observed in both pollen dispersal and seed dispersal patterns. The spatial distribution of the different age stages is most likely the result of little overlap in seed rain, self-thinning, biparental inbreeding and limited gene flow. Our results have important implications for conservation of extant population of S. huangmeiensis. Measures for promoting pollen flow and increasing survival rate of seedlings should be considered for in situ conservation. The presence of SGS in this fragmented population implies that seeds for ex situ conservation should be collected from trees at least 10 m apart to reduce genetic similarity between neighboring individuals.

The RAPD techniques used to assess the genetic diversity in <i>Draba dorneri</i>, a critically endangered plant species

A successful management and preservation of the natural populations is depending on accurate assessment of genetic diversity. Knowledge of genetic diversity within a population is important for the conservation of the species. Our aim was to assess the genetic diversity in Draba dorneri Heuff. population (Brassicaceae family)—an endemic plant species of conservative interest using Random Amplified Polymorphic DNA (RAPD) technique. The plant species is strictly protected at national level as well as at international level through “Convention on the Conservation of European Wildlife and Natural Habitats”, Bern, 1979 European Council. In this study, a total of 52 primers were scored initially. A total of 77 repro- ducible bands with an average of 6.41 bands per primer were obtained from the 12 primers selected. A cluster analysis (UPGAMA) was used to generate a dendrogram based on Dice coefficient. We found 67% similarity between the samples from the two analyzed slopes. Comparing with other rare plants species, our data revealed a higher level of genetic diversity in D. dorneri population in Retezat Mountains.

Relationship between SSR- Based Molecular Marker and Cotton F<SUB>1</SUB> Inter Specific Hybrids Performance for Seed Cotton Yield and Fiber Properties

Knowledge of genetic diversity and relationships among breeding materials has a significant impact on crop improvement. Association between parental divergence and progeny performance has not been well documented in cotton ( Gossypium hirsutum L.). The objectives of this study were to estimate genetic diversity among selected cotton genotypes on the basis of simple sequence repeat (SSR) markers, and to investigate the relationship between genetic diversity and F 1 population performance and heterosis.The present study was conducted to investigate the relationship between parents molecular marker diversity and inter specific hybrids of cotton to evaluate the hybrid performance and heterosis using molecular markers. Twenty eight F 4 lines of ( Gossypium barbadense L.) were crossed with the four common diverse testers ( Gossypium hirsutum L.) viz., DH 98-27 (T 1 ), ZCH8 (T 2 ), 178-24 (T 3 ) and DH 18-31 (T 4 ) to produce 112 F 1 inter specific hybrids during 2010. These 112 F 1 hybrids, their F 5 barbadense lines with 4 hirsutum testers and ruling commercial check (MRC6918 and DCH32) were evaluated for yield and fiber quality traits and sown during kharif 2011 at University of Agricultural Sciences, Dharwad, India. Genetic distances (GD) among the parents were calculated from 40 microsatellite marker data, and their correlation with hybrid performance and heterosis were analysed. The dendrogram constructed from the pooled data revealed three distinct clusters. One cluster involved testers and other clusters showed all lines were placed which are already having proven record in giving good hybrids. The similarity coefficient values between the line DB 533 x DB 534 F 4 IPS 49 and the tester DH 98-27 showed 67%. It revealed that DB 533 x DB 534 F 4 IPS 49 was closely related to DH 98-27 with 67% similarity between parents. The hybrid between DB 533 x DB 534 F4 IPS 49 and DH 98-27 exhibited the highest yield of 2884.26 kg/ha. Similarity coefficient (88%) value between lines and testers showed between the line DB 533 x DB 534 F 4 IPS 52 and the tester ZCH8, the hybrid between these recorded an yield of 2040.757 kg/ha. Lowest similarity coefficient value was noticed between the line DB 533 x DB 534 F 4 IPS 16 and tester DH 98-27 which revealed that they are far distinct from each other. This combination exhibited 2384.62 kg/ha yield. Genetic distance (GD) ranged from 0.041 to 0.429, with an average of 0.183. The result implied that each cluster dendrogram substantially reflected its own genetic relationship among parents. Overall, a low significant correlation of GD with hybrid performance and heterosis was detected in Table 2~6. Highly significant positive correlation were found between genetic distance (GD) and ginning outturn for F 1 performance (0.277) and heterosis over MRC 6918 (0.279) and DCH 32 (0.279), while significant positive correlation were found between genetic distance (GD) and ginning outturn for mid parent heterosis (0.237). Highly significant positive correlation were found between genetic distance (GD) and seed cotton yield for F 1 performance (0.359) and heterosis over Bt check MRC 6918 (0.336) and over non Bt check DCH 32 (0.362), while significant positive correlation were found between genetic distance (GD) and seed cotton yield for mid parent heterosis (0.226). Significant positive correlation were found between genetic distance (GD) and lint index for mid parent heterosis (0.227), F 1 performance (0.251) and heterosis over MRC 6918 (0.250) and DCH 32 (0.250), while significant positive correlation were found only between genetic distance (GD) and fiber micronaire value for F 1 performance (0.241).

Biodiversity of fruit species in the valley of Oued Righ: the case of the area of Touggourt (Algeria)

Introduction . Algerian oases are characterized by a diversification of local fruit species and cultivars. However, this diversity is subject to erosion. To preserve the genetic heritage, we undertook the first work on the inventory of fruit species crops in the region of Touggourt in south-eastern Algeria. Materials and methods . Our working methods were based on surveys carried out on farms in the Oued Righ region according to a questionnaire that met our objectives. For this, we divided the study region into three zones and in each zone we selected ten farms for the inventory of fruit species cultivated. Results and discussion . The results of our investigations allowed us to identify thirteen species, including four species with a wide distribution (pomegranate tree, apricot tree, fig tree and vine). The local genetic diversity of these species is little known. The varieties or cultivars inventoried have local names given by the farmers in the region according to certain morphological characteristics of the fruit. We surveyed five cultivars for the fig tree, two cultivars for the pomegranate tree, two cultivars for the vine, and two apricot tree cultivars. The study of the biodiversity of fruit trees in the Oued Righ region showed high richness of the species and cultivars; some are local and others are endemic to the region. Better knowledge of genetic diversity will begin with tests of behavior and characterization of the different genotypes encountered to dispel the ambiguities and to highlight the actual composition of populations or varieties of different species.

Conservation and management of peripheral populations: Spatial and temporal influences on the genetic structure of wood frog (Rana sylvatica) populations

Peripheral populations of wide-ranging species are often of special conservation concern, and knowledge of genetic diversity, gene flow, and historical population dynamics are critical to informed management of these populations. In this study we evaluate patterns of genetic diversity and gene flow among a series of wood frog populations in east-central Missouri where it is a species of conservation concern. Because these populations are on the periphery of the species’ range and are isolated from one another by fragmented landscapes, we expected to see population subdivision with signatures of range-edge effects and isolation by resistance. Our analyses reveal significant interpopulation differentiation and a distinct gradient in diversity where levels of allelic richness and heterozygosity decline as the species boundary is approached. These patterns likely stem from factors characteristic of peripheral populations, including reduced population size, reduced gene flow, and more frequent extinction–recolonization events. Population structure was evident, but isolation by resistance (i.e. fragmentation) was not a significant factor in our focal landscape. Isolation by distance was significant, but the level of population differentiation suggests that gene flow among populations is limited. We hypothesize that the lack of gene flow is due to the absence of available fishless breeding habitats outside of protected, managed lands, and recommend that future management efforts of the wood frog include increasing population connectivity at the landscape scale via the creation and maintenance of fishless aquatic breeding habitat.

Genetic variations within a collection of anthuriums unraveled by morphological traits and AFLP markers

Abstract In this study, genetic variations among a collection of anthuriums were comparatively investigated using morphological traits and amplified fragment length polymorphism (AFLP) markers. Both morphological and AFLP-based data clustered the accessions from Anthurium andraeanum , Anthurium scherzerianum , and Anthurium clarinervium into three separate groups, with a significant though low correlation ( r = 0.3) observed between the morphological and AFLP-based similarity matrices. The AFLP-based principal coordinate analysis (PCoA) divided the entire accessions into three parts, reinforcing the AFLP-based clustering. Moreover, the Bayesian-based structuring assigned the anthurium accessions to three subgroups but with 27 accessions retained in the admixed groups, probably implying the highly heterozygous genome of the investigated anthuriums. The findings of this study would add new knowledge of genetic diversity among anthuriums as well as embark on a useful beginning for a rational hybridization breeding for anthuriums in future.

Genetic diversity and parentage in farmer varieties of cacao (Theobroma cacao L.) from Honduras and Nicaragua as revealed by single nucleotide polymorphism (SNP) markers

Cacao (Theobroma cacao L.) is the main source for chocolate with an annual production of four million tons worldwide. This Neotropical tree crop was domesticated in Mesoamerica as far back as 3,000 years ago. Knowledge of genetic diversity and population structure in farmer varieties of cacao in the center of domestication is essential for sustainable production of fine-flavored cacao beans and contributes to in situ/on-farm conservation of farmer varieties. Based on 70 single nucleotide polymorphism markers, we analyzed 84 fine-flavored farmer varieties collected from traditional cacao farms in Honduras and Nicaragua. The study also included 31 clones from the international cacao collections to serve as references. The SNP based multilocus matching identified six synonymous groups, including 14 Criollo and two Amelonado varieties. A moderately high level of genetic diversity was observed in these farmer varieties, indicating the possibility to further explore intra-population variation and breed for fine-flavored cocoa. Multivariate analysis showed clustering of the 84 farmer accessions in five genetic groups: ancient Criollo, Amelonado, Trinitario (including Nicaragua Trinitario and Honduras Trinitario) and Upper Amazon Forastero (only one accession). The Honduras Trinitario differed from the Nicaragua Trinitario group. The clustering results largely supported the perceived classification of cacao by local farmers and researchers, which was mainly based on morphological traits. However, the well known traditional variety “Indio” in this region was identified as synonymous with Amelonado. Parentage analysis showed that the variety “Indio” (or Amelonado) contributed more to the Trinitario type farmer varieties, whereas ancient Criollo had less influence. The present study demonstrates the efficacy of using a small set of SNP makers for cacao germplasm characterization, and further depicts the diverse origins and parentage in farmer varieties from Mesoamerica. This information thus will be highly useful for conservation and utilization of cacao germplasm from this region.

Geographic patterns of genetic variation and population structure inPinus aristata, Rocky Mountain bristlecone pine

Pinus aristata Engelm., Rocky Mountain bristlecone pine, has a narrow core geographic and elevational distribution, occurs in disjunct populations, and is threatened by rapid climate change, white pine blister rust, and bark beetles. Knowledge of genetic diversity and population structure will help guide gene conservation strategies for this species. Sixteen sites across four mountain ranges in the core distribution of P. aristata were sampled and genetic diversity was assessed with 21 isozyme loci. Low species and population level genetic diversity (He = 0.070 and 0.062, respectively) occurred with moderate among-population differentiation (FST = 0.131). Genetic diversity correlated with longitude, latitude, and elevation and a strong mountain island effect may contribute to substructuring and isolation. Using multiple complementary analyses, sampled trees were assigned to three genetic lineages that varied in diversity and admixture and were associated with different climatic factors. The distribution of genetic diversity and substructuring of P. aristata may be an outcome of a combination of restricted gene flow due to geographic and phenological isolation, random processes of genetic drift, life history traits, natural selection, and postglacial migrations. The combination of low genetic diversity, moderate population isolation, and a protracted regeneration dynamic puts populations at risk for extirpation by novel stresses.

Genetic Diversity Analysis of Maize Inbred Lines from SCDA Turda - Romania Revealed by RAPD Molecular Markers

Knowledge of genetic diversity and relationships among maize inbred lines is indispensable to a breeding program. Our objective was to investigate the level of genetic diversity among maize inbred lines. Eighty-three maize inbred lines obtained from SCDA Turda were genotyped using 20 decamer primers. These primers generated, among the studied genotypes, a number of polymorphic bands comprised between 17 bands (OPA 03) and 7 bands (OPAB 11). The highest numbers of polymorphic bands were obtained with primer OPA 03, respectively 17 bands, followed by OPA 01, OPB 08 (16 polymorphic bands) and OPX 03 and OPAL 20 (13 polymorphic bands). Genetic distances were established using Nei Li/Dice coefficent and an UPGMA dendrogram was constructed with FreeTree software. The built dendrogram shows phylogenetic relationships between the analysed biological material.

Interview with Sarah Tishkoff: Perspectives for Genetic Research in African Populations

Interview with Sarah Tishkoff:Perspectives for Genetic Research in African Populations Giovanni Destro-Bisol Keywords Sub-Saharan Africa, genetic variation, human origins, genetic epidimiology, African ancestry, natural selection, genetic studies of functional variants, unilinearly transmitted polymorphisms, phylogeography, approximate Bayesian computation methods, next generation sequencing technologies Sarah Tishkoff is the David and Lyn Silfen University Associate Professor in Genetics and Biology at the University of Pennsylvania, holding appointments in the Perelman School of Medicine and the School of Arts and Sciences. Dr. Tishkoff studies genetic variation in ethnically diverse Africans in order to reconstruct modern human origins, African population history, and processes of adaptation. Her research examines how genetic variation influences normal variable traits as well as disease susceptibility and drug response. Dr. Tishkoff has long been an advocate for the need for populations in Africa to be represented in human genetic studies so that they may benefit from knowledge about their population history and development of more effective medical treatments. Dr. Tishkoff received her bachelor's degree in anthropology and genetics from the University of California at Berkeley, and her masters of philosophy and doctorate in genetics from Yale School of Medicine. She taught in the Department of Biology at the University of Maryland at College Park from 2000-2007 and became a faculty member at the University of Pennsylvania in 2008. Dr. Tishkoff is a recipient of an NIH Pioneer Award, a Packard Career Award, and a Burroughs/Wellcome Fund Career Award. She is currently a member of the editorial boards of Genome Research Journal and G3: Genes Genomes Genetics and is an associate editor of Molecular Biology and Evolution Journal and The Quarterly Review of Biology. Her research is supported by grants from the National Institutes of Health and the National Science Foundation. Giovanni Destro-Bisol: Sarah, a significant part of your research work focuses on the genetics of human populations living south of the Sahara desert. Therefore, you can probably explain, better than anyone else, why sub-Saharan Africa is such an important and attractive area for researchers studying human molecular evolution. [End Page 637] Click for larger view View full resolution Figure 1. Sarah Tishkoff is the David and Lyn Silfen Univerity Associate Professor in Genetics and Biology at the University of Pennsylvania. Photo courtesy of Sadie Robinson. Sarah Tishkoff: Africa is an important region to study for genetic variation for a number of reasons. First is that Africa is thought to be the homeland of all modern humans. If we want to learn more about human origins (e.g., when and where did modern humans evolve and how did they adapt to shifting environments?) then we need to study diversity in Africa. Secondly, Africa is the recent homeland of millions of people whose ancestors were brought to the Americas and elsewhere as slaves. Knowledge of genetic diversity across ethnically diverse Africans will be important for reconstructing ancestry in individuals of recent African descent. Thirdly, study of genetic, phenotypic, and environmental variation in Africa will be important for identifying the genetic and environmental factors that play a role in both normal phenotypic variation as well as in diseases common in Africa and in people of recent African descent (e.g., infectious diseases such as malaria, TB, and HIV and other diseases such as hypertension and prostate cancer). Additionally, little is currently known about genetic variation at genes that play a role in drug response across ethnically diverse Africans. Such knowledge will be important for the development of more effective treatments in these populations. Lastly, because of high levels of genetic, cultural, and climatic diversity in Africa there has likely been local adaptation within populations from different regions practicing diverse lifestyles. Therefore, the possibility of geographically restricted rare, as well as common, functional variants requires the inclusion of a broad range of geographically and ethnically diverse African populations in human genetic studies. [End Page 638] GD-B: There have been a number of studies of DNA polymorphisms published in the literature which offer contrasting hypotheses regarding the geographic origin of anatomically modern humans. For example, your Science 2009 paper provides compelling evidence that modern human migration originated in southwestern Africa (Tishkoff et al. 2010). However, a recent...

A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipaënsis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance- and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions and the synthetic amphidiploid grouped separately from most minicore accessions except for COC155, and were eliminated from most subsequent analyses. UPGMA analysis divided the population into four subgroups, two major subgroups representing subspecies fastigiata and hypogaea, a third group containing individuals from each subspecies or possibly of mixed ancestry, and a fourth group, either consisting of COC155 alone if wild species were excluded, or of COC155, the diploid species, and the synthetic amphidiploid. Model-based clustering identified four subgroups- one each for fastigiata and hypogaea subspecies, a third consisting of individuals of both subspecies or of mixed ancestry predominantly from Africa or Asia, and a fourth group, consisting of individuals predominantly of var fastigiata, peruviana, and aequatoriana accessions from South America, including COC155. Analysis of molecular variance (AMOVA) revealed statistically-significant (P<0.0001) genetic variance of 16.87% among subgroups. A total of 4.85% of SSR marker pairs revealed significant LD (at r(2)≥0.1). Of the syntenic marker pairs separated by distances<10cM, 11-20cM, 21-50cM, and>50cM, 19.33, 5.19, 6.25 and 5.29% of marker pairs were found in strong LD (P≤0.01), in accord with LD extending to great distances in self pollinated crops. A threshold value of r(2)>0.035 was found to distinguish mean r(2) values of linkage distance groups statistically from the mean r(2) values of unlinked markers; LD was found to extend to 10cM over the entire minicore collection by this criterion. However, there were large differences in r(2) values among marker pairs even among tightly-linked markers. The implications of these findings with regard to the possibility of using association mapping for detection of genome-wide SSR marker-phenotype association are discussed.

Dissecting Genetic Structure in Farmer Selections of Theobroma Cacao in the Peruvian Amazon: Implications for on Farm Conservation and Rehabilitation

Knowledge of genetic diversity in farmers’ selections is essential for planning on-farm conservation and rehabilitation. Using 15 microsatellite loci, we analyzed parentage and population structure in 220 farmer selections of cacao from the Huallaga valley in Peruvian Amazon. A high level of allele richness and heterozygosity were detected in these selections. Coordination analysis showed that these farmer selections are mainly comprised of hybrids derived from Trinitario and Upper Amazon Forastero germplasm. Bayesian clustering analysis assigned 54 selections as Trinitario and 166 as Upper Amazon Forastero hybrids. Parentage analysis identified 15 international clones as probable parents for 96 farmer selections, which corresponded to a fraction of the known hybrid families disseminated in this region in the late 1980s. Combined analysis of demographic and molecular data revealed a significant spatial autocorrelation (r = 0.235; P = 0.006) at short geographical distances (<5.0 km). This patch-like distribution of spatial heterogeneity suggests a significant “neighborhood effects” in seeds distribution or variety adoption, where closely related hybrid progenies were adopted in the neighboring farms or villages. The outcomes of this study indicate that in spite of the introgressions of exotic germplasm in the past, Upper Amazon Forastero is still the dominant component in the Huallaga valley of Peru. The high level of on-farm diversity can offer needed variability for participatory selection of superior clones in this low input, small-scale production system, where adaptability to specific environment is more preferred than in a high input, large scale production system.

Genetic variation within and among five natural populations of endangered Sclerocarya birrea (A. Rich) subsp. Birrea in Sudan

Knowledge of genetic diversity is important for successful conservation and domestication of species. In order to determine genetic diversity within and among Sclerocarya birrea (A. Rich.) Htochst. subsp. birrea populations in Sudan, random amplified polymorphic DNA (RAPD) markers were used. Leaf materials from 75 seedlings from five populations (Rashad, Alfaid, Alkhwi, Aldamazin and Baw) of this species were used to compare the genetic diversity. A total of 37 bands were generated using four primers. Genetic variation within the populations as estimated by Shannon information index ranged from 0.343 to 0.272 with an overall diversity of 0.306. Analysis of molecular variance revealed that 46% of the variation was attributed to differences among the populations and 54% within the populations (P < 0.001). The gene flow among population was small (Nm = 0.297). UPGMA cluster and principal coordinate analyses (PCA) indicated Alfaid as the most distinct population. Since genetic variation was found to occur among and within the populations of S. birrea (A. Rich.) Hochst. Subsp. birrea, conservation of these populations would help in the maintenance of the species. Key words : Sclerocarya birrea subsp. birrea, genetic variation, conservation, random amplified polymorphic DNA (RAPD), Sudan.

Diversidade genética em acessos do banco de germoplasma de camu-camu (Myrciaria dúbia [H.B.K.] McVaugh) do INPA usando marcadores microssatélites (EST-SSR).

O conhecimento da diversidade genética das espécies amazônicas é de grande importância para a domesticação e melhoramento das culturas. Uma das grandes dificuldades em espécies não domesticadas como o camu-camu é a falta de informação sobre a sua variabilidade genética. Devido ao potencial econômico do camu-camu por sua alta produção de vitamina C, foi realizado o presente trabalho, o qual tem como objetivo estimar a variabilidade genética de 139 acessos de camu-camu oriundos de 17 populações de diferentes rios da Amazônia brasileira, conservados no banco de germoplasma (BAG) de camu-camu do Instituto Nacional de Pesquisa da Amazônia INPA na cidade de Manaus, utilizando marcadores EST-SSR. Oito loci de EST-SSR detectaram um total de 102 alelos com uma média de 12,87 alelos por loco. Os resultados mostram altos níveis de diversidade para todos os locicom uma média de heterozigosidade esperada (He) de 0,797 e heterozigosidade total (Ht) de 0,502. As populações apresentaram altos valores de endogamia, o que sugere déficit de heterozigotos como observado pelos baixos valores de Heterozigosidade observada (H0), provavelmente devido ao isolamento das populações e as distâncias entre elas, o que limita o fluxo gênico favorecendo a endogamia. O valor de diferenciação genética (FST) foi alto 0,21 indicando uma alta variabilidade entre as populações. As medidas baseadas nas freqüências alélicas, amostraram uma maior variabilidade dentro das populações (80,3%) que entre as populações (19,7%). Através das distâncias genéticas entre as populações foi encontrada uma grande variação entre os acessos provenientes de populações de Rondônia (Jarú) e os provenientes de Amazonas (Pirarucu e Tarumã) e Roraima (Urubu). No ordenamento pelo método UPGMA, observou-se a formação de dois grupos principais e cinco sub-grupos os quais estão relacionados geograficamente. Os resultados revelaram a utilidade dos marcadores EST-SSR nos estudos de diversidade genética entre acessos do camu-camu. Estes resultados serão úteis no planejamento de novas coletas e conservação do BAG, no analise de variabilidade de populações, assim como no direcionamento de cruzamentos através da escolha de genótipos geneticamente divergentes, o que contribuirá às atividades de melhoramento de camu-camu nos paises amazônicos.

Geographic Description of Genetic Diversity and Relationships in the USDA Rice World Collection

Knowledge of genetic diversity and relationships among global germplasms of rice collected by the USDA since 1866 is critical for utilization, conservation, and management of the collection. A core subset developed from this collection, including 1794 accessions obtained from 112 countries in 14 geographic regions, was genotyped with one indel and 71 simple sequence repeat (SSR) markers. Total alleles were 1005, averaging 14 alleles per locus. A great majority of genetic variance was due to within instead of among geographic regions and within instead of among countries. The regions and countries were highly and significantly differentiated using these markers. Germplasm accessions obtained from the southern Asia, Southeast Asia, and Africa were highly diversified, while those from North America and western and eastern Europe had the lowest diversity. Different measurements of genetic diversity, including average number of alleles per locus, polymorphism information content (PIC), Nei index, and average number of private alleles per locus uniformly reached this conclusion. Three main clusters were revealed by both analyses of principal coordinates and Nei genetic similarities for the 14 regions. Seventy‐eight countries, from which five or more accessions were collected in the core subset, were differentiated into five main clusters. Germplasm accessions obtained from Myanmar, Indonesia, Cambodia, Malaysia, and Nepal were highly diversified, while those from France, Spain, Romania, Italy, and the United States were poorly diversified. This study proves that the USDA global collection effectively supports the U.S. rice industry with vast genetic diversity responsive to biotic and abiotic stresses.

Genetic diversity and population structure of Ascochyta rabiei from the western Iranian Ilam and Kermanshah provinces using MAT and SSR markers

Knowledge of genetic diversity in A. rabiei provides different levels of information that are important in the management of crop germplasm resources. Gene flow on a regional level indicates a significant potential risk for the regional spread of novel alleles that might contribute to fungicide resistance or the breakdown of resistance genes. Simple sequence repeat (SSR) and mating type (MAT) markers were used to determine the genetic structure, and estimate genetic diversity and the prevalence of mating types in 103 Ascochyta rabiei isolates from seven counties in the Ilam and Kermanshah provinces of western Iran (Ilam, Aseman abad, Holaylan, Chardavol, Dareh shahr, Gilangharb, and Sarpul). A set of 3 microsatellite primer pairs revealed a total of 75 alleles; the number of alleles varied from 15 to 34 for each marker. A high level of genetic variability was observed among A. rabiei isolates in the region. Genetic diversity was high (He = 0.788) within populations with corresponding high average gene flow and low genetic distances between populations. The smallest genetic distance was observed between isolates from Ilam and Chardavol. Both mating types were present in all populations, with the majority of the isolates belonging to Mat1-1 (64%), but within populations the proportions of each mating type were not significantly different from 50%. Results from this study will be useful in breeding for Ascochyta blight-resistant cultivars and developing necessary control measures.

The relic Criollo cacao in Belize – genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank, Trinidad

Cacao (Theobroma cacaoL.) was domesticated in Mesoamerica and is native to the South American rainforest. Belizean Criollo is a group of relic landraces that are thought to be similar to those used by the Olmecs and Mayans during early domestication. Knowledge of genetic diversity is essential for efficient conservation and use of these relic landraces. Using 30 microsatellite markers, we characterized genetic diversity in 77 Belize Criollo accessions collected from the Maya Mountains in Belize, and assessed their relationship with 62 cacao accessions including 25 Trinitario accessions. Genetic diversity and heterozygosity were low in Belizean Criollo germplasm. Eleven distinctive genotypes were identified among the Belizean germplasm. Results of ordination and cluster analysis supported their putative ancestral contribution to the Trinitario cacao. However, results of Bayesian assignment and parentage analysis both suggested that the contribution of Criollo cacao to the Imperial College Selections Trinitario is small. Our preferred hypothesis for the genesis of Trinitario cacao is that a limited population of Criollo × Forastero hybrids emanated from the introduced Forastero population of Trinidad. The present study provides new insights into the origin of the Trinitario cacao, which will be useful in theex situandin situconservation of cacao landraces from Mesoamerica.