Microsatellite Marker Loci Research Articles

Exploring the endangerment mechanisms of Hipposideros pomona based on molecular phylogeographic methods.

The endangerment mechanisms of various species are a focus of studies on biodiversity and conservation biology. Hipposideros pomona is an endangered species, but the reasons behind its endangerment remain unclear. We investigated the endangerment mechanisms of H. pomona using mitochondrial DNA, nuclear DNA, and microsatellite loci markers. The results showed that the nucleotide diversity of mitochondria DNA and heterozygosity of microsatellite markers were high (π = 0.04615, H O = 0.7115), whereas the nucleotide diversity of the nuclear genes was low (THY: π = 0.00508, SORBS2: π = 0.00677, ACOX2: π = 0.00462, COPS7A: π = 0.00679). The phylogenetic tree and median-joining network based on mitochondrial DNA sequences clustered the species into three clades, namely North Vietnam-Fujian, Myanmar-West Yunnan, and Laos-Hainan clades. However, joint analysis of nuclear genes did not exhibit clustering. Analysis of molecular variance revealed a strong population genetic structure; IMa2 analysis did not reveal significant gene flow between all groups (p > .05), and isolation-by-distance analysis revealed a significant positive correlation between genetic and geographic distances (p < .05). The mismatch distribution analysis, neutral test, and Bayesian skyline plots revealed that the H. pomona population were relatively stable and exhibited a contraction trend. The results implied that H. pomona exhibits female philopatry and male-biased dispersal. The Hengduan Mountains could have acted as a geographical barrier for gene flow between the North Vietnam-Fujian clade and the Myanmar-West Yunnan clade, whereas the Qiongzhou Strait may have limited interaction between the Hainan populations and other clades. The warm climate during the second interglacial Quaternary period (c. 0.33 Mya) could have been responsible for species differentiation, whereas the cold climate during the late Quaternary last glacial maximum (c. 10 ka BP) might have caused the overall contraction of species. The lack of significant gene flow in nuclear microsatellite loci markers among the different populations investigated reflects recent habitat fragmentation due to anthropogenic activities; thus, on-site conservation of the species and restoration of gene flow corridors among populations need immediate implementation.

Temporal changes in genetic diversity reveal small-scale invasion dynamics of the eastern redcedar (Juniperus virginiana var. virginiana) in the Lakeside Daisy State Nature Preserve in Ohio

AbstractEastern redcedar (Juniperus virginiana L. var. virginiana; hereafter ERC) is a native species currently invading open areas and grasslands outside of its original range in the United States. We studied ERC’s invasion patterns in the Lakeside Daisy State Nature Preserve (LDSNP), a short grass prairie located on the Marblehead Peninsula in Ohio, examining the changes in the genetic diversity and structure of the encroaching population. We investigated the relative importance of long-distance dispersal versus diffusion in the invasion of this short grass prairie by ERC. We use eight microsatellite marker loci to infer gene flow from external sources versus within-population recruitment. We found that the older trees in this preserve were less than 50 yr old, indicating that the population was established between 1970 and 1980. When we grouped trees into five age categories of 10-yr increments, we found that the allelic diversity, as indicated by the average number of alleles per locus, increased as the age of the trees decreased. We also found that not all loci were in Hardy-Weinberg equilibrium, probably due to the arrival of new variants in the preserve. Moreover, heterozygosity remained high, with an excess of heterozygotes in all age groups (F = −0.163 ± 0.046). Principal coordinate analysis showed two distinct groups of trees in the LDSNP. Analysis of the cryptic population structure of the ERC trees using STRUCTURE revealed four ancestral clusters in the ERC population. All ancestral clusters are present in all age groups, suggesting that all trees sampled are derived from an admixed population. Furthermore, the high observed heterozygosity and lack of inbreeding in this dioecious species maintained all ancestral clusters over time. Overall, our findings indicate that ERC encroachment of the LDSNP results from multiple and reiterated gene flow events from the edge of the range through animal-mediated seed dispersal.

Assessment of Mutation Drift Equilibrium and the Occurrence of a Recent Genetic Bottleneck in South Indian Zebu Cattle.

Simple SummaryThis study was conducted on eight Indian zebu breeds with an objective to reveal any cryptic genetic bottlenecks in the population. The alarming reduction in the effective population size of these breeds was the major reason for conducting this study. Genotyping of 27 FAO/ISAG-recommended microsatellite markers and further statistical analysis using allele frequency data under three different models of mutation revealed the absence of recent genetic bottlenecks in any of the populations under study. The results from the qualitative test of mode shift distortion were in accordance with the above findings. Even though the results of the present study indicated little or no critical loss of rare alleles in any of the breeds understudy, the chances of this happening cannot be completely ignored. One of the plausible explanations for this scenario could be the potential gene flow from commercial taurine cattle through indiscriminate crossbreeding in the native tract of these breeds. Thus, we here emphasize the need of further initiatives for improving selective breeding practices in order to conserve and effectively utilize the existing South Indian zebu cattle genetic diversity.During the last few decades, the effective population size of indigenous zebu cattle breeds has declined drastically, resulting in the classification of some of them into the vulnerable, endangered, or critically endangered category. Drastic reductions in the effective size of a population may result in genetic bottlenecks and can affect within-breed genetic variability and its viability. The present study was undertaken with the objective of evaluating South Indian zebu cattle populations for mutation drift equilibrium and to detect the occurrence of recent genetic bottleneck events. A total of 293 cattle from eight indigenous breeds were genotyped at 27 FAO/ISAG-recommended microsatellite marker loci. Three different statistical tests, viz., the sign test, standardized differences test, and Wilcoxon sign rank test were performed using allele frequency data to detect loci with heterozygosity excess under the infinite alleles, stepwise, and two-phase mutation models. Under the infinite alleles model, the observed number of loci with heterozygosity excess (He > Heq) ranged between 10 and 19 among the investigated cattle breeds. However, the observed heterozygosity excess was not statistically significant (p > 0.05) in any of the studied breeds. Similarly, the standardized differences test and Wilcoxon sign rank test revealed no concrete evidence for the occurrence of a recent genetic bottleneck in South Indian zebu cattle breeds. The qualitative test for mode-shift distortion revealed a normal L-shaped distribution of allele frequencies, suggesting a lack of evidence for the loss of low-frequency alleles in all the investigated South Indian zebu cattle breeds.

Is neutral genetic diversity related to quantitative variation in semen traits in bulls?

Conservation decisions based on neutral genetic diversity have been observed to promote retention of useful quantitative variation in biological populations. An experiment was undertaken to determine the association between microsatellite marker polymorphisms and phenotypic variation in semen production and cryosurvival traits in bulls. Thirty-five ejaculates were collected from ten bulls of two breeds and evaluated before and after cryopreservation for several semen traits. The bulls were also genotyped using a set of sixteen bovine-specific microsatellite marker loci. Fixation indices (FST ), heterozygosity and Nei's genetic distance measures were computed from allele frequency data for each of the bulls. Molecular and phenotypic data were used to compute tri-distance matrices for the ten bulls and correlated using Mantel's test in GenAIEx 6.5. The study revealed extensive heterogeneity in semen traits, heterozygosity and FST values among the bulls. Large pairwise phenotypic and genetic distances were also observed. Correlation between pairwise genetic distances and phenotypic distances was significant and highly positive for sperm viability (r=.61, p<.001) and moderately positive for sperm motility (r=.40-42, p<.05) variables. For sperm morphology, ejaculate volume and sperm concentration, correlation with genetic distances was positive, low and not significantly different from zero (p>.05). A tendency for a triangular-shaped relationship between genetic and phenotypic distances for post-thaw motility and viability traits was also observed. Accordingly, association with neutral genetic diversity was absent for semen production traits and moderate to highly positive for sperm cryosurvival traits. Given these findings, conservation decisions based on neutral genetic diversity may capture variation in some adaptive traits, but not others.

Parâmetros genéticos e teste de paternidade em progênies de Euterpe oleracea produto da hibridação espontânea com Euterpe edulis em clima subtropical

O objetivo deste estudo foi avaliar o sistema de fecundação e a distribuição da variabilidade molecular entre e dentro de três grupos de progênies de polinização aberta de Euterpe oleracea, além de realizar um teste depaternidade para identificação dos genitores masculinos e promover a certificação genética das plântulasbífolioladas. Para tal, foram utilizados seis loci microssatélites em 306 amostras. Os grupos de progênies sãoresultado de um sistema misto de fecundação, com ausência de cruzamentos entre aparentados, sendoalógamos (tm e ts = 1,0), com correlação de autofecundação (rt) igual a 0,110. Foram constatados diferentesgraus de parentescos (rp), entre 15,5 a 26,1% de irmãos completos. A paternidade foi atribuída para 51% e 24% das amostras, com 80 e 95% de confiança respectivamente. Foram identificados 22 doadores de pólen e uma autofecundação, verificou-se que o morfotipo bífoliolado não é garantia de cruzamento intraespecifico, já que quatro progênies foram identificadas como híbridos interespecíficos. Foram detectados em média 7 a 12,3 alelos por locus e uma heterozigosidade média observada entre 0,382 a 0,898 e a esperada entre 0,354 a 0,693. O índice de fixação foi entre -0,053 a -0,319. A variação entre os grupos foi de 5%, sendo 95% dentro deles. Os resultados indicam boas perspectivas para realização de trabalhos futuros relacionados à predição de ganhos genéticos a partir da seleção entre e dentro dos grupos de progênies.

Genetic diversity of Plasmodium knowlesi among human and long-tailed macaque populations in Peninsular Malaysia: The utility of microsatellite markers

It has been discovered that Plasmodium knowlesi (P. knowlesi) is transmitted from macaque to man. Thus, the aim of the present study was to determine P. knowlesi genetic diversity in both human (n = 147) and long-tailed macaque (n = 26) samples from high- and low-endemicity localities. Genotyping was performed using seven neutral microsatellite loci markers. The size of the alleles, multiplicity of infection (MOI), mean number of alleles (Na), expected heterozygosity (HE), linkage disequilibrium (LD), and genetic differentiation (FST) were determined. In highly endemic P. knowlesi localities, the MOI for human and long-tailed macaque isolates was 1.04 and 1.15, respectively, while the Na was 11.14 and 7.86, respectively. Based on the allele frequency distribution for all loci, and with FST < 0.1, no genetic differentiation was seen between human and long-tailed macaque. In localities characterised by lower P. knowlesi endemicity, the MOI for human and long-tailed macaque isolates was 1.05 and 1.11, respectively, while the Na was 6.14 and 2.71, respectively. Further molecular analysis of the allele frequencies indicated that there was a significant genetic differentiation in human P. knowlesi isolates as compared to long-tailed macaque isolates, with a very low fixation index (FST = 0.016, p < .05) based on multiple loci analysis. Our results further indicate that, in Peninsular Malaysia, humans are mostly affected by P. knowlesi of a single genotype, while long-tailed macaque tend to acquire polyclonal infections, which supports the assumption that there is a higher rate of transmission among long-tailed macaque. Understanding the genetic diversity of P. knowlesi isolates can provide invaluable information for characterising patterns of the population structure and the migration rate of P. knowlesi in peninsular Malaysia.

High genetic diversity and differentiation of theBabesia ovispopulation in Turkey

Babesia ovis is a tick-transmitted protozoan haemoparasite causing ovine babesiosis in sheep and goats leading to considerable economic loss in Turkey and neighbouring countries. There are no vaccines available, therapeutic drugs leave toxic residues in meat and milk, and tick vector control entails environmental risks. A panel of eight mini- and micro-satellite marker loci was developed and applied to study genetic diversity and substructuring of B.ovis from western, central and eastern Turkey. A high genetic diversity (He =0.799) was found for the sample of overall B.ovis population (n=107) analyzed. Principle component analysis (PCoA) revealed the existence of three parasite subpopulations: (a) a small subpopulation of isolates from Aydin, western Turkey; (b) a second cluster predominantly generated by isolates from western Turkey; and (c) a third cluster predominantly formed by isolates from central and eastern Turkey. Two B.ovis isolates from Israel included in the analysis clustered with isolates from central and eastern Turkey. This finding strongly suggests substructuring of a major Turkish population into western versus central-eastern subpopulations, while the additional smaller B.ovis population found in Aydin could have been introduced, more recently, to Turkey. STRUCTURE analysis suggests a limited exchange of parasite strains between the western and the central-eastern regions and vice versa, possibly due to limited trading of sheep. Importantly, evidence for recombinant genotypes was obtained in regionally interchanged parasite isolates. Important climatic differences between the western and the central/eastern region, with average yearly temperatures of 21°C versus 15°C, correspond with the identified geographical substructuring. We hypothesize that the different climatic conditions may result in variation in the activity of subpopulations of Rhipicephalus spp. tick vectors, which, in turn, could selectively maintain and transmit different parasite populations. These findings may have important implications for vaccine development and the spread of drug resistance.

De novo Development and Characterization of Tetranucleotide Microsatellite Loci Markers from a Southeastern Population of the House Finch (Haemorhous mexicanus)

De novo Development and Characterization of Tetranucleotide Microsatellite Loci Markers from a Southeastern Population of the House Finch (Haemorhous mexicanus)

Past hybridisation and introgression erased traces of mitochondrial lineages evolution in the Neotropical silver catfish Rhamdia quelen (Siluriformes: Heptapteridae)

The Neotropical species complex Rhamdia quelen is composed of at least six mitochondrial lineages. Three of these occur in sympatry in several regional basins, which encompass La Plata basin, Patos-Merin basin system and the coastal lagoons draining to SW Atlantic Ocean. Based on both mitochondrial cytochrome b gene and 10 nuclear microsatellite loci markers, this study aims to investigate the genetic diversity pattern and the reproductive isolation among R. quelen mitochondrial lineages. Past hybridisation and introgression were evidenced among at least two mitochondrial lineages. The ancestral structure recovered in this study was divided into two groups, which could have diverged in the last marine regression. The recent population structure of R. quelen species complex is mostly recovered following the geographic distribution pattern. We delimited seven management units, three inhabiting riverine environments and four associated to different coastal lagoons. Lagoon populations, unlike the riverine ones, would have diverged in a scenario with null or restricted gene flow and small size population, possibly related to bottleneck events. Population genetic structure should be considered for conservation legislation, fishery management and aquaculture regulation. Additionally, the present genetic structure could aggravate the impact of specimen translocation and escapees from aquaculture farms.

Isolation and characterization of microsatellite marker loci in the Wagner’s mustached bat Pteronotus psilotis (Chiroptera: Mormoopidae) and cross-amplification in other related species

Pteronotus psilotis, a mormoopid bat, is an insectivorous, gregarious and strict cave-dwelling species that is found areas between the sea level and an elevation of about 1000 masl. This species is present in diverse habitats ranging from rain forest to dry deciduous forest. Nine microsatellite loci were developed for Wagner's mustached bat, Pteronotus psilotis using the next-generation sequencing approach, and their utility for population genetics studies was assessed. All loci were polymorphic (7-15 alleles) and characterized in 30 individuals from three P. psilotis populations, with the levels of observed and expected heterozygosity ranging from 0.280 to 0.867 and 0.584 to 0.842, respectively. One locus showed significant departures from Hardy-Weinberg expectations after Bonferroni correction. Cross-amplification in 11 other bat species was tested, for which eight microsatellites were successfully amplified, and of these seven were polymorphic. The development of these new microsatellite loci will contribute to investigations of genetic population structure, genetic diversity and gene flow in P. psilotis populations, as well as in other closely related bat species.

Genetic variability of Akhal-Teke horses bred in Italy.

BackgroundThe Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences.MethodsSeventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences.ResultsNucleic markers showed a high degree of polymorphism (Ho = 0.642; He = 0.649) and a low inbreeding level (FIS = 0.016) in Italian horses, compared to other AKH populations (ranged from −0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy.

Polymorphism analysis of microsatellite marker loci of Plasmodium falciparum from different geographical origins

To compare the genetic diversity of imported Plasmodium falciparum by Polyα and TAA87 microsatellite markers in Southeast Asian and African geographical isolates. Ninety-two and 126 filter paper samples from patients infected with P. falciparum from Southeast Asia (Myanmar) and Africa (Ghana) were collected, respectively. Two neutral microsatellite loci, Polyα and TAA87 were amplified by PCR. The length of PCR fragments was detected by capillary electrophoresis. The allele frequency and expected heterozygosity (He) were calculated by Excel 2010 and GenALEx 6.0 software. A total of 146 P. falciparum samples were analyzed as single infection samples with a total of 26 alleles in locus Polyα and 12 alleles in locus TAA87. The mean He value of the two loci was 0.86 ± 0.02. Ten alleles in locus Polyα and 8 alleles in locus TAA87 were distributed in Myanmar isolates, with the He values of 0.86 and 0.81 respectively. Fifteen alleles in locus Polyα and 11 in locus TAA87 were detected in Ghana isolates, with the He values of 0.91 and 0.86 respectively. In addition, the haplotype of 174 bp (Polyα) and 113 bp (TAA87) were only detected in Myanmar isolates with more than 17% gene frequency, whereas they were absent in Ghana isolates. The two different geographical sources of imported P. falciparum strains have different allele frequencies and haplotypes at the two neutral microsatellite markers, Polyα and TAA87. Therefore, these two microsatellite loci may be considered as the potential molecular marker candidates for identifying P. falciparum strains with different geographical sources.

Microsatellite and SNAP markers used for evaluating pollen dispersal on Pati tall coconuts and Xenia effect on the production of ‘Kopyor’ fruits

Kopyor coconut is one of the many unique coconut types existed in Indonesia. To overcome the problem of low kopyor fruit yield, it is necessary to study xenia effect on the fruit yield of this coconut. The combination of kopyor coconut and normal coconut population selected at infarmers’ coconut plantations consisted of 33 normal coconut trees, and 9 kopyor coconut trees. All adult trees surrounding the 9 kopyor heterozygous (Kk) palms were evaluated as potential male candidate parents (pollen donors). All samples genotypes were determined using four SNAP markers and six microsatellite marker loci, parentage analysis using CERVUS software version 2.0. Results of the analysis indicate that xenia effect reduced kopyor fruit yields. Kopyor heterozygous (Kk) female parents produced low number of kopyor fruits when they were surrounded by many normal homozygous (KK) pollen donors. Out of 99 harvested progeny arrays from the kopyor heterozygous (Kk) female parents, none exhibited kopyor phenotype. The results also indicate that the pollen dispersal from normal homozygous (KK) donor palms range from 0 m (self pollination) to 54 m (outcrossing). The occurence of outcrossing frequency was at least 95% and the selfing frequency is 5%.

Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea

The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.

Extensive gene flow of white-backed planthopper in the Greater Mekong Subregion as revealed by microsatellite markers

The white-backed planthopper (WBPH), Sogatella furcifera (Horváth), is a destructive pest of rice in the Greater Mekong Subregion (GMS) countries including Cambodia, Laos, Myanmar, Thailand, Vietnam, and China’s Yunnan Province. Our previous study not only confirmed the immigration sources of the WBPH in China’s Yunnan Province were from Myanmar, Vietnam, and Laos, but also indicated that Cambodia was likely an additional migration source. To further clarify the migration sources and patterns of the WBPH in the GMS, we investigated the genetic structure of 42 WBPH populations using microsatellite loci markers. The analysis of genetic diversity, heterozygosity deficit, and heterozygosity excess based on the nuclear markers suggest that there is extensive gene flow between the 42 sampled populations from the GMS. The genetic structure confirmed the immigration sources of WBPH as revealed by mitochondrial markers and trajectory analyses methods in previous studies. These findings will aid in the sustainable regional management of this insect pest in the GMS.

Colonization history of the western corn rootworm (Diabrotica virgifera virgifera) in North America: insights from random forest ABC using microsatellite data

First described from western Kansas, USA, the western corn rootworm, Diabrotica virgifera virgifera, is one of the worst pests of maize. The species is generally thought to be of Mexican origin and to have incidentally followed the expansion of maize cultivation into North America thousands of years ago. However, this hypothesis has never been investigated formally. In this study, the genetic variability of samples collected throughout North America was analysed at 13 microsatellite marker loci to explore precisely the population genetic structure and colonization history of D. v. virgifera. In particular, we used up-to-date approximate Bayesian computation methods based on random forest algorithms to test a Mexican versus a central-USA origin of the species, and to compare various possible timings of colonization. This analysis provided strong evidence that the origin of D. v. virgifera was southern (Mexico, or even further south). Surprisingly, we also found that the expansion of the species north of its origin was recent—probably not before 1100 years ago—thus indicating it was not directly associated with the early history of maize expansion out of Mexico, a far more ancient event.

Identification and characterization of microsatellite loci in the tuliptree, Liriodendron tulipifera (Magnoliaceae).

Premise of the study:Twenty-three polymorphic microsatellite loci (simple sequence repeats) were identified and characterized for Liriodendron tulipifera (Magnoliaceae), a species native to eastern North America, to investigate its genetic diversity, population structure, and mating system.Methods and Results:Using Illumina HiSeq paired-end reads from genomic DNA, searches for repeat motifs identified approximately 280,000 potentially amplifiable loci. Of 77 loci tested, 51 amplified consistently. When genotyped using 30 to 52 total adult trees from three old-growth populations in Maryland, Virginia, and New Jersey, USA, 23 loci were polymorphic. These loci exhibited four to 13 alleles, and observed and expected heterozygosities ranged from 0.233 to 0.865 and 0.272 to 0.876, respectively.Conclusions:The microsatellite marker loci presented here will be valuable in population genetic studies of L. tulipifera because they do not suffer from ascertainment bias and show high polymorphism.

Inheritance and Linkage Mapping of Eastern Filbert Blight Disease Resistance in ‘Uebov’ Hazelnut

Eastern filbert blight (EFB) is a serious fungal disease of european hazelnut (Corylus avellana) in North America. The causal agent is the pyrenomycete Anisogramma anomala, which is native in the eastern United States where it occasionally produces small cankers on the wild american hazelnut (C. americana). However, most commercial cultivars of european hazelnut are susceptible. Infection leads to perennial cankers, girdling of branches, and premature tree death. Cultural practices including scouting, pruning out infected branches, and fungicide applications are recommended to slow disease spread but are expensive and not completely effective. EFB resistance from ‘Gasaway’ is conferred by a dominant allele at a single locus and has been extensively used in the Oregon State University hazelnut breeding program, but there is concern that this resistance could be overcome by isolates now present in the eastern United States or that a new race of the pathogen could arise in Oregon. Segregation for EFB resistance from ‘Uebov’, a new source from Serbia, was studied in three progenies by a combination of structure exposure and greenhouse inoculation. The frequency of resistant seedlings following structure exposure was about 20% in all three progenies. The ratios failed to fit the expected 1:1 ratio but did fit a ratio of 1 resistant:3 susceptible, which would be expected if resistance were conferred by dominant alleles at two independent loci. Seedlings from a cross of susceptible selection OSU 741.105 and ‘Uebov’ were used to study correlation of disease response and presence of alleles at microsatellite marker loci. Resistance was highly correlated with the presence of alleles at marker loci on linkage group 6 (LG6), and these markers also showed segregation distortion. We conclude that EFB resistance from ‘Uebov’ maps to a single locus on LG6 in the same region as resistance from ‘Gasaway’, although only about 20% of the seedlings are resistant because of segregation distortion. ‘Uebov’ has large, well-filled, round nuts and is suitable as a parent in breeding for the in-shell market, but its low nut yields and a high frequency of shells with split sutures are the drawbacks. Its use would expand options for breeding and ‘Uebov’ resistance could be combined with other resistance alleles with an expectation of more durable EFB resistance. Durable resistance would not only sustain the hazelnut industry in Oregon but would also allow expansion of plantings to new areas.

Genetic diversity of American hazelnut in the Upper Midwest, USA

World hazelnut production is based on European hazelnut (Corylus avellana) and is limited by the narrow climatic requirements of this species. The cold hardiness and disease resistance of the American hazelnut (Corylus americana) offer opportunities to expand production to new areas including the Upper Midwest (USA). The American hazelnut is a phenotypically diverse species. This study used ten microsatellite marker loci to investigate genetic diversity in 1140 individuals sampled from 25 populations across Wisconsin, Iowa, Minnesota and North Dakota. Overall, the marker loci were highly polymorphic (Ho = 0.69, He = 0.78, PIC = 0.84) with 7–13 alleles per locus. There was very high genetic diversity within populations (90% of the total) and some tendency toward population differentiation. Mantel’s test showed that genetic distance among the populations was not correlated with geographic distance. We conclude that selection of individuals for use in breeding should be based primarily on phenotype (productivity, nut size, percent kernel, ease of harvest), with care to include representatives of genetically differentiated populations.

QTL mapping of domestication and diversifying selection related traits in round-fruited semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis)

QTL analysis revealed 11 QTL underlying flowering time and fruit size variation in the semi-wild Xishuangbanna cucumber, of which, FT6.2 and FS5.2 played the most important roles in determining photoperiod-dependent flowering time and round-fruit shape, respectively. Flowering time and fruit size are two important traits in domestication and diversifying selection in cucumber, but their genetic basis is not well understood. Here we reported QTL mapping results on flowering time and fruit size with F2 and F2:3 segregating populations derived from the cross between WI7200, a small fruited, early flowering primitive cultivated cucumber and WI7167, a round-fruited, later flowering semi-wild Xishuangbanna (XIS) cucumber. A linkage map with 267 microsatellite marker loci was developed with 138 F2 plants. Phenotypic data of male and female flowering time, fruit length and diameter and three other traits (mature fruit weight and number, and seedling hypocotyl length) were collected in multiple environments. Three flowering time QTL, FT1.1, FT5.1 and FT6.2 were identified, in which FT6.2 played the most important role in conferring less photoperiod sensitive early flowering during domestication whereas FT1.1 seemed more influential in regulating flowering time within the cultivated cucumber. Eight consensus fruit size QTL distributed in 7 chromosomes were detected, each of which contributed to both longitudinal and radial growth in cucumber fruit development. Among them, FS5.2 on chromosome 5 exhibited the largest effect on the determination of round fruit shape that was characteristic of the WI7167 XIS cucumber. Possible roles of these flowering time and fruit size QTL in domestication of cucumber and crop evolution of the semi-wild XIS cucumber, as well as the genetic basis of round fruit shape in cucumber are discussed.