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Copyright of Acta Agriculturae Slovenica is the property of Biotechnical Faculty of the University of Ljubljana and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Erzincan University Journal of Science & Technology is the property of Erzincan Binali Yildirim Universitesi and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The study evaluated reliable, easy and an efficient protocol for DNA extraction from young leaves of spine gourd which yielded highly pure with no visible discoloration concentrated genomic DNA ranged from 1202.68 to 3786.92 µg/500 mg of tissue with ratio (A260/A280) of absorbance ranging from 1.34 to 1.95. This method involved modification in original cetyl trimethyl ammonium bromide extraction without liquid nitrogen and by adding high level of β-mercaptoethanol, extracting twofold with chloroform: isoamyl alcohol (24: 1, v/v) and extending the centrifugation time which successfully removes polyphenols, chlorophyll pigments, polysaccharides and dyes. The DNA extracted by this method produced clearly scorable and reproducible definitive PCR fragments authentic exhibiting its compatibility and manifesting its affinity for SSR and ISSR markers. Therefore this method is recommended as an efficient protocol for genomic DNA extraction and microsatellite marker-based genetic analysis in spine gourd for high outp ut sample preparation for diverse PCR-based downstream applications. [ABSTRACT FROM AUTHOR]

Opium poppy (Papaver somniferum L.) is a versatile plant exploited by the pharmaceutical and food industries. Unfortunately, it is also infamously known as a source of highly addictive narcotics, primarily heroin. Drug abuse has devastating consequences for users and also has many direct or indirect negative impacts on human society as a whole. Therefore, developing a molecular genetic tool for the individualization of opium poppy, raw opium or heroin samples could help in the fight against the drug trade by retrieving more information about the source of narcotics and linking isolated criminal cases. Bioinformatic analysis provided insight into the distribution, density and other characteristics of roughly 150 thousand microsatellite loci within the poppy genome and indicated underrepresentation of microsatellites with the desired attributes. Despite this fact, 27 polymorphic STR markers, divided into three multiplexed assays, were developed in this work. Internal validation confirmed species-specific amplification, showed that the optimal amount of DNA is within the range of 0.625–1.25 ng per reaction, and indicate relatively well balanced assays according to the metrics used. Moreover, the stutter ratio (mean + 3 SD 2.28–15.59%) and allele-specific stutters were described. The analysis of 187 individual samples led to the identification of 158 alleles in total, with a mean of 5.85 alleles and a range of 3–14 alleles per locus. Most of the alleles (151) were sequenced by the Sanger method, which enabled us to propose standardized nomenclature and create three allelic ladders. The OpiumPlex system discriminates most of the varieties from each other and pharmaceutical varieties from the others (culinary, dual and ornamental). [ABSTRACT FROM AUTHOR]

Garcinia indica popularly known as 'Kokum' or Murugalu", is a medium sized evergreen tree found in western-ghats of India. This tree species is highly exploited to produce anti-obesity drugs and culinary purposes. Its population is threatened by over exploitation and loss of habitat. Development of microsatellite markers would help in understanding genetic structure and further to develop appropriate conservation strategies. In this study, using next generation sequencing platform Illumina Hiseq 2000, we have sequenced partial genome of G. indica and identified 3725 microsatellites. Forty-eight microsatellite markers were analyzed using 30 accessions. Polymorphism information content (PIC) values ranged from 0.718 to 0.968 with a mean value of 0.922. Allele per locus ranged from 3 to 33 per locus. Probability of identity values ranged from 0.00329 to 0.30489. Cross species amplification SSR primers in the related species, showed a moderate transferability from 12.5 % (for G. morella) to 18.7%(for G. gummigutta). [ABSTRACT FROM AUTHOR]

Microsatellite (SSR) markers have been accepted and employed as useful tools for measuring genetic diversity and divergence within and among populations. In this study, the utility of 15 SSR markers in discrimination of 33 Orobanche cumana (broomrape) populations from different geographical locations (Moldova, Romania, Bulgaria, Serbia, Turkey, China) was assessed. A total of 279 O. cumana plants were genotyped and 110 alleles identified. The level of genetic polymorphism of SSR markers was evaluated by calculating the effective number of alleles per locus (Ne), which demonstrated an average of 5.243, Polymorphic Information Content index (PIC: 0.745), Nei's genetic diversity (H: 0.782) and, Resolving power (Rp: 5.794). Most markers showed PIC values higher than 0.5, indicating a big genetic polymorphism in O. cumana populations. Based on the Rp index and PIC values, genetic diversity in the broomrape populations from Turkey (Rp: 4.774, PIC: 0.722) and Moldova (Rp: 4.394, PIC: 0.716) was higer than in other populations. However, the studied microsatellite markers system characterized very well the genetic structure of all O. cumana populations included in this study. Seven SSR markers (Ocum-052, Ocum-059, Ocum-074, Ocum-081, Ocum-087, Ocum-196, Ocum-197) were selected based on the statistical analysis as the most informative and efficient markers for measuring genetic diversity in O. cumana. [ABSTRACT FROM AUTHOR]

Expanding water shortage, environmental change and decline water table level are the major hindrance for lowland basmati rice variety development in northern parts of India including Haryana. Rice is the absolute most client of fresh irrigated water as it devours 70% of the complete water accessible. More rice is needed to generate to take care of the expanding populace. The promising way to deal with battle the water shortage can be aerobic rice. Aerobic rice is a budding cultivation system that requires no puddling, no transplanting and without need of frequent irrigation than conventional flooded rice. The worth of basmati rice breeding can significantly improve through marker assisted selection (MAS). In the present study, experiments were conducted to assess F2 generation obtained from IB370 × MAS-ARB25 for various agronomic qualities. Grain yield/plant indicated impressive positive relationship (r = 0.25) with root thickness in F2 population. Fifty eight polymorphic SSR markers dispersed on the entire genome of rice were utilized for planning DNA fingerprint data set of the isolating IB370 × MAS-ARB25 F2 population. Composite interval mapping analysis by WinQTL cartographer version 2.5 revealed a sum of 7 quantitative trait loci (QTLs) (three QTL for agronomic traits and four for root traits). The selected promising F2 plants were additionally checked for these putative QTLs recognized in the F2 populace, which were available in homozygous/heterozygous state in high frequencies. [ABSTRACT FROM AUTHOR]

Strawberry (Fragaria x ananassa Duch.) being an important commercial member of Rosaceae family, accounts for high nutritive value in terms of antioxidative and antibacterial properties. Owing to its unique therapeutic values, present study was done with the objective of characterizing 20 Fragaria x ananassa cultivars from Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, India based on their morphological descriptors and expressed sequence tags - simple sequence repeat (EST-SSR) markers of Rubus ellipticus L. (Smith). Broad phenotypic variability among the Fragaria x ananassa cultivars was detected using morphological descriptors. A set of 68 R. ellipticus EST-SSR primers were used for cross transferability analysis in strawberry cultivars for polymorphic marker identification and genetic diversity analysis. Out of 68 EST-SSRs, 51 (75%) showed amplification among the strawberry cultivars. The average (PIC) values of all the polymorphic loci for 20 strawberry cultivars were 0.34. Highest polymorphism information content (PIC) value (0.68) was obtained with contig 218, followed by contig 714 (0.65) and contig 408 (0.63), indicating that contig 218 has the most regions of diversity as amplified with these SSR and was found most suitable for cross transferability. The unweighted pair group method with arithmetic mean (UPGMA) was designed showing two separate groups for 20 cultivars of Fragaria x ananassa. The present study revealed that R. ellipticus microsatellites when used were able to distinguish strawberry cultivars accurately. [ABSTRACT FROM AUTHOR]

Copyright of Bioscience Journal is the property of Bioscience Journal and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Acta Agriculturae Slovenica is the property of Biotechnical Faculty of the University of Ljubljana and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Cactoblastis cactorum, a species of moth native to Argentina, feeds on several prickly pear cactus species (Opuntia) and has been successfully used as a biological control of invading Opuntia species in Australia, South Africa and native ruderal Opuntia species in some Caribbean islands. Since its introduction to the Caribbean its spread was uncontrolled, invading successfully Florida, Texas and Louisiana. Despite this long history of invasion, we are still far from understanding the factors determining the patterns of invasion of Cactoblastis in North America. Here, we explored three non-mutually exclusive explanations: a) a stepping stone model of colonization, b) long distance colonization due to hurricanes, and/or c) hitchhiking through previously reported commercial routes. Genetic diversity, genetic structure and the patterns of migration among populations were obtained by analyzing 10 nuclear microsatellite loci. Results revealed the presence of genetic structure among populations of C. cactorum in the invaded region and suggest that both marine commercial trade between the Caribbean islands and continental USA, as well as recurrent transport by hurricanes, explain the observed patterns of colonization. Provided that sanitary regulations avoiding human-mediated dispersal are enforced, hurricanes probably represent the most important agent of dispersal and future invasion to continental areas. [ABSTRACT FROM AUTHOR]

Genetic gains in forestry are often implemented by producing improved forest seeds in seed orchards. However, unwanted alien genotypes are often accidentally introduced into seed orchards, or genotypes are planted in incorrect locations, both of which can reduce genetic gains. Such errors can be detected using markers, mainly isoenzymatic proteins and microsatellite DNA. These markers differ in their sensitivity, meaning that they can yield different assessments of seed orchard genetic material even when plant material is identical. The main objective of this paper was to compare these two verification methods and their consequences for genetic improvement. Two uneven-aged Scots pine clonal seed orchards were analysed using sets of isoenzymatic and microsatellite loci identified in other studies. The statistical analysis allowed comparison of the actual architecture of seed orchards to the planned layout. The number of clones was also compared to the effective number of clones. The results of microsatellite DNA analysis indicate that misplaced ramets are present from 12.29% to 30.89% of the time. Errors had an impact on breeding efficiency by reducing the relative effective number of clones. Isoenzyme and microsatellite methods had different discriminatory powers, which affected the results of the study. This study indicates that seed orchards can contain large numbers of incorrectly identified individuals. Microsatellite DNA analysis is recommended over isoenzyme analysis for detecting such errors, as the former is a more sensitive analytical method. [ABSTRACT FROM AUTHOR]

Copyright of NaUKMA Research Papers. Biology & Ecology is the property of National University of Kyiv-Mohyla Academy, Faculty of Humanities and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background and aims – The evolutionary history of Amazonia’s hyperabundant tropical tree species, also known as “hyperdominant” species, remains poorly investigated. We assessed whether the hyperdominant Eschweilera coriacea (DC.) S.A.Mori (Lecythidaceae) represents a single genetically cohesive species, and how its genetic constitution relates to other species from the same clade with which it occurs sympatrically in French Guiana. Methods – We sampled 152 individuals in nine forest sites in French Guiana, representing 11 species of the genus Eschweilera all belonging to the Parvifolia clade, with emphasis on E. coriacea. Samples were genotyped at four simple sequence repeat (SSR) markers. We delimited gene pools, i.e., genetically coherent putative taxa, using STRUCTURE software and principal component analysis. We compared the genetic assignment of individuals with their morphological species determination and estimated genetic diversity and differentiation for gene pools and species. We also estimated genome size using flow cytometry. Key results – SSR profiles commonly displayed up to four alleles per genotype, suggesting that the investigated Eschweilera species bear a paleopolyploid signature. Flow cytometry suggested that the studied species are diploid with haploid genome sizes of 871–1046 Mbp. We detected five gene pools and observed a good correspondence between morphological and genetic delimitation for Eschweilera sagotiana Miers and the undescribed morphospecies E. sp. 3 (which resembles E. grandiflora (Aubl.) Sandwith), and to a lesser extent for E. decolorans Sandwith and E. micrantha (O.Berg) Miers. Eschweilera coriacea was the most genetically diverse species and included individuals assigned to each gene pool. Conclusions – We found no conclusive evidence for cryptic species within E. coriacea in French Guiana. SSRs detected fewer gene pools than expected based on morphology in the Parvifolia clade but discriminated evolutionary relationships better than available plastid markers. A positive trend between demographic abundance of species and allelic richness illustrates that hyperdominants may have a high evolutionary potential. This hypothesis can be tested using more powerful genomic data in combination with tree phenotypic trait variation and characterization of niche breadth, to enhance our understanding of the causes of hyperdominance in Amazonian trees. [ABSTRACT FROM AUTHOR]

Great progress has been made during the last decade in clarifying the molecular details of aroma accumulation in grape berries. However, the multigene complex controlling monoterpene accumulation in grape is not well understood. To shed light on this issue, the grapes of 149 F1 progenies from the cross 87-1 (Vitis vinifera L.) × 9-22 (Vitis vinifera L.) were characterized at the mature stage for three representative free monoterpenes during five growing seasons. A total of 202, 184 and 255 polymorphic SSR (simple sequence repeat) markers were contracted on the maternal 87-1, paternal 9-22 and consensus genetic maps, respectively. On the consensus map, we confirmed a major QTL (quantitative trait locus) for free linalool, nerol and a-terpineol content on linkage group (LG) 5, and a stable QTL for free linalool and a-terpineol was detected on LG 10. In addition, two new stable QTLs for free monoterpene (linalool, nerol and a-terpineol) contents were identified on LG 11 and LG 18 that explained up to 42.5 % of the total variance. Eleven promising candidate genes related to pentatricopeptide repeat (PPR)-containing proteins, seed maturation protein, RING finger protein, and AP2/ERF transcription factors might be potentially involved in monoterpene accumulation. The stable QTLs and candidate genes identified in this study provide new insights into free monoterpene accumulation in grape. [ABSTRACT FROM AUTHOR]

In mungbean yield reduction is mainly due to wide spread of powdery mildew disease, which is the most devastating in mungbean. It can be effectively controlled through incorporation of disease resistance genes into susceptible species through Marker Assisted Selection (MAS). In present study, 96 Recombinant Inbred Lines (RIL) derived from cross between Chinamung (highly susceptible topowdery mildew disease) and BL849 (highly resistant) lines were analyzed by PCR technique by using Simple Sequence Repeats (SSR) markers. Phenotypic data was collected by screening the 96 F8 RILs population according to the presence of infections by pathogen. Results revealed that 9 are moderately resistant, 60 are moderately susceptible, 24 are susceptible and 3 are highly susceptible. Parental polymorphism study with 248 SSR primers revealed that 14 showed polymorphic for parents. For Bulked Segregant Analysis (BSA) to identify Polymorphic DNA marker linked to a powdery mildew resistance DNA was pooled from selected segregants and genotyping was followed. The markers association was also studied by Single Marker Analysis (SMA) for 14 polymorphic markers. The SMA revealed that two markers DMBSSR130 and DMBSSR125 showed significant association with powdery mildew resistance with 79 per cent and 73 per cent to total variation, respectively. The DMBSSR130 was confirming the association in both the BSA and SMA but DMBSSR125 showed association in SMA not in BSA. [ABSTRACT FROM AUTHOR]

Crop genetic resources rich in Fe and Zn provide sustainable and cost-effective solution to alleviate micronutrient malnutrition. Maize being the leading staple crop assumes great significance as a target crop for biofortification. We report here wide genetic variation for kernel Fe and Zn among 20 diverse maize inbreds lines, majority of which were bred for quality protein maize (QPM) and provitamin-A. Kernel Fe ranged from 30.0 - 46.13 mg/kg, while kernel Zn ranged from 18.68-39.56 mg/kg. Moderate but positive correlation was observed between the micronutrients. Characterization using 25 Single sequence repeats (SSRs) linked to QTLs for kernel Fe produced 58 alleles. Similarly, 86 alleles were identified from 35 SSRs linked to QTLs for kernel Zn. One unique allele for kernel Fe and three unique alleles for kernel Zn were identified. The mean polymorphic information content (PIC) was 0.40 for both kernel Fe and Zn. Jaccard's dissimilarity coefficients varied from 0.25 - 0.91 with a mean of 0.58 for kernel-Fe while 0.27- 0.88 with a mean of 0.57 for kernel Zn. Principal coordinate analysis depicted diversity of inbreds. Cluster analysis grouped the inbreds into three major clusters for both kernel Fe and Zn. Potential cross combinations have been proposed to develop micronutrient rich hybrids and novel inbreds with higher Fe and Zn. The information generated here would help the maize biofortification programme to develop nutritionally enriched hybrids. [ABSTRACT FROM AUTHOR]

Aim: Distribution‐wide trends in climate variability significantly influence the genetic diversity, differentiation and population structure of tree species. This study investigates the effects of disturbances such as fire, fragmentation and climate on modern‐day genetic patterns and clonal structures of trembling aspen at the transcontinental scale. Location: North American boreal zone. Taxon: Trembling aspen (Populus tremuloides Michx.). Methods: One thousand two hundred individuals in a 30‐site network (40 trees per location) were genotyped with neutral genetic markers and studied in relation to regional differences in climate and surrounding site conditions (aridity, fire cycle, fragmentation). Multiple linear regression models and variance analysis were used to test relationships between genetic indices, structural parameters and the surrounding site factors. Results: Overall, a high percentage of single ramet clones (SRC) and clonal diversity was detected and assumed to be the consequence of multiple sexual reproduction events that took place at all sites, together with suckering, which shapes the clonal structure of populations. Neutral genetic diversity and clonal structure suggested no substantial differences among sites, which were categorized into climate moisture index (CMI) classes; aspen stands across Canada were highly similar from a genetic point of view. Allelic richness (AR) and the average number of alleles (Na) varied significantly among clonal organization groups, and landscape fragmentation and a higher frequency of fires showed a negative influence on the levels of genetic diversity. Main conclusions: Our results are inconsistent with the idea that the genotypic diversity of trembling aspen is related to the intensity of disturbance within the boreal forest. It appears that species‐specific disturbance responses and post‐fire recruitment mechanisms are more important than dominant ecological factors, such as climate and fire regimes, in shaping distribution‐wide patterns of neutral genetic variation and clonal structure. [ABSTRACT FROM AUTHOR]

In this study fourteen microsatellite primer pairs were used to study the genetic diversity of Shishi Date palm in Qatar. A total of 32 date palm (15 Shishi cultivar, 10 Khalas and seven male date palms) were collected from Qatar and 5 Shihi cultivars were collected from Saudi Arabia for comparison. The Shishi set collected from Qatar was selected from different regions to represent the genetic diversity of this cultivar. The results indicated 98 alleles produced from the 14 microsatellite markers, and the cluster analysis showed four major clusters corresponding o the geographical areas. Similarly, the structure analysis indicated four populations according to statistic K value. PCoA analysis showed three groups (A, B and C) separating Shishi (from Qatar) in group A, Khalas in group B and Shishi (from Saudi Arabia) in group C and no clear group separated the male genotypes. This indicates that the sexual propagation by seeds is the main source of variation in the date palm. This is the first study focusing on Shishi cultivar in Qatar and Saudi Arabia by using molecular markers. [ABSTRACT FROM AUTHOR]

Aim: Historical and geological events can impact the genetic structure of species, producing signatures that vary among taxa and among gene pools within taxa. Such signatures can also be affected by local geography and tolerance to environmental conditions. However, disentangling the different drivers of population structure is often difficult. In an attempt to do so, we surveyed two independent gene pools of the same species that followed similar paths of post‐glacial colonization across contrasting landscapes and environmental conditions. We aimed to determine how these differences have affected the post‐glacial population dynamics of each gene pool. Location: The Pacific and Atlantic coasts of Mexico. Taxon: Black mangrove (Avicennia germinans; Avicenniaceae). Methods: Using microsatellite variation, we estimated the divergence time of black mangrove populations through approximated Bayesian computation and implemented a comparative approach to evaluate different demographic hypotheses within and between coasts. Results: The Pacific and Atlantic gene pools diverged long after the rise of the Central American Isthmus (Mid‐Pleistocene), although occasional transisthmian gene exchanges were also inferred. Both coasts showed the characteristic isolation by distance (IBD) pattern expected for expanding gene pools. However, populations from the Atlantic coast were more genetically diverse and admixed than those from the Pacific basin. Both our migration models and the climate data gathered suggested a more ancient establishment and/or more stable conditions for black mangrove on the Atlantic coast. Main conclusions: The Atlantic basin likely bore more favourable climate conditions than the Pacific, allowing for the survival of A. germinans during the Last Glacial Maximum in situ. Populations from the northern Pacific coast became established after the Holocene warming, leading to contrasting genetic patterns between the two gene pools. Nevertheless, the action of environmental factors in determining the contemporary distribution of genetic variation in A. germinans cannot be discarded. [ABSTRACT FROM AUTHOR]

Premise of research. Plant aggregation and pollen origin can profoundly influence pollination success, as measured by fruit initiation and development. The effect of these variables should be more significant in plants with highly specialized pollination systems, as the pool of potential pollinators is assumed to be smaller than in plants with generalized pollination systems, although this possibility has seldom been investigated. Methodology. During two consecutive seasons, we used field observations and hand-pollination experiments in the nursery-pollinated palm Chamaerops humilis to evaluate the effects of pollen origin and the level of plant aggregation on fruit initiation (pollination success) and fruit development. Through nuclear microsatellite markers, we also examined the occurrence of C. humilis spatial genetic structure (SGS) within and between the two populations and its potential effect on pollination success. Pivotal results. Our hand-pollination experiments showed no effect of pollen origin on pollination success and fruit development, which was consistent with the detected lack of C. humilis genetic spatial structure within and between populations. Pollen addition slightly increased fruit initiation, independent of pollen origin. We found differences in fruit initiation/development at the population level. Conclusions. Our results demonstrate that populations in our study were not pollen-quality limited and that plant aggregation did not affect fruit initiation and development. Within our populations, the low fruit initiation was not correlated with the quality of pollen received by the inflorescences and may instead depend on resource allocation to the developing ovaries and competition between siblings. Density-dependent processes influence pollination success, presumably through plants' competition for resources. Long-distance pollen dispersal could compensate for low population density and limit genetic drift, thus maintaining high genetic diversity within populations. [ABSTRACT FROM AUTHOR]

Copyright of Agronomía Colombiana is the property of Universidad Nacional de Colombia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

To quantify the population‐level genetic characteristics of Pedicularis kansuensis, polymorphic microsatellite loci (simple sequence repeats) were identified and characterized. Methods and Results: Using Illumina HiSeq paired‐end reads from genomic DNA, searches for repeat motifs identified 1594 sequences by four softwares simultaneously. We developed and characterized 18 polymorphic microsatellite primers for P. kansuensis using 45 individuals that were collected from three P. kansuensis populations. The number of alleles varied from two to 12. The observed heterozygosity and expected heterozygosity per locus ranged from 0.182 to 0.933 and 0.227 to 0.904 in the pooled population, respectively. All of the primers that were developed were also successfully applied in Pedicularis cheilanthifolia and Pedicularis violascens. These markers should be useful in probing the genetic diversity, genetic structure of P. kansuensis, which could provide information about assessment and prediction of potential risks of this species in its distribution areas. [ABSTRACT FROM AUTHOR]

Premise of the Study: Climate cycles of the Quaternary have impacted plants at a global scale, leaving behind a complex genetic legacy. Species of the northern Rocky Mountains of North America were exposed to more uniform glacial patterns than the central and southern ranges, where synergistic relationships between temperature and precipitation caused differences in the timing and extent of glacier onset. We examined the genetic impacts of climate oscillations on Calochortus gunnisonii (Liliaceae) in the central and southern Rocky Mountains. Methods: Populations were sampled from disjunct mountain ranges across the basins of Wyoming and northern and central Colorado. Allelic data from nuclear microsatellites and plastid sequences (trnV‐ndhC, petA‐psbJ, and rpl16) were used to examine patterns of genetic structure between and among populations along the southern Rocky Mountain corridor. Key Results: We infer considerable population structure concordant with mountain range of origin. Clustering analysis supports separate north and south genetic clusters on either side of major basins in Wyoming, suggesting that populations were maintained in two distinct refugia. Additionally, populations within the Sierra Madre Range of southern Wyoming show localized, divergent genetic signal indicative of a third potential glacial refugium. By contrast, recent genetic admixture is observed in the Laramie, Medicine Bow, and Front ranges, where population expansion from glacial refugia has likely occurred. Conclusions: We conclude that during climate cycles of the Quaternary, C. gunnisonii experienced periods of population expansion and reduction, habitat fragmentation, isolation in three or more refugia, and admixture mirroring genetic impacts of other southern Rocky Mountains organisms. [ABSTRACT FROM AUTHOR]

Premise of the Study: Knowledge about the introduction history (source(s), number and size of introduction events) of an invasive species is a crucial prerequisite to understand invasion success and to facilitate effective and sustainable management approaches, especially for effective biological control. We investigated the introduction history of the Australian legume tree Acacia dealbata in South Africa. Results of this study will not only provide critical information for the management of this species in South Africa, but will also broaden our overall knowledge on the invasion ecology of this globally important invasive tree. Methods: We used nuclear microsatellite markers to compare the genetic diversity and structure between 42 native Australian and 18 invasive South African populations and to test different and competing introduction scenarios using Approximate Bayesian Computation analyses. Key Results: Australian populations were characterized by two distinct genetic clusters, while South African populations lacked any clear genetic structure and showed significantly lower levels of genetic diversity compared to native range populations. South African populations were also genetically divergent from native populations and the most likely introduction scenario indicated an unknown source population. Conclusions: Although we cannot definitely prove the cause of the observed genetic novelty/diversification in South African Acacia dealbata populations, it cannot be attributable to insufficient sampling of native populations. Our study highlights the complexity of unravelling the introduction histories of commercially important alien species. [ABSTRACT FROM AUTHOR]

The disease known as pitch canker results from infection of Pinus species by the fungus Fusarium circinatum. This fungus also causes a serious root disease of Pinus seedlings and cuttings in forestry nurseries. Pinus radiata and P. patula are especially susceptible to the pathogen, but there are no records of pitch canker on P. patula in established plantations. To date, only planting material of this tree species in nurseries or in plantations at the time of establishment have been infected by F. circinatum. Symptoms of pitch canker have recently emerged in an established P. patula plantation in South Africa and this study sought to determine whether the symptoms were caused by F. circinatum. Isolates from cankers were identified as F. circinatum using morphology and DNA-based diagnostic markers. Microsatellite markers were then used to determine the genetic diversity of a collection of 52 isolates. The entire population included 17 genotypes representing 30 alleles, with a greater number of genotypes collected from younger (three- to six-year-old) than older (12- to 19-year-old) trees. Both mating types of F. circinatum were present, but no evidence of sexual recombination was inferred from population genetic analyses. This is the first record globally of pitch canker on P. patula trees in managed plantations. It is of significant concern to South Africa, where P. patula is the most important Pinus species utilised for plantation forestry. [ABSTRACT FROM AUTHOR]

Thousands of species have been introduced to new ranges worldwide. These introductions provide opportunities for researchers to study evolutionary changes in form and function in response to new environmental conditions. However, almost all previous studies of morphological change in introduced species have compared introduced populations to populations from across the species' native range, so variation within native ranges probably confounds estimates of evolutionary change. In this study, we used microsatellites to locate the source population for the beach daisy Arctotheca populifolia that had been introduced to eastern Australia. We then compared four introduced populations from Australia with their original South African source population in a common-environment experiment. Despite being separated for less than 100 years, source and introduced populations of A. populifolia display substantial heritable morphological differences. Contrary to the evolution of increased competitive ability hypothesis, introduced plants were shorter than source plants, and introduced and source plants did not differ in total biomass. Contrary to predictions based on higher rainfall in the introduced range, introduced plants had smaller, thicker leaves than source plants. Finally, while source plants develop lobed adult leaves, introduced plants retain their spathulate juvenile leaf shape into adulthood. These changes indicate that rapid evolution in introduced species happens, but not always in the direction predicted by theory. [ABSTRACT FROM AUTHOR]

The article offers information on the Hall's Beauty, a new, early-ripening, high-quality, firm, and sweet thornless trailing blackberry. Topics discussed include introduced as a machine harvestable, high-quality blackberry that has extremely large, attractive, and ornamental double flowers; mentions in 2009 Hall's Beauty' was planted along with a number of other genotypes in plots at Enfield Farms; and also mentions parentage of ‘Hall's Beauty' was confirmed by microsatellite analysis.

In this study, evolution of the genetic structure of the oldest known population of Dothistroma septosporum in Poland was analysed. Dothistroma needle blight was first recorded in Poland in 1990 in a 5‐year‐old plantation, meaning the population is relatively young in terms of evolution and genetic development. The preservation of DNA extracts from other studies allowed examination of the genetic variation of the pathogen over the span of a decade with the use of highly sensitive microsatellite markers. A number of evolutionary factors were identified that have shaped the genetic structure of this population over time. First, indications of the founder effect and the impact of selection were observed. Secondly, structure analysis provided evidence of the introduction of a new genetic component to the population structure after the pathogen had established. Finally, the impact of the reproductive mode on various components of the Domiarki population was examined, revealing the presence of genetic groups and structure clusters with varying levels of sexual recombination. These results demonstrate how well established and genetically robust a new population of a pathogen may become in just a few decades, given favourable conditions, and how new introductions may facilitate this process. [ABSTRACT FROM AUTHOR]

Mating strategies contributing to a balance between inbreeding and outcrossing are understudied in all but a few model fungal pathogens. This study examined factors that influence the occurrence of the sexual state of Pyrenophora semeniperda. It was consistently found to have functional copies of the MAT1‐1 and MAT1‐2 idiomorphs essential for sexual reproduction, despite considerable polymorphism in both single nucleotide polymorphisms (SNPs) and number of 18‐base minisatellite repeats. The two idiomorphs occurred at approximately equal frequencies across 25 populations on Bromus tectorum seeds in the western United States, suggesting maintenance of sexual reproduction. The putative mating system is described as facultative pseudohomothallism, with only one of the two MAT1 idiomorphs found in a nucleus. Unikaryotic strains of opposite mating type can potentially mate, as can nuclei of opposite mating type in a thallus that results from anastomosis between vegetatively compatible unikaryotic strains. Strains shown to be dikaryotic using simple sequence repeat (SSR) markers may contain either or both MAT1 idiomorphs. Most populations consist of a mixture of MAT1‐1,MAT1‐2 and MAT1‐1/MAT1‐2 genotypes. A possible constraint on recombination is the presence of multiple strain groups characterized by ITS haplotype. These are apparently vegetatively incompatible, as even dikaryotic strains are invariably composed of a single ITS haplotype. Different ITS haplotypes also have unique combinations of MAT1‐1 and MAT1‐2 allelic variants, suggesting that perhaps these strain groups are also sexually incompatible. Phylogenetic analysis using both genome‐wide SNP/indel polymorphisms and SSR markers demonstrated genetic divergence among ITS haplotypes, supporting the hypothesis that these strain groups may represent cryptic species. [ABSTRACT FROM AUTHOR]

Highlights • In present study a set of 361 potentially informative EST-SSR markers have been developed in sugarcane and used to assess genetic diversity and cross-species transferability. • These EST-SSRs exhibited enormous potential and may be useful for genetic improvement and molecular breeding of sugarcane. • Developed SSRs enriches the existing limited DNA marker repertoires which facilitate understanding of the structure and function of the sugarcane complex genome, along with cross-transferability study in other related species of Saccharum complex genera. Abstract Sugarcane expressed sequence tags (ESTs) database (db) offers a great opportunity for developing functional molecular markers associated with the desirable agronomic traits. The aim of the present study was to develop informative simple sequence repeat (SSR) markers in sugarcane using sugarcane expressed sequence tags (ESTs), characterization with respect to their abundance, distribution, variability, and to test their competence in genetic diversity. A total of 361 EST-SSR markers were developed and screened for their ability to detect polymorphism across the wide range of sugarcane germplasm. Among the developed SSRs, TNRs containing motifs were predominant with a frequency of 55%, which followed by TtNRs (22%), PNRs (11%), DNRs (7%), and HNRs (5%). Gene Ontology and homology search was conducted to establish the relevancy of SSRs in functional genomics. Resulting, ∼39% SSRs were found to be functional and confirmed homology with different proteins and transcription factors involved in gene expression. A set of 96 polymorphic primer pairs was used to evaluate genetic diversity among Saccharum species, related genera and cross amplification in other cereal grasses. A total of 710 alleles were generated which ranged from 2 to 15 with an average of 7.40 alleles per locus and showed 100% polymorphism. Polymorphism information content (PIC) value was ranged from 0.35 to 0.91 with an average of 0.71. Majority of the markers developed in current study were related to sucrose metabolism, stress physiology, plant immune responses, signal transduction, biosynthesis of secondary metabolites, ATP generation, growth and other biochemical process. The high degree of polymorphism, cross-species amplification and genetic diversity assessed with these SSR markers suggested their utility for genome mapping, QTL analysis, comparative genomics, gene-based association studies, and marker-assisted selection in sugarcane. Moreover, these informative EST-SSRs described here would enrich existing repertoire of genetic resources for sugarcane and also other related taxa constitute the important secondary genepool for sugarcane genetic improvement. [ABSTRACT FROM AUTHOR]

Licorice (Glycyrrhiza glabra) is an important medicinal herb and has long been used in traditional medicine for the treatment of several diseases worldwide. Understanding the genetic diversity within Glycyrrhiza species is important for the efficient conservation of these medicinal herbs. In this study, we have developed 20 polymorphic chloroplast microsatellite (cpSSR) markers using the chloroplast genome of G. lepidota. The cpSSR markers were tested on a total of 27 Glycyrrhiza individual plants. The number of alleles per locus ranged from two to eight among the Glycyrrhiza accessions. Overall, the Shannon index (I) for each cpSSR ranged from 0.315 to 1.694, the diversity indices (h) were 0.140–0.793 and the unbiased diversity indices (uh) were 0.145–0.825. In addition, the cpSSR markers were successfully divided and classified the 27 Glycyrrhiza individuals into four groups. The cpSSR markers developed in this study could be used in the assessment of genetic diversity and rapid identification of Glycyrrhiza species. [ABSTRACT FROM AUTHOR]

The Australian wheat stem rust (Puccinia graminis f. sp. tritici) population was shaped by the introduction of four exotic incursions into the country. It was previously hypothesized that at least two of these (races 326- 1,2,3,5,6 and 194-1,2,3,5,6 first detected in 1969) had an African origin and moved across the Indian Ocean to Australia on high-altitude winds. We provide strong supportive evidence for this hypothesis by combining genetic analyses and complex atmospheric dispersion modeling. Genetic analysis of 29 Australian and South African P. graminis f. sp. tritici races using microsatellite markers confirmed the close genetic relationship between the South African and Australian populations, thereby confirming previously described phenotypic similarities. Lagrangian particle dispersion model simulations using finely resolved meteorological data showed that long distance dispersal events between southern Africa and Australia are indeed possible, albeit rare. Simulated urediniospore transmission events were most frequent from central South Africa (viable spore transmission on approximately 7% of all simulated release days) compared with other potential source regions in southern Africa. The study acts as a warning of possible future P. graminis f. sp. tritici dispersal events from southern Africa to Australia, which could include members of the Ug99 race group, emphasizing the need for continued surveillance on both continents. [ABSTRACT FROM AUTHOR]

Natural hybridisation has significant ecological, genetic and evolutionary consequences altering morphological and chemical characters of individuals. Quercus glabrescens, Q. rugosa and Q. obtusata are white oak species well separated by their morphological characters when they occur in allopatry in Mexican temperate forests. However, in sympatry, individuals with atypical morphology have been observed, suggesting hybridisation events.In this study, we determined, with microsatellites and secondary metabolites, if interspecific gene flow occurs when these three oak species coexist in sympatry. In total, 180 individuals belonging to seven populations [three allopatric (one for each parental species) and four sympatric sites] were analysed.Allopatric populations represent well‐defined genetic groups and the sympatric populations showed genetic evidence of hybridisation between Q. glabrescens × Q. rugosa and Q. glabrescens × Q. obtusata. The hybridisation percentage varied between sites and combination of involved species. We registered the presence of unique flavonoid compounds for Q. glabrescens (caffeic acid and flavonol 2), Q. rugosa (flavonol 5) and Q. obtusata (flavonol 1). Three compounds (quercetin rhamnoside, flavonol 3 and alkyl coumarate) were expressed in all taxa. Finally, the hybrid genotypes identified in this study (Q. glabrescens × Q. rugosa and Q. glabrescens × Q. obtusata) showed specific chemical profiles, resulting from a combination of those of their parental species.These results show that hybridisation events between these oak species alter chemical expression of secondary metabolites, creating a mosaic of resources and conditions that provide the substrate for different combinations of foliar‐associated species such as herbivores, endophytic fungi or epiphyte plants. [ABSTRACT FROM AUTHOR]

This study presents the results of the first genetic analysis of ancient chestnut trees (Castanea sativa Mill.) in Italy and in the Iberian Peninsula to better understand the effect of grafting on the domestication process of chestnut and to investigate the impacts of early selection and improvement on the genetic diversity retained. We evaluated 105 giant ancient trees from Italy, Spain and Portugal and compared them with the European Union (EU) database of chestnut cultivars by using a set of 24 simple sequence repeats (SSRs; microsatellite markers). We measured the perimeter (girth) at the diameter at breast height (DBH). Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self‐rooted and which were grafted. Diversity was compared using standard metrics and model‐based approaches based on the expected heterozygosity (He) at equilibrium. We could differentiate 91 new genotypes; 9.6% matched known chestnut cultivars. We found the first evidences of cultivation, that is, grafting to produce "instant domestication" in Galicia and in the Douro Valley in trees of 14‐m perimeter (15th century) and in the Basque Country (first report in that area) in a tree of 11.5‐m perimeter (16th century). In Italy, the cultivar "Marrone Fiorentino" was found in some giant trees with perimeters of 8 and 9 m (17th‐18th centuries) in the Toscana and Umbria. Those findings matched with written references in Portugal from the 16th century and from the 18th century in Spain. "Instant domestication" could be dated back to the 15th century and was related to the wild populations existing in the same areas where cultivars are being propagated, without a different genetic structure for wild chestnut trees and with a high diversity maintained through the initiation of domestication. This study presents the results of the first genetic analysis of ancient chestnut trees (Castanea sativa Mill.) in Italy and on the Iberian Peninsula. We could differentiate 91 new genotypes; 9.6% matched known chestnut cultivars. We found the first evidences of cultivation, "Instant domestication" could be dated back to the XVth century and was related to the wild populations existing in the same areas where cultivars are being propagated, without a different genetic structure for wild chestnut trees and with a high diversity maintained through the initiation of domestication. Distribution of 214 European chestnut genotypes showing structure (K = 2). In red, Italian (I) and French (F) genotypes; in green, genotypes from the Iberian Peninsula; in black, admixed genotypes. Numbers are the perimeters of the giant chestnut trees in metres. [ABSTRACT FROM AUTHOR]

Protein content is one of the main nutrition quality traits used to measure nutrition value in rice (Oryza sativa L.) Therefore, improving the protein content is a main target for nutrition quality breeding in rice. Previous studies have mainly focused on the total protein content in brown and polished rice using bi-parental segregating populations. Few researchers have focused on four different protein component traits (glutelin, prolamin, albumin, and globulin) in rice, and little is known regarding association analysis in natural populations. In this study, 329 japonica accessions (Oryza sativa L. subsp. japonica Kato) were collected from worldwide geographic distributions and genotyped using 154 microsatellite markers to detect the association between four protein component traits and relative markers in the tested panel. The Coomassie Brilliant Blue G-250 method was used to measure the phenotype of four protein components. A total of 845 amplified alleles were detected with allele number ranging from 2 to 9. The whole population was divided into three subgroups via software STRUCTURE 2.3.4. The scatterplot showed that the LD (linkage disequilibrium) decay distance was about 30 cM in the whole tested population. A total of 15 simple sequence repeats (SSR) markers were identified by using both the general linear model (GLM) and mixed linear model (MLM). These associated marker loci can provide a higher variety of choices in improving the nutrition quality of rice. In addition, the carrier materials with excellent alleles identified in this study can be used as parental genotypes in rice molecular breeding in the future. [ABSTRACT FROM AUTHOR]

Abstract The ability of mangrove trees to reproduce and disperse in highly dynamic tidal environments is reflected in the contemporary genetic diversity and structure of their populations. Resilience and establishment may occur through either local recruitment (propagule pool model) or over longer distances with mixed origins (migrant pool model), thereby affecting the connectivity between natural populations. Anthropogenic activities such as encroachment and fragmentation or from mitigating reforestation could cause strategy switches and thus the connectivity and genetic structure of populations. In this study, we considered Avicennia officinalis , a dominant component of the Sundarban mangrove forest in Bangladesh to estimate dispersal dynamics over various distances within estuaries. A total of 423 individuals of A. officinalis, distributed over thirteen sites in the Sundarbans were sampled at both large and fine-scaled spatial level, the latter for comparison of natural and dense with fragmented sites. Up to 62 alleles showed a comparable level of allele diversity and gene diversities at both juvenile and adult life stages, assuming overall high levels of outcrossing. Significant inbreeding levels and high kinship values were solely observed at a reforested A. officinalis site. Genetic variables revealed high levels of connectivity between sites at close vicinity, with only a weak structure over larger geographic distances, between natural core Sundarban and coastal edge populations. Kinship coefficients were mostly low though significant up to several kilometers along estuarine branches, thereby suggesting propagule dispersal beyond each site. A fine-scaled analysis of kinship levels estimated for fragmented and natural forest plots along both sides of a river revealed that fragmentation induced higher kinship levels over 25–50 m distance, whereas dense natural populations were composed of less related individuals at shortest distances. A. officinalis populations might stay resilient through a mixture of unrelated propagules, clearly adhering a migrant pool model in natural sites and propagule pool model in fragmented sites. A poor gene diversity of planted trees might jeopardize the sustainability of mangrove plantation practices. Furthermore, high levels of diversity and connectivity indicated that the core Sundarban populations are a relevant source of germplasm in afforestation programmes. Graphical abstract Image 1 [ABSTRACT FROM AUTHOR]

The article discusses the development and cross-amplification of microsatellites for Aquilaria sinensis, an endangered agarwood-producing tree. Topics mentioned include the importance of microsatellite markers for the provenience identification and genetic resource management of the tree, use of restriction site-associated DNA sequencing method to obtain the whole genome DNA sequences of the tree, and calculation of genetic diversity parameters and allelic richness.

In the southern Andes mountains (27-39∘S) Azorella madreporica and Laretia acaulis, two Apiaceae cushion plant species commonly known as yaretas, conform a well-established altitudinal vegetation belt along the lower Andean zone. These species have been considered as fundamental components of several ecological dynamics within their communities; however, high-mountain ecosystems are increasingly threatened worldwide by natural and anthropogenic pressures and the southern Andes are not the exception. Recognizing that genetic information is crucial for the success of any conservation or restoration initiative in wild populations, we developed and cross-amplified 28 specifically designed microsatellite markers (14 in A. madreporica and 14 in L. acaulis), and also tested the cross amplification of 25 markers from the related species Azorella selago. In a region which is particularly vulnerable to global change trends, this new polymorphic microsatellite loci will be useful in the study of the genetic diversity of these high-mountain cushion plants, which are pivotal in the structuring of their native ecosystems. [ABSTRACT FROM AUTHOR]

The veined rapa whelk (Rapana venosa) is an economically important gastropod in China, but is considered as an invasive species globally. Only a few studies have examined the R. venosa genome, a genomewide survey is necessary for improving our understanding of the genome structure and size of this organism. Microsatellite markers are powerful tools for characterizing germplasms, genetic diversity and kinship among individuals. The resultant data are applicable to breeding efforts in commercial aquaculture or for understanding invasion mechanisms. Here, we investigated the genome structure of R. venosa on an Illumina Hi-seq platform with ∼92× sequencing depth. We performed a K-mer analysis to estimate genome size, repeat sequences and heterozygosity. Clean reads were de novo assembled for the identification of simple-sequence repeat (SSR) loci that are suitable as markers. The estimated genome size of R. venosa was 2200.07 Mb, with a 1.41% heterozygosity rate and 67.04% repeats. We detected 5,477,450 simple-sequence repeats (SSRs), with 3,400,602 loci present as pure tandem repeats and 2,076,848 as compound motifs. We further selected and characterized 28 polymorphic markers in 78 individuals from Dandong, Laizhou, Weihai and Zhoushan in China. The range of alleles was 2-28 and the observed heterozygosity was 0.2857-0.8676. The data obtained from our genomic survey will aid the design of R. venosa whole-genome sequencing projects and advance the identification of SSR markers. Both these developments are valuable for further studies on ecological, evolutionary and genetic breeding in R. venosa. [ABSTRACT FROM AUTHOR]

Pinus massoniana is one of the important afforestation and pioneer tree species, which is widely distribute in southern China. Chloroplast simple sequence repeat markers (cpSSRs) have been widely used in studies of tree genetics, phylogenetic and breeding. We sequenced the whole chloroplast genome sequences of P. massoniana using PCR and Sanger sequencing. A total of 71 cpSSRs were identified, among which mononucleotide repeats were predominant (70.42%). Seventeen primer pairs were developed and amplification tests were conducted with 15 P. massoniana individuals. Also, cross-species amplification tests were conducted among 15 individuals per Pinus species, including P. elliottii, P. bungeana, P. armandii, P. caribaea, P. tabulaeformis, P. taiwanensis and P. yunnanensis which revealed polymorphic information content ranging from 0.2 to 0.8 and average of haploid diversity (h) ranging from 0.29 to 0.63. In addition, the polymorphic cpSSRs were useful in distinguishing the sampled pine species, and could be powerful tool in phylogenetic studies. [ABSTRACT FROM AUTHOR]

The article discusses the development and validation of primer pairs for the mulberry-specific simple sequence repeat (SSR) markers in cultivar identification and DUS testing. Topics mentioned include the characterization of a set of diverse mulberry germplasm, use of a set of diverse mulberry accessions for screening the primers, and estimation of allele sizes of the microsatellite markers.

The article explores the identification of novel microsatellite markers in Abelmoschus esculentus L. (Malvaceae), populary known as okra, by next-generation sequencing. Topics mentioned include the partial sequence of genomic DNA using Roche 454 Titanium pyrosequencing technology, the olymorphic information content and heterozygosity of alleles per locus, and assessment of genetic variation in the species.

European hazelnut (Corylus avellana) is a diploid tree species and is widely used in confections. Hazelnuts are, to a large part, produced in Turkey with the cultivar "Tombul" widely grown in the Black Sea region. In this work, the "Tombul" genome was partially sequenced by next-generation sequencing technology yielding 29.2% (111.85 Mb) of the ~ 385 Mb (1C). This sequence information was used to develop genetic markers in order to enable differentiation of material before the long maturation process and to facilitate future breeding strategies. A total of 90,142 simple sequence repeats (SSRs) were identified in the contigs giving a frequency of 1 SSR per 1240 nt in the assembly. Mononucleotides were the most abundant SSR marker type (60.9%) followed by di- and trinucleotides. Primer pairs were designed for 75,139 (83.3%) of the SSRs. Fifty SSR primers were applied to 47 hazelnut accessions from nine countries to test their effectiveness and polymorphism. The markers amplified an average of 3.2 fragments. The highest polymorphism information content value was for cavSSR11062 (0.97) and the lowest (0.04) was for cavSSR13386. Two markers were monomorphic: cavSSR12855 and cavSSR13267. Single-copy SSR primers were also assessed for their ability to discriminate 19 Turkish cultivars, and it was found that seven primer pairs (Cav4217, Cav14875, Cav14418, Cav2704, Cav12862, Cav3909, Cav1361) were sufficient for this task. Thus, this study developed new SSR markers for use in hazelnut breeding and genetic studies and also provide a method to distinguish and identify true-type Turkish cultivars. [ABSTRACT FROM AUTHOR]

Salinity is a major abiotic stress that limits rice productivity worldwide. Due to involvement of multiple genes and multiple mechanisms in salinity tolerance, development of tolerant varieties has been challenging. The present study used 112 introgression lines (ILs) of a salt-tolerant donor 'Nona Bokra' in the genetic background of a US cultivar 'Cheniere' to elucidate the genetic basis of seedling stage salinity tolerance and develop salt-tolerant prebreeding lines for use in breeding program. The ILs were evaluated under salt stress and control conditions and were genotyped using 116 microsatellite markers. A total of 32 QTLs were identified for eight morpho-physiological traits whereas 18 QTLs were detected for salt tolerance indices. Comparison of the QTL results with an earlier study involving the same donor indicated that detection of few common QTLs could be due to genetic background effects. Both studies suggested shoot Na+/K+ homeostasis, Na+ exclusion, and compartmentation as possible salt tolerance mechanisms in 'Nona Bokra'. Candidate gene identification and gene ontology analysis revealed that the genes involved in ion transport, ion homeostasis, and signaling may have important role in improving salinity tolerance. In addition to their utility in isolation of salt-tolerant determinants, the prebreeding lines with enhanced salt tolerance will accelerate development of salt-tolerant varieties by accumulating favorable alleles through marker-assisted selection. [ABSTRACT FROM AUTHOR]

The Ruddy-breasted Crake (Porzana fusca) is an extremely poorly known species. Although it is not listed as globally endangered, in recent years, with the interference of climate change and human activities, its habitat is rapidly disappearing and its populations have been shrinking. There are two different life history traits for Ruddy-breasted Crake in China, i.e., non-migratory population in the south and migratory population in the north of China. In this study, mitochondrial control sequences and microsatellite datasets of 88 individuals sampled from 8 sites were applied to analyze their genetic diversity, genetic differentiation, and genetic structure. Our results indicated that low genetic diversity and genetic differentiation exit in most populations. The neutrality test suggested significantly negative Fu’s Fs value, which, in combination with detection of the mismatch distribution, indicated that population expansion occurred in the interglacier approximately 98,000 years ago, and the time of the most recent common ancestor (TMRCA) was estimated to about 202,705 years ago. Gene flow analysis implied that the gene flow was low, but gene exchange was frequent among adjacent populations. Both phylogenetic and STRUCTURE analyses implied weak genetic structure. In general, the genetic diversity, gene flow, and genetic structure of Ruddy-breasted Crake were low. [ABSTRACT FROM AUTHOR]

We developed novel and polymorphic microsatellite primers for Spathoglottis plicata , a tropical and subtropical terrestrial orchid, to investigate the genetic patterns and population structure among wild populations, and also to identify the varieties and hybrids of S. plicata in horticultural industry. The 12 novel microsatellites from S. plicata were developed by using polymerase chain reaction (PCR)-based isolation of microsatellite arrays. These markers that were successfully PCR amplified exhibited polymorphisms in S. plicata. The number of alleles, observed heterozygosity, expected heterozygosity and polymorphism information content values across loci ranged from 2.000 to 8.000, 0.000 to 0.756, 0.208 to 0.813 and 0.405 to 0.805 in total populations, respectively. The newly developed microsatellite markers exhibited variation in S. plicata. These markers can be used as a tool to further investigate the genetic diversity, conservation genetics and variety/hybrid identification of S. plicata. [ABSTRACT FROM AUTHOR]

Annona crassiflora (Annonaceae) is a protogynous beetle-pollinated savannah tree species, widely distributed in the savannahs of the Cerrado biome. Studies on the mating system and pollen dispersal of protogynous species are very scarce. Here, we used six microsatellite loci to assess the mating system and pollen dispersal of A. crassiflora in a savannah remnant in Central Brazil. We mapped and sampled leaves of 112 adult trees and collected 74 fruits from 20 mother trees (1-4 fruits per plant) to obtain the seeds used (460) for mating system and parentage analyses. Annona crassiflora has predominantly allogamous mating systems, with a high multilocus outcrossing rate (tm = 0.974, SE = 0.011) that did not differ among mother trees (F = 1.32, p = 0.165). However, tm-ts was variable among seed trees, indicating that some seeds were produced by mating among relatives. Our results also showed multiple paternity within fruits. Multilocus correlation of outcrossed paternity was high (rp = 0.302, SE = 0.045), indicating that for each mother tree, the probability that the same pollen donor sired two random sibs was 30.2%, and the mean number of pollen donors per mother tree was high (6.3). We detected a maximum pollen dispersal distance of 360.7 m and an average of 124.3 m (SD = 80 m), but most pollination events (73%) occurred at shorter distances (< 160 m), indicating short-distance pollen dispersal, most likely due to the pollinator behaviour. [ABSTRACT FROM AUTHOR]

Molecular markers are helpful to efficiently protect the plant breeders' rights. Fluorescent simple sequence repeats (SSR) based on DNA sequencing is a powerful and automated platform for the detection of genetic polymorphism. Here, we first reported 13 SSRs using a fluorescent SSR panel according to the reference genome information, and detected the genetic diversity and population structure of 136 pomegranate varieties. The average number of alleles per locus was 6.31, gene diversity ranged from 0.16 to 0.37 with an average of 0.28, and polymorphic information content (PIC) varied from 0.14 to 0.29 with a mean value of 0.22. The mean genetic distance (GD) between varieties was 0.32. Population structure analysis divided the varieties into three different subpopulations (Q1, Q2, and Q3). The cultivars in Q1 all came from China, and almost all cultivars came from foreign countries combined with Chinese were grouped into Q2. The only accession originated from Myanmar was grouped to Q3. The results indicated that 13 SSR markers were polymorphic. The varieties originating from the same geographical region were more closely related, and extensive gene flow had taken place between the varieties from different regions. The results may be useful for the efficient selection breeding and variety protection. [ABSTRACT FROM AUTHOR]

Background: Pod constriction is an important descriptive and agronomic trait of peanut. For the in-shell Virginia marketing-type, this trait has commercial importance as well, since deeply constricted pods have a tendency to break, which makes them unmarketable. Classical genetic studies have indicated that pod constriction in peanut is controlled by one to four genes, depending on the genetic background. In all of those studies, pod constriction was evaluated visually as opposed to quantitatively. Here, we examined the genetic nature of this trait in the Virginia-type background. Our study involved 195 recombinant inbred lines (F7RILs) derived from two closely related cultivars that differ in their degree of pod constriction. Pod constriction was evaluated visually and quantitatively in terms of the pod constriction index (PCI), calculated as the average ratio between the pod's waist and shoulders. Results: ANOVA and genetic parameters for PCI among the F7RILs in three blocks showed very significant genotypic effect (p(F) < 0.0001) and high heritability and genetic gain estimates (0.84 and 0.52, respectively). The mean PCI values of the different RILs had a bimodal distribution with an approximate 1:1 ratio between the two curves. Pod constriction was also determined visually (VPC) by grading the degree of each RIL as 'deep' or 'slight'. The X2 test was found to not be significantly different from a 1:1 ratio (p = 0.79) as well. SNP-array-based technology was used to map this trait in the RIL population. A major locus for the pod constriction trait was found on chromosome B7, between B07_120,287,958 and B07_120,699,791, and the best-linked SNP explained 32% of the total variation within that region. Some discrepancy was found between the SNPs original location and the genetic mapping of the trait. Conclusion: The trait distribution and mapping, together with data from F1 and F2 generations indicate that in this background the pod constriction is controlled by a major recessive gene. The identity of loci controlling the pod constriction trait will allow breeders to apply marker-assisted breeding approaches to shift allelic frequencies towards a slighter pod constriction and will facilitate future effort for map-based gene cloning. [ABSTRACT FROM AUTHOR]