Informative Microsatellite Markers Research Articles

Generation and genetic analysis of a rainbow trout (Oncorhynchus mykiss) clonal line produced by gynogenesis

The efficiency of heat-shock treatments for producing gynogenetic double haploids was evaluated using a rainbow trout (Oncorhynchus mykiss) strain locally adapted in Brazil (2002 broodstock). Eleven and 15 females produced by conventional reproduction (FC) or meiotic gynogenesis (FG) were used as egg donors, respectively. Oocytes from each female were randomly divided into five uneven lots which were submitted to different treatments: (C2n) Normal diploid control, (H) Haploid control, (G-Me) Meiotic gynogenetic, (G-Mi) Mitotic gynogenetic, and (4 n) Control of suppression of the 1st cell cleavage. Homozygous yellow-colored (Dominant albino - DA) males were used as semen donors. Gynogenesis was induced by insemination of eggs with DA semen genetically inactivated by ultraviolet irradiation. Diploidization of gynogenic individuals was induced by an early heat shock to block 2nd polar body extrusion (G-Me), or a late heat shock to suppress first mitosis (G-Mi). Overall mean survival rates to eyed-egg and first feeding stages of treated groups, relative to respective C2n control group were: 19.21 and 14.90%, 13.02 and 8.09%, and 29.94 and 16.48%, for treatments G-Me, G-Mi and 4 n, respectively. When compared with C2n, all treatments showed lower survival rates at both stages. Survival of G-Me and G-Mi progeny from FG females were significantly higher when compared to progeny from FC females for both stages. Progenies from two different females observed to be 100% homozygous in analyzed informative microsatellite markers were used in subsequent cycles of gynogenic reproduction. One line originally derived from a single gynogenic female was reproduced for nine successive generations of meiotic gynogenetic reproduction. Forty animals from the ninth successive generation of gynogenetic reproduction were analyzed with a low-density SNP (Single Nucleotide Polymorphism) panel. All individuals were observed to be homozygous for identical alleles at all SNPs, therefore indicating that the established mitotic gynogenetic line is composed of 100% clonal individuals.

Genome-Wide Informative Microsatellite Markers and Population Structure of Fusarium virguliforme from Argentina and the USA.

Soybean sudden death syndrome (SDS) is a destructive disease that causes substantial yield losses in South and North America. Whereas four Fusarium species were identified as the causal agents, F. virguliforme is the primary SDS-causing pathogen in North America and it also contributes substantially to SDS in Argentina. In this study, we comparatively analyzed genome assemblies of four F. virguliforme strains and identified 29 informative microsatellite markers. Sixteen of the 29 markers were used to investigate the genetic diversity and population structure of this pathogen in a collection of 90 strains from Argentina and the USA. A total of 37 multilocus genotypes (MLGs) were identified, including 10 MLGs in Argentina and 26 in the USA. Only MLG2, the most dominant MLG, was found in both countries. Analyses with three different approaches showed that these MLGs could be grouped into three clusters. Cluster IA consisting of four MLGs exclusively from the USA has much higher genetic diversity than the other two clusters, suggesting that it may be the ancestral cluster although additional data are necessary to support this hypothesis. Clusters IB and II consisted of 13 and 21 MLGs, respectively. MLGs belonging to these two clusters were present in all four sampled states in Argentina and all five sampled states in the USA.

Characterization of Microsatellite Markers in Crossbred Ducks

Background: Chicken represents a valuable genetic resource and protein source, it remains a potential threat to human health as they serve as a reservoir for diseases and food borne pathogens. Diversification of the poultry production is one of the viable options to enhance the food production with less susceptibility to the threats from the emerging diseases and changing climatic conditions. Ducks are promising species suitable for the diversification and will be complimentary with an adaption potential from small to commercial farming. Majority of ducks in the country are desi type with a meagre proportion of improved duck strains. genetic characterization by developing duck specific microsatellite markers and designing suitable improvement program are required to be undertaken at the earliest. The microsatellite markers are extensively used for assessing genetic structure, diversity, and relationships. Information about genetic diversity of indigenous duck breeds is important to design effective improvement and conservation strategies. Therefore, the current studies aim at genetic characterization and evaluation of growth, production and reproduction traits of the crosses of local duck population besides undertaking a suitable duck improvement program. Methods: Spectrophotometric evaluation of DNA extraction, Electrophoretic evaluation of DNA extraction , microsatellite primers- Presently, a panel of 10 informative duck microsatellite markers were identified from database as reported by Alyethodi and Kumar (2010) and Huang et al., (2006) and used for the studies, Polymerase chain reaction (PCR) , Documentation of PCR products by Agarose Gel Electrophoresis, Metaphor agarose gel electrophoresis(MAGE)of microsatellites alleles, Determination of molecular size of microsatellite alleles and genotypes, Statistical analysis of population genetics data, Data on genotype of all experimental birds at ten microsatellites were compiled and analyzed using POPGENE® 3.1 software (Yeh et al., 1999) for their population genetics parameters. Results: The study was conducted at College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, Assam, India. In this study, the genomic DNA was isolated and characterized microsatellite loci in crossbred duck (Pati x White Pekin). Ten microsatellites were used to detect polymorphisms in 50 cross bred ducks. A total of 28 nos of alleles were observed and all loci were polymorphic. The number of alleles ranged from 2 to 5 with an average of 2.6 ±0.08 per microsatellite locus. The observed and expected heterozygosity of these polymorphic makers ranged from 0.00 to 0.42 with an average number of 0.047 and 0.41 to 0.82 with an average number of 0.57, respectively. The Polymorphic markers consist of observed heterozygosities of loci were less than 0.50. The polymorphism information content (PIC) of 10 loci ranged from 0.32 to 0.78 with an average of 0.477. Microsatellite markers will be useful tool for constructing the genetic linkage map of the duck as well as comparative mapping with the chicken.

Development of nuclear microsatellite markers in Yerba mate (Ilex paraguariensis A. St. Hil.) from whole-genome sequence data

AbstractIlex paraguariensis A. St.-Hil. (yerba mate) (Aquifoliaceae Bercht. & J. Presl) is a plant species with great economic and cultural importance because its leaves are processed and ground to make infusions like mate or tereré. The species is distributed in a continuous area that includes Southern Brazil and part of Paraguay and Argentina. Uruguay represents the Southern distribution limit of the species, where small populations can be found as part of ravine forests. Although there are previous reports of molecular markers for this and other species in the genus, the available markers were not informative enough to represent the intra- and interpopulation genetic diversity in marginal Uruguayan populations. In this study, we developed highly informative polymorphic microsatellite markers to be used in genetic studies in I. paraguariensis. Markers were identified in contigs from the genome sequence of two individuals and then tested for amplification and polymorphism content in a diverse panel. Markers which passed these filters were tested on populations from Uruguay. They detected higher diversity within populations (in terms of number of alleles and heterozygosity) than previously reported, and levels of heterozygosity similar to those reported for two Brazilian populations. This subset of seven markers were successfully multiplexed, substantially reducing the costs of the analysis. Combined with previously reported nuclear and plastid markers, they can be used to evaluate the genetic diversity of rear-edge populations, identify genotypes for paternity studies and provide relevant information for the conservation and management of germplasm.

Deep structured populations of geographically isolated nipa (Nypa fruticans Wurmb.) in the Indo-West Pacific revealed using microsatellite markers.

Nipa (Nypa fruticans Wurmb.) is an important mangrove palm species, but it is understudied due to lack of information on genetic patterns within its distribution range. In this study, we identified 18 informative microsatellite markers to assess genetic variations among local populations in the Indo-West Pacific (IWP). Results showed population stratification based on high genetic differentiation (FST = 0.22131) with the Mantel test indicating significance to isolation-by-distance. We found a pronounced differentiation between the west populations in Sri Lanka and east populations in Southeast Asia. The east populations around the South China Sea were more genetically similar than those along the Malacca Strait and Java Sea. These genetic clines were shaped by ocean circulations and seasonal monsoon reversals as plausible factors. The Malacca Strait was confirmed as both a genetic and a geographic barrier rather than a corridor according to the Monmonier plot. Simulations of directional migration indicated a statistically strong contemporary genetic connectivity from west to east where Sri Lankan immigrants were detected as far as central Philippines via long-distance dispersal. This is the first report on the recent migration patterns of nipa using microsatellites. Assignment of first-generation (F0) immigrants suggested Mainland Southeast Asia as a melting pot due to the admixture associated with excess of homozygosity. The western populations were recent expansions that emerged in rapid succession based on a phylogram as supported by footprints of genetic drift based on bottleneck tests.

Parental Polymorphism Survey for Evaluation and Selection of Contrasting Parents for Drought Tolerance in Rice (Oryza sativa L.) by Using SSR Markers

Aim: This study aims to find the informative polymorphic Microsatellite (SSR) markers for drought tolerance between the recipient parent (Pratishya) and donor parent (CR Dhan 801) of rice. The drought tolerant QTLs (qDTY1.1, qDTY2.1, and qDTY3.1) from the donor parent were subsequently introgressed into the popular variety Pratikshya via marker-assisted backcross breeding.
 Place and Duration of Study: The parental polymorphism study was conducted at Molecular Drought Breeding Laboratory, Department of Genetics and Plant Breeding and Central Laboratory, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi; and at Crop Improvement Division, ICAR-NRRI, Cuttack during Rabi 2018-19.
 Methodology: The parents used for the study were Pratikshya (recurrent parent) and CR Dhan 801 (donor parent). The leaf samples were collected from 20-25 days old seedlings which were used for parental polymorphism survey after DNA extraction. The genomic DNA isolation was done by using CTAB method. A set of 510 SSR markers covering all the 12 chromosomes of rice were used for parental polymorphism survey in the present study. The standard protocol of polymerase chain reaction (PCR) and agarose gel electrophoresis was used. The DNA fragments were documented using gel documentation system. The graphical representation of marker data was obtained with GGT 2.0 software.
 Results: Out of 510, total 108 SSR primer pairs exhibited polymorphism between recipient parent (Pratikshya) and donor parent (CR Dhan 801) and remaining 392 SSR primers were monomorphic. The highest percentage of parental polymorphism was observed on chromosome 2 (26.53%) and 3 (26.46%) followed by chromosome 1 (23.08%); and least on chromosome number 10 (14.71%). The average per cent of polymorphism on all the 12 chromosomes were 21.28%. Out of 108 polymorphic markers obtained from screening of 510 SSRs, 69 contained dinucleotide repeats, 32 showed trinucleotide repeats and 5 were having tetranucleotide repeats.
 Conclusion: The screening of markers by parental polymorphism in rice cultivars gives the basis for tagging of the target gene, fine mapping of the gene on the rice chromosome, and subsequent application in Marker Assisted Selection (MAS) programmes. The polymorphic markers identified in this study were be used for genotyping the entire mapping population and for the introgression of the QTLs/genes linked with grain yield during the reproductive stage of drought.

Historical Westward Migration Phases of Ovis aries Inferred from the Population Structure and the Phylogeography of Occidental Mediterranean Native Sheep Breeds.

In this study, the genetic relationship and the population structure of western Mediterranean basin native sheep breeds are investigated, analyzing Maghrebian, Central Italian, and Venetian sheep with a highly informative microsatellite markers panel. The phylogeographical analysis, between breeds’ differentiation level (Wright’s fixation index), gene flow, ancestral relatedness measured by molecular coancestry, genetic distances, divergence times estimates and structure analyses, were revealed based on the assessment of 975 genotyped animals. The results unveiled the past introduction and migration history of sheep in the occidental Mediterranean basin since the early Neolithic. Our findings provided a scenario of three westward sheep migration phases fitting properly to the westward Neolithic expansion argued by zooarcheological, historical and human genetic studies.

Genotypic and Phenotypic Structure of the Population of Phytophthora infestans in Egypt Revealed the Presence of European Genotypes.

Late blight disease of potato and tomato, caused by Phytophthora infestans, results in serious losses to Egyptian and global potato and tomato production. To understand the structure and dynamics of the Egyptian population of P. infestans, 205 isolates were collected from potato and tomato plants during three growing seasons in 2010–2012. The characterization was achieved by mating-type assay, metalaxyl sensitivity assay, and virulence pattern. Additionally, genotyping of 85 Egyptian isolates and 15 reference UK isolates was performed using 12 highly informative microsatellite (SSR) markers David E. L. Cooke and five effector (RxLR) genes. Mating-type testing showed that 58% (118 of 205) of the isolates belonged to mating type A1, 35% (71 isolates) to mating type A2, and the rest 8% (16 isolates) were self-fertile. The phenotype of metalaxyl response was represented as 45% resistant, 43% sensitive, and 12% as intermediate. Structure analysis grouped the 85 identified genotypes into two main clonal lineages. The first clonal lineage comprised 21 isolates belonging to A2 mating type and 8 self-fertile isolates. This clonal lineage was identified as Blue_13 or EU_13_A2. The second main clonal lineage comprised 55 isolates and was identified as EU_23_A1. A single isolate with a novel SSR genotype that formed a distinct genetic grouping was also identified. The effector sequencing showed good correspondence with the virulence data and highlighted differences in the presence and absence of loci as well as nucleotide polymorphism that affect gene function. This study indicated a changing population of P. infestans in Egypt and discusses the findings in the context of late blight management.

Genome-wide SSR markers in bottle gourd: development, characterization, utilization in assessment ofgenetic diversity of National Genebank of India and synteny with other related cucurbits.

Lagenaria siceraria (Molina) Standley is an important cultivated crop with its immense importance in pharmaceutical industry and as vegetable. Its seed, root, stem, leaves, flower, and fruit are used as an ointment for ailment of various diseases throughout Asia. Despite its worldwide importance, informative co-dominant microsatellite markers in the bottle gourd crop are very restricted, impeding genetic improvement, cultivar identification, and phylogenetic studies. Next-generation sequencing has revolutionized the approaches for discovery, assessment, and validation of molecular markers. We conducted a genome-wide analysis, for developing SSR markers by utilizing restriction site-associated DNA sequencing (RAD-Seq) data obtained from NCBI. By performing in silico mining of microsatellite repeat motifs, we developed 45,066 perfect SSR markers. Of which 207 markers were successfully validated and 120 (57.97%) polymorphic primer pairs were utilized for an in-depth genetic diversity and population structure analysis of 96 accessions from the National Genebank of India. Tetranucleotide repeats (∼34.3%) were the most prevalent followed by trinucleotide repeats (∼30.73%), further 21.03%, 9.6%, and 4.3% of di-, penta-, and hexa-nucleotide repeats in the bottle gourd genome, respectively. Synteny of SSR markers on 11 bottle gourd linkage groups was correlated with the 7 chromosomes of cucumber (93.2%), 12 chromosomes of melon (87.4%), and 11 of watermelon (90.8%). The generated SSR markers provide a valuable tool for germplasm characterization, genetic linkage map construction, studying synteny, gene discovery, and for breeding in bottle gourd and other cucurbits species. KEY MESSAGE: Development of 45,066 perfect microsatellite markers as a valuable tool for marker assistedselection (MAS) in plant breeding.

Molecular research in the tomato breeding for resistance to biotic stressors

An urgent problem in tomato breeding is the development of universal varieties and hybrids that combine high yields and good fruit quality with group resistance to a number of diseases. The purpose of this study is to develop tomato breeding material resistant to biotic stressors, basing on modern postgenomic technologies using molecular markers. At the initial stage, we tested microsatellite markers from foreign literature sources, the primers used in the study were synthesized by Syntol LLC, samples from the collection of FSBSI Federal Scientific Center for Biological Plant Protection and FSBSI Federal Scientific Rice Centre were studied under the conditions of Krasnodar region. PCR conditions for identifying the target Ph -3 gene in the tomato plant material used in the breeding process were optimized. Thus, in our study on the testing of microsatellite markers to identify the target Ph-3 resistance gene in the tomato genetic material, we selected 3 informative microsatellite markers R2M1S, G8-1, R1-3U, which reveal the allelic difference between susceptible and resistant samples.

Developing KASP Markers for Identification of Basmati Rice Varieties

Authentication of Basmati rice has relied on microsatellite markers since 2004, but microsatellites cannot distinguish between all of the forty-one Basmati varieties approved in 2017. This study investigated whether single nucleotide polymorphisms (SNP) and insertion/deletion (InDel) variations developed into KASP™ (Kompetitive Allele Specific PCR; LGC Biosearch Technologies) could be used to distinguish between commercial Basmati varieties. Suitable loci were identified by comparing whole genome sequences of 120 diverse rice accessions. Sequences flanking these loci were standardized across a wide range of rice genomes to produce optimal KASP designs. We selected 364 KASP designs to use for genotyping; they were either near to informative microsatellite markers, within the Badh2 and Waxy genes, or distributed throughout the rice genome. Genotypes for 327 KASP were obtained with 255 loci revealing polymorphism in up to 41 samples of approved Basmati varieties and 20 non-Basmati varieties. The varieties genotyped had not been used in the KASP design process. KASP were able to distinguish between commercial Basmati varieties that could not be distinguished with currently available microsatellites. Thirty-seven Basmati varieties could be distinguished from all others with between 3 and 8 KASP markers out of a pool of 98 informative markers. A reduced set of 24 KASP markers could determine whether a sample belongs to one of eight family groups. All of the KASP markers used in this study can be purchased from LGC Biosearch Technologies. These markers have potential to be used by industry for routine testing and regulation.

Parentage assignment in Salmo trutta strains and their crossbreeds with known mating

Brown trout, Salmo trutta is a widespread fish species throughout the Europe yet most of the natural populations of the species is in decline due to the anthropogenic pressures. Hatchery based stock enhancement is commonly used to restore depleted populations. Tracking pedigree information is useful for evaluating performance of stocked offspring and for examining introgression where stocking practices are being implemented. In this study, parentage assignment powers of 16 previously developed microsatellite markers have been evaluated in four brown trout strains and their reciprocal crossbreeds. The number of alleles per locus ranged between 3 (Str73INRA) -24 (T3-13). Observed (HO) and expected heterozygosity (HE) was between 0.188 and 0.854 and 0.175–0.903, respectively. According to the simulation analysis with prior known parental and filial information, of the 204 offspring tested, correct assignment rate of the eight most informative microsatellite marker to their parental pairs was 96.08% and that of 15 loci was 98.04%. Having more than eight markers boosted only 1.96% extra power of assignment. Meanwhile correct assignment rate of five loci was resulted only 85.29%. Our results demonstrate that microsatellite markers are reliable and effective tools for the parentage assignment in brown trout strains and their reciprocal crossbreeds. The findings obtained in the present study would also be useful for performance evaluation of stocked fish, detecting crossbreeds and examining introgression into natural populations.

Population Genetic Analysis for Stock Enhancement of Silver Sea Bream (Rhabdosargus sarba) in Taiwan

Stock enhancement is a method for replenishing depleted wild finfish populations by supplementing them with hatchery-raised fish. In Taiwan, silver sea bream (Rhabdosargus sarba) is a predominant commercial species involved in stock enhancement projects. Although management agencies conduct stock enhancement projects, there are a lot of private releases without records. Stock enhancement is performed by the private aquaculture sector without accurate genetic records, potentially leading to unintended consequences for wild populations. We analyzed the genetics of 459 wild and 701 hatchery-reared specimens from nine batches produced by various hatcheries. Wild and hatchery-reared samples could be considered two separate clades by using a set of stable and informative microsatellite markers including type I (from gene introns and 3′UTR) and type II markers (randomly picked up from genome). Type I microsatellite markers could more sensitively reflect the loss of genetic diversity more than type II markers in the domestication process. All specimens were considered native by using mtDNA COI and microsatellites. The genetic composition of the wild population is relatively simple, and the estimated low contribution rate of the hatchery stock (1.3–10.9%; 6–50/459) indicated a weak but significant genetic effect of stock enhancement. Therefore, establishing standards for the stock enhancement of silver sea bream for more effective supplementation of wild populations is imperative.

Assessing genetic diversity and population structure of sugarcane cultivars, progenitor species and genera using microsatellite (SSR) markers.

Sugarcane is one among the most important commercial crops used to produce sugar, ethanol, and other byproducts, which significantly contributes in the GDP of India and many other countries around the world. Genetic diversity is a platform for any breeding program of a plant species. Estimation of the genetic variability and population structure play a vital role for conservation planning and management of plant genetic resources. Genetic variability serves as a source of noble alleles responsible for key agronomic and quality traits, which ultimately form basis for identification and selection of promising parents for breeding programs. In the present study genetic diversity and population structure of 139 accessions of the genus Saccharum, allied genera of family Poaceae and cultivars were assessed using informative microsatellite (SSR) markers. A sum of 427 alleles was produced using 61 polymorphic primers and number of alleles generated was ranged from 2 to 13 with an average of 7 alleles per locus. PIC values were ranged from 0.35 to 0.90, with a mean value of 0.66 for all the markers evaluated. Cluster analysis based on UPGMA method revealed three major clusters which were further subdivided into nine subclusters. Population structure analysis also established three subpopulations of used accession set, however there were no correlation of sub-groupings with that of place of origin. AMOVA analysis also confirmed that 83% and 17% of total variations were attributed to the within- and between-populations, correspondingly, demonstrating greater exchange of gene pool across places of origin. The principal component analysis (PCA) demonstrated the distribution of accessions in the scatter-plot was substantially dispersed, revealing rich genetic diversity among accessions of different species. The findings from this study will be useful in breeding programs for introgression of noble alleles into modern cultivars by exploiting natural genetic variation existing in sugarcane genetic resources.

Development and characterization of novel microsatellite markers in chestnut tiger butterfly Parantica sita (Lepidoptera: Nymphalidae) using next-generation sequencing

While one subspecies of chestnut tiger butterfly (Parantica sita, Lepitoptera: Nymphalidae) undertakes seasonal migration between Taiwan and Japan, it is still unknown whether the nominate subspecies, P. s. sita, migrates seasonally in southwest China. To understand the potential migration of P. s. sita, it is necessary to investigate the genetic differentiation among populations. In our study, we developed 18 novel microsatellite markers from the transcriptome using next-generation sequencing methods. These polymorphic markers were tested on 89 individuals from 4 populations of P. sita. The allele numbers ranged from 2 to 19. The average polymorphism information content values in each population ranged from 0.34 to 0.40. The observed (Ho) and expected (He) heterozygosity of each locus in each population ranged from 0.043 to 0.870 and 0.043 to 0.833, respectively. These informative microsatellite markers would be helpful for discovering the facts of P. sita long-distance migration in China.

Genetic patterns recognition in crop species using self-organizing map: the example of the highly heterozygous autotetraploid potato (Solanum tuberosum L.)

We tested the ability of the self-organizing map (SOM), a type of artificial neural network, in revealing genetic patterns within the autotetraploid potato (Solanum tuberosum L.). A total of 591 potato varieties, originating from various main European breeder collections and released into different market segments between 1815 and 2015, were examined using a set of 21 informative microsatellite markers. The consistency of this artificial intelligence approach in detecting genetic stratifications in such a homogeneous population was evaluated through the comparison with three other multivariate methods that are widely used for this purpose. Results showed that the SOM was equally suitable for classifying varieties into main detected groups and visualizing inter-group genetic dissimilarities. When it came to reveal the organization of the population structure at the intra-group level, traditional multivariate methods lost in resolution. Contrariwise, the SOM provided additional information on the intra-group diversity by highlighting a multitude of consistent subgroups, which seemed to be mainly related to their common heritage, spatio-temporal features and certain agronomic traits. Relations between computed SOM subgroups and the market segments were subject to certain elucidations. The relevance of using more flexible multivariate statistical approaches for mapping population structures of crop species is considered throughout this paper in terms of current and future prospects for breeding programs.

Understanding the population structure and reproductive behavior of hatchery-produced yellowtail kingfish (Seriola lalandi)

The yellowtail kingfish (Seriola lalandi) is a marine endemic fish, and a key species in the national programme for the diversification of Chilean aquaculture. Since it has been recently developed from wild fish, the biology of this species under production is to a large extent unknown. For example, the structure of the different populations used to create the national breeding programme is not well characterised. Moreover, due to the fact that it is not possible to perform stripping of broodstock in yellowtail kingfish, the genetic contributions of individuals are affected by the reproductive behaviour of this species. To increase our knowledge of the biology of this species under aquaculture conditions, the objectives of this study were: (i) to identify the population structures of wild and commercial populations of yellowtail kingfish obtained from different fisheries off the Chilean coast, and compare these to those of Mexican and Australian specimens and (ii) to study the reproductive behaviour of commercial yellowtail kingfish broodstock through paternity testing, to estimate the genetic contributions of individuals throughout the artificial spawning season in captivity. We used a set of 12 highly informative microsatellite markers optimised for paternity testing. The analysis of the population structure showed at least two clusters of yellowtail kingfish, including a single metapopulation from Chile and Australia (possibly explained by the migratory behaviour of this species in the Pacific Ocean), and the other from Mexico (which is most likely composed of California yellowtail, S. dorsalis). Some degree of admixture, albeit small, was observed between the populations from Mexico and Australia. Paternity analysis showed that the average ratio (male/female) contributing in a spawning event was 2.6, confirming the spawning behaviour observed in other species in this genus. Additionally, we observed that males participated in matings regularly during the whole spawning season. Using the results of this research, we recommend modifying the current implementation of yellowtail kingfish breeding programmes to reduce the effects of random genetic drift. This can be achieved by managing the genetic contributions of broodstock in a two-step breeding programme. This study provides useful genetic information for the long-term development and management of the Chilean yellowtail kingfish industry, which involves a species of high importance for the diversification of Chilean aquaculture.

Population Biology and Genetic Variation of Spongospora subterranea f. sp. subterranea, the Causal Pathogen of Powdery Scab and Root Galls on Potatoes in South Africa.

Spongospora subterranea f. sp. subterranea, causal agent of powdery scab and root galls of potatoes, occurs worldwide and is responsible for quality and yield losses in potato production in South Africa. Despite being one of the most important potato pathogens in South Africa, little information is available on the genetic structure and diversity of S. subterranea f. sp. subterranea, which could provide insight into the factors shaping its evolution and the role of inoculum sources in disease development. A total of 172 samples were collected from four potato growing regions in South Africa. An additional 27 samples obtained from Colombia were included for comparative purposes. The samples were screened against six informative microsatellite (simple-sequence repeat) markers. Of the 172 samples obtained from potato growing regions in South Africa, there were 75 multilocus genotypes (MLGs), only 16 of which were shared between potato growing regions, indicating substantial gene flow and countrywide dispersal of the pathogen. The presence of common MLGs among the root- and tuber-derived samples indicated a lack of specialization of S. subterranea f. sp. subterranea to either tuber or root infection. Nei's unbiased estimates of gene diversity for the clone-corrected data were low and ranged from 0.24 to 0.38. Analysis of molecular variance and discriminant analysis of principal components showed no population differentiation between different potato growing regions in South Africa and between root- and tuber-derived genotypes. The presence of MLGs, high considerable genotypic diversity, and failure to reject the null hypothesis of random mating in most populations are indicative of some kind of recombination, either sexual or asexual, in these S. subterranea f. sp. subterranea populations. Information from this study provides new insights into the genetic structure and diversity of S. subterranea f. sp. subterranea in South Africa. Continuous monitoring of the pathogen population dynamics will be helpful in implementing effective region-specific management strategies for the pathogen, especially in the development of resistant potato cultivars.

Assessment of the genetic relationship between the recently established benthic population and the adjacent floating populations of Sargassum horneri (Phaeophyceae) in Dalian of China by newly developed trinucleotide microsatellite markers

Sargassum horneri is a conspicuous canopy-forming brown seaweed growing on solid substrates or floating on sea surface. A recently established benthic population was discovered in a bay in Dalian, China, in 2016 and suggested to be derived from the earlier floating population. Since 2016, floating populations have kept appearing in the adjacent area. The genetic connectivity between this recently established benthic population and the adjacent floating populations remains unclear. In this study, 10 novel informative trinucleotide microsatellite markers were developed through the high throughput sequencing technology, and employed to analyze the genetic structure of the benthic population (DS16 and DS18) and three adjacent floating populations (DL16, BL16, and DL18) sampled in 2016 and 2018, with one floating population collected from Shidao in 2016 (SD16) as reference. Significant genetic differentiation was found to exist between the benthic and floating populations, and among floating populations from different years. Almost no membership of floating populations was detected in the benthic population and vice versa by the Bayesian model–based structure analysis, indicating very limited genetic connectivity between them. Significant excess of heterozygosity, significant multilocus linkage disequilibrium, high frequency of repeated genotypes, and putative clones were detected in all floating populations, indicating that asexual reproduction is likely dominant in them. Inbreeding and founder effect were revealed to be present in the benthic population. Further studies will focus on tracking the dynamics of genetic structure in the recently established benthic population and investigating the exact reproductive means and patterns of floating populations.

Comparative genomics approach to build a genome-wide database of high-quality, informative microsatellite markers: application on Phytophthora sojae, a soybean pathogen

Microsatellites are a tract of repetitive, short DNA motifs (usually 1 to 6 bp) abundant in eukaryotic genomes. They are robust molecular markers in many areas of studies. Development of microsatellite markers usually involves three steps: (1) obtaining microsatellite-containing sequences, (2) primer design, and (3) screening microsatellite loci for polymorphism. The first and third steps require considerable resources. Next generation sequencing technologies have greatly alleviated the constraint of the first step. In this study, we leveraged the availability of genome assemblies of multiple individuals in many species and designed a comparative genomics approach to bioinformatically identify polymorphic loci. Our approach can eliminate or greatly reduce the need of experimental screening for polymorphism and ensure that the flanking regions do not have length difference that would confound interpretation of genotyping results using microsatellite markers. We applied this approach on Phytophthora sojae, a soybean pathogen, and identified 157 high-quality, informative microsatellite markers in this oomycete. Experimental validation of 20 loci supported bioinformatics predictions. Our approach can be readily applied to other organisms of which the genomes of multiple individuals have been sequenced.