SSR Primer Pairs Research Articles

Molecular Diversity in Flax (Linum usitatissimumL.) as Revealed by DNA Based Markers

The present investigation was undertaken to assess the genetic diversity of flax cultivars using molecular markers. 90 SSR and 10 ISSR flax markers were employed for molecular diversity analysis. Out of these, 25 microsatellite markers were found to be polymorphic giving a total of 99 bands with an average of 3.96 bands per marker ranging from 2 to 12. The polymorphic information content (PIC) value of each SSR primer pair ranged from 0.21 to 0.88 with an average of 0.49 while in case of ISSR primers, out of 10 primers, only 2 were found polymorphic producing a total of 20 bands with an average of 10 bands per marker ranging from 2 to 11. The polymorphic information content (PIC) value of ISSR primer pair ranged from 0.62 to 0.75 with an average of 0.68. Cluster analysis based on Jaccard's similarity coefficient using UPGMA grouped the 48 flax varieties into two clusters. The Jaccard's similarity ranged from 0.56 to 0.97 with an average similarity index of 0.76. The genotype Polf22 showed the highest similarity with LCK-88068 (i.e. 0.96) while Neela showed the least similarity with R-4158 (i.e. 0.68). It was evident from the cluster analysis that two introduced genotypes Neela and R-4158 were the most distantly related to the remaining genotypes followed by PKDL -43, RLC-137, KL-168 and R-4152. So, these genotypes must be further used in breeding programme for developing improved varieties.

Development, characterization and cross-species transferability of genomic SSR markers in berseem (Trifolium alexandrinum L.), an important multi-cut annual forage legume

Egyptian clover (Trifolium alexandrinum), a multi-cut forage legume, is widely grown as an annual feed crop. Genetic improvement in this legume is largely hampered due to limited availability of genomic resources. Hence, a genomic library enriched for GA/CT motif was constructed to develop SSR primers. As a result, 667 SSR primer pairs were developed and 111 were validated in T. alexandrinum cv. Wardan s-99-1. Among these, 45 primer pairs were used for the analysis of genetic diversity among 86 Trifolium accessions, resulting in 220 alleles with an average of 4.88 alleles per locus. Polymorphic information content for these markers ranged from 0.040 to 0.819 with an average of 0.445. The observed and expected heterozygosity for individual loci ranged from 0.39 to 0.89 and 0.368 to 0.80 with an average of 0.675 and 0.659, respectively. The markers exhibited varied levels of cross-species transferability ranging from 93.33 % across T. resupinatum to 40.0 % across T. balansae. Phylogenetic relationships were analyzed using the unweighted pair group method with arithmetic averages (UPGMA)-based dendrogram which was able to establish the uniqueness of each genotype and grouped them into two major clusters. To the best of our knowledge, the SSR markers reported here are among the first to be reported in this important yet neglected forage legume. They were assessed to be highly efficient and polymorphic and found to be useful for distinguishing the closely related genotypes of Trifolium. This large resource of SSR markers would therefore facilitate new avenues for T. alexandrinum genomics.

Influence of Host Shift on Genetic Differentiation of the Oriental Fruit Fly, Bactrocera dorsalis

Invasion of the oriental fruit fly, Bactrocera dorsalis, into new niches containing different food sources (a process referred to as host shift), may cause population genetic differentiation and sympatric speciation. To attempt to infer that experimentally, test populations were established by transferring a subset of the original populations, which had been grown on banana for many generations, onto navel orange, and then subculturing the navel orange population and banana population for at least 20 generations. Four pairs of SSR primers with high polymorphism on laboratory strains were used to detect population genetic differentiation. All six tested populations (the 5th, 10th and 15th generations of B. dorsalis fed on banana and navel orange, respectively) were found to have low genetic diversity. Furthermore, the genetic diversity of the navel orange populations was found to decline after being crossed for several generations. Populations initially were deviated from Hardy-Weinberg equilibrium, however, equilibrium was achieved with increasing numbers of generations in both of the host populations. Limited gene flows were found among the six populations. The Nei's standard genetic distances between the two host populations of the same generation were initially low, but increased with generation number. Genetic distances between banana and navel orange populations of the same generation were lower than genetic distances between different generations grown on the same host plant. Analysis of molecular distance (AMOVA) results based on generation groups and host groups demonstrated that genetic variation among generations was greater than that between the two host populations. The results indicated that population genetic differentiation occurred after the host shift, albeit at low level. Biogeography and taxonomy of the B. dorsalis complex revealed that speciation of B. dorsalis might be tightly associated with host shift or host specialization of B. dorsalis following dispersal.

Mapping of a new wrinkled leaf (wr3) gene in upland cotton.

The phenotype of a wrinkled leaf mutant in upland cotton newly found was different from other analogous mutants reported previously. Genetic analysis indicates that the mutation is controlled by a single recessive gene wr. In this paper, an F₂mapping population derived from the mutation inbred line L037 crossing with Hai7124 (Gossypium babardense) was used. A total of 12 pairs of polymorphic primers were selected from 234 pairs of SSR primers obtained before, which covered 26 pairs of cotton chromosomes at regular intervals. Genetic mapping of the F₂population showed that gene wr₃was linked to the primer BNL3279 on Chr.21 with the distance of 28.7 cM. Further screening of other primers on Chr.21 showed that gene wr₃was flanked by the primers NAU3740 and cgr5428, with genetic distance of 4.8 cM and 10.4 cM, respectively.

Using SSR Markers For Assessment Genetic Diversity And Detection Drought Escape Candidate Genes In Barley Lines (Hordeum Vulgare L.)

Abstract Assessment of genetic diversity using molecular markers is one of the primary and important steps in breeding programs. In this study, genetic diversity of 52 barley lines evaluated using 68 SSR primer pairs and 47 primer pairs produced clear and polymorphic banding pattern. In general, 153 polymorphic alleles detected. The number of observed polymorphic alleles varied from 2 to 9, with an average of 3.26 alleles per locus. Polymorphic Information Content (PIC) ranged from 0.07 to 0.81, with an average of 0.45. In this research, SSR markers differentiated the studied lines efficiently. Using cluster analysis, studied barley lines divided into two groups. Genetic diversity was relatively corresponding with geographical origins, because the lines related to a country somewhat diverged from each other. Two-rowed Iranian and Chinese barleys classified in one subgroup. Also, most six-rowed barleys classified in one subgroup. Association mapping analysis was used to identify candidate genes for drought escape in barley lines and 16 informative markers were identified after which confirmation in other tests could be suitable for marker assisted breeding drought escape.

Genetic map and QTL controlling fiber quality traits in upland cotton (Gossypium hirsutum L.)

Cotton is a leading natural fiber crop in the textile industry worldwide. The improvement of cotton fiber quality has become more important because of changes in spinning technology and ever-increasing demands. Mapping quantitative trait locus (QTL) for fiber quality traits will enable molecular marker-assisted selection (MAS) to improve fiber quality and provide an access to reveal the molecular mechanism of fiber development. A high-density intraspecific genetic map is constructed based on an upland cotton recombinant inbred line (RIL) population. A total of 25,313 SSR primer pairs were used and yielded 1,333 polymorphic markers, with a polymorphic ratio of 5.3 %, producing 1,382 polymorphic loci in the RIL population. The map comprised 1,274 loci and spanned 3,076.4 cM with an average distance of 2.41 cM between two adjacent markers. Based on the phenotypic data of fiber quality traits from five environments, a total of 59 QTL were detected. These QTL comprised 15 QTL for fiber upper half mean length, 10 QTL for fiber length uniformity, 9 QTL for fiber strength, 10 QTL for fiber elongation and 15 QTL for fiber micronaire, respectively. The genetic map constructed in this study is the most detailed upland cotton intraspecific map based on SSR markers to date, and could be used to construct consensus map or as reference genetic map for tetraploid cotton genome assembly. Stable QTL identified across multiple environments reflect some important and favorable alleles shaping fiber quality, and they are valuable candidate alleles for MAS breeding projects as well as for gene function research related to cotton fiber development and quality improvement.

Construction of a genetic map of sunflower using a population of recombinant inbred lines (RILs)

A genetic linkage map of sunflower was constructed by combined applying the SSR and AFLP markers using 187 F5:6 individuals of recombinant inbred lines (RILs) which derived from the cross between Helianthus annuus K55 and Helianthus annuus K58 through single-seed descent (SSD). Using 78 pairs of SSR primers and 48 pairs of AFLP primer, 341 and 1119 bands were amplified, respectively. Among these 1460 bands, 557 bands (39.52%) were polymorphic, including 184 bands by SSR markers and 393 bands by AFLP markers. In the group of these polymorphic bands, 84 bands from SSR markers and 108 bands from AFLP markers showed the genetic distortion (P = 0.05). A total of 192 segregation distortion markers were obtained in this study. By using the JoinMap 4.0 software to do the linkage analysis, a genetic linkage map was established with length of 2759.4 cM, consisted of 17 linkage groups, and comprised of 495 polymorphic molecular markers including 170 segregation distortion markers. The mean marker interval distance is 5.57 cM between markers. In addition, the number of markers in the linkage groups varied from 5 to 72, and the length of linkage groups were from 68.88 cM to 250.17 cM. The genetic map developed in the present study could be used for QTL mapping and gene cloning of sunflower important genes.

Detection of Genome Donor Species of Neglected Tetraploid Crop Vigna reflexo-pilosa (Créole Bean), and Genetic Structure of Diploid Species Based on Newly Developed EST-SSR Markers from Azuki Bean (Vigna angularis)

Vigna reflexo-pilosa, which includes a neglected crop, is the only one tetraploid species in genus Vigna. The ancestral species that make up this allotetraploid species have not conclusively been identified, although previous studies suggested that a donor genome of V. reflexo-pilosa is V. trinervia. In this study, 1,429 azuki bean EST-SSR markers were developed of which 38 EST-SSR primer pairs that amplified one product in diploid species and two discrete products in tetraploid species were selected to analyze 268 accessions from eight taxa of seven Asian Vigna species including V. reflexo-pilosa var. glabra, V. reflexo-pilosa var. reflexo-pilosa, V. exilis, V. hirtella, V. minima, V. radiata var. sublobata, V. tenuicaulis and V. trinervia to identify genome donor of V. reflexo-pilosa. Since both diploid and tetraploid species were analyzed and each SSR primer pair detected two loci in the tetraploid species, we separated genomes of the tetraploid species into two different diploid types, viz. A and B. In total, 445 alleles were detected by 38 EST-SSR markers. The highest gene diversity was observed in V. hirtella. By assigning the discrete PCR products of V. reflexo-pilosa into two distinguished genomes, we were able to identify the two genome donor parents of créole bean. Phylogenetic and principal coordinate analyses suggested that V. hirtella is a species complex and may be composed of at least three distinct taxa. Both analyses also clearly demonstrated that V. trinervia and one taxon of V. hirtella are the genome donors of V. reflexo-pilosa. Gene diversity indicates that the evolution rate of EST-SSRs on genome B of créole bean might be faster than that on genome A. Species relationship among the Vigna species in relation to genetic data, morphology and geographical distribution are presented.

Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis).

Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.

English

The aim of this study was to estimate the genetic diversity in 74 RR soybean cultivars from different Brazilian breeding programs. Analyzes were based on multivariate statistical techniques from phenotypic characteristics and microsatellite molecular markers (SSR). Ten agronomic traits were used in the analysis of the Euclidean distance, Tocher’s clustering, UPGMA clustering and principal component analysis. Eighty-six of 100 SSR primer-pairs studied were selected based on their polymorphism information content, and analyzed using Jaccard Coefficient and UPGMA clustering method. The cultivars were clustered into seven groups according to the UPGMA and Tocher’s methods, based on agronomic traits, while molecular analysis identified six groups. The phenotypic distances ranged from 0.46 to 9.79 and the dissimilarity measurements, based on SSR molecular markers, ranged from 0.07 to 0.73. Both results from agronomic traits and molecular markers showed that there is genetic variability among the RR cultivars and that the Monsanto breeding program has the most divergent germplasm. The analyzed agronomic traits and the chosen SSR markers were effective in assessing the genetic diversity among genotypes, besides proving to be useful for characterizing genetic variability of soybean germplasm. Keywords: Glycine max , genetic variability, phenotypic characteristic, SSR markers. African Journal of Biotechnology , Vol 13(26) 2613-2625

Construction of genetic map and QTL analysis of fiber quality traits for Upland cotton (Gossypium hirsutum L.)

Cotton fiber quality traits are controlled by multiple genes of minor effect. Identification of significant and stable quantitative trait loci (QTL) across environments and populations lays foundation for marker-assisted selection for fiber quality improvement and studies of its molecular regulation. Here, a detailed genetic map is constructed and QTL are detected based on an intraspecific recombinant inbred line population derived from a cross between Upland cotton cultivar/line Yumian 1 and 7235. A total of 25,313 SSR primer pairs, including 5,000 developed from G. raimondii BAC-ends sequences, were used to construct the genetic map which finally contained 1,540 loci, spanning 2,842.06 cM, with an average of 1.85 cM between adjacent markers. With 4 year fiber quality traits data, variance analysis revealed that they were significantly affected by genetic and environmental factors. Significant correlations were also detected between them. A total of 62 QTL were identified with combined analysis and single environment analysis. These QTL explain phenotypic variation from 5.0 to 28.1 %. For each trait, favorable alleles were conferred by both parents. Seventeen QTL were detected in more than one environment. The genetic map and stable QTL are valuable for Upland cotton genome research and breeding projects to improve fiber quality.

Identification of AFLP and SSR markers linked with the male fertility restorer gene of CMS 06J45 in heading Chinese cabbage (Brassica rapa L. ssp. pekinensis)

AbstractIn this study, AFLP and SSR techniques were combined with the bulk segregant analysis (BSA) method to map the restorer gene BrRfp using an F2‐segregating population comprising 258 individuals developed by crossing the polima (pol)‐like cytoplasmic male sterility (CMS) line 06J45 and the restorer line 01S325 of heading Chinese cabbage. A survey of 2048 AFLP primer pairs identified 21 polymorphic fragments, approximately half of which exhibited high similarity with the A09 chromosome sequence of Brassica rapa in the Brassica database (BRAD). Based on the genome sequence, three specific AFLP fragments linked with BrRfp were successfully converted into sequence‐characterized amplified region (SCAR) markers, named SC1233, SC2673 and SC2141. Subsequently, 178 pairs of SSR primers were redesigned for further screening, with five producing polymorphic amplification patterns. Linkage analysis showed that these markers were distributed along both sides of the BrRfp gene, with two markers, SSR03 and SSR2528, co‐segregating with the BrRfp locus in the F2 population. These results may be valuable for marker‐assisted selection and map‐based cloning in heading Chinese cabbage.

Expanding the repertoire of microsatellite markers for polymorphism studies in Indian accessions of mung bean (Vigna radiata L. Wilczek)

Limited availability of validated, polymorphic microsatellite markers in mung bean (Vigna radiata), an important food legume of India, has been a major hurdle towards its improvement and higher yield. The present study was undertaken in order to develop a new set of microsatellite markers and utilize them for the analysis of genetic diversity within mung bean accessions from India. A GA/CT enriched library was constructed from V. radiata which resulted in 1,250 putative recombinant clones of which 850 were sequenced. SSR motifs were identified and their flanking sequences were utilized to design 328 SSR primer pairs. Of these, 48 SSR markers were employed for assessing genetic diversity among 76 mung bean accessions from various geographical locations in India. Two hundred and thirty four alleles with an average of 4.85 alleles per locus were detected at 48 loci. The polymorphic information content (PIC) per locus varied from 0.1 to 0.88 (average: 0.49 per locus). The observed and expected heterozygosities ranged from 0.40 to 0.95 and 0.40 to 0.81 respectively. Based on Jaccard's similarity matrix, a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA) analysis which revealed that one accession from Bundi, Rajasthan was clustered out separately while remaining accessions were grouped into two major clusters. The markers generated in this study will help in expanding the repertoire of the available SSR markers thereby facilitating analysis of genetic diversity, molecular mapping and ultimately broadening the scope for genetic improvement of this legume.

Isolation and characterization of nine polymorphic microsatellite loci in Piper solmsianum (piperaceae).

• Premise of the study: Nine microsatellite (simple sequence repeat [SSR]) loci were characterized for natural populations of Piper solmsianum, a potential source of bioactive secondary metabolites, and analyzed to assess the levels of genetic diversity in this species.• Methods and Results: Based on an enriched library using the oligonucleotides (CT)8 and (GT)8, a total of 19 pairs of SSR primers were designed and nine of them were highly polymorphic after screening of 37 specimens from two populations. The number of alleles per locus ranged from one to six while the observed heterozygosity for polymorphic loci ranged from 0.000 to 0.875.• Conclusions: The SSR regions characterized were informative, and the genetic markers will be useful to assess the genetic diversity and gene flow in populations of P. solmsianum.

Assessment of genetic diversity of Korean Miscanthus using morphological traits and SSR markers

Miscanthus is a potential bioenergy crop due to its C4 perennial growth, rhizomatous propagation, and relatively great resistance to abiotic stress. To obtain genetic diversity for future breeding program, we collected over 69 accessions of miscanthus germplasm from Korea and other East Asian regions and performed morphology-based phenotyping and SSR-based genotyping. There are two distinctive species groups, Miscanthus sinensis and Miscanthus sacchariflorus, the most considered two parental candidates for breeding of high yield cultivars, in both morphological trait and SSR marker analyses. Among 14 morphological traits, we found that three major traits, namely the presence of awn in spikelet, the ratio between the callus hair and spikelet, and new shoot emergence in autumn. In addition, a total of 164 amplicons generated from 31 SSR primer pairs, which were selected out of 122 SSRs, were used to cluster and evaluate the genetic variation and relationships among 69 accessions. The accessions were classified by species followed by region in SSR analysis. Our results suggested that phylogenetic analyses using morphological traits and SSR markers are effective for the diversity assessment and identification of phylogenic groups of Miscanthus species. This phylogenetic group based on morphological traits and SSR markers will provide effective parental selection for future breeding of a highly productive miscanthus cultivar. However, the inconsistency between phylogenic trees using morphological traits and SSR analyses requires further studies using additional SSR markers derived from the miscanthus genome sequence to provide better insight and understanding of the genetic diversity of miscanthus.

Assessment and characterization of genetic relationships of walnut (Juglans regia L.) genotypes by three types of molecular markers

Turkey has a rich walnut germplasm that has arisen from populations of naturally grown seedlings over many years. Despite this enormous genetic potential, only a few studies on molecular characterization studies have been carried out so far. In this study, the genetic relationships among 59 walnut genotypes and cultivars of international and Turkish interest were analyzed by 25 RAPD primers, 25 ISSR primers, and 16 SSR primer pairs. Among the molecular assays tested, SSR provided a very high polymorphism rate of 99.1%, while ISSR and RAPD results showed similar to each other but lower polymorphism (71.1% and 69.1%, respectively). The dendrogram constructed divided the genotypes into three main groups: ‘Group A’ included mainly genotypes originating from the Kahramanmaras and Yalova provinces, while ‘Group B’ contained genotypes originating from the Kırsehir, Tokat and Corum provinces of Turkey. ‘Group C’ contained only cultivars originating from the USA and France. According to the clustering in the dendrogram genotypes grouped largely in accordance with their geographical origin, although certain exceptions were present. The pairs of ‘Akca-2’ with ‘Karabodur’ and ‘Yalova-1’ with ‘Yalova-3’ were the most closely related walnut genotypes in this study. In conclusion, our study indicated that molecular markers are useful tools for use in to determining genetic relationships among walnut genotypes. The results will provide valuable information to walnut cultivar breeding programs for use in parental selection.

Genetic diversity and structure of natural populations of Gossypium mustelinum, a wild relative of cotton, in the basin of the De Contas River in Bahia, Brazil

Gossypium mustelinum is a wild cotton relative found only in the semiarid region of Bahia state in Brazil, and changes caused by humans in the natural habitat of this species have endangered the existence of several natural populations. Information about the occurrence and genetic composition of these populations is necessary to design effective conservation measures. The aim of this study was to characterize the in situ maintenance mode and assess the genetic diversity of G. mustelinum populations in the basin of the De Contas River. A sample of 205 G. mustelinum specimens was collected from the margins of the Jacaré, Riacho Quixaba, Riacho Serra Azul, and Riacho Riachão rivers and genotyped using 13 SSR primer pairs. In general, all G. mustelinum populations exhibit inadequate in situ maintenance, predominantly due to the deforestation of riparian vegetation and herbivory. The observed total genetic diversity of G. mustelinum was significant (H E = 0.489), highly structured (F ST = 0.534), and organized in homozygous genotypes (F IS = 0.873). The high observed inbreeding level is consistent with the predominance of self-fertilization and geitonogamy (t m = 0.234). In addition, the pattern of genetic structure tended to form groups that coincided with the collection sites, i.e., first clustering within subpopulations, then within populations, and finally within the closest populations. Thus, the observed genetic diversity is likely to be rapidly lost, and conservation measures should therefore be undertaken.

Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.

BackgroundFoxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops. Therefore, cost-effective, reliable and highly polymorphic molecular markers covering the entire genome are required for diversity, mapping and functional genomics studies in this model species.ResultA total of 5,020 highly repetitive microsatellite motifs were isolated from the released genome of the genotype 'Yugu1’ by sequence scanning. Based on sequence comparison between S. italica and S. viridis, a set of 788 SSR primer pairs were designed. Of these primers, 733 produced reproducible amplicons and were polymorphic among 28 Setaria genotypes selected from diverse geographical locations. The number of alleles detected by these SSR markers ranged from 2 to 16, with an average polymorphism information content of 0.67. The result obtained by neighbor-joining cluster analysis of 28 Setaria genotypes, based on Nei’s genetic distance of the SSR data, showed that these SSR markers are highly polymorphic and effective.ConclusionsA large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria. The large number of new SSR markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species.

Genetic variation and an estimation of effective population size in the pearl oyster Pinctada martensii

In September 2011, two wild populations of pearl oysters were collected separately from Daya Bay, Shenzhen, and from Beibu Bay, Beihai, China. In April 2012, three cultured stocks were established by sampling breeders from the third-generation selected lines. The genetic variation within the five stocks was analyzed using eight SSR primer pairs. The effective population sizes of the five stocks were analyzed using the sibship reconstruction and multiple summary statistics methods. A total of 22–29 alleles were observed in the five stocks, with two to five alleles per locus and means ranging from 2.750 to 3.625 alleles per locus. The average expected and observed heterozygosities ranged from 0.3387 to 0.5029 and from 0.2917 to 0.4219, respectively. The effective population sizes of the five stocks ranged from 11.0 to 20.0 when estimated using sibship reconstruction and from 13.7 to 179.4 when estimated using multiple summary statistics. The effective population sizes estimated in the three cultured stocks were smaller than the number of breeders used to produce these stocks. Thus, it may be necessary to augment the number of breeders used to produce progeny stocks in selective breeding programs.

Genetic diversity of central and peripheral populations of Toona ciliata var. pubescens, an endangered tree species endemic to China.

Our objective was to examine the genetic diversity of central and peripheral populations of Toona ciliata var. pubescens, to elucidate whether the central-peripheral hypothesis applies to these populations. We analyzed 392 individuals from nine natural populations using eight pairs of polymorphic SSR primers. The results showed that the mean numbers of observed and expected alleles in peripheral populations were higher than in central populations. Common widespread and rare local (RL) alleles were observed in all populations. However, common local alleles were found in five populations and rare widespread alleles were only found in three. The total numbers of the four types of alleles were higher in peripheral than in central populations, and the quantity of the RL allele was obviously higher in the peripheral populations than in the central populations. Both the observed and expected heterozygosities were higher in peripheral populations compared with the central populations. The coefficient of gene differentiation of the peripheral populations was 0.3045, which was significantly higher than that of the central populations. The gene flow between central populations was greater than one, but less than one between peripheral populations. This indicates that frequent gene flow exists between central populations, while terrain and habitat fragmentation prevent gene flow between peripheral populations. A Mantel test indicated that there was no relationship between genetic and geographical distance of T. ciliata var. pubescens.