Seven Simple Sequence Repeat Research Articles

MICROSATELLITE-BASED CHARACTERIZATION OF TRADITIONAL CHESTNUT CULTIVARS OF ITALY

Cultivation of chestnut (Castanea sativa) has a long tradition in Italy, where traditional cultivars have been selected over centuries in function of the best nut traits. Nevertheless, these traditional cultivars are usually described and classified according to geographic origin, ripening period and type of use, thus making cataloguing very difficult. In this work, 87 grafted chestnuts corresponding to 26 cultivar names from Italy were evaluated by seven simple sequence repeats (SSRs) loci to establish if they correspondance to clones. The results showed 20 different genotypes, and 52 alleles were identified, eight of which were exclusive. Some cases of homonymies and synonymies were detected. It was stated that 'Marrone-type' cultivars displayed a considerable genetic uniformity. These results highlighted a high genetic diversity within the material studied and revealed the existence of valuable germplasm within these Italian traditional cultivars.

Genetic variability characterisation of Tanzania sorghum landraces based on simple sequence repeats (ssrs) molecular and morphological markers

Morphological and molecular markers were employed to study the genetic variability among 40 sorghum landraces collected from Tanzania and two from Zambia. A total of 14 morphological markers and seven simple sequence repeats (SSRs) primers were used to (i) determine the genetic relationships among landraces, and (ii) assessimportant agronomic traits. Five principal components accounted for 73.60% of the total variability. There were positive significant correlation between yield and inflorescence width (r = 0.343*), five panicles averages and plot yields (r = 0. 531*), leaf senescence and inflorescence length (r = 0.355*). Negative significant correlationbetween tiller numbers and inflorescence length (r = -0.343*) was recorded. Cluster analysis based on morphological traits revealed three major distinct groups with one landrace forming independent cluster. Based on molecular markers, eleven clusters were observed. Sorghum controls, N13, Ochuti and Adiwo each formed independent clusters. Markers Xgap84 and Xtxp320 had high alleles than other markers. These had seven and eight alleles respectively. Molecular markers clearly separated landraces within and between groups than morphological markers. There were no genotype specific makers with the exceptions of Ochuti and N13 controls.

Combining different resistance components enhances resistance to Fusarium head blight in spring wheat

Fusarium head blight (FHB) is a devastating disease in wheat throughout the world. FHB resistance consists of two components: resistance to initial infection (type I) and resistance to spread within infected spikes (type II). Current wheat breeding programs for FHB focus on type II resistance, which limits pathogen spread but may not be sufficiently durable. To combine type I with existing type II resistance, 113 F9-derived recombinant inbred lines (RILs) were developed from a cross between three wheat genotypes Frontana, W9207, and Alsen. The RILs were evaluated for resistance to initial infection, FHB spread within spike, kernel damage, and deoxynivalenol (DON) content in two independent greenhouse experiments in 2006 and 2007. Among the 113 RILs, 20% lines showed ≤10% initial disease severity (IDS) and ≤11 to 30% final disease severity (FDS), and 19% had DON content ≤5 μg/g. Approximately 11% of the RILs showed tendency of higher resistance (as exhibited by lower IDS, FDS, and DON content) than the resistant parents. The 42 of the FHB-resistant RILs were analyzed with seven simple sequence repeat (SSR) markers or microsatellites known to be linked to FHB resistance. Approximately half of the RILs had molecular markers linked to both types of FHB resistance indicated the presence of type I and II resistance alleles in the RILs. The resistant RILs identified in this study should be useful for the future improvement of FHB resistance in spring wheat.

Adaptation and selection in theSenecio(Asteraceae) hybrid zone on Mount Etna, Sicily

Hybrid zone theory provides a powerful theoretical framework for measuring and testing gene flow and selection. The Senecio aethnensis and Senecio chrysanthemifolius hybrid zone on Mount Etna, Sicily, was investigated to identify phenotypic traits under divergent selection and to assess the contributions of intrinsic and extrinsic selection against hybrids to hybrid zone maintenance. Senecio samples from 14 sites across Mount Etna were analyzed for 24 quantitative traits classified into four groups (QTGs), six allozymes and seven simple sequence repeat (SSR) loci to describe patterns of variation throughout the hybrid zone. Narrower cline widths or shifts in cline centre position were observed for three QTGs relative to the molecular clines, indicating that these traits are likely to be under extrinsic environmental selection. Altitude was key to describing species distributions, but dispersal and intrinsic selection against hybrids explained patterns at smaller spatial scales. The hybrid zone was characterized by strong selection against hybrids, high dispersal rates, recent species contact and few loci differentiating QTGs based on indirect measures. These results support the hypothesis that extrinsic and intrinsic selection against hybrids maintains the hybrid zone and species distinctiveness despite gene flow between the two Senecio species on Mount Etna.

Effects of landscape and demographic history on genetic variation in Picea glehnii at the regional scale

AbstractTo evaluate the effects of landscape and demographic history on genetic variation in Picea glehnii at a regional scale we have investigated the genetic diversity and genetic differentiation of P. glehnii populations in the Furano region, central Hokkaido, Japan, using seven simple sequence repeat (SSR) markers. We found significant correlations between elevation and genetic diversity parameters. The value of A[46] increased and the value of FIS decreased with increasing elevation, while FIS values were not significantly different from 0 in any of the populations. Significant recent bottlenecks were detected for isolated populations at low‐elevation sites and for relatively large populations at moderate‐ and high‐elevation sites. Evolutionary events pre‐dating the Holocene should be taken into consideration, as elevational gradients should be with respect to locally adapted traits such as flowering phenology, However, the palynological data from the Holocene in this region suggest that the distribution pattern of genetic diversity of P. glehnii detected here may have been influenced by past demographic history related to the elevation shifts in this species’ distribution associated with climate change during this period. Population differentiation was low, with FST and G′ST values of 0.022 and 0.065, respectively. However, genetic boundaries were detected around one swamp population (C13). Therefore, significant isolation by distance (IBD) was not detected when all populations were considered, but there was significant IBD when the C13 population was excluded. Information on genetic diversity and genetic differentiation at the regional scale may be useful for selecting seed sources for afforestation programs for P. glehnii.

Construction of a BAC library from cucumber ( Cucumis sativus L.) and identification of linkage group specific clones

A bacterial artificial chromosome (BAC) library consisting of 19,200 clones with an average insert size of 105 kb has been constructed from a cucumber ( Cucumis sativus L.) inbred line S94, derived from a cultivar in North China. The entire library was equivalent to approximately 5 haploid cucumber genomes. To facilitate chromosome engineering and anchor the cucumber genetic linkage map to its chromosomes, 15 sequence-characterized amplified regions (SCAR) and seven simple sequence repeats (SSR) markers from each linkage group of cucumber were used to screen an ordered array of pooled BAC DNA with polymerase chain reaction (PCR). Fifteen markers gave at least two positive clones. As a result, 22 BAC clones representing 7 linkage groups of cucumber were identified, which further validated the genome coverage and utility of the library. This BAC library and linkage group specific clones provide essential resources for future research of the cucumber genome.

The distribution of genetic variation in Norway spruce (Picea abies Karst.) populations in the western Alps

AbstractAim In order to look for a possible centre of survival for the Norway spruce (Picea abies Karst.) in the south‐western Alps, six natural populations of this area were investigated by means of genetic markers in order to assess the degree and the distribution of genetic diversity within the species.Location Western and South‐western Alps.Methods Populations were genotyped using seven simple sequence repeat (SSR) markers. Basic population genetics parameters were estimated and the amount of genetic differentiation calculated.Results A large amount of variability was found (0.59 < He < 0.67); genetic differentiation as measured by FST was 0.05, close to other similar studies; no isolation by distance was detected by a Mantel test. Analysis of molecular variance confirmed a high degree of variability within populations and a low degree of variability among populations. Finally, the number of populations from which those observed could have arisen was estimated by Bayesian analysis.Main conclusions The results presented here suggest that the present populations derive their genetic make‐up from three inferred clusters. The possible existence in this area of a relict/refuge population during the last glaciation is discussed.

Production of haploids and double haploids in annual (Lolium multiflorum) and perennial (L. perenne) ryegrasses

Anthers from 32 genotypes from one line of annual ryegrass (Lolium multiflorum) and 229 genotypes from 15 cultivars of perennial ryegrass (L. perenne) were tested for the production of haploids and double haploids. Six (23%) annual and 71 (31%) perennial ryegrass genotypes produced calli ranging from 1.3-16% and 0.8- 12.2% respectively. However none of the annual ryegrass genotypes produced green plants and only one genotype (Option WH-1) of perennial ryegrass produced 16 (1.8%) green plants. The remaining produced only albino regenerates. Twelve of the 16 green plants were evaluated cytologically for chromosome numbers. Four were haploids thus confirming their origin from haploid pollen. The remaining eight were all diploids. One haploid and one diploid were tested for their homozygous condition using seven simple sequence repeat (SSR) markers and were found to be homozygous at all seven loci. In order to increase the recovery of green regenerates, we have used the responsive genotype Option WH-1 in crosses with three other perennial ryegrass genotypes and the progenies are currently been grown for anther culture

DNA fingerprinting of apple (Malus spp.) rootstocks using Simple Sequence Repeats

Identification of apple clonal rootstocks based on visual morphological characteristics is often difficult because of the genetic similarity of many rootstocks and the restriction of observable characteristics at the nursery stage. In this study, a total of 66 rootstock clones representing a sub-sample of a collection of apple rootstocks from different countries maintained at NIFTS, Morioka, Japan, was screened with seven simple sequence repeat (SSR) markers to establish genetic identities, estimate genetic diversity, verify parentage and examine genetic relationships. All seven SSR loci produced one or two amplified fragments and made it possible to differentiate among the rootstocks, except between virus-free subclones and their original parents as well as between ‘Aotea 40’ and ‘Aotea 106’. The parentage of all but one rootstock clone was confirmed. The placement of individual rootstock clones into subgroups in a phenogram generated from un-weighted pair group average cluster analysis was generally based on parentage or genetic origin. Based upon the ability of the SSR data to differentiate these apple rootstocks and the high level of gene diversity, it is proposed that all commercial apple rootstocks be fingerprinted to provide a mechanism to verify the identity of individual clones.

Geographic isolation of Diplodia scrobiculata and its association with native Pinus radiata

Diplodia pinea (syn. Sphaeropsis sapinea) is a well-known latent pathogen of Pinus spp. with a worldwide distribution. As such, this fungus is native where pines are endemic in the northern hemisphere and it has been introduced into all countries of the Southern Hemisphere where pines are exotic. The newly described D. scrobiculata (formerly known as the B morphotype of D. pinea) is thought to have a much more limited distribution. D. scrobiculata was first reported as an endophyte and weak pathogen of P. banksiana, where it was found to coexist with D. pinea. Diplodia scrobiculata is now known to have a much broader distribution in Northern America and Europe. In this study, seven Simple Sequence Repeat (SSR) markers were used to evaluate genetic diversity and gene flow between populations of D. scrobiculata. Results indicate a strong geographic isolation between populations of D. scrobiculata from different regions in North America, with unique alleles fixed in the different populations. The data fits the isolation by distance model indicating limited dispersal. Geographic isolation in combination with isolation by distance suggests prolonged reproductive isolation. Intensive collections of endophytes from native P. radiata in California have yielded only D. scrobiculata and not the significantly more pathogenic D. pinea. SSR analysis of three populations of D. scrobiculata from native P. radiata identified many shared alleles among the populations and moderate to high gene flow between them. The three Californian populations are distant and distinct from populations of D. scrobiculata from elsewhere. Under stress conditions, P. radiata is known to be very susceptible to D. pinea in plantations in the Southern Hemisphere. Native P. radiata is currently experiencing severe stress due to pitch canker caused by Fusarium circinatum. Such stress would provide ideal conditions for an associated outbreak of D. pinea. Thus, it is critical to prevent the movement of D. pinea into the last remaining native stands of P. radiata.

Transmission disequilibrium mapping at the serotonin transporter gene (SLC6A4) region in autistic disorder.

The serotonin transporter gene (SLC6A4, MIM 182138) is a candidate gene in autistic disorder based on neurochemical, neuroendocrine studies and the efficacy of potent serotonin transporter inhibitors in reducing ritualistic behaviors and related aggression. An insertion/deletion polymorphism (5-HTTLPR) in the promoter region and a variable number of tandem repeat polymorphism (VNTR) in the second intron, were previously identified and suggested to modulate transcription. Six previous family-based association studies of SLC6A4 in autistic disorder have been conducted, with four studies showing nominally significant transmission disequilibrium and two studies with no evidence of nominally significant transmission disequilibrium. In the present study, TDT was conducted in 81 new trios. A previous finding of transmission disequilibrium between a haplotype consisting of the 5-HTTLPR and intron 2 VNTR was replicated in this study, but not preferential transmission of 5-HTTLPR as an independent marker. Because of inconsistent transmission of 5-HTTLPR across studies, SLC6A4 and its flanking regions were sequenced in 10 probands, followed by typing of 20 single nucleotide polymorphisms (SNPs) and seven simple sequence repeat (SSR) polymorphisms in 115 autism trios. When individual markers were analyzed by TDT, seven SNP markers and four SSR markers (six SNPs, 5-HTTLPR and the second intron VNTR from promoter 1A through intron 2 of SLC6A4, one SSR from intron 7 of SLC6A4, one SNP from the bleomycin hydrolase gene (BLMH, MIM 602403) and one SSR telomeric to BLMH) showed nominally significant evidence of transmission disequilibrium. Four markers showed stronger evidence of transmission disequilibrium (TDT(max) P = 0.0005) than 5-HTTLPR.