Transferability and characterization of simple sequence repeat markers from Anacardium occidentale to A. humile (Anacardiaceae)

Analysis of radiographic images and germination of Campomanesia pubescens (Mart. ex DC.) O.Berg (Myrtaceae Juss.) seeds under drying

The objective of this study was to evaluate the internal morphology of seeds of Campomanesia pubescens (Mart. ex DC.) O. Berg with varying water content through X-ray image analysis, and correlate the images with the germination of these seeds. Fruits were collected in Jataí, Goiás, Brazil, and taken to the Seed Laboratory of the Federal Institute Goiano, Rio Verde Campus, where they were processed and the seeds were extracted. To establish the predetermined water content (43%, 37%, 34%, 31%, and 28% wet basis), seeds with an initial water content of 43% were kept in an oven with forced air circulation at a temperature of 40 °C until they reached the predetermined water content levels. Next, the seeds were placed in acrylic holders with double-sided tape and transported to the Federal University of Lavras (UFLA), where they were exposed to different intensities of radiation. The X-ray test was conducted with 200 seeds per treatment, and images of the internal structures of the seeds were evaluated. The seeds were returned to the Seed Laboratory of the Federal Institute Goiano, Rio Verde Campus, where the germination test was initiated. The experimental design was completely randomized, in a factorial design (5 × 4), in which there were five water content levels and four seed classes, with four replications. The X-ray test was efficient in the identification of filled, malformed, damaged and empty seeds, which germination rate above 50% in the filled seeds. This visualization of the internal morphology of the seed can be useful to select seeds of better quality, improving the percentage of germination of C. pubescens seeds.

Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis

BACKGROUND

Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections.

RESULTS

A total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis clustered in another group. Furthermore, structure analysis was consistent with the dendrogram indicating the 134 watermelon accessions were classified into two populations.

CONCLUSION

The large number of genome wide SSR markers developed herein from the watermelon genome provides a valuable resource for genetic map construction, QTL exploration, map-based gene cloning and marker-assisted selection in watermelon which has a very narrow genetic base and extremely low polymorphism among cultivated lines. Furthermore, the cross-species transferable SSR markers identified herein should also have practical uses in many applications in species of Cucurbitaceae family whose whole genome sequences are not yet available.

Transferability of cucumber microsatellite markers used for phylogenetic analysis and population structure study in bottle gourd (Lagenaria siceraria (Mol.) Standl.)

Improved breeding for developing fruit quality in bottle gourd (Lagenaria siceraria (Mol.) Standl.) necessitates knowledge regarding its genetic diversity. To achieve this, a set of 108 locus-specific SSR markers has been developed in bottle gourd by cross-species transferability from 995 mapped Cucumis sativus SSR markers. During screening, 280 primer pairs amplified in the bottle gourd germplasm, which were further evaluated in a diverse set of 42 lines, resulting in 19 polymorphic, 89 monomorphic, 15 with multiple bands, and the rest 157 showed no or very non-specific amplification. The 19 polymorphic primer pairs produced a total of 54 alleles. Gene diversity, Shannon's information index, and Nei's coefficient of differentiation were calculated suggesting a moderate genetic variation at the species level. A model-based population structure analysis divided these germplasm into two subpopulations. This marker set will be applicable for evaluating the genetic structure for association mapping, DNA fingerprinting, and mounting linkage maps and will be a practical tool set for further genetics. This study provides one of the first quantitative views of population genetic variation in bottle gourd.