Pacbio Sequencing Reveals Identical Organelle Genomes between American Cranberry (<i>Vaccinium macrocarpon</i> Ait.) and a Wild Relative

Breeding efforts in the American cranberry (Vaccinium macrocarpon Ait.), a North American perennial fruit crop of great importance, have been hampered by the limited genetic and phenotypic variability observed among cultivars and experimental materials. Most of the cultivars commercially used by cranberry growers today were derived from a few wild accessions bred in the 1950s. In different crops, wild germplasm has been used as an important genetic resource to incorporate novel traits and increase the phenotypic diversity of breeding materials. Vaccinium microcarpum (Turcz. ex Rupr.) Schmalh. and V. oxycoccos L., two closely related species, may be cross-compatible with the American cranberry, and could be useful to improve fruit quality such as phytochemical content. Furthermore, given their northern distribution, they could also help develop cold hardy cultivars. Although these species have previously been analyzed in diversity studies, genomic characterization and comparative studies are still lacking. In this study, we sequenced and assembled the organelle genomes of the cultivated American cranberry and its wild relative, V. microcarpum. PacBio sequencing technology allowed us to assemble both mitochondrial and plastid genomes at very high coverage and in a single circular scaffold. A comparative analysis revealed that the mitochondrial genome sequences were identical between both species and that the plastids presented only two synonymous single nucleotide polymorphisms (SNPs). Moreover, the Illumina resequencing of additional accessions of V. microcarpum and V. oxycoccos revealed high genetic variation in both species. Based on these results, we provided a hypothesis involving the extension and dynamics of the last glaciation period in North America, and how this could have shaped the distribution and dispersal of V. microcarpum. Finally, we provided important data regarding the polyploid origin of V. oxycoccos

Comprehensive analysis of the internal structure and firmness in American cranberry (Vaccinium macrocarpon Ait.) fruit.

BACKGROUND:Cranberry (Vaccinium macrocarpon L.) fruit quality traits encompass many properties. Although visual appearance and fruit nutritional constitution have usually been the most important attributes, cranberry textural properties such as firmness have recently gained importance in the industry. Fruit firmness has become a quality standard due to the recent demand increase for sweetened and dried cranberries (SDC), which are currently the most profitable cranberry product. Traditionally, this trait has been measured by the cranberry industry using compression tests; however, it is poorly understood how fruit firmness is influenced by other characteristics. RESULTS:In this study, we developed a high-throughput computer-vision method to measure the internal structure of cranberry fruit, which may in turn influence cranberry fruit firmness. We measured the internal structure of 16 cranberry cultivars measured over a 40-day period, representing more than 3000 individual fruit evaluated for 10 different traits. The internal structure data paired with fruit firmness values at each evaluation period allowed us to explore the correlations between firmness and internal morphological characteristics. CONCLUSIONS:Our study highlights the potential use of internal structure and firmness data as a decision-making tool for cranberry processing, especially to determine optimal harvest times and ensure high quality fruit. In particular, this study introduces novel methods to define key parameters of cranberry fruit that have not been characterized in cranberry yet. This project will aid in the future evaluation of cranberry cultivars for in SDC production

Assessment of Genetic Diversity of Sweet Potato in Puerto Rico

<div><p>Sweet potato (<i>Ipomoea batatas</i> L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand for food and the need for conservation of agricultural and genetic resources. In Puerto Rico (PR), the genetic diversity of sweet potato has been poorly understood, although it has been part of the diet since Pre-Columbus time. Thus, 137 landraces from different localities around PR were collected and subjected to a genetic diversity analysis using 23 SSR-markers. In addition, 8 accessions from a collection grown in Gurabo, PR at the Agricultural Experimental Station (GAES), 10 US commercial cultivars and 12 Puerto Rican accessions from the USDA repository collection were included in this assessment. The results of the analysis of the 23 loci showed 255 alleles in the 167 samples. Observed heterozygosity was high across populations (0.71) while measurements of total heterozygosity revealed a large genetic diversity throughout the population and within populations. UPGMA clustering method revealed two main clusters. Cluster 1 contained 12 PR accessions from the USDA repository collection, while cluster 2 consisted of PR landraces, US commercial cultivars and the PR accessions from GAES. Population structure analysis grouped PR landraces in five groups including four US commercial cultivars. Our study shows the presence of a high level of genetic diversity of sweet potato across PR which can be related to the genetic makeup of sweet potato, human intervention and out-crossing nature of the plant. The history of domestication and dispersal of sweet potato in the Caribbean and the high levels of genetic diversity found through this study makes sweet potato an invaluable resource that needs to be protected and further studied.</p></div

Polymorphic Index Content (PIC) value of the 23 SSR loci analyzed in 167 accessions of sweet potato (<i>Ipomoea batatas</i>).

<p>Polymorphic Index Content (PIC) value of the 23 SSR loci analyzed in 167 accessions of sweet potato (<i>Ipomoea batatas</i>).</p

Summary statistics of genetic diversity estimators at 23 SSR loci for 167 sweet potato samples.

<p>(NoA: Number of Alleles, H_o: Observed Heterozygosity, H_T: Total Heterozygosity, G_is: Inbreeding Coefficient).</p><p>Summary statistics of genetic diversity estimators at 23 SSR loci for 167 sweet potato samples.</p

Twenty-three SSR marker primers with their respective sequence, annealing temperatures, repeat motifs and allele size.

<p>H_O: Observed heterozygosity.</p><p>H_T: Total heterozygosity.</p><p>SSR Source: ^a Buteler <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116184#pone.0116184-Buteler1" target="_blank">[12]</a>; ^b Tseng <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116184#pone.0116184-Tseng1" target="_blank">[15]</a>; ^c Yañez <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116184#pone.0116184-Yaez1" target="_blank">[18]</a>; ^d Benavides (unpublished data; 2002–2003 at CIP); ^e Solis <i>et al.</i> (unpublished data; 2005–2006 developed at CIP); ^f Yada <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116184#pone.0116184-Yada1" target="_blank">[17]</a>.</p><p>Twenty-three SSR marker primers with their respective sequence, annealing temperatures, repeat motifs and allele size.</p

Distribution of the number of alleles per locus analyzed for 23 SSR loci in 167 accessions of sweet potato (<i>Ipomoea batatas</i>).

<p>Distribution of the number of alleles per locus analyzed for 23 SSR loci in 167 accessions of sweet potato (<i>Ipomoea batatas</i>).</p

Delta K values with respect to K (number of groups) according to the calculation method by Evanno <i>et al</i>. [26].

<p>These results were obtained based on the analysis of 23 SSR markers in 167 accessions of sweet potato from the agricultural experimental station in Gurabo, Puerto Rico (12 accessions), the plant genetic resources conservation unit in Griffin, GA (22 accessions) and 137 Puerto Rico landraces.</p