Biology subjects

Zalapa, J.

Publications and source records attributed to Zalapa, J..

5 recordsLinked to original sources

bioRxiv2023

Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

genomics↗

bioRxiv2019

Pacbio sequencing reveals identical organelle genomes between American cranberry (Vaccinium macrocarpon 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, and given their northern distribution, 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, 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.

genomics↗

bioRxiv2019

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

Cranberry (Vaccinium macrocarpon Ait.) fruit quality traits encompass many properties. Among these, fruit firmness has become a quality standard due to the recent demand increase for sweetened and dried cranberries (SDC). 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. 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. Internal structure data paired with fruit firmness values at each evaluation period allowed us to explore the correlations between firmness and internal morphological characteristics.

plant biology↗

bioRxiv2016

SOFIA: an R package for enhancing genetic visualization with Circos

Visualization of data from any stage of genetic and genomic research is one of the most useful approaches for detecting potential errors, ensuring accuracy and reproducibility, and presentation of the resulting data. Currently software such as Circos, ClicO FS, and RCircos, among others, provide tools for plotting a variety of genetic data types in a concise manner for data exploration and presentation. However, each of the programs have one or more disadvantages that limit their usability in data exploration or construction of publication quality figures, such as inflexibility in formatting and configuration, reduced image quality, lack of potential for automation, or requirements of high-level computational expertise. Therefore, we developed the R package SOFIA, which leverages the capabilities of Circos by manipulating data, preparing configuration files, and running the Perl-native Circos directly from the R environment with minimal user intervention. The advantages of integrating both R and Circos into SOFIA are numerous. R is a very powerful, mid-level programming language widely used among the genetic and genomic research community, while Circos has proven to be a novel software for arranging genomic data to create aesthetical publication quality circular figures. Producing Circos figures in R with SOFIA is simple, requires minimal coding experience, even for complex figures that incorporate high-dimensional genetic information, and allows simultaneous analysis and visual exploration of genomic and genetic data in a single programming environment.

genetics↗

bioRxiv2016

Construction of a high-density American cranberry (Vaccinium macrocarpon Ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping

The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three inter-related cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman Rank Correlations > 0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry.

genomics↗