Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding

Quantitative Trait Loci Analysis and Marker Development for Fruit Rot Resistance in Cranberry Shows Potential Genetic Association with Epicuticular Wax

Fruit rot is a fungal disease complex that threatens cranberry yields in North American growing operations. Management of fruit rot is especially difficult because of the diversity of the infecting fungal species, and although infections take place early in the season, the pathogens usually remain latent in the ovary until the fruit ripen. Control methods heavily rely on fungicide applications, a practice that may be limited in viability long term. Breeding for fruit rot resistance (FRR) is essential for sustainable production. It is likely that field resistance is multifaceted and involves a myriad of traits that fortify cranberry plants against the biotic and abiotic stresses contributing to fruit rot. In this study, we identified quantitative trait loci (QTL) for FRR in a segregating population. Interestingly, a QTL associated with resistance was found to overlap with one associated with fruit epicuticular wax (ECW). A single-nucleotide polymorphism genotyping assay successfully identified accessions that exhibit the desired phenotypes (i.e., less rot and more ECW), thus making it a useful tool for marker-assisted selection. Candidate genes that may contribute to FRR and ECW were also identified. This work will expedite breeding for improved cranberry fruit quality.

Unveiling the evolutionary history of lingonberry (Vaccinium vitis-idaea L.) through genome sequencing and assembly of European and North American subspecies

Lingonberry (Vaccinium vitis-idaea L.) produces tiny red berries that are tart and nutty in flavor. It grows widely in the circumpolar region, including Scandinavia, northern parts of Eurasia, Alaska, and Canada. Although cultivation is currently limited, the plant has a long history of cultural use among indigenous communities. Given its potential as a food source, genomic resources for lingonberry are significantly lacking. To advance genomic knowledge, the genomes for 2 subspecies of lingonberry (V. vitis-idaea ssp. minus and ssp. vitis-idaea var. 'Red Candy') were sequenced and de novo assembled into contig-level assemblies. The assemblies were scaffolded using the bilberry genome (Vaccinium myrtillus) to generate a chromosome-anchored reference genome consisting of 12 chromosomes each with a total length of 548.07 Mb [contig N50 = 1.17 Mb, BUSCO (C%) = 96.5%] for ssp. vitis-idaea and 518.70 Mb [contig N50 = 1.40 Mb, BUSCO (C%) = 96.9%] for ssp. minus. RNA-seq-based gene annotation identified 27,243 and 25,718 genes on the respective assembly, and transposable element detection methods found that 45.82 and 44.58% of the genome were repeats. Phylogenetic analysis confirmed that lingonberry was most closely related to bilberry and was more closely related to blueberries than cranberries. Estimates of past effective population size suggested a continuous decline over the past 1-3 MYA, possibly due to the impacts of repeated glacial cycles during the Pleistocene leading to frequent population fragmentation. The genomic resource created in this study can be used to identify industry-relevant genes (e.g. anthocyanin production), infer phylogeny, and call sequence-level variants (e.g. SNPs) in future research.

Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies

A variety of plant species found in nature contain agrobacterial T-DNAs in their genomes which they transmit in a series of sexual generations. Such T-DNAs are called cellular T-DNAs (cT-DNAs). cT-DNAs have been discovered in dozens of plant genera, and are suggested to be used in phylogenetic studies, since they are well-defined and unrelated to other plant sequences. Their integration into a particular chromosomal site indicates a founder event and a clear start of a new clade. cT-DNA inserts do not disseminate in the genome after insertion. They can be large and old enough to generate a range of variants, thereby allowing the construction of detailed trees. Unusual cT-DNAs (containing the rolB/C-like gene) were found in our previous study in the genome data of two Vaccinium L. species. Here, we present a deeper study of these sequences in Vaccinium L. Molecular-genetic and bioinformatics methods were applied for sequencing, assembly, and analysis of the rolB/C-like gene. The rolB/C-like gene was discovered in 26 new Vaccinium species and Agapetes serpens (Wight) Sleumer. Most samples were found to contain full-size genes. It allowed us to develop approaches for the phasing of cT-DNA alleles and reconstruct a Vaccinium phylogenetic relationship. Intra- and interspecific polymorphism found in cT-DNA makes it possible to use it for phylogenetic and phylogeographic studies of the Vaccinium genus.

Cranberry fruit epicuticular wax benefits and identification of a wax-associated molecular marker

BACKGROUND

As the global climate changes, periods of abiotic stress throughout the North American cranberry growing regions will become more common. One consequence of high temperature extremes and drought conditions is sunscald. Scalding damages the developing berry and reduces yields through fruit tissue damage and/or secondary pathogen infection. Irrigation runs to cool the fruit is the primary approach to controlling sunscald. However, it is water intensive and can increase fungal-incited fruit rot. Epicuticular wax functions as a barrier to various environmental stresses in other fruit crops and may be a promising feature to mitigate sunscald in cranberry. In this study we assessed the function of epicuticular wax in cranberries to attenuate stresses associated with sunscald by subjecting high and low epicuticular wax cranberries to controlled desiccation and light/heat exposure. A cranberry population that segregates for epicuticular wax was phenotyped for epicuticular fruit wax levels and genotyped using GBS. Quantitative trait loci (QTL) analyses of these data identified a locus associated with epicuticular wax phenotype. A SNP marker was developed in the QTL region to be used for marker assisted selection.

RESULTS

Cranberries with high epicuticular wax lost less mass percent and maintained a lower surface temperature following heat/light and desiccation experiments as compared to fruit with low wax. QTL analysis identified a marker on chromosome 1 at position 38,782,094 bp associated with the epicuticular wax phenotype. Genotyping assays revealed that cranberry selections homozygous for a selected SNP have consistently high epicuticular wax scores. A candidate gene (GL1-9), associated with epicuticular wax synthesis, was also identified near this QTL region.

CONCLUSIONS

Our results suggest that high cranberry epicuticular wax load may help reduce the effects of heat/light and water stress: two primary contributors to sunscald. Further, the molecular marker identified in this study can be used in marker assisted selection to screen cranberry seedlings for the potential to have high fruit epicuticular wax. This work serves to advance the genetic improvement of cranberry crops in the face of global climate change.

Crop Wild Relatives: A Valuable Source of Tolerance to Various Abiotic Stresses

Global climate change is one of the major constraints limiting plant growth, production, and sustainability worldwide. Moreover, breeding efforts in the past years have focused on improving certain favorable crop traits, leading to genetic bottlenecks. The use of crop wild relatives (CWRs) to expand genetic diversity and improve crop adaptability seems to be a promising and sustainable approach for crop improvement in the context of the ongoing climate challenges. In this review, we present the progress that has been achieved towards CWRs exploitation for enhanced resilience against major abiotic stressors (e.g., water deficiency, increased salinity, and extreme temperatures) in crops of high nutritional and economic value, such as tomato, legumes, and several woody perennial crops. The advances in -omics technologies have facilitated the elucidation of the molecular mechanisms that may underlie abiotic stress tolerance. Comparative analyses of whole genome sequencing (WGS) and transcriptomic profiling (RNA-seq) data between crops and their wild relative counterparts have unraveled important information with respect to the molecular basis of tolerance to abiotic stressors. These studies have uncovered genomic regions, specific stress-responsive genes, gene networks, and biochemical pathways associated with resilience to adverse conditions, such as heat, cold, drought, and salinity, and provide useful tools for the development of molecular markers to be used in breeding programs. CWRs constitute a highly valuable resource of genetic diversity, and by exploiting the full potential of this extended allele pool, new traits conferring abiotic-stress tolerance may be introgressed into cultivated varieties leading to superior and resilient genotypes. Future breeding programs may greatly benefit from CWRs utilization for overcoming crop production challenges arising from extreme environmental conditions.

Predicted impacts of climate change on wild and commercial berry habitats will have food security, conservation and agricultural implications

Climate change is now a reality and is altering ecosystems, with Canada experiencing 2-4 times the global average rate of warming. This will have a critical impact on berry cultivation and horticulture. Enhancing our understanding of how wild and cultivated berries will perform under changing climates will be essential to mitigating impacts on ecosystems, culture and food security. Our objective was to predict the impact of climate change on habitat suitability of four berry producing Vaccinium species: two species with primarily northern distributions (V. uliginosum, V. vitis-idaea), one species with a primarily southern distribution (V. oxycoccos), and the commercially cultivated V. macrocarpon. We used the maximum entropy (Maxent) model and the CMIP6 shared socioeconomic pathways (SSPs) 126 and 585 projected to 2041-2060 and 2061-2080. Wild species showed a uniform northward progression and expansion of suitable habitat. Our modeling predicts that suitable growing regions for commercial cranberries are also likely to shift with some farms becoming unsuitable for the current varieties and other regions becoming more suitable for cranberry farms. Both V. macrocarpon and V. oxycoccos showed a high dependence on precipitation-associated variables. Vaccinium vitis-idaea and V. uliginosum had a greater number of variables with smaller contributions which may improve their resilience to individual climactic events. Future competition between commercial cranberry farms and wild berries in protected areas could lead to conflicts between agriculture and conservation priorities. New varieties of commercial berries are required to maintain current commercial berry farms.

Genomic-environmental associations in wild cranberry (Vaccinium macrocarpon Ait.)

Understanding the genetic basis of local adaptation in natural plant populations, particularly crop wild relatives, may be highly useful for plant breeding. By characterizing genetic variation for adaptation to potentially stressful environmental conditions, breeders can make targeted use of crop wild relatives to develop cultivars for novel or changing environments. This is especially appealing for improving long-lived woody perennial crops such as the American cranberry (Vaccinium macrocarpon Ait.), the cultivation of which is challenged by biotic and abiotic stresses. In this study, we used environmental association analyses in a collection of 111 wild cranberry accessions to identify potentially adaptive genomic regions for a range of bioclimatic and soil conditions. We detected 126 significant associations between SNP marker loci and environmental variables describing temperature, precipitation, and soil attributes. Many of these markers tagged genes with functional annotations strongly suggesting a role in adaptation to biotic or abiotic conditions. Despite relatively low genetic variation in cranberry, our results suggest that local adaptation to divergent environments is indeed present, and the identification of potentially adaptive genetic variation may enable a selective use of this germplasm for breeding more stress-tolerant cultivars.

Core circadian clock and light signaling genes brought into genetic linkage across the green lineage

The circadian clock is conserved at both the level of transcriptional networks as well as core genes in plants, ensuring that biological processes are phased to the correct time of day. In the model plant Arabidopsis (Arabidopsis thaliana), the core circadian SHAQKYF-type-MYB (sMYB) genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and REVEILLE (RVE4) show genetic linkage with PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7, respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis enabled tracing this genetic linkage back to Amborella trichopoda, a sister lineage to the angiosperm, and identifying an additional evolutionarily conserved genetic linkage in light signaling genes. The LHY/CCA1-PRR5/9, RVE4/8-PRR3/7, and PIF3-PHYA genetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of angiosperm families representing distinct whole-genome duplication and fractionation events. Soybean (Glycine max) maintained all but two genetic linkages, and expression analysis revealed the PIF3-PHYA linkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase, in contrast to the sMYB-PRR morning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae), such as maize (Zea mays), where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation of PRR7 paralogs across heterotic groups. The environmental robustness model is put forward, suggesting that evolutionarily conserved genetic linkages ensure superior microhabitat pollinator synchrony, while wide-hybrids or unlinking the genes, as seen in the grasses, result in heterosis, adaptation, and colonization of new ecological niches.

There and back again; historical perspective and future directions for Vaccinium breeding and research studies

The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have increased worldwide over the crops' relatively short domestication history (~100 years). Other species, including bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and ohelo berry (Vaccinium reticulatum) are largely still harvested from the wild but with crop improvement efforts underway. Here, we present a review article on these Vaccinium berry crops on topics that span taxonomy to genetics and genomics to breeding. We highlight the accomplishments made thus far for each of these crops, along their journey from the wild, and propose research areas and questions that will require investments by the community over the coming decades to guide future crop improvement efforts. New tools and resources are needed to underpin the development of superior cultivars that are not only more resilient to various environmental stresses and higher yielding, but also produce fruit that continue to meet a variety of consumer preferences, including fruit quality and health related traits.