Sporisorium scitamineum is a biotrophic fungus responsible for the sugarcane smut, a worldwide spread disease. This study provides the complete sequence of individual chromosomes of S. scitamineum from telomere to telomere achieved by a combination of PacBio long reads and Illumina short reads sequence data, as well as a draft sequence of a second fungal strain. Comparative analysis to previous available sequences of another strain detected few polymorphisms among the three genomes. The novel complete sequence described herein allowed us to identify and annotate extended subtelomeric regions, repetitive elements and the mitochondrial DNA sequence. The genome comprises 19,979,571 bases, 6,677 genes encoding proteins, 111 tRNAs and 3 assembled copies of rDNA, out of our estimated number of copies as 130. Chromosomal reorganizations were detected when comparing to sequences of S. reilianum, the closest smut relative, potentially influenced by repeats of transposable elements. Repetitive elements may have also directed the linkage of the two mating-type loci. The fungal transcriptome profiling from in vitro and from interaction with sugarcane at two time points (early infection and whip emergence) revealed that 13.5% of the genes were differentially expressed in planta and particular to each developmental stage. Among them are plant cell wall degrading enzymes, proteases, lipases, chitin modification and lignin degradation enzymes, sugar transporters and transcriptional factors. The fungus also modulates transcription of genes related to surviving against reactive oxygen species and other toxic metabolites produced by the plant. Previously described effectors in smut/plant interactions were detected but some new candidates are proposed. Ten genomic islands harboring some of the candidate genes unique to S. scitamineum were expressed only in planta. RNAseq data was also used to reassure gene predictions.

Polyploidization is an ancient and recurrent process in plant evolution, impacting the diversification of natural populations and plant breeding strategies. Polyploidization occurs in many important crops; however, its effects on inheritance of many agronomic traits are still poorly understood compared with diploid species. Higher levels of allelic dosage or more complex interactions between alleles could affect the phenotype expression. Hence, the present study aimed to dissect the genetic basis of fruit-related traits in autotetraploid blueberries and identify candidate genes affecting phenotypic variation. We performed a genome-wide association study (GWAS) assuming diploid and tetraploid inheritance, encompassing distinct models of gene action (additive, general, different orders of allelic interaction, and the corresponding diploidized models). A total of 1,575 southern highbush blueberry individuals from a breeding population of 117 full-sib families were genotyped using sequence capture and next-generation sequencing, and evaluated for eight fruit-related traits. For the diploid allele calling, 77,496 SNPs were detected; while 80,591 SNPs were obtained in tetraploid, with a high degree of overlap (95%) between them. A linear mixed model that accounted for population and family structure was used for the GWAS analyses. By modeling tetraploid genotypes, we detected 15 SNPs significantly associated with five fruit-related traits. Alternatively, seven significant SNPs were detected for only two traits using diploid genotypes, with two SNPs overlapping with the tetraploid scenario. Our results showed that the importance of tetraploid models varied by trait and that the use of diploid models has hindered the detection of SNP-trait associations and, consequently, the genetic architecture of some commercially important traits in autotetraploid species. Furthermore, 14 SNPs co-localized with candidate genes, five of which lead to non-synonymous amino acid changes. The potential functional significance of these SNPs is discussed.

Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses. Furthermore, effector genes are often found in rapidly evolving chromosome compartments which are difficult to assemble. We review how population and comparative genomics toolsets can be combined to address these challenges. We highlight studies that associated genome-scale polymorphisms with pathogen lifestyles and adaptation to different environments. We show how genome-wide association studies can be used to identify effectors and other pathogenicity-related genes underlying rapid adaptation. We also discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes. We argue that an understanding of genome evolution provides important insight into the trajectory of host-pathogen co-evolution.

Plants produce a range of volatile organic compounds (VOCs), some of which are perceived by the human olfactory system, contributing to a myriad flavors. Despite the importance of flavor for consumer preference, most plant breeding programs have neglected it, mainly because of the costs of phenotyping and the complexity of disentangling the role of VOCs in human perception.To develop molecular breeding tools aimed at improving fruit flavor, we carried out target genotyping of and VOC extraction from a blueberry population. Metabolite genome-wide association analysis was used to elucidate the genetic architecture, while predictive models were tested to prove that VOCs can be accurately predicted using genomic information. A historical sensory panel was considered to assess how the volatiles influenced consumers.By gathering genomics, metabolomics, and the sensory panel, we demonstrated that VOCs are controlled by a few major genomic regions, some of which harbor biosynthetic enzymecoding genes; can be accurately predicted using molecular markers; and can enhance or decrease consumers' overall liking.Here we emphasized how the understanding of the genetic basis and the role of VOCs in consumer preference can assist breeders in developing more flavorful cultivars at a more inexpensive and accelerated pace.

The decreasing costs of next-generation sequencing and the improvements in de novo sequence assemblers have made it possible to obtain reference genomes for most eukaryotes, including minor crops such as the blueberry ( Vaccinium corymbosum ). Nevertheless, these genomes are at various levels of completeness and few have been anchored to chromosome scale and/or are haplotype-phased. We highlight the impact of a high-quality genome assembly for plant breeding and genetic research by showing how it affects our understanding of the genetic architecture of important traits and aids marker selection and candidate gene detection. We compared the results of genome-wide association studies and genomic selection that were already published using a blueberry draft genome as reference with the results using the recent released chromosome-scale and haplotype-phased blueberry genome. We believe that the benefits shown herein reinforce the importance of genome assembly projects for other non-model species.

Blueberry (Vaccinium spp.) has been recognized worldwide as a valuable source of health-promoting compounds, becoming a crop with some of the fastest rising consumer demand trends. Fruit firmness is a key target for blueberry breeding as it directly affects fruit quality, consumer preference, transportability, shelf life, and the ability of cultivars to be machine harvested. Fruit softening naturally occurs during berry development, maturation, and postharvest ripening. However, some genotypes are better at retaining firmness than others, and some are crispy, which is a putatively extra-firmness phenotype that provides a distinct eating experience. In this review, we summarized important studies addressing the firmness trait in blueberry, focusing on physiological and molecular changes affecting this trait at the onset of ripening and also the genetic basis of firmness variation across individuals. New insights into these topics were also achieved by using previously available data and historical records from the blueberry breeding program at the University of Florida. The complex quantitative nature of firmness in an autopolyploid species such as blueberry imposes additional challenges for the implementation of molecular techniques in breeding. However, we highlighted some recent genomics-based studies and the potential of a QTL (Quantitative Trait Locus) mapping analysis and genome editing protocols such as CRISPR/Cas9 to further assist and accelerate the breeding process for this important trait.

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Blueberry ( Vaccinium corymbosum and hybrids) is an autotetraploid crop whose commercial relevance has been growing steadily during the last 20 years. However, the ever-increasing cost of labor for hand-picking blueberry is one main constraint in competitive marketing of the fruit. Machine harvestability is, therefore, a key trait for the blueberry industry. Understanding the genetic architecture of traits related to machine harvestability through Quantitative Trait Loci (QTL) mapping is the first step toward implementation of molecular breeding for faster genetic gains. Despite recent advances in software development for autotetraploid genetic mapping, a high-resolution map is still not available for blueberry. In this study, we crafted a map for autotetraploid low-chill highbush blueberry containing 11,292 SNP markers and a total size of 1,953.97 cM (average density of 5.78 markers/cM). This map was subsequently used to perform QTL analyses in 2-year field trials for a trait crucial to machine harvesting: fruit firmness. Preliminary insights were also sought for single evaluations of firmness retention after cold storage, and fruit detachment force traits. Significant QTL peaks were identified for all the traits and overlapping QTL intervals were detected for firmness across the years. We found low-to-moderate QTL effects explaining the phenotypic variance, which suggest a quantitative nature of these traits. The QTL intervals were further speculated for putative gene repertoire. Altogether, our findings provide the basis for future fine-mapping and molecular breeding efforts for machine harvesting in blueberry.