Biology subjects

Yocca, A. E.

Publications and source records attributed to Yocca, A. E..

7 recordsLinked to original sources

bioRxiv2026

Landrace and bred accessions of allotetraploid sour cherry (Prunus cerasus L.) reveal variation in subgenome dosage and subgenome expression bias

Subgenome dominance is a phenomenon observed in many allopolyploids where one parental genome exhibits stronger influence over phenotype than the other parental genomes. This may present as preferential retention of one subgenome through fractionation, replacement via homoeologous exchange, or as subgenome expression bias, where one subgenome is expressed at a higher abundance compared to other subgenomes. Sour cherry (Prunus cerasus) is an allotetraploid fruit tree species resulting from an interspecific cross between extant relatives of ground cherry (P. fruticosa) and sweet cherry (P. avium). Prior comparative genomic analyses suggest that the sour cherry cultivar Montmorency contains three subgenomes. Subgenomes A and A, each present in one copy, are derived from a P. fruticosa-like ancestor, and B, present in two copies, is derived from a P. avium-like ancestor. In this study we investigated the subgenome dynamics of the three subgenomes of sour cherry in four diverse landraces and two cultivars, including Montmorency. We found evidence of 26 homoeologous exchange events and five whole-homoeolog replacements relative to Montmorency in three of the six accessions. We also detected subgenome expression bias favoring the A and A subgenomes over the B subgenome, the magnitude of which differs between accessions and changes over the course of fruit development. Lastly, we show differences in dosage variation and expression bias of four previously-described genes in Montmorency associated with fruit softening, a key trait in this crop. These findings on subgenome dominance offer valuable insights into how this phenomenon may influence traits important for sour cherry breeding.

genetics↗

bioRxiv2023

A chromosome-scale assembly for dAnjou pear

Cultivated pear consists of several Pyrus species with P. communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate a fully-phased chromosome-scale genome assembly of P. communis cv. dAnjou. Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totalling nearly 540 Megabases and a contig N50 of nearly 14 Mb. Both haplotypes are highly syntenic to each other, and to the Malus domestica Honeycrisp apple genome. Nearly 45,000 genes were annotated in each haplotype, over 90% of which have direct RNA-seq expression evidence. We detect signatures of the known whole-genome duplication shared between apple and pear, and we estimate 57% of dAnjou genes are retained in duplicate derived from this event. This genome highlights the value of generating phased diploid assemblies for recovering the full allelic complement in highly heterozygous crop species.

genomics↗

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↗

bioRxiv2021

Blueprint for Phasing and Assembling the Genomes of Heterozygous Polyploids: Application to the Octoploid Genome of Strawberry

The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated strawberry (Fragaria x ananassa) and its wild progenitors are outbred octoploids (2n = 8x = 56) in which up to eight homologous and homoeologous alleles are preserved. This introduces significant risk of haplotype collapse, switching, and chimeric fusions during assembly. Using third generation HiFi sequences from PacBio, we assembled the genome of the day-neutral octoploid F. x ananassa hybrid Royal Royce from the University of California. Our goal was to produce subgenome-and haplotype-resolved assemblies of all 56 chromosomes, accurately reconstructing the parental haploid chromosome complements. Previous work has demonstrated that partitioning sequences by parental phase supports direct assembly of haplotypes in heterozygous diploid species. We leveraged the accuracy of HiFi sequence data with pedigree-informed sequencing to partition long read sequences by phase, and reduce the downstream risk of subgenomic chimeras during assembly. We were able to utilize an octoploid strawberry recombination breakpoint map containing 3.6 M variants to identify and break chimeric junctions, and perform scaffolding of the phase-1 and phase-2 octoploid assemblies. The N50 contiguity of the phase-1 and phase-2 assemblies prior to scaffolding and gap-filling was 11 Mb. The final haploid assembly represented seven of 28 chromosomes in a single contiguous sequence, and averaged fewer than three gaps per pseudomolecule. Additionally, we re-annotated the octoploid genome to produce a custom F. x ananassa repeat library and improved set of gene models based on IsoSeq transcript data and an expansive RNA-seq expression atlas. Here we present FaRR1, a gold-standard reference genome of F. x ananassa cultivar Royal Royce to assist future genomic research and molecular breeding of allo-octoploid strawberry.

genomics↗

bioRxiv2021

Machine learning approaches to identify core and dispensable genes in pangenomes

A gene in a given taxonomic group is either present in every individual (core), or absent in at least a single individual (dispensable). Previous pangenomic studies have identified certain functional differences between core and dispensable genes. However, identifying if a gene belongs to the core or dispensable portion of the genome requires the construction of a pangenome, which involves sequencing the genomes of many individuals. Here we aim to leverage the previously characterized core and dispensable gene content for two grass species (Brachypodium distachyon and Oryza sativa) to construct a machine learning model capable of accurately classifying genes as core or dispensable using only a single annotated reference genome. Such a model may mitigate the need for pangenome construction, an expensive hurdle especially in orphan crops which often lack the adequate genomic resources.

bioinformatics↗

bioRxiv2019

Disease Resistance Genetics and Genomics in Octoploid Strawberry

Octoploid strawberry (Fragaria x ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberrys complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, eQTL analysis and RenSeq analysis in cultivars. Octoploid fruit transcript expression quantitative trait loci (eQTL) were identified for 77 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. x ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance towards exploiting variation for strawberry cultivar improvement.

genomics↗

bioRxiv2019

Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia

Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Despite its overall importance to small-scale farmers and communities in Africa, teff suffers from low production compared to other cereals because of limited intensive selection and molecular breeding. Here we report a chromosome-scale genome assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintained as syntenic gene pairs. Through analyzing the history of transposable element activity, we estimate the teff polyploidy event occurred [~]1.1 million years ago (mya) and the two subgenomes diverged [~]5.0 mya. Despite this divergence, we detected no large-scale structural rearrangements, homoeologous exchanges, or bias gene loss, contrasting most other allopolyploid plant systems. The exceptional subgenome stability observed in teff may enable the ubiquitous and recurrent polyploidy within Chloridoideae, possibly contributing to the increased resilience and diversification of these grasses. The two teff subgenomes have partitioned their ancestral functions based on divergent expression patterns among homoeologous gene pairs across a diverse expression atlas. The most striking differences in homoeolog expression bias are observed during seed development and under abiotic stress, and thus may be related to agronomic traits. Together these genomic resources will be useful for accelerating breeding efforts of this underutilized grain crop and for acquiring fundamental insights into polyploid genome evolution.

plant biology↗