Biology subjects

Hulse-Kemp, A. M.

Publications and source records attributed to Hulse-Kemp, A. M..

6 recordsLinked to original sources

bioRxiv2026

Breedbase 2.0 - expanding the functionality for traditional breeding and transgenics

Breedbase ( is a comprehensive, web-based, open-source breeding management and analysis software for plant breeding that was introduced to address gaps with existing software for plant breeding data. Breedbase is continually improved and developed, with new features being added as required by the breeding community. Since its inception, the capabilities of Breedbase were improved to better serve the diverse data modeling needs of additional crops beyond our original ensemble of cassava, banana, yam, sweet potato, tomato, rice, and wheat. We describe here major updates that have been made in the past 4 years, including (1) improved handling of repetitive measurements; (2) a redesigned experimental treatments interface; (3) a more fine-grained user permission system; (4) improved trial quality control workflows; (5) intercropping support; (6) the addition of a decision meeting feature that helps decision makers make the best selection with the available data; (7) transgenics and tracking tools and finally, (8) an improved field layout tool which consolidates several trials in one field. These new features integrate seamlessly with the previous feature set of Breedbase - making it one of the most feature rich breeding management softwares available.

bioinformatics↗

bioRxiv2025

Chromosome-Scale Assemblies of Flowering Dogwood Cultivars Enable Identification of Candidate Genes Regulating Anthocyanin Biosynthesis in Leaves and Bracts

O_LIThe North American-native ornamental tree, flowering dogwood (Cornus florida L.), has a showy bract display that can range in color from white to pink to deep red. Although many trees have white bracts, there is consumer demand for novel pigmentation in the bracts combined with other traits of interest. Because the genetic basis of all traits in flowering dogwood is unknown, combining them using traditional breeding efforts is time, labor, and space-intensive. C_LIO_LIWe developed foundational genomic resources to establish marker-assisted selection within flowering dogwood breeding. We generated diploid, chromosome-scale, annotated genome assemblies for one pink-bracted and red-leafed tree and one white-bracted and green-leafed tree. Additionally, a phenotyping protocol for bract color and presence/absence diagnostic SNPs for bract and leaf color were established. C_LIO_LIWe leveraged these resources to evaluate linkage associations and differential gene expression related to anthocyanin biosynthesis to identify candidate genes regulating bract and leaf pigmentation. Within a 14Mb locus we identified 14 anthocyanin-related candidate genes. Two genes, with MYB (g19533) and RING finger (g19556) binding domains, had both differential gene expression and variants with the expected segregation pattern. C_LIO_LIThese resources will be valuable in combining pink-red bracts with other traits to advance flowering dogwood breeding. C_LI

genomics↗

bioRxiv2025

Pangenome analysis provides insights into the evolution of mango (Mangifera spp.)

Mango (Mangifera spp.) is a major tropical fruit crop of global economic importance, but advanced genomic resources are needed to support its breeding, conservation, and sustainable cultivation. In this study, a mango pangenome was constructed using high-quality, telomere-to-telomere genomes of four cultivated mango (M. indica) accessions representing distinct genetic origins, and one wild relative, M. odorata. Genome-wide analyses revealed a significant reduction in heterozygosity among elite commercial cultivars, indicating a genetic bottleneck resulting from long-term artificial selection. Core genes were enriched in fundamental biological pathways, including primary metabolism, photosynthesis, transcriptional regulation, and cellular signaling. Variable genes were primarily associated with secondary metabolite biosynthesis, reflecting local environmental adaptations. Pangenome and comparative genomic analyses identified structural variations among accessions. Additionally, 10,482 high-confidence single nucleotide polymorphisms (SNPs) were detected and utilized for population genomic analysis of 197 mango accessions, delineating four genetically distinct groups. Southeast Asian accessions exhibited unique genetic diversity and divergence from Caribbean, Indian, and U.S. groups. Comparative analyses revealed differentiation in specialized metabolic pathways, particularly alkaloid and diterpenoid biosynthesis, likely reflecting adaptive responses to the complex ecological interactions and high biodiversity of Southeast Asian tropical rainforests. Genomic analysis of the MiRWP gene, associated with apomixis, provided comprehensive insights into this important mango trait, demonstrating the potential of the pangenome for future mango breeding efforts. The genomic resources generated in this study establish a critical foundation for advancing mango genetic research, facilitating trait improvement, and informing conservation strategies.

genomics↗

bioRxiv2024

De novo whole-genome assembly and annotation of a high-quality coffee variety from the primary origin of coffee, Coffea arabica var. Geisha

Geisha coffee is recognized for its unique aromas and flavors and accordingly, has achieved the highest prices in the specialty coffee markets. We report the development of a chromosome-level, well-annotated, genome assembly of Coffea arabica var. Geisha, considered an Ethiopian landrace thatrepresents germplasm from the Ethiopian center of origin of coffee. We used a hybrid de novo assembly approach combining two long-reads single molecule sequencing technologies, Oxford Nanopore and Pacific Biosciences, together with scaffolding with Hi-C libraries. The final assembly is 1.03GB in size with BUSCO assessment of the assembly completeness of 97.7% of single-copy orthologs clusters. RNAseq and IsoSeq data were used as transcriptional experimental evidence for annotation and gene prediction revealing the presence of 47,062 gene loci encompassing 53,273 protein-coding transcripts. Comparison of the assembly to the progenitor subgenomes, separated the set of chromosome sequences inherited from C. canephora from those of C. eugenioides., Corresponding orthologs between Geisha and Red Bourbon had a 99.67% median identity, higher than what we observe with the progenitor assemblies (median 97.28%). Both, Geisha and Red Bourbon contain an inversion on Chromosome 10 relative to the pseudomolecules of the genetic material inherited from the two progenitors that must have happened before the separation in the geographical migration of the two varieties. Lending support of a single allopolyploidization event that gave origin to C. arabica after the hybridization event with the two progenitor lines. Broadening the availability of high-quality genome assemblies of Coffea arabica varieties, paves the way for understanding the evolution and domestication of coffee, as well as the genetic basis and environmental interactions of why a variety like Geisha is capable of producing beans with such exceptional and unique high-quality.

genomics↗

bioRxiv2022

Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance

The genomic sequences segregating in experimental populations are often highly divergent from the community reference and from one another. Such divergence is problematic under various short-read-based genotyping strategies. In addition, large structural differences are often invisible despite being strong candidates for causal variation. These issues are exacerbated in specialty crop breeding programs with fewer, lower-quality sequence resources. We examined the benefits of complete genomic information, based on long-read assemblies, in a biparental mapping experiment segregating at numerous disease resistance loci in the non-model crop, melon (Cucumis melo). We find that a graph-based approach, which uses both parental genomes, results in 19% more variants callable across the population and raw allele calls with a 2 to 3-fold error-rate reduction, even relative to single reference approaches using a parent genome. We show that structural variation has played a substantial role in shaping two Fusarium wilt resistance loci with known causal genes. We also report on the genetics of powdery mildew resistance, where copy number variation and local recombination suppression are directly interpretable via parental genome alignments. Benefits observed, even in this low-resolution biparental experiment, will inevitably be amplified in more complex populations.

genetics↗

bioRxiv2017

Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library

BackgroundLinked-Read sequencing technology has recently been employed successfully for de novo assembly of multiple human genomes, however the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5 gigabase (Gb) diploid pepper (Capsicum annuum) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F1 derived from a wide cross to assess the ability to derive both haplotypes for a pungency gene characterized by a large insertion/deletion.\n\nResultsThe Supernova software generated a highly ordered, more contiguous sequence assembly than all currently available C. annuum reference genomes. Eighty-four percent of the final assembly was anchored and oriented using four de novo linkage maps. A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly. The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5 kb insertion/deletion haplotypes of the PUN1 locus in the F1 sample that represents pungent and non-pungent peppers.\n\nConclusionsThe most contiguous pepper genome assembly to date has been generated through this work which demonstrates that Linked-Read library technology provides a rapid tool to assemble de novo complex highly repetitive heterozygous plant genomes. This technology can provide an opportunity to cost-effectively develop high-quality reference genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.

genomics↗