Biology subjects

Scheffler, B. E.

Publications and source records attributed to Scheffler, B. E..

7 recordsLinked to original sources

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

The genome assembly of the westslope cutthroat trout, Oncorhynchus lewisi, reveals interspecific chromosomal rearrangements with the rainbow trout

Cutthroat trout (Oncorhynchus clarkii) are popular among anglers throughout their native range along the West Coast and interior of North America. As they colonized the interior of North America, cutthroat trout diverged into several genetically distinct groups. Many of these groups are now threatened by habitat destruction, hybridization with rainbow trout (O. mykiss), and competition from introduced species. These groups were previously classified as subspecies, but recent research suggests they may represent distinct species. In this study, we produced a chromosomal-level genome assembly and a genetic map for one of the species in the cutthroat trout species complex, the westslope cutthroat trout (O. lewisi--formerly O. clarki lewisi). We also constructed haplotype-resolved assemblies from a westslope cutthroat-rainbow trout F1 hybrid. We used the new genome assemblies to identify major interspecific chromosomal rearrangements between the two sister species, including fusions, fissions, and inversions. These genome assemblies and chromosome data provide valuable insights regarding genetic variation within cutthroat trout and in hybrids between rainbow and cutthroat trout. Article SummaryWestslope cutthroat trout inhabit bodies of water in several states and provinces near the Rocky Mountains and are well-known among anglers. In this study, we produced the first publicly available genome assemblies and a high-density genetic map for this species. These are research tools that allow detailed genetic analyses, including identifying differences among the genomes of related species. These comparisons allow researchers to understand the evolution of these species better and may provide insight into why successful interbreeding is possible among cutthroat and rainbow trout.

genomics↗

bioRxiv2022

Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton

The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae), is a major global pest of cotton. Current management practices include chemical insecticides, cultural strategies, sterile insect releases, and transgenic cotton producing crystalline (Cry) protein toxins of the bacterium Bacillus thuringiensis (Bt). These strategies have contributed to eradication of P. gossypiella from the cotton growing areas of the United States and northern Mexico. However, this pest has evolved resistance to Bt cotton in Asia, where it remains a critical pest, and the benefits of using transgenic Bt crops have been lost. A complete annotated reference genome is needed to improve global Bt resistance management of the pink bollworm. We generated the first chromosome-level genome assembly for pink bollworm from a Bt-susceptible laboratory strain (APHIS-S) using PacBio continuous long reads for contig generation, Illumina Hi-C for scaffolding, and Illumina whole-genome re-sequencing for error-correction. The psuedohaploid assembly consists of 29 autosomes and the Z sex chromosome. The assembly exceeds the minimum Earth BioGenome Project quality standards, has a low error-rate, is highly contiguous at both the contig and scaffold level (L/N50 of 18/8.26 MB and 14/16.44 MB, respectively), and complete, with 98.6% of lepidopteran single-copy orthologs represented without duplication. The genome was annotated with 50% repeat content and 14,107 protein-coding genes, further assigned to 41,666 functional annotations. This assembly represents the first publicly available complete annotated genome of pink bollworm and will serve as the foundation for advancing molecular genetics of this important pest species.

genomics↗

bioRxiv2022

The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for North American Atlantic salmon

Given the genetic and genomic differences between Atlantic salmon of European origin and North American (N.A.) origin, it is crucial to develop unique genomic resources for each lineage. Here we describe the resources that we recently developed for genomic and genetic research in N.A. Atlantic salmon. Firstly, a new single nucleotide polymorphism (SNP) database for N.A. Atlantic salmon consisting of 3.1 million putative SNPs was generated using data from whole genome resequencing of 80 N.A. Atlantic salmon individuals; Secondly, a high density 50K SNP array enriched for the genic regions of the genome and containing three sex determination and 61 continent of origin markers was developed and validated; Thirdly, a genetic map composed of 27 linkage groups with 36K SNP markers, was generated from 2,512 individuals in 141 full-sib families; Finally, a chromosome level de-novo assembly of a male N.A. Atlantic salmon genome was generated using PacBio long-reads. Information from Hi-C proximity ligation sequences and Bionano optical mapping was used to concatenate the contigs into scaffolds. The assembly contains 1,755 scaffolds and only 1,253 gaps, with a total length of 2.83 Gb and N50 of 17.2 Mb. A BUSCO analysis detected 96.2% of conserved Actinopterygii genes in the assembly and the genetic linkage information was used to guide the formation of 27 chromosome sequences. In contrast, the karyotype of the European Atlantic salmon lineage is composed of 29 chromosomes. Comparative analysis with the reference genome assembly of the European Atlantic salmon confirmed that the karyotype differences between the two linages are caused by a fission in chromosome Ssa01 and three chromosome fusions including the p arm of chromosome Ssa01 with Ssa23, Ssa08 with Ssa29 and Ssa26 with Ssa28. The genomic resources we have generated for Atlantic salmon provide a crucial boost for genetic research and for management of farmed and wild populations in this highly valued species.

genomics↗

bioRxiv2020

Gene disruption by structural mutations drives selection in US rice breeding over the last century

The genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropical japonica rice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion is the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection. Significance StatementSome crop varieties have superior performance across years and environments. In hybrids, harmful mutations in one parent are masked by the ancestral alleles in the other parent, resulting in increased vigor. Unfortunately, these mutations are very difficult to identify precisely because, individually, they only have a small effect. In this study, we use long-read sequencing to characterize the entire mutational spectrum between two rice varieties. We then track these mutations through the last century of rice breeding. We show that large structural mutations in exons are selected against at a greater rate than any other mutational class. These findings illuminate the nature of deleterious alleles and will guide attempts to predict variety vigor based solely on genomic information.

genetics↗

bioRxiv2018

An EST-SSR based genetic linkage map and identification of QTLs for anthracnose disease resistance in water yam (Dioscorea alata L.)

Water yam (Dioscorea alata L.) is one of the most important food yams with wide geographical distribution in tropics. One of the major constraints to water yam production is anthracnose disease caused by a fungus, Colletotrichum gloesporioides (Penz.). There are no economically feasible solutions as chemical sprays or cultural practices, such as crop rotation are seldom convenient for smallholder farmers for sustainable control of the disease. Breeding for development of durable genetic resistant varieties is known to offer lasting solution to control endemic disease threats to crop production. However, breeding for resistance to anthracnose has been slow considering the biological constraints related to the heterozygous and vegetative propagation of the crop. The development of saturated linkage maps with high marker density, such as SSRs, followed by identification of QTLs can accelerate the speed and precision of resistance breeding in water yam. A total of 380 EST-SSRs were used to generate a saturated linkage map. About 60.19% of SSRs showed Mendelian segregation pattern, however, it had no effect on the construction of linkage map. All 380 EST-SSRs were mapped into 20 linkage groups covering a total length of 2559.66 cM, which agrees with the diploid nature (2n = 2x = 20) of the parents used in the cross. Majority of the markers were mapped on linkage group 1 comprising of 97 EST-SSRs. This is the first genetic linkage map of water yam constructed using EST-SSRs. QTL localization was based on phenotypic data collected over a 3-year period of inoculating the mapping population with the most virulent strain of C. gloeosporoides from West Africa. Using the mean permutation value of LOD scores as threshold value for declaring a putative QTL on all linkage groups, one QTL was consistently observed on linkage group (LG) 14 in all the three years and average score data. This QTL was found at position interval of 71.12 - 84.76 cM explaining 68.94% of the total phenotypic variation in the average score data. The high marker density allowed identification of QTLs and association for anthracnose disease, which could be validated in other mapping populations and used in marker-assisted breeding in D. alata improvement programmes.

molecular biology↗