Search bioRxiv⌕ Search

Biology subjects

Humphries, A.

Publications and source records attributed to Humphries, A..

2 recordsLinked to original sources
bioRxiv2026

Leveraging whole-genome re-sequencing for diversity, population structure, and a public mid-density genotyping enrichment panel in crimson clover (Trifolium incarnatum L.) for breeding purposes

AO_SCPLOWBSTRACTC_SCPLOWCrimson clover (Trifolium incarnatum L.) is an obligately outcrossing, cool-season annual legume valued for forage and cover cropping, yet genomic resources to support systematic improvement are limited. We performed the first and most comprehensive whole-genome resequencing (WGR) of global crimson clover germplasm to (i) characterize diversity and population structure and (ii) develop a public mid-density enrichment capture panel for breeding applications. A core set of 45 accessions sequenced at [~]50X generated 5.84 million variants, while 149 additional accessions sequenced at [~]2.54X yielded 17.05 million variants. After stringent filtering, we retained 542,790 high-confidence SNPs from the high-coverage dataset and [~]2.4 million from the low-pass cohort. Population analyses (PCA, ADMIXTURE) revealed compact clustering of cultivars, broader dispersion of wild and uncertain-status accessions, and low overall differentiation (FST = 0.0105) with excess heterozygosity (FIS = -0.0592), consistent with obligate outcrossing. Guided by these resources, we designed a 28,913-SNP TWIST hybrid-capture panel enriched for genic regions and evenly distributed across seven chromosomes. This panel is being deployed within Auburn Universitys crimson clover breeding program to support population improvement and cultivar development. The resulting genomic resources provide a reproducible, mid-density genotyping platform for trait discovery, predictive breeding, and diversity monitoring. Together, these advances bring crimson clover genomic resources on par with other legumes such as soybean (Glycine max (L.) Merr.) and alfalfa (Medicago sativa), establishing a robust foundation for genomics-assisted improvement of this key cover and forage crop in U.S. sustainable agriculture. CORE IDEASO_LIWhole-genome re-sequencing of 194 crimson clover accessions revealed >21 M variants. C_LIO_LIHigh-confidence SNP catalogs from 50X and 2X data enable cost-effective genotyping. C_LIO_LIGenetic diversity is weakly structured, with cultivars clustering narrowly by origin. C_LIO_LIA 28,913 SNP enrichment panel delivers uniform genome coverage and >75% genic content. C_LIO_LIThese genomic tools accelerate GWAS, genomic selection, and breeding innovation. C_LI

genomics↗
bioRxiv2019

Using a collaborative data collection method to update life-history values for snapper and grouper in Indonesia’s deep-slope demersal fishery

The deep-slope demersal fishery that targets snapper and grouper species is an important fishery in Indonesia. Boats operate at depths between 50-500 m using drop lines and bottom long lines. There are few data, however, on the basic characteristics of the fishery which impedes accurate stock assessments and the establishment of harvest control rules. To address this gap, we developed a collaborative data collection and recording system for species and length composition of commercial catches. The Crew-Operated Data Recording System (CODRS) involves fishers who take photos of each individual fish in the catch along with a low-cost vessel tracking system. As it relies on fishers collaboration and willingness to share data, CODRS is comparable with a logbook system but enables verification of species identification with greater spatial resolution. We implemented this system from 2015 to 2018 and gathered data from 251 captains and 2,707 fishing trips, which yielded more than one million individual fish, or 2,680 tons. While there were over 100 species in the fishery, we found that the top five species accounted for approximately half of the total catch. We also unveiled fifteen species previously not associated with the fishery due to the fish being eaten on-board, used as bait, or sold prior to being recorded by traders. Using these data, we updated life-history parameters (length at maturity, optimum fishing length, asymptotic length, and maximum length) of the top 50 species in the fishery based on the maximum observed length; this study resulted in higher estimates for maximum length, most likely due to the high sampling size. For some species, the discrepancies between different sources were large, whereas others were not. This collaborative data collection method and findings are useful for scientists and managers interested in conducting length-based stock assessments to establish harvest control rules for data-poor fisheries.

ecology↗