Biology subjects

Jones, C. S.

Publications and source records attributed to Jones, C. S..

8 recordsLinked to original sources

bioRxiv2026

Large-scale phenotyping and multi-trait selection identify low-methane Napier grass (Cenchrus purpureus) accessions under contrasting environmental conditions

Abstract Napier grass (Cenchrus purpureus, NG) is an important forage in tropical and subtropical livestock systems, but the extent of naturally occurring variation in its methane (CH4) production and its potential for selecting low-CH4 emitting genotypes remains poorly characterised. This study evaluated variation in CH4 yield among NG accessions, examined the effects of season and water stress, validated contrasting CH4 phenotypes across donor cows, and identified elite accessions combining low CH4 yield with favourable digestibility. A total of 750 NG samples representing 84 accessions grown under dry and wet seasons and moderate and severe water-stress were evaluated using a high-throughput in-vitro fermentation system. To further identify forages combining low-CH4 production with acceptable digestibility, a multi-trait selection approach was applied using biologically defined thresholds for CH4 yield and in vitro organic matter digestibility (IVOMD), followed by a weighted index assigning 60% weight to CH4 yield and 40% to IVOMD. Methane yield varied widely among accessions, ranging from 0.02 to 5.07 mL/g DM and was affected by growing conditions. Methane production was generally lower during the wet season, while water stress was associated with changes in forage quality and fermentation characteristics. Low-CH4 producing accessions generally had lower IVOMD, crude protein and metabolizable energy and relatively higher fibre than high-CH4 producing accessions. Accessions initially classified as low and high-CH4 emitters based solely on CH4 yield were subsequently validated using rumen inoculum from three individual donor cows. Although the magnitude of CH4 production varied among donors, the contrast between low- and- high-CH4 accessions was generally retained, supporting the robustness of accession differences in CH4 production. Several accessions also maintained relatively low CH4 production across contrasting season and water-stress conditions, indicating that favourable CH4 phenotypes were not entirely environment dependent. A multi-trait selection identified ten elite accessions that produced 0.019-0.810 mL CH4/g DM and had 55.2-69.0% IVOMD, whereas ten poor-performing accessions produced 2.80-3.89 mL CH4/g DM and had 50.1-54.7% IVOMD. Differences in hexose fermentation and CH4 produced per unit of fermented substrate further indicated contrasting fermentation efficiency between the groups. These results demonstrate substantial variation in NG and identify accessions with low-CH4 production, favourable digestibility and relatively stable performance across growing conditions. In conclusion, incorporating CH4 yield and digestibility into forage selection could support the development of lower-emission forage cultivars for sustainable climate-smart livestock production.

plant biology↗

bioRxiv2025

Genetic Diversity and Phylogenetic Relationships of Cultivated and Wild Urochloa Species Conserved in the ILRI Forage Genebank

Understanding the genetic diversity and evolutionary relationships within the genus Urochloa is essential for effective germplasm conservation and the development of improved forage cultivars. In this study, we assessed the genetic diversity, population structure, and phylogenetic relationships of 545 accessions representing 17 Urochloa species conserved in the ILRI Forage Genebank for the last four decades at its Zway field site in Ethiopia. Large numbers of genome-wide SNP and SilicoDArT markers were generated by the GBS based Diversity Arrays Technology (DArT)seq platform, providing valuable resources for genetic analysis in Urochloa spp. From these, we filtered a subset of high-quality SNP and SilicoDArT markers suitable for cross-species analysis, which was then used to characterize species differentiation and to detect admixture patterns across wild and cultivated species. Hierarchical clustering grouped all 545 accessions into two major groups, clearly separating the brizantha complex (U. brizantha, U. decumbens, and U. ruziziensis) from the rest of the species, which were primarily wild and less domesticated relatives. The analysis further identified four well-defined phylogenetic clades, largely consistent with previously reported evolutionary relationships within the genus. The three clades, primarily composed of wild species, exhibited clear genetic separation, high diversity, and strong geographic structuring with limited admixture, reflecting reproductive isolation (their apomictic nature) and differing ploidy levels that have driven local adaptation. In contrast, the brizantha complex exhibited extensive admixture and comparatively lower genetic variation, consistent with their historical polyploidization events, shared ancestry, and domestication (particularly in the key forage species U. brizantha and U. decumbens). Population structure analysis using the admixture model revealed multiple genetically distinct clusters and populations across clades, including species-specific clusters, mixed-species groups, and within-species populations, highlighting substantial genetic variation within and among species shaped by historical gene flow (particularly among diploid and sexual types), differences in ploidy levels, and adaptive divergence. The identification of genetically differentiated populations in wild species underscores their potential as reservoirs of unique adaptive traits such as drought tolerance, waterlogging and disease resistances, and nutrient-use efficiency. Meanwhile, the genetically diverse cultivated gene pool provides valuable resources for improving biomass productivity, nutritional quality, and resilience to environmental stress. Our findings provide a comprehensive genetic overview of one of the most important tropical forage genera and offer strategic insights for the conservation and utilization of Urochloa genetic resources.

plant biology↗

bioRxiv2025

Genome-wide association mapping for grain and forage quality traits in a subtropical oat germplasm collection adapted to highland regions of Eastern Africa

Oat (Avena sativa L.) is a globally important cereal cultivated for both livestock feed and human nutrition. However, its productivity is increasingly constrained by both biotic and abiotic stresses, exacerbated by rapid climate change. To support the development of dual-usage, stress-resilient and high-yielding cultivars adapted to subtropical agroecologies, we evaluated the genetic structure and agronomic performance of a 169-member oat association panel. This panel was phenotyped for key vegetative, forage feed quality and grain related traits across three subtropical locations in Sub-Saharan Africa (SSA) over two growing seasons and genotyped using Genotyping-by-Sequencing (GBS). Diversity analysis, based on filtered SNPs, showed moderate genetic diversity (He = 0.39 and PIC = 0.3), and population structure analysis identified two main sub-groups with varying degrees of admixture, suggesting gene flow among different groups. Genome-wide association analysis uncovered 42 SNPs significantly associated with sixteen traits (false discovery rate, FDR, <0.05), along with 46 candidate genes located near these loci. Notably, candidate genes associated with seed traits included a homolog of rice OsAK3, encoding adenylate kinase, and a UDP-glucosyltransferase homologous to rice GSA1, both previously shown to regulate grain size. These genes were located near QTL linked to seed length, width, and thousand-grain weight. Another key candidate, encoding a subunit of the ESCRT-II complex (VPS25), was identified near a separate QTL and is implicated in intracellular trafficking, endosperm development, and overall seed quality. By illuminating the genetic architecture of economically important traits and identifying molecular markers linked to yield, quality and resilience, this study provides valuable genomic resources to support genomics-based breeding aimed at developing climate-resilient, productive oats varieties adapted to sub-tropical agro-ecologies.

genomics↗

bioRxiv2024

Population genomics uncover loci for trait improvement in the indigenous African cereal tef (Eragrostis tef)

Tef (Eragrostis tef) is an indigenous African cereal that is gaining global attention as a gluten-free "superfood" with high protein, mineral, and fibre contents. However, tef yields are limited by lodging and by losses during harvest owing its small grain size (150x lighter than wheat). Breeders must also consider a strong cultural preference for white-grained over brown-grained varieties. Tef is relatively understudied with limited "omics" resources. Here, we resequenced 220 tef accessions from an Ethiopian diversity collection and also conducted multi-locational phenotyping for 25 agronomic and grain traits. Grain metabolome profiling revealed differential accumulation of fatty acids and flavonoids between white and brown grains. We conducted k-mer and SNP-based genome wide association and uncovered novel marker-trait associations. A significant 70 kb peak for panicle morphology contained the tef orthologue of rice qSH1, a transcription factor regulating inflorescence morphology in cereals. We also observed a previously unknown relationship between grain size, colour, and fatty acids. These traits were highly associated with retrotransposon insertions in homoeologues of TRANSPARENT TESTA 2, a known regulator of grain colour. Our study provides valuable resources for tef research and breeding, facilitating the development of improved cultivars with desirable agronomic and nutritional properties.

genomics↗

bioRxiv2023

MaUGT79 confers drought tolerance by regulating scopolin biosynthesis in plants

The coumarin scopoletin and its glycosylated form scopolin constitute a vast class of natural products that are considered to be high-value compounds, distributed widely in the plant kingdom, they help plants adapt to environmental stresses. However, the underlying molecular mechanism of how scopolin is involved in the regulation of plant drought tolerance remains largely unexplored. Here, UDP-glycosyltransferase 79 (MaUGT79) was genetically mapped as the target gene by bulk segregant analysis sequencing (BSA-seq) from two Melilotus albus near-isogenic lines (NILs). MaUGT79 exhibits glucosyltransferase activity toward scopoletin. The expression of MaUGT79 is induced by drought stress and it was found to mediate scopolin accumulation and reactive oxygen species (ROS) scavenging under drought stress. Moreover, the transcription of MaUGT79 was demonstrated to be directly and positively regulated by MaMYB4, which is a key integrator of both scopolin biosynthesis and drought tolerance. Collectively, this study reveals that MaMYB4 is a positive regulator in drought stress by targeting the MaUGT79 promoter and activating its expression to coordinately mediate scopolin biosynthesis and drought tolerance, providing insights into the regulatory mechanism for plant growth adaption to environmental changes through accumulation of scopolin.

physiology↗

bioRxiv2022

Chromosome-scale assembly of the lablab genome - A model for inclusive orphan crop genomics

Orphan crops (also described as underutilised and neglected crops) hold the key to diversified and climate-resilient food systems. After decades of neglect, the genome sequencing of orphan crops is gathering pace, providing the foundations for their accelerated domestication and improvement. Recent attention has however turned to the gross under-representation of researchers in Africa in the genome sequencing efforts of their indigenous orphan crops. Here we report a radically inclusive approach to orphan crop genomics using the case of Lablab purpureus (L.) Sweet (syn. Dolichos lablab, or hyacinth bean) - a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led South-North plant genome collaboration produced a high-quality chromosomescale assembly of the lablab genome - the first chromosome-scale plant genome assembly locally sequenced in Africa. We also re-sequenced cultivated and wild accessions of lablab from Africa confirming two domestication events and examined the genetic diversity in lablab germplasm conserved in Africa. Our approach provides a valuable resource for lablab improvement and also presents a model that could be explored by other researchers sequencing indigenous crops particularly from Low and middle income countries (LMIC).

genomics↗

bioRxiv2021

Feeding ecology of broadbill swordfish (Xiphias gladius) in the California Current

The feeding ecology of broadbill swordfish (Xiphias gladius) in the California Current was described based on analysis of stomach contents collected by federal fishery observers aboard commercial drift gillnet boats from 2007 to 2014. Prey were identified to the lowest taxonomic level and diet composition was analyzed using univariate and multivariate methods. Of 299 swordfish sampled (74 to 245 cm eye-to-fork length), 292 non-empty stomachs contained remains from 60 prey taxa. Diet consisted mainly of cephalopods but also included epipelagic and mesopelagic teleosts. Jumbo squid (Dosidicus gigas) and Gonatopsis borealis were the most important prey based on the geometric index of importance. Swordfish diet varied with body size, location and year. Jumbo squid, Gonatus spp. and Pacific hake (Merluccius productus) were more important for larger swordfish, reflecting the ability of larger specimens to catch large prey. Jumbo squid, Gonatus spp. and market squid (Doryteuthis opalescens) were more important in swordfish diet in inshore waters, while G. borealis and Pacific hake predominated offshore. Jumbo squid was more important from 2007-2010 than in 2011-2014, with Pacific hake the most important prey item in the latter period. Diet variation by area and year probably reflects differences in swordfish preference, prey availability, prey distribution, and prey abundance. The range expansion of jumbo squid that occurred during the first decade of this century may particularly explain their prominence in swordfish diet from 2007-2010. Some factors that may influence dietary variation in swordfish were identified. Standardization could make future studies more comparable for conservation monitoring purposes.

ecology↗

bioRxiv2021

Insights into the genetic architecture of complex traits in Napier grass (Cenchrus purpureus) and QTL regions governing forage biomass yield, water use efficiency and feed quality traits

Napier grass is the most important perennial tropical grass native to Sub-Saharan Africa and widely grown in tropical and subtropical regions around the world, primarily as a forage crop for animal feed, but with potential as an energy crop and in a wide range of other areas. Genomic resources have recently been developed for Napier grass that need to be deployed for genetic improvement and molecular dissection of important agro-morphological and feed quality traits. From a diverse set of Napier grass genotypes assembled from two independent collections, a subset of 84 genotypes that best represents the genetic diversity of the collections were selected and evaluated for two years in dry (DS) and wet (WS) seasons under three soil moisture conditions: moderate water stress in DS (DS-MWS); severe water stress in DS (DS-SWS) and, under rainfed (RF) conditions in WS (WS-RF). Data for agro-morphological and feed quality traits, adjusted for the spatial heterogeneity in the experimental blocks, were collected over a two-year period from 2018 to 2020. A total of 135,706 molecular markers were filtered, after removing markers with missing values > 10% and a minor allele frequency (MAF) < 5 %, from the high-density genome-wide markers generated previously using the genotyping by sequencing (GBS) method of the DArTseq platform. A genome-wide association study (GWAS), using two different mixed linear model algorithms, identified more than 58 QTL regions and markers associated with agronomic, morphological and water-use efficiency traits. QTL regions governing purple pigmentation and feed quality traits were also identified. The identified markers will be useful in the genetic improvement of Napier grass through the application of marker-assisted selection and for further characterization and map-based cloning of the QTLs.

genetics↗