Biology subjects

Kitony, J. K.

Publications and source records attributed to Kitony, J. K..

4 recordsLinked to original sources

bioRxiv2026

Efficient genomic prediction at reduced training size and moderate marker density in an expanded aus-NAM population of rice

Genomic selection (GS) can accelerate genetic gain in crops, but its effectiveness depends on training population design and marker density. Nested association mapping (NAM) populations provide a structured framework that captures broad allelic diversity within a controlled genetic background. Here, we evaluated genomic prediction (GP) and genome-wide association study (GWAS) performance in an expanded aus-NAM population of rice comprising 1,818 recombinant inbred lines across 14 families and 11 agronomic traits, using genotyping-by-sequencing (GBS) markers and projected whole-genome sequence variants. Prediction accuracy plateaued at moderate marker densities ([~]20k SNPs) and with training populations of [~]500 lines ([~]40-60% of the available pool), with trait heritability emerging as the strongest determinant of predictive performance rather than model choice or marker density. In contrast, GWAS resolution continued to improve with increasing marker density, enabling detection of additional loci, including a chromosome 12 locus associated with heading date, while consistently recovering well-characterized genes such as EARLY HEADING DATE 1 (Ehd1) and SEMIDWARF 1 (SD1). These contrasting patterns indicate that GP reaches near-optimal performance once genome-wide variation is adequately represented, whereas GWAS benefits from higher marker density through improved locus resolution. The present study establishes a benchmark for implementing breeding programs involving japonica/indica crosses using GP in a single environment.

plant biology↗

bioRxiv2025

Pangenome of U.S. ex-PVP and Wild Sorghum Reveals Structural Variants and Selective Sweeps Shaping Adaptation and Trait Improvement

Sorghum is a cereal crop grown for food, feed, and biofuel, yet the genomic diversity of elite commercial lines remains underexplored. Here, we assembled a sorghum pangenome from long-read sequences of 46 U.S. ex-Plant Variety Protection Act (ex-PVP) cultivars and a haplotype-resolved assembly of one wild accession. The pangenome revealed largely conserved genomic architecture across elite lines but identified presence-absence variations (PAVs) in 28% of gene families, including genes involved in stress responses and starch metabolism, such as STARCH BRANCHING ENZYME I (SBE1). Selective sweep analyses detected strong signals at key flowering-time loci (Ma1/SbPRR37, Ma2, Ma6) and circadian/light regulators (PHOT1, DET1, XAP5), with PHYA showing copy number variations (CNVs). Analysis of 24 wild accessions, beyond the core pangenome panel, detected CNVs in MULTIDRUG AND TOXIC COMPOUND EXTRUSION (MATE) transporters, potentially reflecting selection or breeding for enhanced herbicide detoxification. These results highlight breeding-shaped regions and position the pangenome as a resource for sorghum improvement.

genomics↗

bioRxiv2024

Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome

Cannabis sativa is a globally significant seed-oil, fiber, and drug-producing plant species. However, a century of prohibition has severely restricted legal breeding and germplasm resource development, leaving potential hemp-based nutritional and fiber applications unrealized. Existing cultivars are highly heterozygous and lack competitiveness in the overall fiber and grain markets, relegating hemp to less than 200,000 hectares globally1. The relaxation of drug laws in recent decades has generated widespread interest in expanding and reincorporating cannabis into agricultural systems, but progress has been impeded by the limited understanding of genomics and breeding potential. No studies to date have examined the genomic diversity and evolution of cannabis populations using haplotype-resolved, chromosome-scale assemblies from publicly available germplasm. Here we present a cannabis pangenome, constructed with 181 new and 12 previously released genomes from a total of 156 biological samples from both male (XY) and female (XX) plants, including 42 trio phased and 36 haplotype-resolved, chromosome-scale assemblies. We discovered widespread regions of the cannabis pangenome that are surprisingly diverse for a single species, with high levels of genetic and structural variation, and propose a novel population structure and hybridization history. Conversely, the cannabinoid synthase genes contain very low levels of diversity, despite being embedded within a variable region containing multiple pseudogenized paralogs and distinct transposable element arrangements. Additionally, we identified variants of acyl-lipid thioesterase (ALT) genes2 that are associated with fatty acid chain length variation and the production of the rare cannabinoids, tetrahydrocannabinol varin (THCV) and cannabidiol varin (CBDV). We conclude the Cannabis sativa gene pool has only been partially characterized, and that the existence of wild relatives in Asia remains likely, while its potential as a crop species remains largely unrealized.

plant biology↗

bioRxiv2024

Chromosome-level baobab (Adansonia digitata) genome illuminates its evolutionary insights

AbstractBaobab, Adansonia digitata, is a long-lived tree endemic to Africa that holds great economic, ecological, and cultural value. However, our knowledge of its genomic features, evolutionary history, and diversity is limited, rendering it orphaned scientifically. We generated a haploid chromosome-level reference genome anchored into 42 chromosomes for A. digitata, as well as draft assemblies for a sibling tree, two trees from distinct locations in Africa, and a related species, A. za from Madagascar. Unlike any other plant to date, DNA transposable elements (TEs) make up 33% of the A. digitata genome compared to only 10% long terminal repeat retrotransposons (LTR-RTs), which are usually predominant in plant genomes. Baobab has undergone a whole genome duplication (WGD) shared with the Malvoideae [~]30 million years ago (MYA), as well as a confirmed autotetraplody event 3-4 million MYA that coincides with the most recent burst of TE insertions. Resequencing 25 A. digitata trees from Africa revealed three subpopulations that suggest gene flow through most of West Africa but separated from East Africa. Gene enrichment analysis for baobab-specific and high fixation index (Fst) suggested baobab may have retained multiple copies of circadian, light and growth genes to coordinate genome protection for longevity through the UV RESISTANCE LOCUS 8 (UVR8) and synchronizing flower development with pollinators. This study lays the groundwork for the creation of breeding resources and the conservation of baobab biodiversity.

genomics↗