Biology subjects

Lynch, R. C.

Publications and source records attributed to Lynch, R. C..

3 recordsLinked to original sources

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

The evolution of heteromorphic sex chromosomes in plants

Sex chromosomes in cannabis and hop were identified a century ago because of their obvious visible differences in size (heteromorphy). However, we know little about the genes they contain that control the development of the inflorescences. Here we assembled genomes, with phased sex chromosomes, for hop and cannabis. The XY chromosomes share an origin prior to the divergence between the genera >36 MYA. Due to the inheritance patterns of the XYs, the male-specific region of the Y is highly-degenerated, with substantial gene loss, while the X shows faster rates of molecular evolution. Consistent with the theory that these species lack an active-Y system, no clear sex-determining genes reside on the Y. Instead, an X-linked homolog of aminocyclopropane-1-carboxylate synthase (ACS), that is involved in the ethylene biosynthesis pathway, determines the fate of the female inflorescence. Beyond sex determination, the sex chromosomes contribute to the sexual dimorphism in ecology and physiology and have played a role in the domestication and breeding of these species.

evolutionary biology↗

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↗