Biology subjects

Rice, B. R.

Publications and source records attributed to Rice, B. R..

4 recordsLinked to original sources

bioRxiv2025

Developing future resilience from signatures of adaptation across the sorghum pangenome

While the green revolution adapted a handful of crops to homogenous and high-input industrialized agriculture, much of the global population still relies on local food production from low-input smallholder farms that grow highly variable crop cultivars. The high diversity of the grain and bioenergy crop sorghum 1-4, and many other crops that were not homogenized during the green revolution 5, not only provides the raw materials for breeders to make substantial gains in cultivar improvement, but also constrains breeding efforts due to highly specialized locally adapted plant phenotypes 6. Here, we construct a 33-member pangenome and identify trait-associated variants in 1,988 cultivars and landraces. We then apply these resources to explore the complex interplay between historical contingency, ongoing adaptation, and the potential for future gains through climate-aware genome-enabled breeding. Specifically, our analyses conclusively demonstrate that multiple nested, deeply diverged, and previously uncharacterized structural variants in the domestication gene SHATTERING1 distinguish the previously established multicentric origin of sorghum. We then apply landscape genomics tests to reveal how gene flow, adaptation, and secondary contact created the complex genetic mosaic in current global breeding networks. Further analysis of climate-gene associations highlights candidate loci underlying adaptation, including the biosynthetic gene cluster for the cyanogenic glucoside dhurrin. Combined, the pangenome-informed variants developed here will enable both trait discovery and subsequent marker assays to accelerate breeding and provide a framework for similar applications in other diverse and non-model crops.

genomics↗

bioRxiv2025

Genomic approaches to build de novo elite breeding gene pools from locally-adapted landraces

Many nascent breeding programs aim to achieve genetic gain by crossing locally elite germplasm, but a lack of systematic approaches to develop elite gene pools from locally-adapted varieties hinders their progress. Motivated by the observation of undesirable transgressive segregation in presumed elite crosses in Senegalese cereal breeding programs, we designed approaches for de novo development of elite gene pools from locally-adapted landrace-derived germplasm. We first define two types of "elite" germplasm: cis-elite, phenotypically similar and genetically homogeneous for locally-adapted traits ("acquired traits"); versus trans-elite, phenotypically similar, but genetically heterogeneous for acquired traits. Next, we defined two genomic approaches for de novo inference of elite gene pools: population-based genotypic inference (PGI) and QTL-based genotypic inference (QGI), and compared to a family-based phenotypic inference (FPI) approach. Using simulations that trace the evolution from locally-adapted landraces to elite breeding lines, we evaluate the effectiveness of these strategies in nascent forward breeding programs. QGI accurately and cost-effectively identifies both cis- and trans-elite pairs, regardless of the underlying trait architecture, while PGI is less sensitive when trait architecture is oligogenic. Over ten cycles of phenotypic recurrent selection, programs based on cis-elite crosses consistently outperformed those based on trans-elite crosses for genetic gain. The findings highlight the value of trait genetic architecture knowledge for elite gene pool development and provide a practical roadmap for elite germplasm development in modernizing breeding programs.

genetics↗

bioRxiv2023

Regulatory variation controlling architectural pleiotropy in maize

An early event in plant organogenesis is establishment of a boundary between the meristem and differentiating lateral organ. In maize (Zea mays), evidence suggests a common gene network functions at boundaries of distinct organs and contributes to pleiotropy between leaf angle and tassel branch number, two agronomic traits. To uncover regulatory variation at the nexus of these two traits, we used regulatory network topologies derived from specific developmental contexts to guide multivariate genome-wide association analyses. In addition to defining network plasticity around core pleiotropic loci, we identified new transcription factors that contribute to phenotypic variation in canopy architecture, and structural variation that contributes to cis-regulatory control of pleiotropy between tassel branching and leaf angle across maize diversity. Results demonstrate the power of informing statistical genetics with context-specific developmental networks to pinpoint pleiotropic loci and their cis-regulatory components, which can be used to fine-tune plant architecture for crop improvement.

plant biology↗

bioRxiv2019

The regulatory landscape of early maize inflorescence development

BackgroundThe functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments. ResultHere, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen- and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profile accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classify at least 1.6 percent of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3 ends of maize genes. This approach maps regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor occupancy data are used to annotate regulatory factors, such as combinatorial transcription factor binding motifs and long non-coding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based solely on functional regions delineated by MNase hypersensitivity reveals new SNP-trait associations in known regulators of inflorescence development as well as new candidates. ConclusionsThese analyses provide a comprehensive look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.

plant biology↗