Biology subjects

Miller, B. A.

Publications and source records attributed to Miller, B. A..

2 recordsLinked to original sources

bioRxiv2024

Leveraging Soil Mapping and Machine Learning to Improve Spatial Adjustments in Plant Breeding Trials

Spatial adjustments are used to improve the estimate of plot seed yield across crops and geographies. Moving mean and P-Spline are examples of spatial adjustment methods used in plant breeding trials to deal with field heterogeneity. Within trial spatial variability primarily comes from soil feature gradients, such as nutrients, but study of the importance of various soil factors including nutrients is lacking. We analyzed plant breeding progeny row and preliminary yield trial data of a public soybean breeding program across three years consisting of 43,545 plots. We compared several spatial adjustment methods: unadjusted (as a control), moving means adjustment, P-spline adjustment, and a machine learning based method called XGBoost. XGBoost modeled soil features at (a) local field scale for each generation and per year, and (b) all inclusive field scale spanning all generations and years. We report the usefulness of spatial adjustments at both progeny row and preliminary yield trial stages of field testing, and additionally provide ways to utilize interpretability insights of soil features in spatial adjustments. These results empower breeders to further refine selection criteria to make more accurate selections, and furthermore include soil variables to select for macro- and micro-nutrients stress tolerance.

plant biology↗

bioRxiv2023

A bioinformatics screen reveals Hox and chromatin remodeling factors at the Drosophila histone locus

Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets and 27 factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax, Abdominal-A and Abdominal-B, suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other transcription factors that target the histone gene array: JIL-1, Hr78, the long isoform of fs(1)h as well as the generalized transcription factors TAF-1, TFIIB, and TFIIF. Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.

molecular biology↗