Biology subjects

Wang, Y.-w.

Publications and source records attributed to Wang, Y.-w..

5 recordsLinked to original sources

bioRxiv2026

Unlocking the potential of Capsicum Germplasm Collections for Climate Resilience and Fruit Quality

Climate change increasingly threatens global Capsicum (pepper) production. Accelerating the deployment of climate-resilient cultivars requires effective use of genetic diversity conserved in genebanks. We implement a "turbocharging" strategy in Capsicum by integrating genome-wide association studies and genomic prediction in a core collection (n = 423), followed by genomic prediction across the global collection (n = 10,250) using the core as a training population. We generated genomic estimated breeding values (GEBVs) for 31 high-accuracy traits (r > 0.5) encompassing hyperspectral phenotypes (heat/control), agronomic performance (heat/control) and fruit quality. To enhance accessibility and decision-making, we developed a large language model (LLM) integrated application that enables flexible, preference-based selection of candidates. By narrowing the parental decision space, this framework streamlines screening of large germplasm collections while balancing climate resilience, quality attributes and market demands. Our approach provides a scalable decision-support system to accelerate climate-resilient Capsicum breeding and maximize global genetic resources.

plant biology↗

bioRxiv2024

Temporal cohort number, neural composition, and connectivity vary along the Drosophila larval body axis

Neural stem cells are inherently flexible, producing different lineages of neurons in different contexts; yet in vivo, development must be highly regulated because aberrant stem cell development leads to microcephalies, tumors, and neurodevelopmental disorders. However, the full complement of in vivo flexibility in neural stem cell development remains poorly understood. Within the Drosophila CNS, 30 types of neural stem cells or neuroblasts repeat in each segment with segment-specific differences in development. We studied NB3-3 neuroblast in each of the 14 segments where it is present. In different segments, NB3-3 produces different types of neurons in different numbers but always produces Even-skipped Lateral (EL) neurons. Prior work showed that in abdominal segments, ELs comprise two types of temporal cohorts. Temporal cohorts are small sets of neurons within a lineage that are born within a tight time window. In the abdomen, EL neurons in the early-born temporal cohort all receive mechanosensory input, whereas EL neurons in the late-born temporal cohort all receive proprioceptive input. Herein, we find that NB3-3 generates an early-born EL temporal cohort in all segments. In specific regions, NB3-3 neuroblasts produce additional types of temporal cohorts, including but not limited to the late-born EL temporal cohort. We show that variations in NB3-3 division pattern determine the number and type of temporal cohorts. Later in development, the number of neurons within a temporal cohort is refined by a variety of post-mitotic mechanisms: regulation of molecular identity markers, cell death, and differentiation status, acting in complex combinations in different segments. Post-mitotic refinement of neuron numbers occurs most often for neurons of the early-born EL temporal cohort. Further, neurons of the early-born EL temporal cohort are incorporated into different circuits, depending on segment. Together, our results show how a single neural stem cell type can flexibly generate segment-specific lineages and contribute to various circuits. We offer the following framework for understanding how a given type of neural stem cell generates diverse temporal cohorts: a stem cell type invariably generates one type of temporal cohort, regardless of location or pattern of division. For neurons in this invariant temporal cohort, post-mitotic mechanisms introduce diversity in number. The stem cell, on a segment-by-segment basis, can also produce additional types of temporal cohorts simply by altering its division pattern. This framework is valuable for motor circuit development, the development of sexual dimorphisms, nervous system evolution, and in vitro stem cell applications.

neuroscience↗

bioRxiv2022

Comprehensive evaluation of harmonization on functional brain imaging for multisite data-fusion

To embrace big-data neuroimaging, harmonization of site effect in resting-state functional magnetic resonance imaging (R-fMRI) data fusion is a fundamental challenge. Comprehensive evaluation of potentially effective harmonization strategies, particularly with specifically collected data has been rare, especially for R-fMRI metrics. Here, we comprehensively assess harmonization strategies from multiple perspectives, including efficiency, individual identification, test-retest reliability and replicability of group-level statistical results, on widely used R-fMRI metrics across multiple datasets including data obtained from the same participants scanned at several sites. For individual identifiability (i.e., whether the same subject could be identified across R-fMRI data scanned across different sites), we found that, while most methods decreased site effects, the Subsampling Maximum-mean-distance based distribution shift correction Algorithm (SMA) outperformed linear regression models, linear mixed models, ComBat series and invariant conditional variational auto-encoder. Test-retest reliability was better for SMA and adjusted ComBat series than alternatives, while SMA was superior to the latter in replicability, both in terms of Dice coefficient and the scale of brain areas showing sex differences reproducibly observed across datasets. Moreover, we examined test-retest datasets to identify the best target site features to optimize SMA identifiability and test-retest reliability. We noted that both sample size and distribution of the target site matter and introduced a heuristic target site selection formula. In addition to providing practical guidelines, this work can inform continuing improvements and innovations in harmonizing methodologies for big R-fMRI data.

neuroscience↗

bioRxiv2022

Sequential addition of neuronal stem cell temporal cohorts generates a feed-forward circuit in the Drosophila larval nerve cord

Understanding how circuits self-assemble starting from neuronal stem cells is a fundamental question in developmental biology. Here, we addressed how neurons from different lineages wire with each other to form a specific circuit motif. To do so, we combined developmental genetics--Twin spot MARCM, Multi-color Flip Out, permanent labeling--with circuit analysis--calcium imaging, connectomics, and network science analyses. We find many lineages are organized into temporal cohorts, which are sets of lineage-related neurons born within a tight time window, and that temporal cohort boundaries have sharp transitions in patterns of input connectivity. We identify a feed-forward circuit motif that encodes the onset of vibration stimuli. This feed-forward circuit motif is assembled by preferential connectivity between temporal cohorts from different neuronal stem cell lineages. Further, connectivity does not follow the often-cited early-to-early, late-to-late model. Instead, the feed-forward motif is formed by sequential addition of temporal cohorts, with circuit output neurons born before circuit input neurons. Further, we generate multiple new tools for the fly community. Ultimately, our data suggest that sequential addition of neurons (with outputs neurons being oldest and input neurons being youngest) could be a fundamental strategy for assembling feed-forward circuits.

developmental biology↗

bioRxiv2020

Reproductive Compatibility in Capsicum is not Reflected in Genetic or Phenotypic Similarity Between Species Complexes

Wild relatives of domesticated Capsicum represent substantial genetic diversity and thus sources of traits of potential interest. Furthermore, the hybridization compatibility between members of Capsicum species complexes remains unresolved. Improving our understanding of the relationship between Capsicum species relatedness and their ability to form hybrids is a highly pertinent issue. Through the development of novel interspecific hybrids in this study, we demonstrate interspecies compatibility is not necessarily reflected in relatedness according to established Capsicum genepool complexes. Based on a phylogeny constructed by genotyping using single sequence repeat (SSR) markers and with a portion of the waxy locus, and through principal component analysis (PCA) of phenotypic data, we clarify the relationships among wild and domesticated Capsicum species. Together, the phylogeny and hybridization studies provide evidence for the misidentification of a number of species from the World Vegetable Center genebank included in this study. The World Vegetable Center holds the largest collection of Capsicum genetic material globally, therefore this may reflect a wider issue in the misidentification of Capsicum wild relatives. The findings presented here provide insight into an apparent disconnect between compatibility and relatedness in the Capsicum genus, which will be valuable in identifying candidates for future breeding programs.

plant biology↗