Biomedical subjects

Feng Guo

Publications and source records attributed to Feng Guo.

3 recordsLinked to original sources

PubMed2026

Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut.

The cultivated peanut is a crucial global legume crop that is essential for food security and nutrition, particularly in developing regions. However, its limited genetic variation hampers breeding progress and yield improvement. Here we constructed a graph-based pan-genome for peanut, incorporating 14 genomes that represent all 6 peanut varieties. Using this pan-genome, we genotyped 2,320 accessions, covering 88.03% of ICRISAT and 59.21% of USDA core germplasm, enriching valuable resources for genomic studies and breeding. We cataloged genomic structural variations and investigated the role of homoeologous exchanges in population divergence. Through our pan-genome approach, we overcame the challenges of genotyping posed by homoeologous exchanges and identified key genes associated with flowering and dwarfism in peanut. By integrating superior haplotypes and germplasm resources guided by the pan-genome, we further developed high-yield dwarf lines. This work provides essential genomic resources to accelerate functional gene discovery and modern peanut breeding.

Journal Article↗

PubMed2026

Interrogation of functional variants in COPD GWAS loci by massively parallel reporter assays.

RATIONALE: Genome-wide association study (GWAS) loci often contain many linked variants, making it difficult to determine which variant is functionally relevant. Massively parallel reporter assays (MPRA) allow experimental testing of candidate variants to identify those with regulatory activity. Prior chronic obstructive pulmonary disease (COPD) MPRA studies have largely focused on individual loci, whereas broader multi-locus, multi-cell-type interrogation remains limited. OBJECTIVES: We aim to identify functional variants in five COPD GWAS loci across three lung-relevant cell types. METHODS: We screened 1120 variants using MPRA in epithelial (16HBE), fibroblast (MRC5), and endothelial (HUVEC) cells followed by reporter assay validation. Public Hi-C, ChIP-seq and ATAC-seq datasets were analyzed to evaluate chromatin context near candidate variants. We further performed CRISPR interference (CRISPRi) targeting variant-containing regions and measured gene expression by RT-qPCR in primary normal human bronchial epithelial (NHBE) cells using two gRNAs per variant. Co-immunoprecipitation was performed to test interaction between selected candidate genes. MEASUREMENTS AND MAIN RESULTS: In MPRA, we identified 25 variants with allele-specific effects (∼2% of tested variants). Enrichment of H3K27Ac and open chromatin near rs35421223 was detected in 16HBE cells. CRISPRi identified two SNP-gene pairs, RUVBL1 and RAB7A regulated by rs35421223 in both the 16HBE cell line and primary NHBE cells. We detected interaction between RUVBL1 and the known COPD gene product FAM13A. CONCLUSIONS: Screening COPD loci across three cell types identified functional regulatory variants and linked them to candidate target genes for future mechanistic studies.

Journal Article↗

PubMed2025

The mutation landscape of Daphnia obtusa reveals evolutionary forces shaping genome stability.

Spontaneous mutations are the primary source of genetic variation and play a central role in shaping evolutionary processes. To investigate mutational dynamics in Daphnia obtusa, we generated a chromosome-level genome assembly spanning 129.4 Mb across 12 chromosomes, encompassing 15,321 predicted protein-coding genes. Leveraging whole-genome sequencing of eight mutation accumulation (MA) lines propagated for an average of 482 generations (spanning over 20 years), we estimated a spontaneous single nucleotide mutation (SNM) rate of 2.23 × 10-9 and an indel mutation rate of 2.75 × 10-10 per site per generation. The SNM spectrum was strongly biased toward C:G > T:A transitions. Comparative analyses with natural population data revealed that exonic mutations observed in the MA lines were significantly less likely to be present in standing variation than intronic or intergenic mutations, suggesting that purifying selection in natural populations acts to remove deleterious alleles. We also identified 48 de novo loss-of-heterozygosity (LOH) events, comprising 8 heterozygous deletions and 40 gene conversion events. The genome-wide gene conversion rate was estimated at 2.62 × 10-5 per heterozygous site per generation. These findings provide a comprehensive view of the mutation spectrum, selective pressures, and mechanisms underlying genome stability in D. obtusa.

Daphnia obtusa↗