Biology subjects

Yerka, M.

Publications and source records attributed to Yerka, M..

3 recordsLinked to original sources

bioRxiv2025

Integrative metabolome-genome analysis reveals the genetic architecture of metabolic diversity in sorghum grain

Natural variation in the grain metabolome plays a central role in shaping nutritional quality and end-use traits in grass crops. Understanding the genetic basis of this metabolic diversity is therefore essential, yet population-scale integration of metabolomics and genomics remains limited in sorghum, a climate-resilient C4 crop renowned for its exceptional heat and drought tolerance. Here, we integrated large-scale untargeted metabolomic profiling, population genomics, and artificial intelligence (AI)-based machine learning to systematically dissect grain metabolic diversity and its genetic architecture in sorghum. Untargeted metabolomic profiling of mature grains of the Sorghum Association Panel (SAP) identified 4,877 compounds, revealing extensive quantitative variation relevant to grain nutritional improvement. Metabolite-based genome-wide association studies (mGWAS) identified [~]4.15 million significant SNP-metabolite associations, revealing the heterogeneous genetic architecture of metabolic traits. Associated variants were enriched in genic and regulatory regions but depleted in intergenic regions, consistent with functional constraint. A total of 38 metabolite gene clusters revealed coordinated genetic control of core metabolic pathways. We further applied machine learning to identify key metabolites that underlie grain color variation and to prioritize associated candidate genes, demonstrating the utility of predictive models integrating genotype, metabolome, and end trait. Collectively, this work establishes a population-scale atlas of sorghum grain metabolomic and genetic diversity, available through the Sorghum Grain Metabolite Diversity Atlas (SorGMDA). This resource enables integrated metabolomics and genomic analyses and supports systems-level breeding strategies for improving grain nutritional quality.

genomics↗

bioRxiv2024

Identification and characterization of a temperature sensitive chlorotic soybean mutant

Screening a transposon-mutagenized soybean population led to the discovery of a recessively inherited chlorotic phenotype. This "vir1" phenotype results in smaller stature, weaker stems, and a smaller root system with smaller nodules. Genome sequencing identified 15 candidate genes with mutations likely to result in a loss of function. Amplicon sequencing of a segregating population was then used to narrow the list to a single candidate mutation, a single-base change in Glyma.07G102300 that disrupts splicing of the second intron. Single cell transcriptomic profiling indicates that this gene is expressed primarily in mesophyll cells and RNA sequencing data indicates it is upregulated in germinating seedlings by cold stress. Previous studies have shown that mutations to Os05g34040, the rice homolog of Glyma.07G102300, produced a chlorotic phenotype that was more pronounced in cool temperatures. Growing soybean vir1 mutants at lower temperatures also resulted in a more severe phenotype. In addition, transgenic expression of wild type Glyma.07G102300 in the knockout mutant of the Arabidopsis homolog At4930720 rescues the chlorotic phenotype, further supporting the hypothesis that the mutation in Glyma.07G102300 is causal of the vir1 phenotype.

plant biology↗

bioRxiv2019

Genome wide analysis of Ga1-s modifiers in maize

A one way reproductive barrier exists between most popcorn varieties and dent corn varieties grown in the United States. This barrier is predominantly controlled by the ga1 locus. Using data from a diverse population of popcorn accessions pollinated by a dent corn tester, we found that the non-reciprocal pollination barrier conferred by ga1 is more complex than previously described. Individual accessions ranged from 0% to 100% compatible with dent corn pollen. Using conventional genotyping-by-sequencing data from 371 popcorn accessions carrying Ga1-s, seven significant modifiers of dent pollen compatibility were identified on five chromosomes. One locus may either be a nonfunctional ga1 allele present within popcorn, or second necessary gene for the reproductive barrier in genetic linkage with ga1, while the other modifiers are clearly genetically unlinked. The existence of ga1 modifiers segregating in a popcorn genetic background may indicate selective pressure to allow gene flow between populations, which should be incorporated into future models of the impact of genetic incompatibility loci on gene flow in natural and agricultural plant populations.

plant biology↗