Biology subjects

Linders, K.

Publications and source records attributed to Linders, K..

4 recordsLinked to original sources

bioRxiv2026

Nitrogen adaptation and phenotypic transitions from wild to improved sorghum

Crop domestication and subsequent improvement under modern agronomic conditions have altered the nitrogen (N) regimes experienced by crops, yet how selection has reshaped the genetic architecture of phenotypic responses to N availability remains poorly understood. Here, we integrated population genomic analyses of n = 289 sorghum accessions spanning multiple stages of domestication and improvement with N-response (NR) trait-associated variants identified through genome-wide association studies (GWAS) of phenotypic data collected under two contrasting N conditions in n = 347 diverse sorghum accessions. Unlike maize and sunflower, sorghum showed a reduced deleterious burden both genome-wide and within historically balanced and recently selected regions following domestication and improvement. Additionally, we identified 470 trait-associated loci (TALs), including 273 associated with NR traits. The effects of these NR-associated loci showed no apparent bias toward derived alleles, suggesting that selection on NR traits in sorghum has not been sufficiently strong or directional to consistently overcome genetic drift. Together, these results reveal distinct patterns of selection in sorghum and provide promising genetic targets for improving N-use efficiency in sustainable agricultural systems.

genomics↗

bioRxiv2025

Assessing the impact of yield plasticity on hybrid performance in maize

Improving crop resilience in the face of increasingly extreme and unpredictable weather and reduced access to agricultural inputs such as nitrogen fertilizer and water will require an improved understanding of phenotypic plasticity in crops. To understand the roles of different component traits in determining overall plasticity for grain yield, we generated data from a panel of 122 maize (Zea mays) hybrids grown in replicated field trials in 34 environments spanning 700 miles (1126 km) of the U.S. Corn Belt. We observed that the levels of genetic versus environmental control and the relationships between mean parent release year, overall performance, and linear plasticity were trait-dependent across the 18 agronomic and yield components studied. Importantly and unexpectedly, we observed no clear tradeoff between linear plasticity and mean performance and found only rare examples where genotype-by-environment interactions would alter selection decisions based on the environments tested in our dataset. Furthermore, we showed that overall plasticity was repeatable and appears to be under considerable genetic control but that plasticity in response to nitrogen fertilization was not, which may help explain the limited success in breeding for nitrogen use efficiency. Together, these findings improve our understanding of phenotypic plasticity, with implications for maize breeding.

plant biology↗

bioRxiv2024

Genes and pathways determining flowering time variation in temperate adapted sorghum

The timing of the transition from vegetative to reproductive growth is determined by a complex genetic architecture integrating signals from a diverse set of external and internal stimuli and plays a key role in determining plant fitness and adaptation. However, significant divergence in the identities and functions of many flowering time pathway components has been reported among plant species. Here we employ a combination of genome and transcriptome wide association studies to identify genetic determinants of variation in flowering time across multiple environments in a large panel of primarily photoperiod-insensitive sorghum (Sorghum bicolor), a major crop that has, to date, been the subject of substantially less genetic investigation than its relatives. Gene families that form core components of the flowering time pathway in other species, FT-like and SOC1-like genes, appear to play similar roles in sorghum, but the genes identified are not orthologous to the primary FT-like or SOC1-like genes which play similar roles in related species. The aging pathway appears to play a significant role in determining non-photoperiod determined variation in flowering time in sorghum. Two components of this pathway were identified in a transcriptome wide association study, while a third was identified via genome wide association. Our results demonstrate that, while the functions of larger gene families are conserved, functional data from even closely related species is not a reliable guide to which gene copies will play roles in determining natural variation in flowering time.

plant biology↗

bioRxiv2024

Off-the-shelf image analysis models outperform human visual assessment in identifying genes controlling seed color variation in sorghum

Seed color is a complex phenotype linked to both the impact of grains on human health and consumer acceptance of new crop varieties. Today seed color is often quantified via either qualitative human assessment or biochemical assays for specific colored metabolites. Imaging-based approaches have the potential to be more quantitative than human scoring while lower cost than biochemical assays. We assessed the feasibility of employing image analysis tools trained on rice (Oryza sativa) or wheat (Triticum aestivum) seeds to quantify seed color in sorghum (Sorghum bicolor ) using a dataset of > 1,500 images. Quantitative measurements of seed color from images were substantially more consistent across biological replicates than human assessment. Genome-wide association studies conducted using color phenotypes for 682 sorghum genotypes identified more signals near known seed color genes in sorghum with stronger support than manually scored seed color for the same experiment. Previously unreported genomic intervals linked to variation in seed color in our study co-localized with a gene encoding an enzyme in the biosynthetic pathway leading to anthocyanins, tannins, and phlobaphenes - colored metabolites in sorghum seeds - and with the sorghum ortholog of a transcription factor shown to regulate several enzymes in the same pathway in rice. The cross-species transferability of image analysis tools, without the retraining, may aid efforts to develop higher value and health-promoting crop varieties in sorghum and other specialty and orphan grain crops.

plant biology↗