Understanding the genetic basis of shattering in pearl millet

Over the last years, genes involved in several traits targeted during domestication have been studied in crops. Because shattering is an important domestication and agronomic trait, it has been intensively studied in crops such as rice, sorghum, Setaria, maize, wheat, and barley. However, shattering-related genes found in major cereal crops such as rice and wheat have not been validated in other crops. Additionally, recent transcriptomic analysis of abscission zone tissues from three grasses; a de-domesticated Oryza accession, and accessions of the wild species Setaria viridis and phylogenetically distant from each other have further supported the hypothesis of independent selection on genes for shattering between different grass species. However, it leaves the question of whether closely related genera might share similar shattering mechanisms. Hence, I have chosen to identify genomic regions associated with reduced shattering in pearl millet and compare them to identified genomic regions for shattering in the closely related genus, Setaria, as well as in the distantly related cereal species, rice. The wild relative, Cenchrus americanus ssp. violaceum (monodii), easily shatters by breaking at the base of the primary branch where the pedicel of the spikelet joins the rachis. Domesticated pearl millet, Cenchrus americanus ssp. americanus, does not break at this location, making it non-shattering. A histological and SEM analysis of the shattering zone shows a unique indentation of the epidermis that is present from early development of the primary rachis branches in both domesticated and wild accessions. I crossed accessions of domesticated pearl millet and wild pearl millet; and created an F2 population of 387 plants. Phenotyping of the F2 and F2:3 populations through a simple hand grasping method suggested that it followed a 15:1 segregation ratio (p=0.223) suggesting that two loci might be responsible for the non-shattering trait in pearl millet. I measured the force to detach the primary branch with a force gauge 28 days after heading, and mapped genetic loci associated with this trait using a high-density linkage map to identify quantitative trait loci associated with shattering. QTL mapping revealed a major QTL on chromosome 3 and a minor QTL on chromosome 5 associated with the shattering phenotype. This was confirmed by QTL analysis of the qualitative hand-shattering phenotyping trait identified in the F2 and F2:3 populations. Comparative genomics of QTL positions amongst grasses showed no conservation, which suggests, along with the histological details, that the shattering mechanism in wild millet is unique in grasses

Pearl millet response to drought: A review

The C4 grass pearl millet is one of the most drought tolerant cereals and is primarily grown in marginal areas where annual rainfall is low and intermittent. It was domesticated in sub-Saharan Africa, and several studies have found that it uses a combination of morphological and physiological traits to successfully resist drought. This review explores the short term and long-term responses of pearl millet that enables it to either tolerate, avoid, escape, or recover from drought stress. The response to short term drought reveals fine tuning of osmotic adjustment, stomatal conductance, and ROS scavenging ability, along with ABA and ethylene transduction. Equally important are longer term developmental plasticity in tillering, root development, leaf adaptations and flowering time that can both help avoid the worst water stress and recover some of the yield losses via asynchronous tiller production. We examine genes related to drought resistance that were identified through individual transcriptomic studies and through our combined analysis of previous studies. From the combined analysis, we found 94 genes that were differentially expressed in both vegetative and reproductive stages under drought stress. Among them is a tight cluster of genes that are directly related to biotic and abiotic stress, as well as carbon metabolism, and hormonal pathways. We suggest that knowledge of gene expression patterns in tiller buds, inflorescences and rooting tips will be important for understanding the growth responses of pearl millet and the trade-offs at play in the response of this crop to drought. Much remains to be learnt about how pearl millet’s unique combination of genetic and physiological mechanisms allow it to achieve such high drought tolerance, and the answers to be found may well be useful for crops other than just pearl millet

Plot-level satellite imagery can substitute for UAVs in assessing maize phenotypes across multistate field trials.

Accurate genotype-specific early yield estimates at fields and plots offer potential benefits to farmers in optimizing their agronomic practices, breeders in screening thousands of varieties, and policymakers in decision-making contributing to the improvement of agriculture and food production systems. Effective approaches to track plant growth and predict yield require large datasets of remote sensing and ground truth data collected across multiple environments. Low-altitude drone flights are increasingly being used to collect data from field evaluations of new crop varieties, while satellite imagery is being explored to track yield and management practices at the regional scales. Despite their lower spatial resolution, satellite platforms exhibit logistical and technical advantages in scalability and accessibility, and could facilitate plot-level predictions, especially with steadily improving spatial resolution. However, genotype-specific, plot-level, high-resolution satellite images from multiple environments with ground truth measurements are not yet publicly available. Here we generated, described, and evaluated over 20,000 plot-level images of over 80 hybrid maize varieties grown across the US corn belt under various management practices collected from (near simultaneous) satellite and drone flights integrated with ground truth yield measurement. Of the six baseline models examined, models employing data collected from satellite images often matched or exceeded the performance of models employing drone images for both within and cross-environment yield prediction. Large, multi-environment, genetically diverse datasets such as those generated in this study, along with more complex models could help unlock the power of satellite imagery as an important addition to the tool of farmers, plant geneticists, breeders, and policymakers.This is a preprint from Shrestha, Nikee, Anirudha Powadi, Jensina Davis, Timilehin T. Ayanlade, Hu-yu Liu, Michael C. Tross, Ramesh K. Mathivanan et al. "Plot-level satellite imagery can substitute for UAVs in assessing maize phenotypes across multistate field trials." agriRxiv 2024 (2024): 20240201322. doi: https://doi.org/10.31220/agriRxiv.2024.00251. Copyright 2024, The Authors

Pearl millet response to drought: A review

The C4 grass pearl millet is one of the most drought tolerant cereals and is primarily grown in marginal areas where annual rainfall is low and intermittent. It was domesticated in sub-Saharan Africa, and several studies have found that it uses a combination of morphological and physiological traits to successfully resist drought. This review explores the short term and long-term responses of pearl millet that enables it to either tolerate, avoid, escape, or recover from drought stress. The response to short term drought reveals fine tuning of osmotic adjustment, stomatal conductance, and ROS scavenging ability, along with ABA and ethylene transduction. Equally important are longer term developmental plasticity in tillering, root development, leaf adaptations and flowering time that can both help avoid the worst water stress and recover some of the yield losses via asynchronous tiller production. We examine genes related to drought resistance that were identified through individual transcriptomic studies and through our combined analysis of previous studies. From the combined analysis, we found 94 genes that were differentially expressed in both vegetative and reproductive stages under drought stress. Among them is a tight cluster of genes that are directly related to biotic and abiotic stress, as well as carbon metabolism, and hormonal pathways. We suggest that knowledge of gene expression patterns in tiller buds, inflorescences and rooting tips will be important for understanding the growth responses of pearl millet and the trade-offs at play in the response of this crop to drought. Much remains to be learnt about how pearl millet’s unique combination of genetic and physiological mechanisms allow it to achieve such high drought tolerance, and the answers to be found may well be useful for crops other than just pearl millet