Genomics of sorghum local adaptation to a parasitic plant.

Host-parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR-Cas9-edited sorghum further indicate that the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.

Comparative Analysis of Phosphoproteome Remodeling After Short Term Water Stress and ABA Treatments versus Longer Term Water Stress Acclimation.

Several studies have used short term dehydration, osmotic stress or Abscisic Acid (ABA) treatments to identify the initial protein phosphorylation-dephosphorylation responses to drought and low water potential or ABA treatments. However, longer term drought acclimation leads to altered expression of many kinases and phosphatases suggesting that it may also produce unique changes in phosphoproteome composition. To get a better overview of the state of drought-related phosphoproteomics and investigate this question of short versus longer term phosphoproteome regulation, we compared three Arabidopsis thaliana studies analyzing short term phosphoproteome changes to recent data from our laboratory analyzing phosphoproteome changes after a longer drought acclimation treatment. There was very little overlap of phosphoproteins with putative stress-induced phosphorylation or dephosphorylation among these studies. While some of this is due to technical limitations and limited coverage of the phosphoproteome achieved by each study, biological differences and the type of stress treatment used also play a role. This comparative analysis emphasized how both short and long term analysis of physiologically relevant stress treatments, as well as validation of phosphoproteomic data, will be needed to move past just scratching the surface of the stress phosphoproteome. In drought acclimation experiments, distinguishing between changes in protein abundance versus phosphorylation stoichiometry is a key challenge. We discuss initial work in using Arabidopsis seedling transient expression combined with Phos-tag gel analysis as a way to validate drought-induced phosphorylation-dephosphorylation of candidate proteins.

Dynamic proline metabolism: importance and regulation in water limited environments.

Drought-induced proline accumulation observed in many plant species has led to the hypothesis that further increases in proline accumulation would promote drought tolerance. Here we discuss both previous and new data showing that proline metabolism and turnover, rather than just proline accumulation, functions to maintain growth during water limitation. Mutants of Δ (1)-Pyrroline-5-Carboxylate Synthetase1 (P5CS1) and Proline Dehydrogenase1 (PDH1), key enzymes in proline synthesis and catabolism respectively, both have similar reductions in growth during controlled soil drying. Such results are consistent with patterns of natural variation in proline accumulation and with evidence that turnover of proline can act to buffer cellular redox status during drought. Proline synthesis and catabolism are regulated by multiple cellular mechanisms, of which we know only a few. An example of this is immunoblot detection of P5CS1 and PDH1 showing that the Highly ABA-induced (HAI) protein phosphatase 2Cs (PP2Cs) have different effects on P5CS1 and PDH1 protein levels despite having similar increases in proline accumulation. Immunoblot data also indicate that both P5CS1 and PDH1 are subjected to unknown post-translational modifications.