The transcription factors Adr1 and Cat8 act in concert to regulate the expression of numerous yeast genes after the diauxic shift. Their activities are regulated by Snf1, the yeast homolog of the AMP-activated protein kinase of higher eukaryotes. Cat8 is regulated directly by Snf1, but how Snf1 regulates Adr1 is unknown. Mutations in Adr1 that alleviate glucose repression are clustered between amino acids 227 and 239. This region contains a consensus sequence for protein kinase A, RRAS 230 F, and Ser230 is phosphorylated in vitro by both protein kinase A and Ca 11 calmodulin-dependent protein kinase. Using an antiphosphopeptide antibody, we found that the level of Adr1 phosphorylated on Ser230 was highest in glucose-grown cells and decreased in a Snf1-dependent manner when glucose was depleted. A nonphosphorylatable Ser230Ala mutant was no longer Snf1 dependent for activation of Adr1-dependent genes and could suppress Cat8 dependence at genes coregulated by Adr1 and Cat8. Contrary to expectation, neither protein kinase A (PKA) nor Ca 11 calmodulin-dependent protein kinase appeared to have an important role in Ser230 phosphorylation in vivo, and a screen of 102 viable kinase deletion strains failed to identify a candidate kinase. We conclude that either Ser230 is phosphorylated by multiple protein kinases or its kinase is encoded by an essential gene. Using the Ser230Ala mutant, we explain a long-standing observation of synergy between Adr1 constitutive mutants and Snf1 activation and conclude that dephosphorylation of Ser230 via a Snf1-dependent pathway appears to be a major component of Adr1 regulation.

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Key messageQTLstm9controlling rapid-onset water stress tolerance inS. habrochaiteswas high-resolution mapped to a chromosome 9 region that contains genes associated with abiotic stress tolerances.AbstractWild tomato (Solanum habrochaites) exhibits tolerance to abiotic stresses, including drought and chilling. Root chilling (6 °C) induces rapid-onset water stress by impeding water movement from roots to shoots. S. habrochaites responds to such changes by closing stomata and maintaining shoot turgor, while cultivated tomato (S. lycopersicum) fails to close stomata and wilts. This response (shoot turgor maintenance under root chilling) is controlled by a major QTL (designated stm9) on chromosome 9, which was previously fine-mapped to a 2.7-cM region. Recombinant sub-near-isogenic lines for chromosome 9 were marker-selected, phenotyped for shoot turgor maintenance under root chilling in two sets of replicated experiments (Fall and Spring), and the data were used to high-resolution map QTL stm9 to a 0.32-cM region. QTL mapping revealed a single QTL that was coincident for both the Spring and Fall datasets, suggesting that the gene or genes contributing to shoot turgor maintenance under root chilling reside within the marker interval H9–T1673. In the S. lycopersicum reference genome sequence, this chromosome 9 region is gene-rich and contains representatives of gene families that have been associated with abiotic stress tolerance.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-015-2540-y) contains supplementary material, which is available to authorized users.

A wild tomato species (Solanum habrochaites S. Knapp & D.M. Spooner) is tolerant to many abiotic stresses, including limited water, and can serve as a valuable genetic resource for breeding cultivated tomato (S. lycopersicum L.). Previously, we developed and used a set of 18 sub‐near‐isogenic lines (sub‐NILs) containing introgressions from chromosome 9 of S. habrochaites to determine the genetic basis of tolerance to rapid‐onset water stress imposed by root chilling. In this study, we used this same set of 18 sub‐NILs to investigate the genetic basis of tolerance to slow‐onset water stress in the field imposed by restricted irrigation (with full water treatment as control) in replicated experiments for 2 yr in Davis, CA. The sub‐NILs were evaluated for C isotope discrimination (Δ13C), specific leaf area (SLA), shoot dry weight (SDW), yield, and other horticultural traits. A total of 19 QTL for Δ13C, SLA, SDW, yield, and maturity traits were mapped on chromosome 9. Significant genotype × environment interactions were detected for Δ13C, SLA, yield, and maturity. Agriculturally beneficial effects were conferred by S. habrochaites alleles at QTL for traits associated with water‐stress tolerance: low Δ13C, low SLA, and high SDW. The majority of QTL mapped to the centromeric end of the introgression, suggesting a gene‐rich region containing valuable wild alleles for breeding tomato for improved abiotic stress tolerance.

More than 150 Ma, the avian lineage separated from that of other dinosaurs and later diversified into the more than 10,000 species extant today. The early neoavian bird radiations most likely occurred in the late Cretaceous (more than 65 Ma) but left behind few if any molecular signals of their archaic evolutionary past. Retroposed elements, once established in an ancestral population, are highly valuable, virtually homoplasy-free markers of species evolution; after applying stringent orthology criteria, their phylogenetically informative presence/absence patterns are free of random noise and independent of evolutionary rate or nucleotide composition effects. We screened for early neoavian orthologous retroposon insertions and identified six markers with conflicting presence/absence patterns, whereas six additional retroposons established before or after the presumed major neoavian radiation show consistent phylogenetic patterns. The exceptionally frequent conflicting retroposon presence/absence patterns of neoavian orders are strong indicators of an extensive incomplete lineage sorting era, potentially induced by an early rapid successive speciation of ancestral Neoaves.