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Arbuscular mycorrhizal fungi (AMF), the mutualistic symbionts with most crops, constitute a research system of human-associated fungi whose relative simplicity and synchrony are conducive to experimental ecology. However, little is known about the shifts in adaptive strategies of sorghum associated AMFs where strong AMF succession replaces initially ruderal species with competitive ones and where the strongest plant response to drought is to manage these AMF. First, we hypothesize that, when irrigation is stopped to mimic drought, competitive AMF species should be replaced by AMF species tolerant to drought stress. We then, for the first time, correlate AMF abundance and host plant transcription to test two novel hypotheses about the mechanisms behind the shift from ruderal to competitive AMF. Surprisingly, despite imposing drought stress, we found no stress tolerant AMF. Remarkably, we found strong and differential correlation between the successional shift from ruderal to competitive AMF and sorghum genes whose products (i) produce and release strigolactone signals, (ii) perceive mycorrhizal-lipochitinoligosaccharide (Myc-LCO) signals, (iii) provide plant lipid and sugar to AMF and, (iv) import minerals and water provided by AMF. These novel insights into host gene expression and succession of AMF show adaptive strategies evolved by AMF and their hosts and provide a rationale for selecting AMF to reduce inputs and maximize yield in commercial agriculture. Future research opportunities include testing the specifics and generality of our hypotheses by employing genetically modified host plants, and exploring additional genes underlying the adaptive strategies in natural succession.

Recent studies have demonstrated that drought leads to dramatic, highly conserved shifts in the root microbiome. At present, the molecular mechanisms underlying these responses remain largely uncharacterized. Here we employ genome-resolved metagenomics and comparative genomics to demonstrate that carbohydrate and secondary metabolite transport functionalities are overrepresented within drought-enriched taxa. These data also reveal that bacterial iron transport and metabolism functionality is highly correlated with drought enrichment. Using time-series root RNA-Seq data, we demonstrate that iron homeostasis within the root is impacted by drought stress, and that loss of a plant phytosiderophore iron transporter impacts microbial community composition, leading to significant increases in the drought-enriched lineage, Actinobacteria. Finally, we show that exogenous application of iron disrupts the drought-induced enrichment of Actinobacteria, as well as their improvement in host phenotype during drought stress. Collectively, our findings implicate iron metabolism in the root microbiome’s response to drought and may inform efforts to improve plant drought tolerance to increase food security., Advances in omics provide a tool to understand mechanisms for plant–microbial interactions under stress. Here the authors apply genome-resolved metagenomics to investigate sorghum and its microbiome responses to drought, identifying an unexpected role of iron metabolism.

Histones belong to a family of highly conserved proteins in eukaryotes. They pack DNA into nucleosomes as functional units of chromatin. Post-translational modifications (PTMs) of histones, which are highly dynamic and can be added or removed by enzymes, play critical roles in regulating gene expression. In plants, epigenetic factors, including histone PTMs, are related to their adaptive responses to the environment. Understanding the molecular mechanisms of epigenetic control can bring unprecedented opportunities for innovative bioengineering solutions. Herein, we describe a protocol to isolate the nuclei and purify histones from sorghum leaf tissue. The extracted histones can be analyzed in their intact forms by top-down mass spectrometry (MS) coupled with online reversed-phase (RP) liquid chromatography (LC). Combinations and stoichiometry of multiple PTMs on the same histone proteoform can be readily identified. In addition, histone tail clipping can be detected using the top-down LC-MS workflow, thus, yielding the global PTM profile of core histones (H4, H2A, H2B, H3). We have applied this protocol previously to profile histone PTMs from sorghum leaf tissue collected from a large-scale field study, aimed at identifying epigenetic markers of drought resistance. The protocol could potentially be adapted and optimized for chromatin immunoprecipitation-sequencing (ChIP-seq), or for studying histone PTMs in similar plants.

Diseases such as Fusarium wilt caused by Fusarium oxysporum f.sp. vasinfectum (FOV), a soil borne fungal pathogen, represent expanding threats to cotton (Gossypium spp.) production around the world. For over a decade, FOV race 4 (FOV4) has adversely impacted cotton production in California’s San Joaquin Valley causing plant wilt and death. With this disease formally identified in 2019 in New Mexico and in 2017 in El Paso, TX region in proximity to the High Plains of west Texas—the largest Upland cotton producing region in the USA, the need to expand the genetic base of Upland (G. hirsutum L.) cotton and develop cultivars resistant/tolerant to FOV4 has become urgent. Our previous research in Pima (G. barbadense L.) cotton identified high levels of resistance to FOV4 in ‘Pima S-6’ germplasm, and our program publicly released Pima germplasm with improved FOV4 resistance. However, the search for resistant Upland cotton has proved more challenging compared to the effort in Pima. More than 1000 Upland accessions from the USDA-ARS Cotton Germplasm Collection were evaluated for reaction to FOV4 in artificial-greenhouse conditions and in naturally infested grower fields. Less than 0.1% of the tested accessions were selected to develop highly resistant FOV4 progeny. Two sources (NM12Y1004–NM12Y1005 and SA-3208) of Asiatic breeding origin were identified with tolerance to FOV4 and used to introgress and increase resistance. Pedigree information from other parental lines used to develop progeny revealed their sources to be exotic and wild Upland germplasm. That is triple/multiple crosses included the origin of these obsolete SA cultivars ‘Auburn M’, ‘DES 920’, ‘MARSPD202085’, ‘S.N.0503-1’, PD 2165, and ‘Stoneville 14’, among others. A range of severity of foliar symptoms, vascular root staining, and plant mortality occurred in the infested fields based on tested accessions and observations of susceptible germplasm/cultivar-checks, indicating moderate to severe inoculum levels with the sites. Many FOV4 infected Upland cultivars typically showed fewer leaf symptoms and much lower plant mortality in early stages of the disease compared to Pima cultivars. The inheritance of FOV4 resistance/tolerance in Upland cotton ranges from recessive to intermediate, unlike in Pima cotton where resistance seems to be dominant or more complete in the host plant. Highly resistant/tolerant Upland breeding lines were developed from this breeding research effort and will be publicly released to reduce the vulnerability of the cotton industry to this pathogen.

Background Sorghum bicolor is the fifth most commonly grown cereal worldwide and is remarkable for its drought and abiotic stress tolerance. For these reasons and the large size of biomass varieties, it has been proposed as a bioenergy crop. However, little is known about the genes underlying sorghum’s abiotic stress tolerance and biomass yield. Results To uncover the genetic basis of drought tolerance in sorghum at a genome-wide level, we undertook a high-density phenomics genome wide association study (GWAS) in which 648 diverse sorghum lines were phenotyped at two locations in California once per week by drone over the course of a growing season. Biomass, height, and leaf area were measured by drone for individual field plots, subjected to two drought treatments and a well-watered control. The resulting dataset of ~ 171,000 phenotypic data-points was analyzed along with 183,989 genotype by sequence markers to reveal 213 high-quality, replicated, and conserved GWAS associations. Conclusions The genomic intervals defined by the associations include many strong candidate genes, including those encoding heat shock proteins, antifreeze proteins, and other domains recognized as important to plant stress responses. The markers identified by our study can be used for marker assisted selection for drought tolerance and biomass. In addition, our results are a significant step toward identifying specific sorghum genes controlling drought tolerance and biomass yield.

Chromosome substitution (CS) lines in plants are a powerful genetic resource for analyzing the contribution of chromosome segments to phenotypic variance. In this study, a series of interspecific cotton (Gossypium spp.) CS lines were used to identify a new germplasm resource, and to validate chromosomal regions and favorable alleles associated with nematode or fungal disease resistance traits. The CS lines were developed in the G. hirsutum L. TM-1 background with chromosome or chromosome segment substitutions from G. barbadense L. Pima 3-79 or G. tomentosum. Root-knot nematode (Meloidogyne incognita) and fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) (races 1 and 4) resistance alleles and quantitative trait loci (QTL) previously placed on cotton chromosomes using SSR markers in two interspecific recombinant inbred line populations were chosen for testing. Phenotypic responses of increased resistance or susceptibility in controlled inoculation and infested field assays confirmed the resistance QTLs, based on substitution with the positive or negative allele for resistance. Lines CS-B22Lo, CS-B04, and CS-B18 showed high resistance to nematode root-galling, confirming QTLs on chromosomes 4 and 22 (long arm) with resistance alleles from Pima 3-79. Line CS-B16 had less fusarium race 1-induced vascular root staining and higher percent survival than the TM-1 parent, confirming a major resistance QTL on chromosome 16. Lines CS-B(17-11) and CS-B17 had high fusarium race 4 vascular symptoms and low survival due to susceptible alleles introgressed from Pima 3-79, confirming the localization on chromosome 17 of an identified QTL with resistance alleles from TM1 and other resistant lines. Analyses validated regions on chromosomes 11, 16, and 17 harboring nematode and fusarium wilt resistance genes and demonstrated the value of CS lines as both a germplasm resource for breeding programs and as a powerful genetic analysis tool for determining QTL effects for disease resistance. CS lines carrying small alien chromosome segments with favorable QTL alleles could be used for effective introgression of biotic stress resistance or many other desirable traits by targeting gene interactions and reducing linkage drag effects.

Chemical defoliation is a necessary pre-harvest practice in Pima cotton (Gossypium barbadense L.) production in California. Growers begin defoliating as early as possible but yield and quality loss can occur if the bolls are not fully mature. Harvest aids can advance harvest dates, avoid late-season pests, and adverse weather conditions in California. A study was conducted on Pima cotton, cv. ‘Phytogen-802’. Different rates of Ginstar (ai thidiazuron/diuron, Bayer CropScience) or Ginstar plus Finish 6-Pro (ai ethephon/cyclanilide, Bayer CropScience) were applied at 6 to 7 nodes above cracked boll (NACB) or 4 to 5 NACB at various rates. Results showed that these harvest aids could be applied at the tested rates at both timings without any adverse effects on percent open bolls, and lint yield and quality. Therefore, application of these harvest-aid materials starting at 6 to 7 NACB can benefit Pima cotton growers in California as early harvests can be achieved without compromising lint yield or quality.

Diseases such as Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans] represent expanding threats to cotton production. Integrating disease resistance into high-yielding, high-fiber quality cotton (Gossypium spp.) cultivars is one of the most important objectives in cotton breeding programs worldwide. In this study, we conducted a comprehensive analysis of gene action in cotton governing FOV race 4 resistance by combining conventional inheritance and quantitative trait loci (QTL) mapping with molecular markers. A set of diverse cotton populations was generated from crosses encompassing multiple genetic backgrounds. FOV race 4 resistance was investigated using seven parents and their derived populations: three intraspecific (G. hirsutum × G. hirsutum L. and G. barbadense × G. barbadense L.) F1 and F2; five interspecific (G. hirsutum × G. barbadense) F1 and F2; and one RIL. Parents and populations were evaluated for disease severity index (DSI) of leaves, and vascular stem and root staining (VRS) in four greenhouse and two field experiments. Initially, a single resistance gene (Fov4) model was observed in F2 populations based on inheritance of phenotypes. This single Fov4 gene had a major dominant gene action and conferred resistance to FOV race 4 in Pima-S6. The Fov4 gene appears to be located near a genome region on chromosome 14 marked with a QTL Fov4-C141, which made the biggest contribution to the FOV race 4 resistance of the generated F2 progeny. Additional genetic and QTL analyses also identified a set of 11 SSR markers that indicated the involvement of more than one gene and gene interactions across six linkage groups/chromosomes (3, 6, 8, 14, 17, and 25) in the inheritance of FOV race 4 resistance. QTLs detected with minor effects in these populations explained 5–19 % of the DSI or VRS variation. Identified SSR markers for the resistance QTLs with major and minor effects will facilitate for the first time marker-assisted selection for the introgression of FOV race 4 resistance into elite cultivars during the breeding process.

Four Pima cotton (Gossypium barbadense L.) germplasm lines, SJ-07P-FR01 (Reg. No. GP-910, PI 654065), SJ-07P-FR02 (Reg. No. GP-911, PI 654066), SJ-07P-FR03 (Reg. No. GP-912, PI 654067), and SJ-07P-FR04 (Reg. No. GP-913, PI 654068), were developed by the USDA-ARS and New Mexico State University Agricultural Experiment Station and jointly released with the University of California in 2008. The primary purpose for these releases is to provide germplasm with good levels of resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum Atk. Sny & Hans) (FOV) race 4 to cotton breeders in California. Lines SJ-07P-FR01 to -FR03 originated from a cross made at New Mexico State University in 1997 of germplasm lines 8810 and NMSI 1601. The germplasm line SJ-07P-FR04 originated from reselection within the publicly released USDA- ARS germplasm line P 73. The lines were evaluated for resistance to race 4 in two fi eld and three greenhouse trials conducted in 2003 and 2005. Five replicated fi eld evaluations for yield potential, fi ber characteristics, and other agronomic traits were conducted at Five Points, CA, Shafter, CA, and Maricopa, AZ, in 2005 and 2006. The SJ-07P-FR series possesses good resistance, moderate lint yield potential, and good to superior fi ber length and strength. Caution should be applied when using these lines, and it should not be assumed that the lines provide complete resistance against FOV race 4.

Knowledge of the inheritance of disease resistance and genomic regions housing resistance (R) genes is essential to prevent expanding pathogen threats such as Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans] in cotton (Gossypium spp.). We conducted a comprehensive study combining conventional inheritance, genetic and quantitative trait loci (QTL) mapping, QTL marker-sequence composition, and genome sequencing to examine the distribution, structure and organization of disease R genes to race 1 of FOV in the cotton genome. Molecular markers were applied to F2 and recombinant inbred line (RIL) interspecific mapping populations from the crosses Pima-S7 (G. barbadense L.) × ‘Acala NemX’ (G. hirsutum L.) and Upland TM-1 (G. hirsutum) × Pima 3-79 (G. barbadense), respectively. Three greenhouse tests and one field test were used to obtain sequential estimates of severity index (DSI) of leaves, and vascular stem and root staining (VRS). A single resistance gene model was observed for the F2 population based on inheritance of phenotypes. However, additional inheritance analyses and QTL mapping indicated gene interactions and inheritance from nine cotton chromosomes, with major QTLs detected on five chromosomes [Fov1-C06, Fov1-C08, (Fov1-C11 1 and Fov1-C11 2) , Fov1-C16 and Fov1-C19 loci], explaining 8–31% of the DSI or VRS variation. The Fov1-C16 QTL locus identified in the F2 and in the RIL populations had a significant role in conferring FOV race 1 resistance in different cotton backgrounds. Identified molecular markers may have important potential for breeding effective FOV race 1 resistance into elite cultivars by marker-assisted selection. Reconciliation between genetic and physical mapping of gene annotations from marker-DNA and new DNA sequences of BAC clones tagged with the resistance-associated QTLs revealed defenses genes induced upon pathogen infection and gene regions rich in disease-response elements, respectively. These offer candidate gene targets for Fusarium wilt resistance response in cotton and other host plants.

The purpose of this research was to determine the magnitude of photorespiration in field-grown cotton ( Gossypium hirsutum L.) as a function of environmental and plant-related factors. Photorespiration rates were estimated as the difference between measured gross and net photosynthetic rates. A linear increase in photorespiration was observed as air temperature increased from 22 to 40°C at saturating photon flux density. At 22°C, photorespiration was less than 15 per cent of net photosynthesis and very comparable to the dark respiration rate. At 40°C, photorespiration represented about 50 per cent of net photosynthesis. Gross photosynthesis had a temperature optimum of 32 to 34°C. Water stress, as indicated by Ψ L , did not alter the ratio of gross photosynthesis to net photosynthesis when the confounding effects of leaf temperature differences were accounted for in the data analyses. A reduction in both gross and net photosynthesis was apparent as Ψ L declined from −2.0 megapascals indicating direct effects of water stress on the photosynthetic process. Photorespiration expressed as a proportion of net photosynthesis increased as water stress intensified. Cotton cultivars possessing a fruit load had significantly higher gross and net photosynthetic rates and lower photorespiration rates than did photoperiod-sensitive cotton strains without a fruit load. Within the fruiting types, which were genetically very similar, only minor differences were observed in the photorespiration:net photosynthesis ratios. However, in the photoperiod-sensitive strains, considerable genetic variability existed when photorespiration was expressed as a proportion of net photosynthesis. These results suggest that the kinetics of ribulose-1,5-bisphosphate carboxylase:oxygenase may be different and, thus, the possibility of genetically reducing photorespiration exists.

Seasonal and diurnal measurements of leaf water potential (ψ1), relative water content (RWC) and stomatal conductance (gs) were made in the field on 19-year old Prunus salicina (L.) cv. Santa Rosa, a deciduous fruit tree species, irrigated with 3 different concentrations of saline water over a 3 year period (1985-1987). With the exception of stage III of fruit growth, little or no treatment difference in Φ1, leaf turgor potential (Φp), or RWC was noted during the day. Seasonal averages of morning (0700-0900) and afternoon (1500-1700) Φp did not decline with increasing salinity, indicating long-term osmotic adjustment in this species. Maintenance of leaf water status under saline conditions was in part a consequence of increased stomatal closure, with a subsequent reduction in leaf transpiration rate. However, during stage III of fruit growth, an increase in mean afternoon (1200-1700) stomatal conductance of 26-117%, independent of salinity treatment, was observed in 1985 and again in 1987. Higher conductance values during this period may be associated with rapid fruit expansion and greater assimilate demand. The observed increase in conductance resulted in greater leaf water loss and larger measured differences in midday ψ1 between salinity treatments. This research indicates that for Prunus salicina in the field, salinity stress resulted in leaf water deficits only during the final period of fruit expansion and ripening.

The relationship between single leaf photosynthesis and conductance was examined in cotton ( Gossypium hirsutum L.) across a range of environmental conditions. The purpose of this research was to separate and define the degree of stomatal and nonstomatal limitations in the photosynthetic process of field-grown cotton. Photosynthetic rates were related to leaf conductance of upper canopy leaves in a curvilinear manner. Increases in leaf conductance of CO 2 in excess of 0.3 to 0.4 mole per square meter per second did not result in significant increases in gross or net photosynthetic rates. No tight coupling between environmental influences on photosynthetic rates and those affecting conductance levels was evident, since photosynthesis per unit leaf conductance did not remain constant. Slowly developing water stress caused greater reductions in photosynthesis than in leaf conductance, indicating nonstomatal limitations of photosynthesis. Increases in external CO 2 concentration to levels above ambient did not produce proportional increases in photosynthesis even though substomatal or intercellular CO 2 concentration increased. The lack of a linear increase in photosynthetic rate in response to increases in leaf conductance and in response to increases in external CO 2 concentration demonstrated that nonstomatal factors are major photosynthetic rate determinants of cotton under field conditions.