Robert B. Hutmacher

Analysis of root-knot nematode and fusarium wilt disease resistance in cotton (Gossypium spp.) using chromosome substitution lines from two alien species

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.

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria

Significance Drought remains a critical obstacle to meeting the food demands of the coming century. Understanding the interplay between drought stress, plant development, and the plant microbiome is central to meeting this challenge. Here, we demonstrate that drought causes enrichment of a distinct set of microbes in roots, composed almost entirely of monoderms, which lack outer membranes and have thick cell walls. We demonstrate that under drought, roots increase the production of many metabolites, and that monoderms inhabiting the drought-treated rhizosphere exhibit increased activity of transporters connected with some of these same compounds. The discovery of this drought-induced enrichment and associated shifts in metabolite exchange between plant and microbe reveal a potential blueprint for manipulating plant microbiomes for improved crop fitness. Drought stress is a major obstacle to crop productivity, and the severity and frequency of drought are expected to increase in the coming century. Certain root-associated bacteria have been shown to mitigate the negative effects of drought stress on plant growth, and manipulation of the crop microbiome is an emerging strategy for overcoming drought stress in agricultural systems, yet the effect of drought on the development of the root microbiome is poorly understood. Through 16S rRNA amplicon and metatranscriptome sequencing, as well as root metabolomics, we demonstrate that drought delays the development of the early sorghum root microbiome and causes increased abundance and activity of monoderm bacteria, which lack an outer cell membrane and contain thick cell walls. Our data suggest that altered plant metabolism and increased activity of bacterial ATP-binding cassette (ABC) transporter genes are correlated with these shifts in community composition. Finally, inoculation experiments with monoderm isolates indicate that increased colonization of the root during drought can positively impact plant growth. Collectively, these results demonstrate the role that drought plays in restructuring the root microbiome and highlight the importance of temporal sampling when studying plant-associated microbiomes.

Glufosinate Safety in WideStrike® Acala Cotton

Abstract WideStrike® Acala cotton is a two-gene, in-plant trait that provides broad-spectrum and season-long control of lepidopteran insect pests, and the varieties available in California also have resistance to glyphosate. There have been indications that WideStrike cotton has some glufosinate tolerance as well, so the level of tolerance to glufosinate needed to be ascertained. A 2-yr (2008 and 2009) study was conducted in California to evaluate the potential crop injury caused by three different rates (0.59, 0.88, and 1.76 kg ai ha−1) of glufosinate–ammonium at four different growth stages (cotyledon, 2-node, 5- to 6-node, and 18- to 19-node stages) of WideStrike Acala cotton. The effects of these treatments on the cotton plants and yield were closely monitored. Glyphosate at 1.54 kg ae ha−1 was applied at all cotton growth stages as a standard application, and a nontreated control was included. The greatest level of injury (58%) was observed with the highest rate of glufosinate applied at both the cotyledon and the two-node stage of cotton. However, injury was less than 10% following glufosinate at 0.59 kg ha−1 applied at the 18- to 19-node stage. The level of injury increased with the higher application rate of glufosinate at all crop growth stages. In 2008 and 2009, the glufosinate treatments had no effect on cotton lint yield. Therefore, the study showed that glufosinate can be applied safely topically at 0.59 kg ha−1 at the cotyledon- to 2-node stage or as POST-directed spray between the 5- to 19-node stages. Although injury occurred at this rate, the plants recovered within 2 to 3 wk of the treatment. Increasing glufosinate rates beyond 0.59 kg ha−1 can increase the possibility of greater crop injury. Nomenclature: Glufosinate-ammonium; glyphosate; cotton; Gossypium hirsutum L. Resumen El algodón Acala WideStrike® posee dos genes que brindan control de amplio espectro de plagas insectiles-lepidóptera a lo largo de la temporada de crecimiento, y las variedades disponibles en California también tienen resistencia a glyphosate. Han habido indicaciones de que el algodón WideStrike también tiene algo de tolerancia a glufosinate, así que es necesario definir el nivel de tolerancia a este herbicida. Se realizó un estudio de dos años de duración (2008 y 2009) en California, para evaluar el potencial de daño al cultivo causado por tres dosis diferentes (0.59, 0.88, y 1.76 kg ai ha−1) de glufosinate ammonium en cuatro estadios de crecimiento (cotiledón, 2 nudos, 5 a 6 nudos, y 18 a 19 nudos) de algodón Acala WideStrike. Se le dio seguimiento detallado a los efectos de estos tratamientos en las plantas y el rendimiento del algodón. Se aplicó glyphosate a 1.54 kg ae ha−1 en todos los estadios de crecimiento como estándar de aplicación, y se incluyó un testigo sin tratamiento. El mayor nivel de daño (58%) se observó con la dosis mayor de glufosinate aplicada en los estadios de cotiledón y 2 nudos del algodón. Sin embargo, el daño fue menos de 10% después de aplicaciones de glufosinate a 0.59 kg ha−1 en el estadio de 18 a 19 nudos. El nivel de daño incrementó con la dosis mayor de glufosinate en todos los estadios de crecimiento del cultivo. En 2008 y 2009, los tratamientos de glufosinate no tuvieron ningún efecto en el rendimiento de fibra del algodón. Así, el estudio mostró que se puede aplicar glufosinate tópicamente en forma segura a 0.59 kg ha−1 en los estadios de cotiledón y de 2 nudos, o en forma POST-dirigida en los estadios de 5 a 19 nudos. Aunque hubo daños con esta dosis, las plantas se recuperaron 2 a 3 semanas después del tratamiento. Aumentar las dosis de glufosinate más allá de 0.59 kg ha−1 puede incrementar la posibilidad de observar un mayor daño en el cultivo.

Impact of Early Defoliation on California Pima Cotton Boll Opening, Lint Yield, and Quality

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.

Crop Choices with Limiting Water Supplies: Deficit Irrigation and Sensitive Crop Growth Stages

Limited supplies of good-quality water in semi-arid and arid crop production regions often results in intense competition for water supplies among agricultural, municipal, and environmental interests. This increased competition can provide motivation for agricultural water users to reduce planted acreage, change practices or use equipment to control water losses, improve efficiencies of water application or irrigation scheduling, and consider changes in water management to impose some periods of deficit irrigation. Each of these choices has consequences for the crop, land and producer, the magnitude of which often depends on the knowledge of the agent making the choice as well as other factors outside of their control. For instance, if deficit irrigation is to be effective, it requires identification of growth stages sensitive to reduced water applications. Additionally, deficit irrigation requires development of new irrigation scheduling approaches that are based on a reduction of applications, at least during a large portion of the less-sensitive crop-growth stages. Crop species have different sensitivities to water deficit and, therefore, the potential impact on crop productivity (yield) will likewise be different. Crop-quality characteristics can also be adversely affected, some of which can impact marketability and the relative value of the crop. Objectives of this analysis are to describe crop and water management issues that can arise when deficit irrigation is considered as a water-saving approach. This chapter also provides examples of crop species characteristics that impact the suitability of deficit irrigation as a workable management option when irrigation water is scarce.

Strong succession in arbuscular mycorrhizal fungal communities

The ecology of fungi lags behind that of plants and animals because most fungi are microscopic and hidden in their substrates. Here, we address the basic ecological process of fungal succession in nature using the microscopic, arbuscular mycorrhizal fungi (AMF) that form essential mutualisms with 70–90% of plants. We find a signal for temporal change in AMF community similarity that is 40-fold stronger than seen in the most recent studies, likely due to weekly samplings of roots, rhizosphere and soil throughout the 17 weeks from seedling to fruit maturity and the use of the fungal DNA barcode to recognize species in a simple, agricultural environment. We demonstrate the patterns of nestedness and turnover and the microbial equivalents of the processes of immigration and extinction, that is, appearance and disappearance. We also provide the first evidence that AMF species co-exist rather than simply co-occur by demonstrating negative, density-dependent population growth for multiple species. Our study shows the advantages of using fungi to test basic ecological hypotheses (e.g., nestedness v. turnover, immigration v. extinction, and coexistence theory) over periods as short as one season.

Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought

BackgroundSorghum 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.ResultsTo 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.ConclusionsThe 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.

Low-pressure drip system in reduced tillage cotton.

Research has shown the soil and water conservation advantages of subsurface drip irrigation. Low-pressure drip system (LPS) technology has shown a high potential for economically improving application efficiency of irrigation systems under sandy soil conditions in areas where water is scarce and/or expensive. Energy costs are reduced as less than 70 grams per square cm is needed for system operation. The low-pressure system is installed just below the soil surface, it operates at very low flow and pressure, and it can stay on for longer periods of time without generating runoff or deep percolation. This study is designed to assess LPS under a reduced tillage system without the use of any other irrigation method for stand establishment. This combines the benefits of increased water use efficiency and lower energy costs for improved irrigation efficiency and fewer tillage operations resulting in lower production costs and less airborne dust. Since the drip tape was installed two years ago, only 3 cultivation passes have been made. No major tillage operations, the kind that generate lots of dust, have been performed. LPS water usage was 15% less than furrow irrigation and yields of cotton (Gossypium hirsutum) and blackeye beans (Vigna unguiculata) were comparable to yields from furrow irrigation. This system does present some challenges in stand establishment on very sandy soils and with weed control, which continue to be investigated. Herbicides requiring incorporation were not used. Weeds can be controlled in cotton using glyphosate and other herbicides. Fewer chemical weed control options are available for blackeye beans. The LPS technology has many potential technical, energy and economic advantages over standard drip and subsurface drip irrigation.

Response of Acala Cotton to Nitrogen Rates in the San Joaquin Valley of California

The responses of Acala cotton (Gossypium hirsutum L.) in California to a range of applied nitrogen (N) treatments were investigated in a 5-year, multisite experiment. The experiment’s goals were to identify crop growth and yield responses to applied N and provide information to better assess the utility of soil residual N estimates in improving fertilizer management. Baseline fertilizer application rates for the lowest applied N treatments were based on residual soil nitrate-N (NO3-N) levels determined on soil samples from the upper 0.6 m of the soil collected prior to spring N fertilization and within 1 week postplanting each year. Results have shown positive cotton lint yield responses to increases in applied N across the 56 to 224 kg N/ha range in only 41% (16 out of 39) of test sites. Soil NO3-N monitoring to a depth of 2.4 m in the spring (after planting) and fall (postharvest) indicate most changes in soil NO3 occur within the upper 1.2 m of soil. However, some sites (those most prone to leaching losses of soluble nutrients) also exhibited net increases in soil NO3-N in the 1.2- to 2.4-m depth zone when comparing planting time vs. postharvest data. The lack of yield responses and soil NO3-N accumulations at some sites indicate that more efforts should be put into identifying the amount of plant N requirements that can be met from residual soil N, rather than solely from fertilizer N applications.