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Potential carbon mineralization (Cmin) is a commonly used indicator of soil health, with greater Cmin values interpreted as healthier soil. While Cmin values are typically greater in agricultural soils managed with minimal physical disturbance, the mechanisms driving the increases remain poorly understood. This study assessed bacterial and archaeal community structure and potential microbial drivers of Cmin in soils maintained under various degrees of physical disturbance. Potential carbon mineralization, 16S rRNA sequences, and soil characterization data were collected as part of the North American Project to Evaluate Soil Health Measurements (NAPESHM). Results showed that type of cropping system, intensity of physical disturbance, and soil pH influenced microbial sensitivity to physical disturbance. Furthermore, 28% of amplicon sequence variants (ASVs), which were important in modeling Cmin, were enriched under soils managed with minimal physical disturbance. Sequences identified as enriched under minimal disturbance and important for modeling Cmin, were linked to organisms which could produce extracellular polymeric substances and contained metabolic strategies suited for tolerating environmental stressors. Understanding how physical disturbance shapes microbial communities across climates and inherent soil properties and drives changes in Cmin provides the context necessary to evaluate management impacts on standardized measures of soil microbial activity. Foundation for Food and Agricultural Research [523926]; Samuel Roberts Noble Foundation; General Mills Published version Foundation for Food and Agricultural Research (grant ID 523926), General Mills, and The Samuel Roberts Noble Foundation.

Appropriate agronomic management of breeding trials plays an important role in creating selection conditions that lead to clear expression of trait differences between genotypes. Good trial management reduces experimental error to a minimum and in this way facilitates the detection of the best genotypes. The field site should be representative for the target environment of the breeding program, including soil and climatic conditions, photoperiod, and pest and disease prevalence. Uniformity of a field site is important to provide similar growing conditions to all plants. Field variability is affected by natural and management factors and leads to variability in crop performance. Additionally, pest and disease incidence tend to concentrate in patches, introducing variability not necessarily related to the susceptibility of affected genotypes. Precise agronomic management of breeding trials can reduce natural field variability and can contribute to reduce variability of crop performance. Through specialized agronomic management, contrasting selection conditions can be created in the same experimental station. The use of adequate machinery like plot seeders and harvesters contributes to precise trial management and facilitates operation. Machine seeding assures even seeding depth and density. Plot combines can be equipped with grain cleaners, on-board weighing systems and sensors to measure grain humidity and weight, which can greatly facilitate data collection.

In Central America, population and food demands are rising rapidly, while yields of staple crops, maize and beans, remain low. To identify the main factors limiting production, field trials were established in six maize- and bean-producing regions in Guatemala, Honduras and El Salvador, representing about three-quarters of the maize-producing area. Potential yield-limiting factors were evaluated in 2017 and included: water stress, nutrient deficiency, pest and disease pressure, and/or inter-plant competition. When considering all sites, improved fertilization and pest and disease control significantly improved yields in maize by 11 and 16%, respectively but did not have a significant effect in beans. Irrigation had no effect due to good rainfall distribution over the growing season. Optimized planting arrangement resulted in an average 18% increase in maize yield, making it the most promising factor evaluated. The treatment and site combinations that increased both crop productivity and net profit included management changes that improved resource use efficiency. However, the contribution of each limiting factor to yield gaps varied across sites and no treatment was effective at increasing yield consistently across sites. Production constraints are highly dependent on local management practices and agroecological location. Therefore, public and private development efforts that seek to increase production should conduct multi-year, participatory experiments to identify limitations pertinent to the area in question. The next step is then to evaluate sustainable and profitable practices, to address those limitations and provide sound recommendations to farmers while decreasing the environmental and economic costs.

Agronomic systems based on zero tillage and residue retention are becoming more important due to their potential for climate change adaptation through the reduction of soil erosion and improved water availability. Denser soil surface conditions and large amounts of crop residues, however, may be a constraint for early plant establishment, especially in irrigated production areas with high yield potential. Genotype by tillage interactions for yield are not well understood and it is unknown whether tillage should be an evaluation factor in breeding programs. Twenty-six CIMMYT bread ( Triticum aestivum ) and durum ( Triticum turgidum ) wheat genotypes, created between 1964 and 2009, were tested for yield and agronomic performance at CIMMYT’s experimental station near Ciudad Obregon, Mexico, over six years. Treatments included conventional and permanent raised beds with full and reduced irrigation. The objectives were to study breeding progress in distinct agronomic systems and to elucidate the importance of tillage and genotype by tillage interaction for yield and agronomic traits. Breeding progress was achieved irrespective of agronomic treatment. Tillage influenced plant growth and number of grains per m 2 in both wheat types. In bread wheat, genotype by tillage interaction was significant for yield, test weight, and growth parameters. However, no cross-over effects were detected and rank changes were small. In durum wheat, genotype by tillage interaction was only significant for plant growth. The results do not indicate the need for separate breeding programs. However, the question of a need for selection under zero tillage to increase breeding progress is yet to be answered.

Permanent raised beds (PB) are a conservation agriculture option for irrigated conditions that can improve soil quality, increase soil moisture conservation and stabilize yields compared to conventional furrow irrigation. In irrigated wheat (Triticum sp.) production, wet sowing (i.e. applying irrigation before sowing) is most widely used. It allows pre-sowing weed control but reduces sowing time flexibility. Dry sowing, i.e. applying irrigation after sowing, reduces options for weed control but improves water use efficiency and sowing time flexibility. This study evaluated the performance of durum wheat (Triticum durum L.) under conventionally tilled (CTB) and PB with wet and dry sowing in northwestern Mexico. In those four tillage-sowing irrigation environments (ENV), five nitrogen (N) fertilization treatments were tested. Plant stand, grain yield, and grain quality were measured for ten years and fertilizer-based N use efficiency indices were assessed in three years. Plant stand, wheat yield and quality were significantly affected by ENV. The lowest plant stand and yield were found in PB-Dry sowing. On average, only 54 plants m-2 emerged in PB-Dry whereas 159 plants m-2 emerged in CTB-Wet. Plant stand showed high yearly fluctuations, with plant stand in dry sowing favored by lower reference evapotranspiration, with CTB-Dry favored more by high minimum temperature and PB-Dry by high maximum temperature. Yield ranged between 4.20 and 7.94 t ha-1. Yield in PB-Dry was on average 0.35 to 0.50 t ha-1 lower than in the remaining ENV, but positive interactions between year and dry sowing systems were associated with high minimum temperatures at germination and tillering. N fertilization management affected wheat quality, but not wheat yield, possibly due to high levels of soil mineral N available at sowing that were not measured in this study. Split application of N increased grain N content compared to basal N application. Research should address reduced plant stands with dry sowing in conservation agriculture to find management options that improve wheat emergence. Further efforts to optimize N fertilizer management in PB are required to improve grain quality components.

The combination of zero tillage (ZT) and crop residue retention can substantially improve soil structure and reduce the risk of erosion. Growing conditions for crops are substantially altered in such systems and the question whether specific varieties adapted to ZT conditions need to be developed is not answered. Most published research assessed Genotype by Tillage interactions, which are rarely significant, using genotypes generally developed under CT conditions. CIMMYT’s durum wheat breeding program went beyond this approach and performed parallel early generation selection within 16 crosses both in conventional tilled (CT) and ZT soils with the aim of comparing the effect of selection environment (either CT or ZT) on the performance of selected progenies. From 16 initial crosses, 234 lines were selected under CT and 250 under ZT. All 484 lines were subsequently tested for yield and growth traits during three seasons near Ciudad Obregon, Sonora, Mexico in three different testing environments. Those included ZT and CT with full irrigation and CT with reduced irrigation. Early vegetative growth was slightly improved with selection under ZT in all testing environments. Grain yield was highest in ZT testing environment, with a very small average difference in 2013 (0.11 t ha-1) and larger differences in 2014 (0.65 t ha-1) and 2015 (0.42 t ha-1). The differences between selection streams observed for yield were marginal and in most cases not significant. We conclude that, within the germplasm pool handled in CIMMYT’s durum wheat breeding program, selection can be conducted under either tillage conditions without affecting negatively the performance of resulting progenies. The neutrality of selection under ZT in relation to performance of progenies is a likely hypothesis that should be tested in other ZT conditions and germplasm pool combinations.

Drought is a major stress which can seriously limit yield in many crops including barley. Wild barley introgression lines (ILs) like the S42IL library may enhance drought stress tolerance of barley cultivars through the introduction of exotic alleles. The S42IL library was already characterized with 636 Illumina SNPs. New approaches like genotyping by sequencing (GBS) are available for barley to enhance the characterization of ILs. We generated an improved genetic map of the S42IL library, consisting of 4,201 SNPs by adding GBS data. The new map with a total length of 989.2 cM confirmed the extent of wild barley introgressions. Adding GBS data increased the resolution of the S42IL map tenfold from 0.4 to 4.2 markers/cM. This may assist to select possible candidate genes that improve drought tolerance. In four greenhouse experiments, juvenile drought stress response of 52 barley S42ILs was tested to identify quantitative trait loci (QTL). Thirteen S42ILs showed effects for plant biomass and leaf senescence. Subsequently, two verification experiments were conducted with these S42ILs. Nine out of eleven QTL were verified, and 22 additional QTL were detected. For 21 QTL, the Hsp allele increased trait performance, indicating the value of wild barley introgressions. For example, S42IL-107 and S42IL-123 produced more biomass under drought. Two different water-saving strategies were observed. S42IL-143 and S42IL-129 both revealed increased relative water content under drought. While S42IL-143 reduced biomass under drought, S42IL-129 maintained a high biomass production. We recommend using S42IL-107, S42IL-123 and S42IL-129 in barley breeding programs to enhance drought tolerance.

Drought is a major abiotic stress impeding the yield of cereal crops globally. Particularly in Mediterranean environments, water becomes a limiting factor during the reproductive developmental stage, causing yield losses. The wild progenitor of cultivated barley Hordeum vulgare ssp spontaneum (Hsp) is a potentially useful source of drought tolerance alleles. Wild barley introgression lines like the S42IL library may facilitate the introduction of favorable exotic alleles into breeding material. The complete set of 83 S42ILs was genotyped with the barley 9k iSelect platform in order to complete genetic information obtained in previous studies. The new map comprises 2,487 SNPs, spanning 989.8 cM and covering 94.5% of the Hsp genome. Extent and positions of introgressions were confirmed and new information for ten additional S42ILs was collected. A subset of 49 S42ILs was evaluated for drought response in four greenhouse experiments. Plants were grown under well-watered conditions until ten days post anthesis. Subsequently drought treatment was applied by reducing the available water. Several morphological and harvest parameters were evaluated. Under drought treatment, trait performance was reduced. However, there was no interaction effect between genotype and treatment, indicating that genotypes, which performed best under control treatment, also performed best under drought treatment. In total, 40 QTL for seven traits were detected in this study. For instance, favorable Hsp effects were found for thousand grain weight (TGW) and number of grains per ear under drought stress. In particular, line S42IL-121 is a promising candidate for breeding improved malting cultivars, displaying a TGW, which was increased by 17% under terminal drought stress due to the presence of an unknown wild barley QTL allele on chromosome 4H. The introgression line showed a similar advantage in previous field experiments and in greenhouse experiments under early drought stress. We, thus, recommend using S42IL-121 in barley breeding programs to enhance terminal drought tolerance.

Drought is one of the most severe stresses, endangering crop yields worldwide. In order to select drought tolerant genotypes, access to exotic germplasm and efficient phenotyping protocols are needed. In this study the high-throughput phenotyping platform “The Plant Accelerator”, Adelaide, Australia, was used to screen a set of 47 juvenile (six week old) wild barley introgression lines (S42ILs) for drought stress responses. The kinetics of growth development was evaluated under early drought stress and well watered treatments. High correlation (r = 0.98) between image based biomass estimates and actual biomass was demonstrated, and the suitability of the system to accurately and non-destructively estimate biomass was validated. Subsequently, quantitative trait loci (QTL) were located, which contributed to the genetic control of growth under drought stress. In total, 44 QTL for eleven out of 14 investigated traits were mapped, which for example controlled growth rate and water use efficiency. The correspondence of those QTL with QTL previously identified in field trials is shown. For instance, six out of eight QTL controlling plant height were also found in previous field and glasshouse studies with the same introgression lines. This indicates that phenotyping juvenile plants may assist in predicting adult plant performance. In addition, favorable wild barley alleles for growth and biomass parameters were detected, for instance, a QTL that increased biomass by approximately 36%. In particular, introgression line S42IL-121 revealed improved growth under drought stress compared to the control Scarlett. The introgression line showed a similar behavior in previous field experiments, indicating that S42IL-121 may be an attractive donor for breeding of drought tolerant barley cultivars.

QTL mapping by association analysis has recently gained interest in plant breeding research as an alternative to QTL mapping in segregating populations from biparental crosses. In a first experiment on whole-genome association analysis in rapeseed, 684 mapped AFLP markers were tested for association with 14 traits in a set of 84 canola quality winter rapeseed cultivars. For association analysis a general linear model was used. By testing significance of marker-trait associations against a false discovery rate of 0.2, between 1 and 34 associated markers were found for 10 of the 14 traits. Taking into account linkage disequilibrium between the significant markers, these markers represent between 1 and 22 putative QTL for the respective traits. The minimum phenotypic variance explained by the QTL for the different traits ranged from 15% to 53%. A subset of 27 markers were significantly associated with two or more traits. These markers were predominantly shared between traits that were significantly correlated at the phenotypic level. The results show clearly that in rapeseed, QTL mapping by association analysis is a viable alternative to QTL mapping in segregating populations.