Wheat Sequences Research Articles

Long-Term Manuring and Fertilization Influence on Soil Properties and Wheat Productivity in Semi-Arid Regions

Information on the long-term effects of the addition of organics and fertilizers to wheat under the pearl millet–wheat cropping system with semi-arid conditions in north-western India is still lacking. The present research was conducted in an ongoing field experiment initiated during Rabi 1995 at the Research Farm of Chaudhary Charan Singh at Haryana Agricultural University, Hisar. After 25 years, the impacts of nutrient management practices on soil fertility and wheat productivity were evaluated. The experiment comprised a total of eight treatment combinations viz. half and full doses of recommended fertilizers (N and P), organic manures (FYM: farmyard manure, POM: poultry manure, and PRM: press mud) alone and in combination with NP fertilizers. The conjoint application of organic manure and chemical fertilizers resulted in a positive influx of nutrients via increasing total organic carbon (TOC), available N, P, K, and S, which ranged from 0.46 to 1.42%, 122.70 to 194.70, 15.66 to 74.92, 340.5 to 761.2, and 15.26 to 54.63 kg ha−1 in surface soil (0–15 cm), respectively. Carbon fractions and crop yield were significantly improved by adopting integrated nutrient management (INM). The TOC showed a positive and significant correlation with C fractions (r > 0.92) and with soil-available N, P, K, and S (r > 0.77) content. The data also revealed a strong relationship between TOC and soil-available (0–15 cm) nutrients i.e., available N (R2= 0.769), available P (R2 = 0.881), available K (R2 = 0.758), and available S (R2 = 0.914), respectively. Thus, practices that increased TOC were also beneficial in enhancing the availability of the nutrients in the soil. A positive and highly significant correlation was also found among wheat yield, nutrient (NPKS) content, and uptake. A polynomial relationship between grain yield and grain N (R2 = 0.962), P (R2 = 0.946), and K (R2 = 0.967) content, and between straw yield and straw N (R2 = 0.830), P (R2 = 0.541) and K (R2 = 0.976) content was obtained. Integrated use of PRM7.5 followed by FYM15 and POM5 coupled with NP fertilizers proved best, which could be beneficial for obtaining nutritious and highest wheat yield (grain: 6.01 t ha−1 and straw: 7.70 t ha−1) coupled with improved fertility within a sustained manner under the pearl millet–wheat sequence in prevailing semi-arid conditions of the North Indian state of Haryana.

Crop rotation diversity and tillage effects on soil and wheat grain nutrient concentration in an organically-managed system

Consumer demand for high quality organic produce in Canada has in recent years contributed to the development of a more sustainable organic agriculture system that increased productivity without decreasing soil fertility. The objective of this 4-yr field study was to determine if an organic system with diversified crop rotations under reduced tillage would produce high quality spring wheat (Triticum aestivum L.) grain and improve soil fertility. A simplified rotation (SR) consisting of a forage pea (Pisum sativum L.) green manure (GM)-spring wheat sequence and a diversified rotation (DR, forage pea GM-oilseed-pulse crop-spring wheat sequence) were compared under two tillage intensities (high tillage [HT] and low tillage [LT]). The oilseed alternated between mustard (Sinapis alba L.) and flax (Linum usitatissimum L.), and the pulse alternated between field pea and lentil (Lens culinaris L.). Generally, nutrient concentrations in wheat grain were mostly significantly higher under LT than HT and in the DR compared with the SR. In addition, tillage-rotation system influenced soil zinc, calcium, magnesium, and sodium concentrations. However, grain Cd concentration was higher in the LT treatment under the DR sequence relative to other treatments. Our results indicate that organically managed diversified crop rotations under reduced tillage can produce wheat grains with high nutritional value for humans and livestock but may not increase soil micronutrient concentrations.

Effect of Organic Manures on Productivity in a Groundnut-Wheat Sequence under Organic Farming

An experiment was conducted during two consecutivekharif and rabi season from the year 2016-17 to 2018-19 for three years on to evaluate different organic sources performance on groundnut and wheat sequence under organic farming at Agronomy Instructional Farm, Chimanbhai Patel College of Agriculture, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar. The soil of experiment was loamy sand. Experiment was carried out in Large plot technique design and with eight replication for four treatments. From three years experiment result revealed that in kharif season, application of 100% nitrogen through castor cake sequring higher pod yield of groundnut and application of 75% nitrogen through castor cake for succeding wheat in rabi season for getting higher seed yield. Application of castor cake in both season sequred higher groundnut equivalent yield. Maximum gross (Rs 150300/ha) and net neturn (Rs 67922/ha) with BCR of 1.82 was obtained under Treatment T3 (100% RDN through castor cake in groundnut and 75% RDN through castor cake in succeeding wheat) under organic farming under North Gujarat Agro climatic conditions.

An Accurate Representation of the Number of bZIP Transcription Factors in the Triticum aestivum (Wheat) Genome and the Regulation of Functional Genes during Salt Stress.

Climate change is dramatically increasing the overall area of saline soils around the world, which is increasing by approximately two million hectares each year. Soil salinity decreases crop yields and, thereby, makes farming less profitable, potentially causing increased poverty and hunger in many areas. A solution to this problem is increasing the salt tolerance of crop plants. Transcription factors (TFs) within crop plants represent a key to understanding salt tolerance, as these proteins play important roles in the regulation of functional genes linked to salt stress. The basic leucine zipper (bZIP) TF has a well-documented role in the regulation of salt tolerance. To better understand how bZIP TFs are linked to salt tolerance, we performed a genome-wide analysis in wheat using the Chinese spring wheat genome, which has been assembled by the International Wheat Genome Sequencing Consortium. We identified 89 additional bZIP gene sequences, which brings the total of bZIP gene sequences in wheat to 237. The majority of these 237 sequences included a single bZIP protein domain; however, different combinations of five other domains also exist. The bZIP proteins are divided into ten subfamily groups. Using an in silico analysis, we identified five bZIP genes (ABF2, ABF4, ABI5, EMBP1, and VIP1) that were involved in regulating salt stress. By scrutinizing the binding properties to the 2000 bp upstream region, we identified putative functional genes under the regulation of these TFs. Expression analyses of plant tissue that had been treated with or without 100 mM NaCl revealed variable patterns between the TFs and functional genes. For example, an increased expression of ABF4 was correlated with an increased expression of the corresponding functional genes in both root and shoot tissues, whereas VIP1 downregulation in root tissues strongly decreased the expression of two functional genes. Identifying strategies to sustain the expression of the functional genes described in this study could enhance wheat's salt tolerance.

Changes in Biological Soil Health Properties in Response to Increased Crop Diversity in a Dryland Wheat-Based Cropping System

ABSTRACT Diversifying wheat (Triticum aestivum L.)-based cropping systems is important for the sustainability of dryland agriculture. Research has focused on the agronomic benefits of increased crop diversity in semi-arid environments, but less is known about the impacts of increased crop diversity on the soil microbial community. This work compared soil health parameters between a continuous wheat crop sequence to a diverse sequence that included pea (Pisum sativum L.), proso millet (Panicum miliaceum L.), safflower (Carthamus tinctorius, L.), and spring wheat. Respiration was higher (p < .005) in the diverse sequence while activity of N-acetyl-β-d-glucosaminidase was lower (p < .05) with a mean rate of 26.3 and 16.3 mg ρ-nitrophenol kg−1 soil h−1 for the continuous wheat and diverse sequences, respectively. The mean net nitrogen mineralized during the growing season was 33.2 ± 2.5 kg ha−1 and was not different between treatments (p > .05). No difference was observed in bacterial alpha diversity, while fungal community diversity was 52% lower in the diverse rotation. The results of this work suggest that specific crops in a rotation may impact microbial processes related to nitrogen mineralization and that the soil fungal community may be more sensitive to changes in crop sequence than the soil bacterial community.

A near-complete genome sequence of einkorn wheat provides insight into the evolution of wheat A subgenomes

A near-complete genome sequence of einkorn wheat provides insight into the evolution of wheat A subgenomes

Performance of different rice-based cropping systems in the wet temperate zone of Himachal Pradesh

A field experiment to diversify the rice‒wheat system to increase employment and income was conducted during 2017-18 at the research farm of CSK Himachal Pradesh Krishi Vishwavidyalaya Palampur with eight cropping systems that were replicated four times. One-year results revealed that the highest rice grain yield (16477 kg/ha), net returns (₹ 219828/ha) and marginal returns (₹80946) were recorded from the rice – palak – cucumber sequence. Okra – radish – onion resulted in maximum food availability (55.16 kg/ha/day), whereas employment generation was maximum from rice – lettuce – potato + coriander (102.91%). In terms of carbohydrate yield (5146 kg/ha), protein yield (640.6 kg/ha) and energy equivalent (23919 MJ/ha), it was highest from the rice – wheat sequence; however, in the case of carbohydrate and energy equivalent, it was on par with rice – lettuce – potato + coriander.

LysM Proteins TaCEBiP and TaLYK5 are Involved in Immune Responses Mediated by Chitin Coreceptor TaCERK1 in Wheat.

Plant lysin motif (LysM) ectodomain receptors interact with pathogen-associated molecular patterns (PAMPs) and have critical functions in plant-microbe interactions. In this study, 65 LysM family genes were identified using the recent version of the reference sequence of bread wheat (Triticum aestivum), in which 23, 16, 20, and 6 members belonged to LysM-containing receptor-like kinases (LYKs), LysM-containing receptor-like proteins (LYPs), extracellular LysM proteins (LysMes), and intracellular nonsecretory LysM proteins (LysMns), respectively. The study found that TaCEBiP, TaLYK5, and TaCERK1 were highly responsive to PAMP elicitors and phytopathogens, with TaCEBiP and TaLYK5 binding directly to chitin. TaCERK1 acted as a coreceptor with TaCEBiP and TaLYK5 at the plasma membrane. Overexpression of TaCEBiP, TaLYK5, and TaCERK1 in Nicotiana benthamiana leaves exhibited enhanced resistance to Sclerotinia sclerotiorum. Subsequently, knocking down TaCEBiP, TaLYK5, and TaCERK1 genes with barley stripe mosaic virus-VIGS compromised the wheat defense response to an avirulent strain of Puccinia striiformis. The study concluded that wheat has two synergistic chitin perception systems for detecting pathogen elicitors, with the activated CERK1 intracellular kinase domain leading to signaling transduction. This research provides valuable insights into the functional roles and regulatory mechanisms of wheat LysM members under biotic stress.

Analysis of nucleotide sequences of the &lt;i&gt;GT47&lt;/i&gt; glycosyltransferase gene in rye cultivars differing in the content of water-soluble pentosans in grain

Rye (Secale cereale L.) is the most important crop in Russia, its grain quality depends on the content of water-soluble pentosans. The grain of rye cultivars with high content of water-soluble pentosans has good baking properties, but low fodder qualities. Methods of marker-assisted selection for this trait in rye remain undeveloped. For Triticeae, the content of pentosans in grain may be associated with the GT47 glycosyltransferase genes, but the genes of this family have not been identified in rye. The aim of this study was amplification, sequencing, and search for single nucleotide substitutions or other mutations in the GT47 gene in various rye cultivars differing in the content of water-soluble pentosans in their grain and the viscosity of their aqueous extract. DNA from rye leaves was isolated by the standard CTAB method. Based on the nucleotide sequences of the bread wheat and barley GT47 genes, universal primers were selected, then a fragment of the open reading frames of the studied gene was amplified, and the nucleotide sequences were determined by automatic capillary sequencing. The population cultivars of rye, ‘Chulpan 7’ and ‘Podarok’, and F1 hybrids ‘KVS Aviator’, ‘KVS Magnifico’ and ‘KVS Eterno’ were analyzed. The highest content of pentosans and the highest kinematic viscosity of the aqueous extract were found in cv. ‘Chulpan 7’. The lowest values of these indicators were shown by the hybrid cv. ‘KVS Aviator’. The analysis of the nucleotide sequences of the GT47 gene revealed the presence of single-nucleotide substitutions in seven loci, in which the studied rye cultivars differed. Of these, the high-pentosan cv. ‘Chulpan 7’ and the low-pentosan cv, ‘KVS Aviator’ differed in three nucleotide substitutions: 159 (G/A), 204 (C/T), and 327 (G/A). It is suggested that these SNPs can be used for genotyping rye cultivars for the content of water-soluble pentosans in grain.

CRISPR/Cas9-guided knockout of eIF4E improves Wheat yellow mosaic virus resistance without yield penalty.

CRISPR/Cas9-guided knockout of eIF4E improves Wheat yellow mosaic virus resistance without yield penalty.

Do cover crops on the Canadian prairies affect soil nitrogen cycling?

For one of Canada’s most important regions of crop production—the prairies—it’s uncertain if cover crops can be successfully integrated into rotations; if so, will soil nitrogen (N) cycling be influenced to benefit main crops? To address these gaps, we compared a crop rotation with cover crops (CC) vs. without cover crops (LR) from 2018 to 2021 in Saskatoon, SK. The main crops were grown in sequence of wheat–canola–potato–pea; the cover crops included red clover, berseem clover/oat mix, fall rye, and a brassica cover. Yield and aboveground biomass were collected each year and analyzed to determine crop yield and N use efficiency (NUE). Soil N availability was monitored in various ways, that is, by assessing pre-plant soil nitrate, soil inorganic N (SIN) supply rate, and potentially mineralizable N (PMN). We found that the influence on soil N dynamics was restricted to the non-growing season where cover crops reduced SIN supply rate and nitrate content compared to the conventional practice without cover crops. Yet, rotations with vs. without cover crop did not differ in crop NUEs, yields, or in-season N dynamics. We found some evidence that diversifying rotations with cover crops may help the system to function more like perennial systems in terms of regulating N in the long run; but had limited impact during the three years studied. To ensure that cover crops are effective and functional on the prairies, innovative design approaches are needed to adapt cover crops to reach soil health goals under prairie conditions.

Integrating long fallow into wheat-based cropping systems in Western Australia: Spatial pattern of yield and economic responses

CONTEXTLong fallow, once a common management practice in the low-rainfall of Mediterranean-type environments, may provide growers with an opportunity to switch cropping sequence and reduce the risk of yield and income losses during the recent drought period. However, such benefits are usually not uniform across a spatially variable environment. It is important to identify where long fallow would have a role in increasing crop yield and economic return. OBJECTIVETo examine the spatial pattern of yield and economic performance of integrating long fallow into a wheat cropping system in dryland Mediterranean environments of Western Australia. METHODSThe Agricultural Production Systems Simulator (APSIM) driven by 0.05° gridded climate over the dry period of 1990–2020 was used to simulate five rotations (fallow followed by one, two, three or four wheat crops, respectively) and continuous wheat. With offset simulations, simulated wheat yields, plant available water at sowing after a wheat crop or long fallow and N fertilizer requirement were compared and analysed for fallow-wheat and wheat-wheat. Wheat yields and economic returns were also calculated for each rotation and compared with continuous wheat. RESULTS AND CONCLUSIONSWheat yield and economic responses to long fallow showed clear geographic patterns that increased from the south-west to north-east across the wheatbelt, which could be explained by climate and soil conditions. Yield increase from fallow could be >6%, equivalent to 13% of economic increase, in the areas where growing season rainfall was <230 mm and the difference in plant available soil water at sowing between fallowed and continuously cropped soil was >30 mm. Although fallow resulted in overall reduction in crop production, integrating one fallow into a continuous wheat sequence every three or more years might achieve similar profit to continuous wheat for fields with weeds and diseases challenges in the north-eastern wheatbelt. SIGNIFICANCEThe results of yield and economic performance after fallow in the context of space and crop sequence provide a systematic analysis to map where and how fallow could be adopted into cropping systems.

Genome-wide identification and expression analysis of the TaRRA gene family in wheat (Triticum aestivum L.).

Cytokinin is an important endogenous hormone in plants performing a wide spectrum of biological roles. The type-A response regulators (RRAs) are primary cytokinin response genes, which are important components of the cytokinin signaling pathway and are involved in the regulation of plant growth and development. By analysis of the whole genome sequence of wheat, we identified 20 genes encoding RRAs which were clustered into eight homologous groups. The gene structure, conserved motifs, chromosomal location, and cis-acting regulatory elements of the TaRRAs were analyzed. Quantitative real-time polymerase chain reaction (qRT-PCR) results showed that the expression levels of most of the TaRRAs increased rapidly on exogenous cytokinin application. Moreover, the TaRRA family members displayed different expression profiles under the stress treatments of drought, salt, cold, and heat. This study provides valuable insights into the RRA gene family in wheat and promotes the potential application of these genes in wheat genetic improvement.

Production of Conjoined Transgenic and Edited Barley and Wheat Plants for Nud Genes Using the CRISPR/SpCas9 System.

The Nudum (Nud) gene controls the caryopsis type of cereal crops by regulating lipid biosynthetic pathways. Based on the HvNud sequence and its homologous gene sequences in wheat, a conserved sgRNA was designed to obtain the mutants from the barley variety “Vlamingh” and the wheat variety “Fielder” via Agrobacterium-mediated transformation. A total of 19 and 118 transgenic plants were obtained, and 11 and 61 mutant plants were identified in T0 transgenic plants in barley and wheat after PCR-RE detection, and the editing efficiencies of the targeted gene were 57.9 and 51.7% in barley and wheat, respectively. The grain shape of the barley mutants was naked. Five different combinations of mutations for wheat TaNud genes were identified in the T0 generation, and their homozygous-edited plants were obtained in the T1 generation. Interestingly, the conjoined plants in which one plant has different genotypes were first identified. The different tillers in an individual T0 plant showed independent transgenic or mutant events in both barley and wheat, and the different genotypes can stably inherit into T1 generation, indicating that the T0 transgenic plants were the conjoined type. In addition, we did not find any off-target mutations in both barley and wheat. A candidate method for detecting putative-edited wheat plants was suggested to avoid losing mutations in this investigation. This study provides not only materials for studying the function of the Nud gene in barley and wheat but also a system for detecting the mutants in wheat.

Depthwise variation in selected soil properties as influenced by tillage and residue management in sandy loam soil of North-West Himalayas, India

The present study aimed to determine the effect of varying tillage and residue management in a sandy loam soil under maize (Zea mays L.)-wheat (Triticum aestivum L.) sequence. The research was carried out at ICAR- Indian Institute of Soil and Water Conservation, Research Centre, Chandigarh, research farm, located at Panchkula, Haryana, in maize (kharif)-wheat (rabi) cropping sequence during 2009–2017. Six treatments implemented were Conventional tillage (CT); Deep tillage once in three years (DT); Conventional tillage with integrated nutrient management (CT-INM); Conventional tillage with brown manuring in maize + cowpea (1:2) and wheat + pea (4:1) ratio (CT-BM); Conservation tillage (CST) ; Conservation tillage with brown manuring (CST-BM). The compaction level attained under conservation tillage based systems were lower than the corresponding levels in the conventional tillage control. The highest percentage of macro aggregates was found in CST-BM treatment (48%), followed by CST (45%) and CT, DT and CT-INM recorded much lesser macro aggregate (29.3, 28 and 31%). Conventional tillage (CT) reduced macroaggregates with a concomitant increase in microaggregates (&lt;0.25 mm) percentage. The mean soil moisture percentage average in surface (0–15 cm) and sub surface soil (15–30 cm) were found to be higher under DT, CST and CST-BM treatments over CT and CT-INM treatments. In general, the soil moisture was found to be proportional to the amount of biomass added under various treatments. The mean soil available nitrogen were 15.4% and 17.5% higher under CT-BM and CST-BM treatments respectively, over the control (CT).

Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale.

The genetic diversity and loci underlying agronomic traits were analyzed by the reads coverage and genome-wide association study based genotyping-by-sequencing in a diverse population consisting of 199 accessions. Triticale (× Triticosecale Wittmack) is an economically important grain forage and energy crop planted worldwide for its high biomass. Little is known about the genetic diversity and loci underlying agronomic traits in triticale. We performed genotyping-by-sequencing of 199 cultivars and mapped reads to the A, B, D, and R genomes for karyotype analysis. These cultivars could mostly be grouped into five types. Some chromosome abnormalities occurred with high frequency, such as 2D (2R) substitution, deletion of the long arm of chromosome 2D or the short arm of 5R, and translocation of the long arms of 7D/7A, the short arms of 6D/6A, or the long arms of 1D/1A. We chose only widely planted hexaploid triticale cultivars (153) for genome-wide association study. These cultivars could be divided into nine distinct groups, and the linkage disequilibrium decay was 25.4kb in this population. We identified 253 significant marker-trait associations (MTAs) on 20 chromosomes, except 7R. Twenty-one reliable MTAs were identified repeatedly over two environments. We predicted 16 putative candidate genes involved in plant growth and development using the genome sequences of wheat and rye. These results provide a basis for understanding the genetic mechanisms of agronomic traits and will benefit the breeding of improved hexaploid triticale.

Candidate powdery mildew resistance gene in wheat landrace cultivar Hongyoumai discovered using SLAF and BSR-seq

BackgroundWheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is an important disease affecting wheat production. Planting resistant cultivars is an effective, safe, and economical method to control the disease. Map construction using next-generation sequencing facilitates gene cloning based on genetic maps and high-throughput gene expression studies. In this study, specific-locus amplified fragment sequencing (SLAF) was used to analyze Huixianhong (female parent), Hongyoumai (male parent) and two bulks (50 homozygous resistant and 50 susceptible F2:3 segregating population derived from Huixianhong × Hongyoumai to determine a candidate gene region for resistance to powdery mildew on the long arm of chromosome 7B in wheat landrace Hongyoumai. Gene expressions of candidate regions were obtained using bulked segregant RNA-seq in 10 homozygous resistant and 10 susceptible progeny inoculated by Bgt.. Candidate genes were obtained using homology-based cloning in two parents.ResultsA 12.95 Mb long candidate region in chromosome 7BL was identified, and five blocks in SLAF matched the scaffold of the existing co-segregation marker Xmp1207. In the candidate region, 39 differentially expressed genes were identified using RNA-seq, including RGA4 (Wheat_Chr_Trans_newGene_16173)—a disease resistance protein whose expression was upregulated in the resistant pool at 16 h post inoculation with Bgt. Quantitative reverse transcription (qRT)-PCR was used to further verify the expression patterns in Wheat_Chr_Trans_newGene_16173 that were significantly different in the two parents Hongyoumai and Huixianhong. Two RGA4 genes were cloned based on the sequence of Wheat_Chr_Trans_newGene_16173, respectively from two parent and there was one amino acid mutation: S to G in Huixianhong on 510 loci.ConclusionThe combination of SLAF and BSR-seq methods identified a candidate region of pmHYM in the chromosome 7BL of wheat landrace cultivar Hongyoumai. Comparative analysis between the scaffold of co-segregating marker Xmp1207 and SLAF-seq showed five matching blocks. qRT-PCR showed that only the resistant gene Wheat_Chr_Trans_newGene_16173 was significantly upregulated in the resistant parent Hongyoumai after inoculation with Bgt, and gene cloning revealed a difference in one amino acid between the two parent genes, indicating it was involved in the resistance response and may be the candidate resistance gene pmHYM.

Genome sequencing-based coverage analyses facilitate high-resolution detection of deletions linked to phenotypes of gamma-irradiated wheat mutants

BackgroundGamma-irradiated mutants of Triticum aestivum L., hexaploid wheat, provide novel and agriculturally important traits and are used as breeding materials. However, the identification of causative genomic regions of mutant phenotypes is challenging because of the large and complicated genome of hexaploid wheat. Recently, the combined use of high-quality reference genome sequences of common wheat and cost-effective resequencing technologies has made it possible to evaluate genome-wide polymorphisms, even in complex genomes.ResultsTo investigate whether the genome sequencing approach can effectively detect structural variations, such as deletions, frequently caused by gamma irradiation, we selected a grain-hardness mutant from the gamma-irradiated population of Japanese elite wheat cultivar “Kitahonami.” The Hardness (Ha) locus, including the puroindoline protein-encoding genes Pina-D1 and Pinb-D1 on the short arm of chromosome 5D, primarily regulates the grain hardness variation in common wheat. We performed short-read genome sequencing of wild-type and grain-hardness mutant plants, and subsequently aligned their short reads to the reference genome of the wheat cultivar “Chinese Spring.” Genome-wide comparisons of depth-of-coverage between wild-type and mutant strains detected ~ 130 Mbp deletion on the short arm of chromosome 5D in the mutant genome. Molecular markers for this deletion were applied to the progeny populations generated by a cross between the wild-type and the mutant. A large deletion in the region including the Ha locus was associated with the mutant phenotype, indicating that the genome sequencing is a powerful and efficient approach for detecting a deletion marker of a gamma-irradiated mutant phenotype. In addition, we investigated a pre-harvest sprouting tolerance mutant and identified a 67.8 Mbp deletion on chromosome 3B where Viviparous-B1 and GRAS family transcription factors are located. Co-dominant markers designed to detect the deletion-polymorphism confirmed the association with low germination rate, leading to pre-harvest sprouting tolerance.ConclusionsShort read-based genome sequencing of gamma-irradiated mutants facilitates the identification of large deletions linked to mutant phenotypes when combined with segregation analyses in progeny populations. This method allows effective application of mutants with agriculturally important traits in breeding using marker-assisted selection.

Disentangling the impact of contrasting agricultural management practices on soil microbial communities – Importance of rare bacterial community members

Agriculture has a strong effect on soil microbial communities, but it is still unclear how different management practices drive their diversity and composition. To disentangle the effects of temporally contrasting crop management practices on soil microbial abundance and prokaryotic diversity, we analysed samples from a long-term agricultural field experiment, in which plant residues were exported (RE) or returned to soil, i.e., restituted (RR), over a period of 60 years. For 2.5 years, we followed a cropping sequence of maize, winter wheat and barley, in which, as an additional treatment, wheat cultivation was diversified once with pea intercropping. Based on soil-extracted DNA, abundances of bacteria, archaea and fungi were analysed by domain-specific qPCR and the diversity and composition of the prokaryotic community by 16S rRNA gene amplicon sequencing. The abundance of bacteria and fungi, but not for archaea, increased with the long-term restitution, but this effect was only detectable in spring due to their stabilized abundance during winter. The long-term effect of crop restitution on bacterial diversity became tangible when rare and dominant community members were differentiated, with higher sensitivity shown for the rare. In contrast, the cropping sequence equally affected members of both groups. The short-term effect of crop diversification by intercropping was much stronger in the C-depleted RE soils, than in RR soils where the C-loss was compensated, indicating that crop residue restitution increased the environmental resilience of soil microbial communities. Finally, we could confirm that rare bacterial community members, suspected to represent more oligotrophs and synergistic bacteria, formed stronger network structures to each other than the dominant, suspected to be more copiotrophic and competitive. Therefore, our results emphasize the importance to consider the response of rare microbial community members when evaluating long-term effects of agricultural management on the soil microbiome.

Economic returns from three‐year crop rotations under low precipitation in Pacific Northwest

AbstractSome producers in the inland Pacific Northwest (PNW) are interested in diversifying the traditional 2‐yr sequence of winter wheat (Triticum aestivum L.) (WW)–summer fallow (SF) with oilseed crops to capture break crop effects. The objective of this study was to compare production costs and economic returns of 2‐yr sequences with those of intensified 3‐yr sequences at a low‐precipitation (&lt;300 mm) site where the long‐term rotation has been WW‐SF. A 5‐year (2014–2018) cropping sequence study was conducted that included summer fallow with intensive tillage (SF) and reduced tillage (RTF) in 2‐yr rotations with WW; and RTF in 3‐yr rotations with WW, winter canola (WN; Brassica napus L.), or spring carinata (SC; Brassica carinata A. Braun) as a primary crop and spring wheat (SW), spring barley (SB; Hordeum vulgare L.), or SC as a secondary crop. Reduced tillage fallow increased WW yields by 14% compared with SF. Production of WN and SC in WN‐SW‐RTF and SC‐SW‐RTF, expressed by equivalent WW yield, was 42%, and 35% of WW in WW‐RTF vs. 67% needed to compensate for 1/3 less cropping with WW. Production of SC in WW‐SC‐RTF was 21% of WW in WW‐RTF vs. 33% needed to compensate. Mean net returns over total costs were negative with WW‐RTF least unprofitable at −US$162 ha−1 followed by WW‐SB‐RTF at −$167 ha−1, WW‐SF at −$180 ha−1, WW‐SC‐RTF at −$191 ha−1, SC‐SW‐RTF at −$205 ha−1, and WN‐SW‐RTF at −$229 ha−1. Including oilseeds in 3‐yr rotations with WW and fallow apparently may be less profitable than WW in 2‐yr rotations with fallow.