ResearchPad - grasses https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Evaluation of residue management practices on barley residue decomposition]]> https://www.researchpad.co/article/elastic_article_13875 Optimizing barley (hordeum vulgare L.) production in Idaho and other parts of the Pacific Northwest (PNW) should focus on farm resource management. The effect of post-harvest residue management on barley residue decomposition has not been adequately studied. Thus, the objective of this study was to determine the effect of residue placement (surface vs. incorporated), residue size (chopped vs. ground-sieved) and soil type (sand and sandy loam) on barley residue decomposition. A 50-day(d) laboratory incubation experiment was conducted at a temperature of 25°C at the Aberdeen Research and Extension Center, Aberdeen, Idaho, USA. Following the study, a Markov-Chain Monte Carlo (MCMC) modeling approach was applied to investigate the first-order decay kinetics of barley residue. An accelerated initial flush of residue carbon(C)-mineralization was measured for the sieved (Day 1) compared to chopped (Day 3 to 5) residues for both surface incorporated applications. The highest evolution of carbon dioxide (CO2)-C of 8.3 g kg-1 dry residue was observed on Day 1 from the incorporated-sieved application for both soils. The highest and lowest amount of cumulative CO2-C released and percentage residue decomposed over 50-d was observed for surface-chopped (107 g kg-1 dry residue and 27%, respectively) and incorporated-sieved (69 g kg-1 dry residue and 18%, respectively) residues, respectively. There were no significant differences in C-mineralization from barley residue based on soil type or its interactions with residue placement and size (p >0.05). The largest decay constant k of 0.0083 d-1 was calculated for surface-chopped residue where the predicted half-life was 80 d, which did not differ from surface sieved or incorporated chopped. In contrast, incorporated-sieved treatments only resulted in a k of 0.0054 d-1 and would need an additional 48 d to decompose 50% of the residue. Future residue decomposition studies under field conditions are warranted to verify the residue C-mineralization and its impact on residue management.

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<![CDATA[SNP markers for low molecular glutenin subunits (LMW-GSs) at the <i>Glu-A3</i> and <i>Glu-B3</i> loci in bread wheat]]> https://www.researchpad.co/article/elastic_article_13817 The content and composition of seed storage proteins is largely responsible for wheat end-use quality. They mainly consist of polymeric glutenins and monomeric gliadins. According to their electrophoretic mobility, gliadins and glutenins are subdivided into several fractions. Glutenins are classified as high molecular weight or low molecular weight glutenin subunits (HMW-GSs and LMW-GSs, respectively). LMW-GSs are encoded by multigene families located at the orthologous Glu-3 loci. We designed a set of 16 single-nucleotide polymorphism (SNP) markers that are able to detect SDS-PAGE alleles at the Glu-A3 and Glu-B3 loci. The SNP markers captured the diversity of alleles in 88 international reference lines and 27 Mexican cultivars, when compared to SDS-PAGE and STS markers, however, showed a slightly larger percent of multiple alleles, mainly for Glu-B3. SNP markers were then used to determine the Glu-1 and Glu-3 allele composition in 54 CIMMYT historical lines and demonstrated to be useful tool for breeding programs to improve wheat end product properties.

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<![CDATA[Nutritional and physicochemical characteristics of purple sweet corn juice before and after boiling]]> https://www.researchpad.co/article/elastic_article_7720 Sweet corn juice is becoming increasingly popular in China. In order to provide valuable health-related information to consumers, the nutritional and physicochemical characteristics of raw and boiled purple sweet corn juices were herein investigated. Sugars, antinutrients, total free phenols, anthocyanins, and antioxidant activity were analyzed by conventional chemical methods. The viscosity and stability of juices were determined by Ubbelohde viscosity meter and centrifugation, respectively. Boiling process could elevate viscosity, stability and sugar content, and reduce antinutrients, total free phenols, anthocyanins, and antioxidant activity in corn juice. In addition, short time boiling efficiently reduced the degradation of anthocyanins during subsequent refrigeration. The content of amino acids, vitamin B1/B2 and E were detected by High Performance Liquid Chromatography. Gas Chromatography Mass Spectrometry was used for the analysis of fatty acids and aroma compounds. Several aroma compounds not previously reported in corn were identified, including 1-heptanol, 2-methyl-2-butenal, (Z)-3-nonen-1-ol, 3-ethyl-2-methyl-1,3-hexadiene, and 2,4-bis(1,1-dimethylethyl)phenol. Interestingly, the boiling process had no apparent effect on the amino acids profile, but it caused a 45.8% loss of fatty acids in the juice by promoting the retention of fatty acids in the corn residue. These results provide detailed information that could be used for increasing consumers’ knowledge of sweet corn juice, further development of sweet corn juice by food producers, and maize breeding programs.

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<![CDATA[Impacts of arbuscular mycorrhizal fungi on nutrient uptake, N2 fixation, N transfer, and growth in a wheat/faba bean intercropping system]]> https://www.researchpad.co/article/5c900d39d5eed0c48407e3a9

Arbuscular mycorrhizal fungi (AMF) can play a key role in natural and agricultural ecosystems affecting plant nutrition, soil biological activity and modifying the availability of nutrients by plants. This research aimed at expanding the knowledge of the role played by AMF in the uptake of macro- and micronutrients and N transfer (using a 15N stem-labelling method) in a faba bean/wheat intercropping system. It also investigates the role of AMF in biological N fixation (using the natural isotopic abundance method) in faba bean grown in pure stand and in mixture. Finally, it examines the role of AMF in driving competition and facilitation between faba bean and wheat. Durum wheat and faba bean were grown in pots (five pots per treatment) as sole crops or in mixture in the presence or absence of AMF. Root colonisation by AMF was greater in faba bean than in wheat and increased when species were mixed compared to pure stand (particularly for faba bean). Mycorrhizal symbiosis positively influenced root biomass, specific root length, and root density and increased the uptake of P, Fe, and Zn in wheat (both in pure stand and in mixture) but not in faba bean. Furthermore, AMF symbiosis increased the percentage of N derived from the atmosphere in the total N biomass of faba bean grown in mixture (+20%) but not in pure stand. Nitrogen transfer from faba bean to wheat was low (2.5–3.0 mg pot-1); inoculation with AMF increased N transfer by 20%. Overall, in terms of above- and belowground growth and uptake of nutrients, mycorrhization favoured the stronger competitor in the mixture (wheat) without negatively affecting the companion species (faba bean). Results of this study confirm the role of AMF in driving biological interactions among neighbouring plants.

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<![CDATA[Perceived socio-economic impacts of the marbled crayfish invasion in Madagascar]]> https://www.researchpad.co/article/N7a6c5db8-4016-4d26-87a6-87422e70e8c1

The negative environmental and economic impacts of many invasive species are well known. However, given the increased homogenization of global biota, and the difficulty of eradicating species once established, a balanced approach to considering the impacts of invasive species is needed. The marbled crayfish (Procambarus virginalis) is a parthenogenetic freshwater crayfish that was first observed in Madagascar around 2005 and has spread rapidly. We present the results of a socio-economic survey (n = 385) in three regions of Madagascar that vary in terms of when the marbled crayfish first arrived. Respondents generally considered marbled crayfish to have a negative impact on rice agriculture and fishing, however the animals were seen as making a positive contribution to household economy and food security. Regression modeling showed that respondents in regions with longer experience of marbled crayfish have more positive perceptions. Unsurprisingly, considering the perception that crayfish negatively impact rice agriculture, those not involved in crayfish harvesting and trading had more negative views towards the crayfish than those involved in crayfish-related activities. Food preference ranking and market surveys revealed the acceptance of marbled crayfish as a cheap source of animal protein; a clear positive in a country with widespread malnutrition. While data on biodiversity impacts of the marbled crayfish invasion in Madagascar are still completely lacking, this study provides insight into the socio-economic impacts of the dramatic spread of this unique invasive species. Biby kely tsy fantam-piaviana, mahavelona fianakaviana” (a small animal coming from who knows where which supports the needs of the family). Government worker Analamanga, Madagascar.

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<![CDATA[A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene]]> https://www.researchpad.co/article/N8aa5bdf2-6390-43c2-aef2-b7a76659179a

We used three approaches to map the yellow rust resistance gene Yr7 and identify associated SNPs in wheat. First, we used a traditional QTL mapping approach using a double haploid (DH) population and mapped Yr7 to a low-recombination region of chromosome 2B. To fine map the QTL, we then used an association mapping panel. Both populations were SNP array genotyped allowing alignment of QTL and genome-wide association scans based on common segregating SNPs. Analysis of the association panel spanning the QTL interval, narrowed the interval down to a single haplotype block. Finally, we used mapping-by-sequencing of resistant and susceptible DH bulks to identify a candidate gene in the interval showing high homology to a previously suggested Yr7 candidate and to populate the Yr7 interval with a higher density of polymorphisms. We highlight the power of combining mapping-by-sequencing, delivering a complete list of gene-based segregating polymorphisms in the interval with the high recombination, low LD precision of the association mapping panel. Our mapping-by-sequencing methodology is applicable to any trait and our results validate the approach in wheat, where with a near complete reference genome sequence, we are able to define a small interval containing the causative gene.

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<![CDATA[Identification and expression analysis of miRNAs and elucidation of their role in salt tolerance in rice varieties susceptible and tolerant to salinity]]> https://www.researchpad.co/article/N52f944dc-26d8-4e67-9222-1bf646d955e0

Soil salinization is a serious problem for cultivation of rice, as among cereals rice is the most salt sensitive crop, and more than 40% of the total agricultural land amounting to approximately 80 million ha the world over is salt affected. Salinity affects a plant in a varieties of ways, including ion toxicity, osmotic stress and oxidative damage. Since miRNAs occupy the top place in biochemical events determining a trait, understanding their role in salt tolerance is highly desirable, which may allow introduction of the trait in the rice cultivars of choice through biotechnological interventions. High throughput sequencing of sRNAs in the root and shoot tissues of the seedlings of the control and NaCl treated Pokkali, a salt-tolerant rice variety, identified 75 conserved miRNAs and mapped 200 sRNAs to the rice genome as novel miRNAs. Expression of nine novel miRNAs and two conserved miRNAs were confirmed by Northern blotting. Several of both conserved and novel miRNAs that expressed differentially in root and/or shoot tissues targeted transcription factors like AP2/EREBP domain protein, ARF, NAC, MYB, NF-YA, HD-Zip III, TCP and SBP reported to be involved in salt tolerance or in abiotic stress tolerance in general. Most of the novel miRNAs expressed in the salt tolerant wild rice Oryza coarctata, suggesting conservation of miRNAs in taxonomically related species. One of the novel miRNAs, osa-miR12477, also targeted L-ascorbate oxidase (LAO), indicating build-up of oxidative stress in the plant upon salt treatment, which was confirmed by DAB staining. Thus, salt tolerance might involve miRNA-mediated regulation of 1) cellular abundance of the hormone signaling components like EREBP and ARF, 2) synthesis of abiotic stress related transcription factors, and 3) antioxidative component like LAO for mitigation of oxidative damage. The study clearly indicated importance of osa-miR12477 regulated expression of LAO in salt tolerance in the plant.

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<![CDATA[Mutations on ent-kaurene oxidase 1 encoding gene attenuate its enzyme activity of catalyzing the reaction from ent-kaurene to ent-kaurenoic acid and lead to delayed germination in rice]]> https://www.researchpad.co/article/N3fbe67d9-408b-4f07-a6d8-c659dfb628bd

Rice seed germination is a critical step that determines its entire life circle, with seeds failing to germinate or pre-harvest sprouting both reduce grain yield. Nevertheless, the mechanisms underlying this complex biological event remain unclear. Previously, gibberellin has been shown to promote seed germination. In this study, a delayed seed germination rice mutant was obtained through screening of the EMS induced mutants. Besides of delayed germination, it also shows semi-dwarfism phenotype, which could be recovered by exogenous GA. Through re-sequencing on the mutant, wild-type and their F2 populations, we identified two continuous mutated sites on ent-kaurene oxidase 1 (OsKO1) gene, which result in the conversion from Thr to Met in the cytochrome P450 domain. Genetic complementary analysis and enzyme assay verified that the mutations in OsKO1 gene block the biosynthesis of GA and result in the defect phenotypes. Further analyses proved that OsKO1 could catalyze the reaction from ent-kaurene into ent-kaurenoic acid in GA biosynthesis mainly at seed germination and seedling stages, and the mutations decrease its activity to catalyze the step from ent-kaurenol to ent-kaurenoic acid in this reaction. Transcriptomic and proteomic data indicate that the defect on GA biosynthesis decreases its ability to mobilize starch and attenuate ABA signaling, therefore delay the germination process. The results provide some new insights into both GA biosynthesis and seed germination regulatory pathway in rice.

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<![CDATA[Bund removal to re-establish tidal flow, remove aquatic weeds and restore coastal wetland services—North Queensland, Australia]]> https://www.researchpad.co/article/Neac5db12-b809-4a22-afa7-0c243544d6ab

The shallow tidal and freshwater coastal wetlands adjacent to the Great Barrier Reef lagoon provide a vital nursery and feeding complex that supports the life cycles of marine and freshwater fish, important native vegetation and vital bird habitat. Urban and agricultural development threaten these wetlands, with many of the coastal wetlands becoming lost or changed due to the construction of artificial barriers (e.g. bunds, roads, culverts and floodgates). Infestation by weeds has become a major issue within many of the wetlands modified (bunded) for ponded pasture growth last century. A range of expensive chemical and mechanical control methods have been used in an attempt to restore some of these coastal wetlands, with limited success. This study describes an alternative approach to those methods, investigating the impact of tidal reinstatement after bund removal on weed infestation, associated changes in water quality, and fish biodiversity, in the Boolgooroo lagoon region of the Mungalla wetlands, East of Ingham in North Queensland. High resolution remote sensing, electrofishing and in-water logging was used to track changes over time– 1 year before and 4 years after removal of an earth bund. With tides only penetrating the wetland a few times yearly, gross changes towards a more natural system occurred within a relatively short timeframe, leading to a major reduction in infestation of olive hymenachne, water hyacinth and salvina, reappearance of native vegetation, improvements in water quality, and a tripling of fish diversity. Weed abundance and water quality does appear to oscillate however, dependent on summer rainfall, as changes in hydraulic pressure stops or allows tidal ingress (fresh/saline cycling). With an estimated 30% of coastal wetlands bunded in the Great Barrier Reef region, a passive remediation method such as reintroduction of tidal flow by removal of an earth bund or levee could provide a more cost effective and sustainable means of controlling freshwater weeds and improving coastal water quality into the future.

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<![CDATA[A conserved regulatory mechanism mediates the convergent evolution of plant shoot lateral organs]]> https://www.researchpad.co/article/N38f7a2a5-9838-4ae0-b206-f959ee03524f

Land plant shoot structures evolved a diversity of lateral organs as morphological adaptations to the terrestrial environment, with lateral organs arising independently in different lineages. Vascular plants and bryophytes (basally diverging land plants) develop lateral organs from meristems of sporophytes and gametophytes, respectively. Understanding the mechanisms of lateral organ development among divergent plant lineages is crucial for understanding the evolutionary process of morphological diversification of land plants. However, our current knowledge of lateral organ differentiation mechanisms comes almost entirely from studies of seed plants, and thus, it remains unclear how these lateral structures evolved and whether common regulatory mechanisms control the development of analogous lateral organs. Here, we performed a mutant screen in the liverwort Marchantia polymorpha, a bryophyte, which produces gametophyte axes with nonphotosynthetic scalelike lateral organs. We found that an Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 and Oryza G1 (ALOG) family protein, named M. polymorpha LATERAL ORGAN SUPRESSOR 1 (MpLOS1), regulates meristem maintenance and lateral organ development in Marchantia. A mutation in MpLOS1, preferentially expressed in lateral organs, induces lateral organs with misspecified identity and increased cell number and, furthermore, causes defects in apical meristem maintenance. Remarkably, MpLOS1 expression rescued the elongated spikelet phenotype of a MpLOS1 homolog in rice. This suggests that ALOG genes regulate the development of lateral organs in both gametophyte and sporophyte shoots by repressing cell divisions. We propose that the recruitment of ALOG-mediated growth repression was in part responsible for the convergent evolution of independently evolved lateral organs among highly divergent plant lineages, contributing to the morphological diversification of land plants.

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<![CDATA[Modified shape index for object-based random forest image classification of agricultural systems using airborne hyperspectral datasets]]> https://www.researchpad.co/article/5c8acce5d5eed0c484990263

This paper highlights the importance of optimized shape index for agricultural management system analysis that utilizes the contiguous bands of hyperspectral data to define the gradient of the spectral curve and improve image classification accuracy. Currently, a number of machine learning methods would resort to using averaged spectral information over wide bandwidths resulting in loss of crucial information available in those contiguous bands. The loss of information could mean a drop in the discriminative power when it comes to land cover classes with comparable spectral responses, as in the case of cultivated fields versus fallow lands. In this study, we proposed and tested three new optimized novel algorithms based on Moment Distance Index (MDI) that characterizes the whole shape of the spectral curve. The image classification tests conducted on two publicly available hyperspectral data sets (AVIRIS 1992 Indian Pine and HYDICE Washington DC Mall images) showed the robustness of the optimized algorithms in terms of classification accuracy. We achieved an overall accuracy of 98% and 99% for AVIRIS and HYDICE, respectively. The optimized indices were also time efficient as it avoided the process of band dimension reduction, such as those implemented by several well-known classifiers. Our results showed the potential of optimized shape indices, specifically the Moment Distance Ratio Right/Left (MDRRL), to discriminate between types of tillage (corn-min and corn-notill) and between grass/pasture and grass/trees, tree and grass under object-based random forest approach.

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<![CDATA[Genome-wide haplotype-based association analysis of key traits of plant lodging and architecture of maize identifies major determinants for leaf angle: hapLA4]]> https://www.researchpad.co/article/5c89773ed5eed0c4847d27e7

Traits related to plant lodging and architecture are important determinants of plant productivity in intensive maize cultivation systems. Motivated by the identification of genomic associations with the leaf angle, plant height (PH), ear height (EH) and the EH/PH ratio, we characterized approximately 7,800 haplotypes from a set of high-quality single nucleotide polymorphisms (SNPs), in an association panel consisting of tropical maize inbred lines. The proportion of the phenotypic variations explained by the individual SNPs varied between 7%, for the SNP S1_285330124 (located on chromosome 9 and associated with the EH/PH ratio), and 22%, for the SNP S1_317085830 (located on chromosome 6 and associated with the leaf angle). A total of 40 haplotype blocks were significantly associated with the traits of interest, explaining up to 29% of the phenotypic variation for the leaf angle, corresponding to the haplotype hapLA4.04, which was stable over two growing seasons. Overall, the associations for PH, EH and the EH/PH ratio were environment-specific, which was confirmed by performing a model comparison analysis using the information criteria of Akaike and Schwarz. In addition, five stable haplotypes (83%) and 15 SNPs (75%) were identified for the leaf angle. Finally, approximately 62% of the associated haplotypes (25/40) did not contain SNPs detected in the association study using individual SNP markers. This result confirms the advantage of haplotype-based genome-wide association studies for examining genomic regions that control the determining traits for architecture and lodging in maize plants.

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<![CDATA[Genome-wide analysis, expansion and expression of the NAC family under drought and heat stresses in bread wheat (T. aestivum L.)]]> https://www.researchpad.co/article/5c897798d5eed0c4847d30f2

The NAC family is one of the largest plant-specific transcription factor families, and some of its members are known to play major roles in plant development and response to biotic and abiotic stresses. Here, we inventoried 488 NAC members in bread wheat (Triticum aestivum). Using the recent release of the wheat genome (IWGS RefSeq v1.0), we studied duplication events focusing on genomic regions from 4B-4D-5A chromosomes as an example of the family expansion and neofunctionalization of TaNAC members. Differentially expressed TaNAC genes in organs and in response to abiotic stresses were identified using publicly available RNAseq data. Expression profiling of 23 selected candidate TaNAC genes was studied in leaf and grain from two bread wheat genotypes at two developmental stages in field drought conditions and revealed insights into their specific and/or overlapping expression patterns. This study showed that, of the 23 TaNAC genes, seven have a leaf-specific expression and five have a grain-specific expression. In addition, the grain-specific genes profiles in response to drought depend on the genotype. These genes may be considered as potential candidates for further functional validation and could present an interest for crop improvement programs in response to climate change. Globally, the present study provides new insights into evolution, divergence and functional analysis of NAC gene family in bread wheat.

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<![CDATA[Modern botanical analogue of endangered Yak (Bos mutus) dung from India: Plausible linkage with extant and extinct megaherbivores]]> https://www.researchpad.co/article/5c897796d5eed0c4847d30d6

The study reports the micro- and macrobotanical remains on wild Yak dung, providing evidence for understanding the diet, habitat, and ecology of extant and extinct megaherbivores. Grasses are the primary diet of the yak as indicated by the abundance of grass pollen and phytoliths. Other associated non-arboreal and arboreal taxa namely, Cyperacaeae, Rosaceae, Chenopodiaceae, Artemisia, Prunus, and Rhododendron are also important dietary plants for their living. The observation of plant macrobotanical remains especially the vegetative part and seeds of the grasses and Cyperaceae is also in agreement with the palynodata. The documented micro- and macrobotanical data are indicative of both Alpine meadow and steppe vegetation under cold and dry climate which exactly reflected the current vegetation composition and climate in the region. The recovery of Botryococcus, Arcella, and diatom was observed in trace amounts in the palynoassemblage which would have been incorporated in the dung through the ingestion of water and are indicative of the presence of perennial water system in the region. Energy dispersive spectroscopy analysis marked that the element contained in dung samples has variation in relation to the summer and winter, which might be due to the availability of the food plants and vegetation. This generated multiproxy data serves as a strong supplementary data for modern pollen and vegetation relationships based on surface soil samples in the region. The recorded multiproxy data could also be useful to interpret the relationship between the coprolites of herbivorous fauna and the palaeodietary, the palaeoecology in the region, and to correlate with other mega herbivores in a global context.

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<![CDATA[How elevated CO2 affects our nutrition in rice, and how we can deal with it]]> https://www.researchpad.co/article/5c8823f8d5eed0c48463945d

Increased concentrations of atmospheric CO2 are predicted to reduce the content of essential elements such as protein, zinc, and iron in C3 grains and legumes, threatening the nutrition of billions of people in the next 50 years. However, this prediction has mostly been limited to grain crops, and moreover, we have little information about either the underlying mechanism or an effective intervention to mitigate these reductions. Here, we present a broader picture of the reductions in elemental content among crops grown under elevated CO2 concentration. By using a new approach, flow analysis of elements, we show that lower absorption and/or translocation to grains is a key factor underlying such elemental changes. On the basis of these findings, we propose two effective interventions—namely, growing C4 instead of C3 crops, and genetic improvements—to minimize the elemental changes in crops, and thereby avoid an impairment of human nutrition under conditions of elevated CO2.

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<![CDATA[Analysis of genetic control and QTL mapping of essential wheat grain quality traits in a recombinant inbred population]]> https://www.researchpad.co/article/5c897730d5eed0c4847d2663

Wheat cultivars are genetically crossed to improve end-use quality for traits as per demands of baking industry and broad consumer preferences. The processing and baking qualities of bread wheat are influenced by a variety of genetic make-ups, environmental factors and their interactions. Two wheat cultivars, WL711 and C306, derived recombinant inbred lines (RILs) with a population of 206, were used for phenotyping of quality-related traits. The genetic analysis of quality traits showed considerable variation for measurable quality traits, with normal distribution and transgressive segregation across the years. From the 206 RILs, few RILs were found to be superior to those of the parental cultivars for key quality traits, indicating their potential use for the improvement of end-use quality and suggesting the probability of finding new alleles and allelic combinations from the RIL population. Mapping analysis identified 38 putative QTLs for 13 quality-related traits, with QTLs explaining 7.9–16.8% phenotypic variation spanning over 14 chromosomes, i.e., 1A, 1B, 1D, 2A, 2D, 3B, 3D, 4A, 4B, 4D, 5D, 6A, 7A and 7B. In-silico analysis based on homology to the annotated wheat genes present in database, identified six putative candidate genes within QTL for total grain protein content, qGPC.1B.1 region. Major QTL regions for other quality traits such as TKW have been identified on 1B, 2A, and 7A chromosomes in the studied RIL population. This study revealed the importance of the combination of stable QTLs with region-specific QTLs for better phenotyping, and the QTLs presented in our study will be useful for the improvement of wheat grain and bread-making quality.

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<![CDATA[Analysis of transcriptional responses in root tissue of bread wheat landrace (Triticum aestivum L.) reveals drought avoidance mechanisms under water scarcity]]> https://www.researchpad.co/article/5c89770fd5eed0c4847d238d

In this study, high-throughput sequencing (RNA-Seq) was utilized to evaluate differential expression of transcripts and their related genes involved in response to terminal drought in root tissues of bread wheat landrace (L-82) and drought-sensitive genotype (Marvdasht). Subsets of 460 differentially expressed genes (DEGs) in drought-tolerant genotype and 236 in drought-sensitive genotype were distinguished and functionally annotated with 105 gene ontology (GO) terms and 77 metabolic pathways. Transcriptome profiling of drought-resistant genotype “L-82” showed up-regulation of genes mostly involved in Oxidation-reduction process, secondary metabolite biosynthesis, abiotic stress response, transferase activity and heat shock proteins. On the other hand, down-regulated genes mostly involved in signaling, oxidation-reduction process, secondary metabolite biosynthesis, auxin-responsive protein and lipid metabolism. We hypothesized that the drought tolerance in “L-82” was a result of avoidance strategies. Up-regulation of genes related to the deeper root system and adequate hydraulic characteristics to allow water uptake under water scarcity confirms our hypothesis. The transcriptomic sequences generated in this study provide information about mechanisms of acclimation to drought in the selected bread wheat landrace, “L-82”, and will help us to unravel the mechanisms underlying the ability of crops to reproduce and keep its productivity even under drought stress.

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<![CDATA[Combining biophysical parameters, spectral indices and multivariate hyperspectral models for estimating yield and water productivity of spring wheat across different agronomic practices]]> https://www.researchpad.co/article/5c897762d5eed0c4847d2b85

Manipulating plant densities under different irrigation rates can have a significant impact on grain yield and water use efficiency by exerting positive or negative effects on ET. Whereas traditional spectral reflectance indices (SRIs) have been used to assess biophysical parameters and yield, the potential of multivariate models has little been investigated to estimate these parameters under multiple agronomic practices. Therefore, both simple indices and multivariate models (partial least square regression (PLSR) and support vector machines (SVR)) obtained from hyperspectral reflectance data were compared for their applicability for assessing the biophysical parameters in a field experiment involving different combinations of three irrigation rates (1.00, 0.75, and 0.50 ET) and five plant densities (D1: 150, D2: 250, D3: 350, D4: 450, and D5: 550 seeds m-2) in order to improve productivity and water use efficiency of wheat. Results show that the highest values for green leaf area, aboveground biomass, and grain yield were obtained from the combination of D3 or D4 with 1.00 ET, while the combination of 0.75 ET and D3 was the best treatment for achieving the highest values for water use efficiency. Wheat yield response factor (ky) was acceptable when the 0.75 ET was combined with D2, D3, or D4 or when the 0.50 ET was combined with D2 or D3, as the ky values of these combinations were less than or around one. The production function indicated that about 75% grain yield variation could be attributed to the variation in seasonal ET. Results also show that the performance of the SRIs fluctuated when regressions were analyzed for each irrigation rate or plant density specifically, or when the data of all irrigation rates or plant densities were combined. Most of the SRIs failed to assess biophysical parameters under specific irrigation rates and some specific plant densities, but performance improved substantially for combined data of irrigation rates and some specific plant densities. PLSR and SVR produced more accurate estimations of biophysical parameters than SRIs under specific irrigation rates and plant densities. In conclusion, hyperspectral data are useful for predicting and monitoring yield and water productivity of spring wheat across multiple agronomic practices.

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<![CDATA[Origins and geographic diversification of African rice (Oryza glaberrima)]]> https://www.researchpad.co/article/5c897765d5eed0c4847d2be9

Rice is a staple food for the majority of the world’s population. Whereas Asian rice (Oryza sativa) has been extensively studied, the exact origins of African rice (Oryza glaberrima) are still contested. Previous studies have supported either a centric or a non-centric geographic origin of African rice domestication. Here we review the evidence for both scenarios through a critical reassessment of 206 whole genome sequences of domesticated and wild African rice. While genetic diversity analyses support a severe bottleneck caused by domestication, signatures of recent and strong positive selection do not unequivocally point to candidate domestication genes, suggesting that domestication proceeded differently than in Asian rice–either by selection on different alleles, or different modes of selection. Population structure analysis revealed five genetic clusters localising to different geographic regions. Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Although genome-wide phylogenetic relationships support an origin in the eastern cultivation range followed by diversification along the Atlantic coast, further analysis of domestication genes shows distinct haplotypes in the southwest—suggesting that at least one of several key domestication traits might have originated there. These findings shed new light on an old controversy concerning plant domestication in Africa by highlighting the divergent roots of African rice cultivation, including a separate centre of domestication activity in the Guinea Highlands. We thus suggest that the commonly accepted centric origin of African rice must be reconsidered in favour of a non-centric or polycentric view.

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<![CDATA[Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles]]> https://www.researchpad.co/article/5c76fe27d5eed0c484e5b5dd

Many plants have natural partnerships with microbes that can boost their nitrogen (N) and/or phosphorus (P) acquisition. To assess whether wheat may have undiscovered associations of these types, we tested if N/P-starved Triticum aestivum show microbiome profiles that are simultaneously different from those of N/P-amended plants and those of their own bulk soils. The bacterial and fungal communities of root, rhizosphere, and bulk soil samples from the Historical Dryland Plots (Lethbridge, Canada), which hold T. aestivum that is grown both under N/P fertilization and in conditions of extreme N/P-starvation, were taxonomically described and compared (bacterial 16S rRNA genes and fungal Internal Transcribed Spacers—ITS). As the list may include novel N- and/or P-providing wheat partners, we then identified all the operational taxonomic units (OTUs) that were proportionally enriched in one or more of the nutrient starvation- and plant-specific communities. These analyses revealed: a) distinct N-starvation root and rhizosphere bacterial communities that were proportionally enriched, among others, in OTUs belonging to families Enterobacteriaceae, Chitinophagaceae, Comamonadaceae, Caulobacteraceae, Cytophagaceae, Streptomycetaceae, b) distinct N-starvation root fungal communities that were proportionally enriched in OTUs belonging to taxa Lulworthia, Sordariomycetes, Apodus, Conocybe, Ascomycota, Crocicreas, c) a distinct P-starvation rhizosphere bacterial community that was proportionally enriched in an OTU belonging to genus Agrobacterium, and d) a distinct P-starvation root fungal community that was proportionally enriched in OTUs belonging to genera Parastagonospora and Phaeosphaeriopsis. Our study might have exposed wheat-microbe connections that can form the basis of novel complementary yield-boosting tools.

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