Annual Crop Species Research Articles

Tree species and drought: Two mysterious long-standing counterparts.

Around 252 million years ago (Late Permian), Earth experienced one of its most significant drought periods, coinciding with a global climate crisis, resulting in a devastating loss of forest trees with no hope of recovery. In the current epoch (Anthropocene), the worsening of drought stress is expected to significantly affect forest communities. Despite extensive efforts, there is significantly less research at the molecular level on forest trees than on annual crop species. Would it not be wise to allocate equal efforts to woody species, regardless of their importance in providing essential furniture and sustaining most terrestrial ecosystems? For instance, the poplar genome is roughly quadruple the size of the Arabidopsis genome and has 1.6 times the number of genes. Thus, a massive effort in genomic studies focusing on forest trees has become inevitable to understand their adaptation to harsh conditions. Nevertheless, with the emerging role and development of high-throughput DNA sequencing systems, there is a growing body of literature about the responses of trees under drought at the molecular and eco-physiological levels. Therefore, synthesizing these findings through contextualizing drought history and concepts is essential to understanding how woody species adapt to water-limited conditions. Comprehensive genomic research on trees is critical for preserving biodiversity and ecosystem function. Integrating molecular insights with eco-physiological analysis will enhance forest management under climate change.

Phenotypic limits of crop diversity: a data exploration of functional trait space.

Relationships between crop genetic and functional diversity are key to addressing contemporary agricultural challenges. Yet, there are few approaches for quantifying the relationship between genetic diversity and crop functional trait expression. Here, we introduce 'functional space accumulation curves' to analyze how trait space increases with the number of crop genotypes within a species. We explore the potential for functional space accumulating curves to quantify genotype-trait space relationships in four common annual crop species: barley (Hordeum vulgare), rice (Oryza sativa), soybean (Glycine max), and durum wheat (Triticum durum). We also employ these curves to describe genotype-trait space relationships in the wild annual Arabidopsis thaliana, which has not been subjected to artificial selection. All five species exhibited asymptotic functional space accumulation curves, suggesting a limit to intraspecific functional crop diversity, likely due to: dominant phenotypes represented by several genotypes;or functional redundancy that might exist among genotypes. Our findings indicate that there is a diminishing return of functional diversity with increasing number of genotypes. Our analysis demonstrates the efficacy of functional space accumulation curves in quantifying trait space occupancy of crops, with implications for managing crop diversity in agroecosystems, and genetic diversity in crop breeding programs.

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding.

Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.

Phytochrome-interacting factors play shared and distinct roles in regulating shade avoidance responses in Populus trees.

Plants adjust their growth and development in response to changing light caused by canopy shade. The molecular mechanisms underlying shade avoidance responses have been widely studied in Arabidopsis and annual crop species, yet the shade avoidance signalling in woody perennial trees remains poorly understood. Here, we first showed that PtophyB1/2 photoreceptors serve conserved roles in attenuating the shade avoidance syndrome (SAS) in poplars. Next, we conducted a systematic identification and characterization of eight PtoPIF genes in Populus tomentosa. Knocking out different PtoPIFs led to attenuated shade responses to varying extents, whereas overexpression of PtoPIFs, particularly PtoPIF3.1 and PtoPIF3.2, led to constitutive SAS phenotypes under normal light and enhanced SAS responses under simulated shade. Notably, our results revealed that distinct from Arabidopsis PIF4 and PIF5, which are major regulators of SAS, the Populus homologues PtoPIF4.1 and PtoPIF4.2 seem to play a minor role in controlling shade responses. Moreover, we showed that PtoPIF3.1/3.2 could directly activate the expression of the auxin biosynthetic gene PtoYUC8 in response to shade, suggesting a conserved PIF-YUC-auxin pathway in modulating SAS in tree. Overall, our study provides insights into shared and divergent functions of PtoPIF members in regulating various aspects of the SAS in Populus.

Harnessing Hyper-Accumulator Plants for an Innovative Green Technology to Recover Nickle from Serpentine Soils in Sri Lanka

Phyto-mining is an environmentally sound green technique that has been employed for metal recovery from low-grade sources using hyperaccumulator plants. Due to its economic viability and wide social acceptance, this technology has been favoured over many conventional mining applications. Nickel (Ni) phyto-mining was introduced to the world with the identification of many Ni hyperaccumulator species grown in Ni-enriched metalliferous soils like serpentine, where they accumulate more than 1,000 mg/kg of Ni. Along the boundary of Highland and Vijayan Complexes in Sri Lanka, Ginigalpelessa, Indikolapelessa, and Ussangoda serpentinite deposits are closely located by showing similar geographical features. According to previous studies, these deposits contain a high concentration of Ni in the soil causing the evolution of serpentinite flora unique to these areas. This study aimed to identify the diversity and the presence of hyperaccumulator species that can be employed in Ni phyto-mining. More importantly, the study focused on identifying annual or biannual crop species with short lifespans that can be used in phyto-mining. The plant diversity and abundance analysis were carried out using a grid sampling method (3×3 m), and the highly abundant species were harvested and subjected to aqua regia digestion to determine hyperaccumulator levels using Inductively Coupled Plasma Mass Spectrometer (ICP-MS). Ginigalpelessa and Indikolapelessa showed similar diversity, abundant with grass and small herb species, such as Apluda mutica, Imperata cylindrica, Eupatorium odoratum, and Tephrosia villosa, where the A. mutica was dominant. In addition, plants like Morinda tinctoria, Vitex pinnata, and Azadirachta indica were dispersed throughout the deposit. Ussangoda deposit exhibited few herb species, including Hybanthus enneaspermus, Evolvulus alsinoides, and Desmodium triflorum, and localized thick vegetation patches. Diversity analysis of all the deposits showed very low plant diversity, ranging from 0.1 to 1.3. Moreover, the areas containing high Ni concentrations (6,000- 10,000 mg/kg) were abundant with stunted trees and grass species. The present study identified the Apluda grass species as a potential Ni hyperaccumulator for phytomining since it accumulates a high concentration of Ni (900-2,800 mg/kg) and can be grown biannually. Even though the grass species was dominant in both Ginigalpelessa and Indikolapelessa deposits, it was not observed in Ussangoda deposit, probably due to the arid climate and the deposition of salt spray from the coast. The findings of this study would be promising to establish phytomining in serpentine soils to support the increasing demand for Ni in the global market, especially for clean energy transition.
 
 Keywords: Low-grade soils, Clean energy transition, Ni phyto-mining, Serpentinite deposits
 
 Financial assistance from SR/LT/2021/15 grant from University of Moratuwa is acknowledged

A RESEARCH ON THE HAY YIELD AND QUALITY OF ALFALFA CULTIVARS WITH DIFFERENT FALL DORMANCY RATES UNDER MEDITERRANEAN CLIMATE CONDITIONS

This research was carried out as two separate trials established in two different years to determine the effects
 of different seed ratios and harvest stages of different annual companion crop species on the hay yield and
 botanical composition of a pasture mixture under Mediterranean climate conditions. The field trials were
 established in a randomized complete block with a split-plot arrangement in three replications. The research
 results showed that barley, annual ryegrass, and berseem clover can be utilized as companion crops in
 artificial pasture systems. The inclusion of these companion crop species in the pasture mixture resulted in an
 increase in forage yield and a significant decrease in weed infestation. While delaying the harvest stage of the
 companion crop does not have a notable effect on the proportion of legumes and weeds in the total biomass, it
 significantly enhances the dry forage yield and the proportion of grasses in the overall biomass of the mixture.

EFFECTS OF COMPANION CROP ON THE HAY YIELD AND BOTANICAL COMPOSITION OF PASTURE UNDER MEDITERRANEAN CLIMATE CONDITIONS

This research was carried out as two separate trials established in two different years to determine the effects of different seed ratios and harvest times of different annual companion crop species on the hay yield and botanical composition of a pasture mixture under Mediterranean climate conditions. The field trials were established in a randomized complete block with a split-plot arrangement in three replications. The research results showed that barley, annual ryegrass, and berseem clover can be utilized as companion crops in artificial pasture systems. The inclusion of these companion crop species in the pasture mixture resulted in an increase in forage yield and a significant decrease in weed infestation. While delaying the harvest time of the companion crop does not have a notable effect on the proportion of legumes and weeds in the total biomass, it significantly enhances the dry forage yield and the proportion of grasses in the overall biomass of the mixture.

A temporal analysis and response to nitrate availability of 3D root system architecture in diverse pennycress (Thlaspi arvense L.) accessions.

Roots have a central role in plant resource capture and are the interface between the plant and the soil that affect multiple ecosystem processes. Field pennycress (Thlaspi arvense L.) is a diploid annual cover crop species that has potential utility for reducing soil erosion and nutrient losses; and has rich seeds (30-35% oil) amenable to biofuel production and as a protein animal feed. The objective of this research was to (1) precisely characterize root system architecture and development, (2) understand plastic responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity. Using a root imaging and analysis pipeline, the 4D architecture of the pennycress root system was characterized under four nitrate regimes, ranging from zero to high nitrate concentrations. These measurements were taken at four time points (days 5, 9, 13, and 17 after sowing). Significant nitrate condition response and genotype interactions were identified for many root traits, with the greatest impact observed on lateral root traits. In trace nitrate conditions, a greater lateral root count, length, density, and a steeper lateral root angle was observed compared to high nitrate conditions. Additionally, genotype-by-nitrate condition interaction was observed for root width, width:depth ratio, mean lateral root length, and lateral root density. These findings illustrate root trait variance among pennycress accessions. These traits could serve as targets for breeding programs aimed at developing improved cover crops that are responsive to nitrate, leading to enhanced productivity, resilience, and ecosystem service.

Olive agroforestry shapes rhizosphere microbiome networks associated with annual crops and impacts the biomass production under low-rainfed conditions.

Agroforestry (AF) is a promising land-use system to mitigate water deficiency, particularly in semi-arid areas. However, the belowground microbes associated with crops below trees remain seldom addressed. This study aimed at elucidating the effects of olive AF system intercropped with durum wheat (Dw), barely (Ba), chickpea (Cp), or faba bean (Fb) on crops biomass and their soil-rhizosphere microbial networks as compared to conventional full sun cropping (SC) under rainfed conditions. To test the hypothesis, we compared the prokaryotic and the fungal communities inhabiting the rhizosphere of two cereals and legumes grown either in AF or SC. We determined the most suitable annual crop species in AF under low-rainfed conditions. Moreover, to deepen our understanding of the rhizosphere network dynamics of annual crops under AF and SC systems, we characterized the microbial hubs that are most likely responsible for modifying the microbial community structure and the variability of crop biomass of each species. Herein, we found that cereals produced significantly more above-ground biomass than legumes following in descending order: Ba > Dw > Cp > Fb, suggesting that crop species play a significant role in improving soil water use and that cereals are well-suited to rainfed conditions within both types of agrosystems. The type of agrosystem shapes crop microbiomes with the only marginal influence of host selection. However, more relevant was to unveil those crops recruits specific bacterial and fungal taxa from the olive-belowground communities. Of the selected soil physicochemical properties, organic matter was the principal driver in shaping the soil microbial structure in the AF system. The co-occurrence network analyses indicated that the AF system generates higher ecological stability than the SC system under stressful climate conditions. Furthermore, legumes' rhizosphere microbiome possessed a higher resilient capacity than cereals. We also identified different fungal keystones involved in litter decomposition and drought tolerance within AF systems facing the water-scarce condition and promoting crop production within the SC system. Overall, we showed that AF reduces cereal and legume rhizosphere microbial diversity, enhances network complexity, and leads to more stable beneficial microbial communities, especially in severe drought, thus providing more accurate predictions to preserve soil diversity under unfavorable environmental conditions.

ANNUAL AND PERENNIAL SPECIES PREFERENCE IN DIFFERENT CROPPING SYSTEMS IN RAJSHAHI DISTRICT OF BANGLADESH

Different types of annual and perennial crop species have been detected in cropland agroforestry (CAF), homestead agroforestry (HAF) and annual cropping (AC) system in four Upazilas (Bagha, Charghat, Puthia and Tanore) under Rajshahi district of Bangladesh. The objectives of the study were to assess and compare farmer’s preference to different types of annual and perennial species in homestead agroforestry, cropland agroforestry and annual cropping systems, and to find out the financial values of the species among different cropping systems. The sample size was 150 small agroforestry farmers of which 50 were from cropland agroforestry, 50 from homestead agroforestry and 50 from annual cropping system. Banana (BCR = 3.85) was found as the most financially profitable species in AC system in the study area. However, four types of paddy (41% of total preference) were identified as the most preferred species in AC system. Farmers usually grew 25 different annual crop species on their croplands. Blackgram was the most profitable (BCR = 4.02) annual crop species in CAF system. Sugarcane was the most financially profitable species as a crop combination and also as sole crop. For getting quick return farmers grow sissoo in their croplands. Among 19 HAF species, sweet gourd (27%) was the most preferred species (14%) and financially beneficial annual crop. Out of total 21 tree species in HAF system, mahogany was planted by 21% farmers 21%. However, mango was recorded as the most planted and profitable species in respect to the plot number (90%).

Interest of phenomic prediction as an alternative to genomic prediction in grapevine

BackgroundPhenomic prediction has been defined as an alternative to genomic prediction by using spectra instead of molecular markers. A reflectance spectrum provides information on the biochemical composition within a tissue, itself being under genetic determinism. Thus, a relationship matrix built from spectra could potentially capture genetic signal. This new methodology has been mainly applied in several annual crop species but little is known so far about its interest in perennial species. Besides, phenomic prediction has only been tested for a restricted set of traits, mainly related to yield or phenology. This study aims at applying phenomic prediction for the first time in grapevine, using spectra collected on two tissues and over two consecutive years, on two populations and for 15 traits, related to berry composition, phenology, morphological and vigour. A major novelty of this study was to collect spectra and phenotypes several years apart from each other. First, we characterized the genetic signal in spectra and under which condition it could be maximized, then phenomic predictive ability was compared to genomic predictive ability.ResultsFor the first time, we showed that the similarity between spectra and genomic relationship matrices was stable across tissues or years, but variable across populations, with co-inertia around 0.3 and 0.6 for diversity panel and half-diallel populations, respectively. Applying a mixed model on spectra data increased phenomic predictive ability, while using spectra collected on wood or leaves from one year or another had less impact. Differences between populations were also observed for predictive ability of phenomic prediction, with an average of 0.27 for the diversity panel and 0.35 for the half-diallel. For both populations, a significant positive correlation was found across traits between predictive ability of genomic and phenomic predictions.ConclusionNIRS is a new low-cost alternative to genotyping for predicting complex traits in perennial species such as grapevine. Having spectra and phenotypes from different years allowed us to exclude genotype-by-environment interactions and confirms that phenomic prediction can rely only on genetics.

STUDY REGARDING THE QUALITY AND PRODUCTIVITY POTENTIAL OF SOME PERSPECTIVE MAIZE HYBRIDS CREATED AT ARDS LOVRIN

Zea mays L. is an important annual crop species, belonging to Poaceae family, a species that comes from teosinte (Zea mays L. spp Mexicana). Maize kernel is an edible and nutritive part of the plant, this crop being an essential source of various phytochemicals, vitamins, minerals and other micro- and macronutrients. Maize breeding is considered to be an important and complex program that has has unique elements, which are different from other cultivated self-pollinated crops, each obtained hybrid having its own combination of genetic effects. Therefore, this paper aims to study a comparative culture with 20 maize hybrids created at ARDS Lovrin, hybrids from indurata and dentata convarieties, in order to highlight hybrids with a high productive or qualitative potential. Regarding to production capacity, the analyzed hybrids had a different behavior, the highest values being recorded at H10-1010 (9767 kg*ha-1) and H13-1013 (9631 kg*ha-1) hybrids. The highlighted hybrids differs significantly from the other ones, registering an increase of 32.6%, respectively 30.8% compared to the experience average. In terms of quality, the following hybrids H1, H3 and H19 were evidentiated. H1-1001 hybrid registered a protein content in kernel of 11.30% and oil by 6.55%; H3-1003 hybrid registering close values, of 11.35% protein and 6.65% oil content and H19 hybrid with 10.95% protein content, respectively 6.50% oil content in kernel. Summing up, from the results obtained for the hybrids taken in study, the hybrids mentioned above were highlighted, from both qualitative and productive point of view.

Yield Potential and Water Use Efficiency of Alternate Rotation Crops in the Semiarid Environment of Southwestern United States

Highlights Water use efficiency and yield potential of 10 rotation crops were tested under dryland and fully irrigated conditions. Pearl millet in grasses, cowpea and sesbania in legumes had great potential as rotation crops with greater yields and WUEs. Irrigation improved water use efficiency of crops compared to dryland conditions. Abstract. Unpredictability in weather patterns prompted a need for testing diverse crops with broad range adaptability to introduce into the existing cropping systems or to innovate alternate cropping systems in the southwestern United States. Such crops suitable for system integration should preferably be dual-purpose and resource-use efficient. Keeping this in view, a two-year study was conducted at NMSU Rex E. Kirksey Agricultural Science Center, Tucumcari, New Mexico, comprised of 10 annual crop species including grasses, legumes, and oilseed crops. The study aimed at researching yield potential and water use efficiency of the selected crops under dryland and limited irrigated conditions in the semiarid, subtropical environment. Results suggest that both crop species and water regime (irrigated vs. dryland) had significant effects on seed and biomass yield and water use efficiencies (WUE) (P<0.05). Seed and biomass production under dryland conditions were significantly influenced each year by amount of precipitation received. Pearl millet [Pennisetum glaucum (L.) R. Br.] had consistently greater seed and biomass yields and WUEs than the other crops. Cowpea (Vigna unguiculata) and sesbania (Sesbania sesban) proved to be viable legumes with the advantage of greater biomass yields and water-use efficiency (WUEs) compared to other the legumes tested (P<0.05). For a balanced livestock diet, pearl millet+cowpea intercrop combination is a good option with greater yields and WUEs. Integrating these rotation crops into the traditional winter wheat cropping systems or alternate cropping systems may provide a significant benefit to producers in the semiarid southwestern United States. Keywords: Alternate crops, Summer rotation, Water-use efficiency, Yield potential.

Root traits of crop species contributing to soil shear strength

Roots of annual species would be able to conserve soil properties during traffic induced compaction. The objective of this study was to determine and compare root traits and soil shear strength for three crop species with contrasted root types and morphological traits to see if roots of annual species are able to increase soil shear strength and thus explain the soil properties conservation. The experiment was performed under controlled conditions in steel cylinders containing a repacked loamy sand, with initial dry bulk density of 1.2 g cm−3 and that was kept moist. Soil shear strength parameters, i.e. cohesion and angle of internal friction, were determined from direct shear tests for soil cores at a soil matric potential of −10 kPa (i.e. water content at field capacity). The direct shear tests were performed with six external normal stress levels (25, 34, 44, 63, 83 and 93 kPa) and at a constant shear rate of 3 mm.min−1, and applying Mohr Coulomb equation. The difference of root type, root length density, root density, specific root length and root dry matter content among crop species was not related to a difference in soil shear strength. The root volume density was the main trait involved in both soil cohesion and the angle of internal friction. This study highlights the effect of roots of annual crop species on soil shear strength by comparing their root traits to the apparent cohesion of soil core where they grow. Vicia faba would be a good candidate to improve soil shear strength for soil conservation. This study constitutes a step towards improving the understanding of plants’ effects on soil shear strength with regards to selecting species and designing cropping systems for soil conservation.

Light Quality Environment and Photomorphological Responses of Young Olive Trees

Tree densities have increased greatly in olive orchards over the last few decades. In many annual crop species, increased density reduces the horizontal red/far-red (R/FR) and blue/green (B/G) ratios during canopy development even before direct shading occurs, and such changes are known to alter plant morphology. This study with olive trees evaluated: (1) whether the leaf area index (LAI) of neighboring trees modifies the light quality environment prior to a tree being directly shaded and (2) the potential morphological responses of three olive cultivars to changes in light quality. Increasing LAI using different spatial arrangements of potted, three-year-old trees reduced the horizontal R/FR ratio more than that of the B/G ratio. Cultivar-specific responses to low R/FR ratio were observed for individual leaf area and aboveground/belowground biomass ratio using laterally positioned FR mirrors or green fences. No statistically significant responses were detected in response to green vegetation fences that reduced both horizontal R/FR and B/G ratios, but a cluster analysis grouped together the overall morphological responses to both FR mirrors and green fences. These results in olive trees suggest that cultivar differences in response to light quality may be relevant for understanding adaptation to dense orchards and identifying cultivars best suited to them.

Cereal-legume mixtures increase net CO2 uptake in a forage crop system in the Eastern Pyrenees

• Cereal-legume mixtures increased net CO 2 uptake and productivity compared to cereal monocultures. • Cereal-legume mixtures increased gross uptake, while respiration did not change. • Management associated to cereal-legume mixtures enhanced net CO 2 uptake. • Cereal-legume mixtures provide enormous opportunities to mitigate climate change. Forage systems are the major land use and provide essential resources for animal feeding. Assessing the influence of annual forage crop species on net ecosystem CO 2 exchange (NEE) is key to develop management strategies that can help to mitigate climate change, while optimizing productivity of these systems. However, little is known about the effect of annual forage crop species on CO 2 exchange fluxes, considering separately net CO 2 balances during the growth and fallow periods, and species ecophysiological responses. Our study assesses the influence of cereal monocultures vs. cereal‑legume mixtures on (1) ecosystem‑scale CO 2 fluxes, for the whole crop season and separately for the two periods of growth and fallow; and (2) potential sensitivities of CO 2 exchange related to short-term variations in light, temperature, and soil water content. This is the first mid‑term (seven years) ecosystem‑scale CO 2 fluxes assessment of an intensively managed forage system in the Pyrenees region. Our results provide strong evidence that cereal‑legume mixtures lead to higher net CO 2 uptake than cereal monocultures, as a result of higher gross CO 2 uptake, while respiratory fluxes did not significantly increase. Also, cereal-legume mixtures favoured a higher voluntary regrowth during the fallow period, which was decisive for the cumulative net CO 2 uptake of the entire crop season. Overall, cereal‑legume mixtures enhanced net CO 2 sink capacity of the forage crop, while ensuring productivity and forage quality.

Interspecific interactions regulate plant reproductive allometry in cereal–legume intercropping systems

Abstract Calls for the application of ecological principles in agriculture have gained momentum. Intercropping systems are designed by growing two, or more, annual crop species in the same field, aiming for a better resource use efficiency. However, assembly rules for their design are lacking. Notably, it is unknown whether species performances are maximized during both the vegetative and reproductive phases given the sensitivity of reproductive allocation rules to resource limitation. Interestingly, ecological theory provides expectations regarding putative invariance of plant reproductive allometry (PRA) under non‐limiting conditions for plant growth. Here we examined whether and how PRA changes in response to plant–plant interactions in intercropping systems, which can inform both ecological theory and the understanding of the functioning of intercropping systems. We analysed a dataset of 28 field cereal–legume intercropping trials from various climatic and management conditions across Western Europe. PRA was quantified in both mixing and single‐species situations. Plant reproductive allometry was positively impacted in specific management conditions, leading to a greater increase in yield for a given increase in plant size. Variations in PRA were more beneficial to legumes grown in unfertilized mixtures, which explains their use as a key component in actual intercropping systems. The response for cereals was similar but less pronounced in magnitude, and was greater under resource‐limiting conditions. Focusing on intercropping conditions, hierarchical competition (indicated by biomass difference between intercropped species) appears as a strong driver of the reproductive output of a given species. Synthesis and applications. Plant reproductive allometry (PRA) behaves in crop species in the same way as it does in wild species. However, contrary to theoretical expectations about an overall invariance of PRA, we highlighted taxon‐specific and context‐dependent effects of plant–plant interactions on PRA. This systematic deviation to PRA expectations could be leveraged to cultivate each species up to its reproductive optimum while accounting for the performance of the other, whether farmer's objective is to favour one species or to reach an equilibrium in seed production. Sowing density and cultivar choice could regulate the biomass of each component, with specific targets derived from allometric relationships, aiming for an optimal reproductive allocation in mixtures.

MFCIS: an automatic leaf-based identification pipeline for plant cultivars using deep learning and persistent homology

Recognizing plant cultivars reliably and efficiently can benefit plant breeders in terms of property rights protection and innovation of germplasm resources. Although leaf image-based methods have been widely adopted in plant species identification, they seldom have been applied in cultivar identification due to the high similarity of leaves among cultivars. Here, we propose an automatic leaf image-based cultivar identification pipeline called MFCIS (Multi-feature Combined Cultivar Identification System), which combines multiple leaf morphological features collected by persistent homology and a convolutional neural network (CNN). Persistent homology, a multiscale and robust method, was employed to extract the topological signatures of leaf shape, texture, and venation details. A CNN-based algorithm, the Xception network, was fine-tuned for extracting high-level leaf image features. For fruit species, we benchmarked the MFCIS pipeline on a sweet cherry (Prunus avium L.) leaf dataset with >5000 leaf images from 88 varieties or unreleased selections and achieved a mean accuracy of 83.52%. For annual crop species, we applied the MFCIS pipeline to a soybean (Glycine max L. Merr.) leaf dataset with 5000 leaf images of 100 cultivars or elite breeding lines collected at five growth periods. The identification models for each growth period were trained independently, and their results were combined using a score-level fusion strategy. The classification accuracy after score-level fusion was 91.4%, which is much higher than the accuracy when utilizing each growth period independently or mixing all growth periods. To facilitate the adoption of the proposed pipelines, we constructed a user-friendly web service, which is freely available at http://www.mfcis.online.

Root secondary growth: an unexplored component of soil resource acquisition.

Despite recent progress in elucidating the molecular basis of secondary growth (cambial growth), the functional implications of this developmental process remain poorly understood. Targeted studies exploring how abiotic and biotic factors affect this process, as well as the relevance of secondary growth to fitness of annual dicotyledonous crop species under stress, are almost entirely absent from the literature. Specifically, the physiological role of secondary growth in roots has been completely neglected yet entails a unique array of implications for plant performance that are distinct from secondary growth in shoot tissue. Since roots are directly responsible for soil resource capture, understanding of the fitness landscape of root phenotypes is important in both basic and applied plant biology. Interactions between root secondary growth, edaphic conditions and soil resource acquisition may have significant effects on plant fitness. Our intention here is not to provide a comprehensive review of a sparse and disparate literature, but rather to highlight knowledge gaps, propose hypotheses and identify opportunities for novel and agriculturally relevant research pertaining to secondary growth of roots. This viewpoint: (1) summarizes evidence from our own studies and other published work; (2) proposes hypotheses regarding the fitness landscape of secondary growth of roots in annual dicotyledonous species for abiotic and biotic stress; and (3) highlights the importance of directing research efforts to this topic within an agricultural context. Secondary growth of the roots of annual dicots has functional significance with regards to soil resource acquisition and transport, interactions with soil organisms and carbon sequestration. Research on these topics would contribute significantly toward understanding the agronomic value of secondary growth of roots for crop improvement.

Integrated farming systems influence soil organic matter dynamics in southeastern Brazil

Integrated farming systems are sustainable strategies to intensify land productivity by combining annual crop, livestock and/or forestry activities in different spatio-temporal arrangements. Therefore, they may help tackle global food and energy insecurity and climate change in the coming decades. We investigated the effects of integrated crop-livestock (ICL) and integrated crop-livestock-forestry (ICLF) systems on quantity, quality, and origin of soil organic matter (SOM) in southeastern Brazil. A native forest and an extensive low-grazing intensity pasture system were used as references. In integrated systems, corn (Zea mays) was alternated with two consecutive years of piatã grass (Urochloa bryzantha) for cattle grazing. In ICLF, eucalyptus trees (Eucalyptus urograndis) were planted in simple rows of 15 × 2 m. Soil sampling was performed three times; in 2014, after two years of grazing; in 2015, after crop cultivation; and in 2016, after a successive grazing year, to evaluate chemical and physical composition changes of organic matter (C, N, δ13C, δ15N, and organic matter fractions) with time. Our findings showed that from 2010 to 2016, all systems (extensive grazing, ICL and ICLF) promoted increments on soil C and N stocks. However, land intensification converting extensive low-grazing intensity pasture to ICL was the most promising strategy, increasing soil C stocks at the rate of 0.28 Mg C ha−1 yr−1 from 2010 to 2016. Annual crop cultivation (corn intercropped with piatã grass) promoted high organic matter inputs on the soil, increasing the amount of soil labile organic matter fractions, which presented higher δ13C and lower δ15N values over time. SOM in the integrated farming systems was originated mainly from C4 plants. Therefore, optimizing development of piatã grass and corn increases organic residue inputs and then, soil C and N stocks. In addition, the crop period increased soil fertility parameters, which favors plant growth, thus providing high labile C inputs to the soil. In contrast, land intensification by adding the forestry component into the system (i.e., conversion from ICL to ICLF) reduced soil C (-0.22 Mg C ha−1 yr−1) and N (-0.03 Mg N ha−1 yr−1) stocks from 2010 to 2016, likely due to the reduction of C and N inputs to the soil caused by limited growth of annual crop and grass species under tree shades. In conclusion, land use intensification through ICL system contributes towards a more efficient and low-C agriculture, whereas the studied ICLF system did not bring further benefits to increase the quantity and/or quality of SOM.