Corrigendum: The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization

[This corrects the article DOI: 10.3389/fpls.2022.992663.].

The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization

The OMICAS alliance is part of the Colombian government's Scientific Ecosystem, established between 2017-2018 to promote world-class research, technological advancement and improved competency of higher education across the nation. Since the program's kick-off, OMICAS has focused on consolidating and validating a multi-scale, multi-institutional, multi-disciplinary strategy and infrastructure to advance discoveries in plant science and the development of new technological solutions for improving agricultural productivity and sustainability. The strategy and methods described in this article, involve the characterization of different crop models, using high-throughput, real-time phenotyping technologies as well as experimental tissue characterization at different levels of the omics hierarchy and under contrasting conditions, to elucidate epigenome-, genome-, proteome- and metabolome-phenome relationships. The massive data sets are used to derive in-silico models, methods and tools to discover complex underlying structure-function associations, which are then carried over to the production of new germplasm with improved agricultural traits. Here, we describe OMICAS' R&D trans-disciplinary multi-project architecture, explain the overall strategy and methods for crop-breeding, recent progress and results, and the overarching challenges that lay ahead in the field.

Greenhouse gas emissions from cattle dung depositions in two Urochloa forage fields with contrasting biological nitrification inhibition (BNI) capacity

Grazing-based production systems are a source of soil greenhouse gas (GHG) emissions triggered by excreta depositions. The adoption of Urochloa forages (formerly known as Brachiaria) with biological nitrification inhibition (BNI) capacity is a promising alternative to reduce nitrous oxide (N₂O) emissions from excreta patches. However, how this forage affects methane (CH₄) or carbon dioxide (CO₂) emissions from excreta patches remains unclear. This study investigated the potential effect of soils under two Urochloa forages with contrasting BNI capacity on GHG emissions from cattle dung deposits. Additionally, the N₂O and CH₄ emission factors (EF) for cattle dung under tropical conditions were determined. Dung from cattle grazing star grass (without BNI) was deposited on both forage plots: Urochloa hybrid cv. Mulato and Urochloa humidicola cv. Tully, with a respectively low and high BNI capacity. Two trials were conducted for GHG monitoring using the static chamber technique. Soil and dung properties and GHG emissions were monitored in trial 1. In trial 2, water was added to simulate rainfall and evaluate GHG emissions under wetter conditions. Our results showed that beneath dung patches, the forage genotype influenced daily CO₂ and cumulative CH₄ emissions during the driest conditions. However, no significant effect of the forage genotype was found on mitigating N₂O emissions from dung. We attribute the absence of a significant BNI effect on N₂O emissions to the limited incorporation of dung-N into the soil and rhizosphere where the BNI effect occurs. The average N₂O EFs was 0.14%, close to the IPCC 2019 uncertainty range (0.01-0.13% at 95% confidence level). Moreover, CH₄ EFs per unit of volatile solid (VS) averaged 0.31 g CH₄ kgVS^-1, slightly lower than the 0.6 g CH₄ kgVS^-1 developed by the IPCC. This implies the need to invest in studies to develop more region-specific Tier 2 EFs, including farm-level studies with animals consuming Urochloa forages to consider the complete implications of forage selection on animal excreta based GHG emissions.

Perspectives on Reducing the National Milk Deficit and Accelerating the Transition to a Sustainable Dairy Value Chain in Zimbabwe

The Zimbabwean dairy industry is massively underperforming, as evidenced by a reduction in milk yield from 262 million liters in 1990 to <37 million liters in 2009 and a steady but slow increase to 82 million liters in 2021. The current demand for milk in Zimbabwe stands at 130 million liters, and there is a national capacity for processing 400 million liters per annum. This study used literature, stakeholder inputs and expert knowledge to provide a perspective on practical options to reduce the national milk deficit and, simultaneously, accelerate the transition to a sustainable dairy value chain in Zimbabwe. Following a discussion on the key barriers and constraints to developing the milk value chain, we explored opportunities to improve the performance of the underperforming smallholder and medium-scale dairy farmers. Specifically, we discussed innovative management, creative policy instruments and alternative technological options to maximize milk production in Zimbabwe. We also highlight the need for an inclusive and creatively organized dairy value chain to optimize stakeholder linkages and improve information flow and equity. Examples of crucial investments and incentive structures for upgrading the existing value chain and monitoring greenhouse gas emissions and carbon uptake are discussed. Furthermore, the socio-economic effects (i.e., profitability, women empowerment and employment creation), milk quality, safety and traceability issues linked to a better organized and performing dairy value chain are highlighted.

In vitro Fermentation Profile and Methane Production of Kikuyu Grass Harvested at Different Sward Heights

Highly digestible forages are associated with an in vitro low-methane (CH4) rumen fermentation profile and thus the possibility of reducing CH4 emissions from forage-based systems. We aimed to assess the in vitro ruminal fermentation profile, including CH4 production, of the top stratum of Kikuyu grass (Cenchrus clandestinus - Hochst. ex Chiov) harvested at different sward heights (10, 15, 20, 25, and 30 cm). Herbage samples (incubating substrate) were analyzed for their chemical composition, in vitro organic matter digestibility (IVOMD), and morphological components. In vitro incubations were performed under a randomized complete block design with four independent runs of each treatment. Gas production (GP), in vitro dry matter digestibility (IVDMD), CH4 production, total volatile fatty acid (VFA) concentration, and their acetate, propionate, and butyrate proportions were measured following 24 and 48 h of incubation. Herbage samples had similar contents of organic matter, neutral detergent fiber, and crude protein for all treatments. However, a higher acid detergent fiber (ADF) content in taller sward heights than in smaller sward heights and a tendency for metabolizable energy (ME) and IVOMD to decrease as sward height increased were found. Similarly, the stem + sheath mass tended to increase with increasing sward height. Amongst the nutrients, ME (r = −0.65) and IVDMD (r = −0.64) were negatively correlated with sward height (p < 0.001) and ADF was positively correlated with sward height (r = 0.73, p < 0.001). Both the GP and IVDMD were negatively related to the sward height at both incubation times. Sward heights of Kikuyu grass below 30 cm display an in vitro profile of VFAs high in propionate and low in acetate, with a trend toward lower methane production of CH4 per unit of IVDMD. These findings are important to aid decision-making on the optimal sward height of Kikuyu grass and manage animal grazing with the opportunity to reduce CH4 production.

Tapping Into the Environmental Co-benefits of Improved Tropical Forages for an Agroecological Transformation of Livestock Production Systems

Livestock are critical for incomes, livelihoods, nutrition and ecosystems management throughout the global South. Livestock production and the consumption of livestock-based foods such as meat, cheese, and milk is, however, under global scrutiny for its contribution to global warming, deforestation, biodiversity loss, water use, pollution, and land/soil degradation. This paper argues that, although the environmental footprint of livestock production presents a real threat to planetary sustainability, also in the global south, this is highly contextual. Under certain context-specific management regimes livestock can deliver multiple benefits for people and planet. We provide evidence that a move toward sustainable intensification of livestock production is possible and could mitigate negative environmental impacts and even provide critical ecosystem services, such as improved soil health, carbon sequestration, and enhanced biodiversity on farms. The use of cultivated forages, many improved through selection or breeding and including grasses, legumes and trees, in integrated crop-tree-livestock systems is proposed as a stepping stone toward agroecological transformation. We introduce cultivated forages, explain their multi-functionality and provide an overview of where and to what extent the forages have been applied and how this has benefited people and the planet alike. We then examine their potential to contribute to the 13 principles of agroecology and find that integrating cultivated forages in mixed crop-tree-livestock systems follows a wide range of agroecological principles and increases the sustainability of livestock production across the globe. More research is, however, needed at the food system scale to fully understand the role of forages in the sociological and process aspects of agroecology. We make the case for further genetic improvement of cultivated forages and strong multi-disciplinary systems research to strengthen our understanding of the multidimensional impacts of forages and for managing agro-environmental trade-offs. We finish with a call for action, for the agroecological and livestock research and development communities to improve communication and join hands for a sustainable agri-food system transformation.

Environmental impact of primary beef production chain in Colombia: Carbon footprint, non-renewable energy and land use using Life Cycle Assessment

In Colombia, the beef production chain accounts for approximately 11.6 million cattle heads and annually produces 933 million kg of the beef carcass. There are no life cycle assessment (LCA) studies that have evaluated the environmental performance of Colombian beef systems. The present study aimed to estimate the carbon footprint (CF), non-renewable energy use, and land use of 251 cow-calf and 275 fattening farms in Colombia. The study also aimed to identify the main hotspots of adverse environmental impacts and propose possible mitigation options and their cost-effectiveness. The impact categories were estimated using the 2006 IPCC and the 2019 Refinement to 2006 IPCC guidelines, databases, and locally estimated emission factors. The functional units used were 1 kg fat and protein corrected milk (FPCM) and 1 kg live weight gain (LWG), leaving the farm gate. Three methods of allocating environmental burdens to meat and milk products were applied: economic, energy, and mass allocation. The adoption of improved pastures was considered a mitigation measure, and an economic assessment was performed to estimate the relative cost-effectiveness of its establishment. A principal component multivariate analysis and a Hierarchical Clustering on Principal Components were performed. The economic allocation method assigned a greater environmental burden to meat (83%), followed by energy content (80%) and mass production (73%). The largest sources of GHG emissions were enteric fermentation and manure deposited on pasture. Both cow-calf and fattening systems had a cluster of farms with better productivity, pasture and cattle management practices, and environmental performance. The CF for meat could be reduced by 33 to 56% for cow-calf and 21 to 25% for fattening farms, by adopting improved pastures. Therefore, our results suggest that GHG emissions can be reduced by adopting improved pastures, better agricultural management practices, efficient fertilizer usage, using the optimal stocking rate, and increasing productivity.

Nutritional Evaluation of Tropical Forage Grass Alone and Grass-Legume Diets to Reduce in vitro Methane Production

Forage grass nutritional quality directly affects animal feed intake, productivity, and enteric methane (CH4) emissions. This study evaluated the nutritional quality, in vitro enteric CH4 emission potential, and optimization of diets based on two widely grown tropical forage grasses either alone or mixed with legumes. The grasses Urochloa hybrid cv. Cayman (UHC) and U. brizantha cv. Toledo (UBT), which typically have low concentrations of crude protein (CP), were incubated in vitro either alone or mixed with the legumes Canavalia brasiliensis (CB) and Leucaena diversifolia (LD), which have higher CP concentrations. Substitution of 30% of the grass dry matter (DM) with CB or LD did not affect gas production or DM degradability. After 96 h of incubation, accumulated CH4 was 87.3 mg CH4 g−1 DM and 107.7 mg CH4 g−1 DM for the grasses alone (UHC and UBT, respectively), and 100.7 mg CH4 g−1 DM and 113.2 mg CH4 g−1 DM for combined diets (70% grass, 15% CB, and 15% LD). Diets that combined legumes (CB or LC) and grass (UHC or UBT) had higher CP contents, gross, and metabolizable energy (GE, ME, respectively) densities, as well as lower concentrations of neutral detergent fiber (NDF) and acid detergent lignin (ADL). The ME and nutritional variables such as NFD, tannins (T), and CP showed a positive correlation with in vitro net gas production, while ruminal digestibility was affected by CP, ADL, T, and GE. Optimal ratios of components for ruminant diets to reduce rumen net gas production and increase protein content were found with mixtures consisting of 60% grass (either UHC or UBT), 30% CB, and 10% LD. However, this ratio did not result in a decrease in CH4 production.

Covid-19 management by farmers and policymakers in Burkina Faso, Colombia and France: Lessons for climate action

CONTEXT

During crises, adaptation or recovery measures or plans at local or national scales may not necessarily address longer-term or structural problems such as climate change mitigation.

OBJECTIVE

This article describes farmers and policymakers' responses to mitigate the adverse effects of Covid-19 on the agricultural sector. We then assess the responses' possible effects on greenhouse gas (GHG) emissions.

METHODS

The study is based on surveys conducted with farmers, traders, and extension staff in Burkina Faso, Colombia, and France, and literature. We used the Cool Farm Tool calculator to assess GHG emissions associated with fertilizer production, crop production and produce transportation to international markets for the three main cash crops in the three countries.

RESULTS AND CONCLUSIONS

We identified contrasting responses by the agricultural sector mostly driven by changes in the consumption patterns at local or international levels. We also identified contrasting state responses to mitigate Covid-19. These responses at farm and policy scales led to similar trends in decreasing carbon dioxide (CO₂) emissions across the studied countries. However, none of the studied countries linked Covid-19 response measures to long-term climate change mitigation actions. Therefore, an opportunity to sustain Covid-19 induced short-term decreases in GHG emissions was overlooked.

SIGNIFICANCE

Analyzing the impacts that Covid-19 had on agricultural systems and the decision taken by policymakers to handle its direct and indirect effects can help society draw lessons on how to improve climate action.

Apparent Nitrogen Recovery in Milk and Early Dry Season Nitrous Oxide Emission Factors for Urine Deposited by Dual-Purpose Cattle on Different Soil Types

Pasture conditions influence the nutrients use efficiency and nitrogen (N) losses from deposited excreta. Part of the N is lost as nitrous oxide (N2O), a potent greenhouse gas. The objective of this study was to characterize apparent N recovery in milk of dual-purpose cattle and to quantify N2O emissions from the urine they deposit following grazing on Megathyrsus maximus cv. Mombasa. The N content in the grass and the milk produced by the cattle and the milk urea N (MUN) content were quantified in two contrasting regions of Colombia (Casanare and Atlántico). Dry matter intake (DMI) by the cattle was estimated using the Cornell Net Carbohydrate and Protein System. We used a closed static chamber technique to measure N2O emissions from soils in areas with and without urine patches (21 days in Atlántico and 35 Days in Casanare). Estimated DMI values were 11.5 and 11.6 kg DM day−1, milk production was 6.5 and 5.9 L day−1, apparent N recovery in milk was 24 and 23%, and the MUN content was 4.4 and 17.2 mg N dl−1 in Casanare and Atlántico, respectively. N applied to soil in the form of urine corresponded at rates of 20 and 64 g N m−2 and net cumulative N2O emissions were 350 and 20 mg N2O-N m−2 in Casanare and Atlántico, respectively. Despite low digestibility of offered diet, N recovery in milk was above the values reported at dairy cattle in tropical conditions. High urine-N inputs at Atlántico site did not result in high N2O emissions suggesting that the default Tier 1 emission factor (EF) which is based on N inputs would have overestimated urine-based N2O emissions in Atlántico. Comparing previous studies conducted in Colombia, we observed inter-regional differences by urine-based N2O emissions. This observation suggests that to increase certainty in estimating urine-based N2O emissions, Colombia needs to move toward more region-specific Tier 2 EF and reduce its dependence on the default IPCC Tier 1 EF. In addition, the adoption of Tier 2 EF in the cattle sector will facilitate accounting for the effect of animal diets on N2O inventories.

Nutritional Quality, Voluntary Intake and Enteric Methane Emissions of Diets Based on Novel Cayman Grass and Its Associations With Two Leucaena Shrub Legumes

Methane (CH4) emissions from enteric fermentation in cattle are an important source of greenhouse gases, accounting for about 40% of all agricultural emissions. Diet quality plays a fundamental role in determining the magnitude of CH4 emissions. Specifically, the inclusion of feeds with high digestibility and nutritional value have been reported to be a viable option for reducing CH4 emissions and, simultaneously, increase animal productivity. The present study aimed to evaluate the effect of the nutritional composition and voluntary intake of diets based on tropical forages upon CH4 emissions from zebu steers. Five treatments (diets) were evaluated: Cay1: Urochloa hybrid cv. Cayman (harvested after 65 days of regrowth: low quality); Cay2: cv. Cayman harvested after 45 days of regrowth; CayLl: cv. Cayman + Leucaena leucocephala; CayLd: cv. Cayman + Leucaena diversifolia; Hay: Dichantium aristatum hay as a comparator of common naturalized pasture. For each diet representing different levels of intensification (naturalized pasture, improved pasture, and silvopastoral systems), CH4 emissions were measured using the polytunnel technique with four zebu steers housed in individual chambers. The CH4 accumulated was monitored using an infrared multigas analyzer, and the voluntary forage intake of each animal was calculated. Dry matter intake (DMI, % of body weight) ranged between 0.77 and 2.94 among diets offered. Emissions of CH4 per kg of DMI were significantly higher (P < 0.0001) in Cay1 (60.4 g), compared to other treatments. Diets that included Leucaena forage legumes had generally higher crude protein contents and higher DMI. Cay1 and Hay which had low protein content and digestibility had a higher CH4 emission intensity (per unit live weight gain) compared to Cay2, CayLl and CayLd. Our results suggest that grass consumed after a regrowth period of 45 days results in lower CH4 emissions intensities compared to those observed following a regrowth period of 65 days. Diets with Leucaena inclusion showed advantages in nutrient intake that are reflected in greater live weight gains of cattle. Consequently, the intensity of the emissions generated in the legume-based systems were lower suggesting that they are a good option for achieving the emission reduction goals of sustainable tropical cattle production.

Caracterización técnica y ambiental de fincas de cría con doble utilización de la vaca, pertenecientes a muy pequeños, pequeños, medianos y grandes productores

En Colombia, la cría bovina representa el 15% del inventario ganadero, siendo un eslabón importante en la cadena de producción de carne. La carencia de estudios de caracterización limita la adecuada planificación técnica y ambiental de esta actividad. El objetivo de este estudio fue caracterizar los parámetros técnicos y ambientales de fincas de cría con doble utilización de la vaca, pertenecientes a muy pequeños (MPG), pequeños (PG), medianos (MG) y grandes productores (GG). La información se obtuvo de los proyectos Ganadería Colombiana Sostenible y Livestock – Plus. La muestra total fue de 2618 fincas, que fueron clasificadas de acuerdo con su orientación productiva: cría, ceba, doble propósito, lechería especializada e integral. Las 251 fincas de cría se estratificaron en MPG (1 a 30 bovinos), PG (31 a 50), MG (51 a 250) y GG (más de 251). Se consideraron variables numéricas y categóricas, las cuales fueron clasificadas en cinco componentes: información general, composición y manejo del hato, manejo de potreros, información productiva y reproductiva e información ambiental. Cada componente se analizó mediante un Análisis Factorial para Datos Mixtos (AFDM). En los primeros cuatro componentes, las variables conllevaron a una separación espacial del centroide de cada categoría de productores. Los MG y GG estuvieron asociados con variables que indicaron la existencia de mejor infraestructura, maquinarias y equipos, y mejores prácticas y parámetros reproductivos y productivos. No existieron diferencias en el desarrollo de prácticas ambientales. Las características identificadas pueden servir para el establecimiento de políticas públicas de desarrollo tecnológico y gestión ambiental. 

How to measure, report and verify soil carbon change to realize the potential of soil carbon sequestration for atmospheric greenhouse gas removal

There is growing international interest in better managing soils to increase soil organic carbon (SOC) content to contribute to climate change mitigation, to enhance resilience to climate change and to underpin food security, through initiatives such as international '4p1000' initiative and the FAO's Global assessment of SOC sequestration potential (GSOCseq) programme. Since SOC content of soils cannot be easily measured, a key barrier to implementing programmes to increase SOC at large scale, is the need for credible and reliable measurement/monitoring, reporting and verification (MRV) platforms, both for national reporting and for emissions trading. Without such platforms, investments could be considered risky. In this paper, we review methods and challenges of measuring SOC change directly in soils, before examining some recent novel developments that show promise for quantifying SOC. We describe how repeat soil surveys are used to estimate changes in SOC over time, and how long-term experiments and space-for-time substitution sites can serve as sources of knowledge and can be used to test models, and as potential benchmark sites in global frameworks to estimate SOC change. We briefly consider models that can be used to simulate and project change in SOC and examine the MRV platforms for SOC change already in use in various countries/regions. In the final section, we bring together the various components described in this review, to describe a new vision for a global framework for MRV of SOC change, to support national and international initiatives seeking to effect change in the way we manage our soils.

Genetic mitigation strategies to tackle agricultural GHG emissions: The case for biological nitrification inhibition technology

Accelerated soil-nitrifier activity and rapid nitrification are the cause of declining nitrogen-use efficiency (NUE) and enhanced nitrous oxide (N₂O) emissions from farming. Biological nitrification inhibition (BNI) is the ability of certain plant roots to suppress soil-nitrifier activity, through production and release of nitrification inhibitors. The power of phytochemicals with BNI-function needs to be harnessed to control soil-nitrifier activity and improve nitrogen-cycling in agricultural systems. Transformative biological technologies designed for genetic mitigation are needed, so that BNI-enabled crop-livestock and cropping systems can rein in soil-nitrifier activity, to help reduce greenhouse gas (GHG) emissions and globally make farming nitrogen efficient and less harmful to environment. This will reinforce the adaptation or mitigation impact of other climate-smart agriculture technologies.