Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

Agricultural crops benefit from resistance to pathogens that endures over years and generations of both pest and crop. Durable disease resistance, which may be partial or complete, can be controlled by several genes. Some of the most devastating fungal pathogens in wheat are leaf rust, stripe rust, and powdery mildew. The wheat gene Lr34 has supported resistance to these pathogens for more than 50 years. Lr34 is now shared by wheat cultivars around the world. Here, we show that the LR34 protein resembles adenosine triphosphate-binding cassette transporters of the pleiotropic drug resistance subfamily. Alleles of Lr34 conferring resistance or susceptibility differ by three genetic polymorphisms. The Lr34 gene, which functions in the adult plant, stimulates senescence-like processes in the flag leaf tips and edges.

As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.

Race Ug99 of the fungus Puccinia graminis tritici that causes stem or black rust disease on wheat was first detected in Uganda in 1998. Seven races belonging to the Ug99 lineage are now known and have spread to various wheat-growing countries in the eastern African highlands, as well as Zimbabwe, South Africa, Sudan, Yemen, and Iran. Because of the susceptibility of 90% of the wheat varieties grown worldwide, the Ug99 group of races was recognized as a major threat to wheat production and food security. Its spread, either wind-mediated or human-aided, to other countries in Africa, Asia, and beyond is evident. Screening in Kenya and Ethiopia has identified a low frequency of resistant wheat varieties and breeding materials. Identification and transfer of new sources of race-specific resistance from various wheat relatives is underway to enhance the diversity of resistance. Although new Ug99-resistant varieties that yield more than current popular varieties are being released and promoted, major efforts are required to displace current Ug99 susceptible varieties with varieties that have diverse race-specific or durable resistance and mitigate the Ug99 threat.

Seven years after the introduction of genomic selection in the United States, it is now possible to evaluate the impact of this technology on the population. Selection differential(s) (SD) and generation interval(s) (GI) were characterized in a four-path selection model that included sire(s) of bulls (SB), sire(s) of cows (SC), dam(s) of bulls (DB), and dam(s) of cows (DC). Changes in SD over time were estimated for milk, fat, and protein yield; somatic cell score (SCS); productive life (PL); and daughter pregnancy rate (DPR) for the Holstein breed. In the period following implementation of genomic selection, dramatic reductions were seen in GI, especially the SB and SC paths. The SB GI reduced from ∼7 y to less than 2.5 y, and the DB GI fell from about 4 y to nearly 2.5 y. SD were relatively stable for yield traits, although modest gains were noted in recent years. The most dramatic response to genomic selection was observed for the lowly heritable traits DPR, PL, and SCS. Genetic trends changed from close to zero to large and favorable, resulting in rapid genetic improvement in fertility, lifespan, and health in a breed where these traits eroded over time. These results clearly demonstrate the positive impact of genomic selection in US dairy cattle, even though this technology has only been in use for a short time. Based on the four-path selection model, rates of genetic gain per year increased from ∼50-100% for yield traits and from threefold to fourfold for lowly heritable traits.

Common beans (Phaseolus vulgaris L.) originated in the New World and are the grain legume of greatest production for direct human consumption. Common bean production is subject to frequent droughts in highland Mexico, in the Pacific coast of Central America, in northeast Brazil, and in eastern and southern Africa from Ethiopia to South Africa. This article reviews efforts to improve common bean for drought tolerance, referring to genetic diversity for drought response, the physiology of drought tolerance mechanisms, and breeding strategies. Different races of common bean respond differently to drought, with race Durango of highland Mexico being a major source of genes. Sister species of P. vulgaris likewise have unique traits, especially P. acutifolius which is well adapted to dryland conditions. Diverse sources of tolerance may have different mechanisms of plant response, implying the need for different methods of phenotyping to recognize the relevant traits. Practical considerations of field management are discussed including: trial planning; water management; and field preparation.

Wheat is grown worldwide in diverse geographical regions, environments, and production systems. Although many diseases and pests are known to reduce grain yield potential and quality, the three rusts and powdery mildew fungi have historically caused major crop losses and continue to remain economically important despite the widespread use of host resistance and fungicides. The evolution and fast spread of virulent and more aggressive race lineages of rust fungi have only worsened the situation. Fusarium head blight, leaf spotting diseases, and, more recently, wheat blast (in South America and Bangladesh) have become diseases of major importance in recent years largely because of intensive production systems, the expansion of conservation agriculture, undesirable crop rotations, or increased dependency on fungicides. High genetic diversity for race-specific and quantitative resistance is known for most diseases; their selection through phenotyping reinforced with molecular strategies offers great promise in achieving more durable resistance and enhancing global wheat productivity.

Studies have documented biodiversity losses due to intensification of coffee management (reduction in canopy richness and complexity). Nevertheless, questions remain regarding relative sensitivity of different taxa, habitat specialists, and functional groups, and whether implications for biodiversity conservation vary across regions.We quantitatively reviewed data from ant, bird, and tree biodiversity studies in coffee agroecosystems to address the following questions: Does species richness decline with intensification or with individual vegetation characteristics? Are there significant losses of species richness in coffee-management systems compared with forests? Is species loss greater for forest species or for particular functional groups?and Are ants or birds more strongly affected by intensification? Across studies, ant and bird richness declined with management intensification and with changes in vegetation. Species richness of all ants and birds and of forest ant and bird species was lower in most coffee agroecosystems than in forests, but rustic coffee (grown under native forest canopies) had equal or greater ant and bird richness than nearby forests. Sun coffee(grown without canopy trees) sustained the highest species losses, and species loss of forest ant, bird, and tree species increased with management intensity. Losses of ant and bird species were similar, although losses of forest ants were more drastic in rustic coffee. Richness of migratory birds and of birds that forage across vegetation strata was less affected by intensification than richness of resident, canopy, and understory bird species. Rustic farms protected more species than other coffee systems, and loss of species depended greatly on habitat specialization and functional traits. We recommend that forest be protected, rustic coffee be promoted,and intensive coffee farms be restored by augmenting native tree density and richness and allowing growth of epiphytes. We also recommend that future research focus on potential trade-offs between biodiversity conservation and farmer livelihoods stemming from coffee production.

The locus Lr34/Yr18/Pm38 confers partial and durable resistance against the devastating fungal pathogens leaf rust, stripe rust, and powdery mildew. In previous studies, this broad-spectrum resistance was shown to be controlled by a single gene which encodes a putative ATP-binding cassette transporter. Alleles of resistant and susceptible cultivars differed by only three sequence polymorphisms and the same resistance haplotype was found in the three independent breeding lineages of Lr34/Yr18/Pm38. Hence, we used these conserved sequence polymorphisms as templates to develop diagnostic molecular markers that will assist selection for durable multi-pathogen resistance in breeding programs. Five allele-specific markers (cssfr1-cssfr5) were developed based on a 3 bp deletion in exon 11 of the Lr34-gene, and one marker (cssfr6) was derived from a single nucleotide polymorphism in exon 12. Validation of reference genotypes, well characterized for the presence or absence of the Lr34/Yr18/Pm38 resistance locus, demonstrated perfect diagnostic values for the newly developed markers. By testing the new markers on a larger set of wheat cultivars, a third Lr34 haplotype, not described so far, was discovered in some European winter wheat and spelt material. Some cultivars with uncertain Lr34 status were re-assessed using the newly derived markers. Unambiguous identification of the Lr34 gene aided by the new markers has revealed that some wheat cultivars incorrectly postulated as having Lr34 may possess as yet uncharacterised loci for adult plant leaf and stripe rust resistance.

Biocontrol agents (BCA) have been an important tool in agriculture to prevent crop losses due to plant pathogens infections and to increase plant food production globally, diminishing the necessity for chemical pesticides and fertilizers and offering a more sustainable and environmentally friendly option. Fungi from the genus Trichoderma are among the most used and studied microorganisms as BCA due to the variety of biocontrol traits, such as parasitism, antibiosis, secondary metabolites (SM) production, and plant defense system induction. Several Trichoderma species are well-known mycoparasites. However, some of those species can antagonize other organisms such as nematodes and plant pests, making this fungus a very versatile BCA. Trichoderma has been used in agriculture as part of innovative bioformulations, either just Trichoderma species or in combination with other plant-beneficial microbes, such as plant growth-promoting bacteria (PGPB). Here, we review the most recent literature regarding the biocontrol studies about six of the most used Trichoderma species, T. atroviride, T. harzianum, T. asperellum, T. virens, T. longibrachiatum, and T. viride, highlighting their biocontrol traits and the use of these fungal genera in Trichoderma-based formulations to control or prevent plant diseases, and their importance as a substitute for chemical pesticides and fertilizers.

Few studies have attempted to isolate the various factors that may cause the observed increases in peak flows and erosion after high‐severity wildfires. This study evaluated the effects of burning by: (i) comparing soil water repellency, surface cover, and sediment yields from severely burned hillslopes, unburned hillslopes, and hillslopes where the surface cover was removed by raking; and (ii) conducting rainfall simulations to compare runoff, erosion, and surface sealing from two soils with varying ash cover. The fire‐enhanced soil water repellency was only stronger on the burned hillslopes than the unburned hillslopes in the first summer after burning. For the first 5 yr after burning, the mean sediment yield from the burned hillslopes was 32 Mg ha −1 , whereas the unburned hillslopes generated almost no sediment. Sediment yields from the raked and burned hillslopes were indistinguishable when they had comparable surface cover, rainfall erosivity, and soil water repellency values. The rainfall simulations on ash‐covered plots generated only 21 to 49% as much runoff and 42 to 67% as much sediment as the plots with no ash cover. Soil thin sections showed that the bare plots rapidly developed a structural soil seal. Successive simulations quickly eroded the ash cover and increased runoff and sediment yields to the levels observed from the bare plots. The results indicate that: (i) post‐fire sediment yields were primarily due to the loss of surface cover rather than fire‐enhanced soil water repellency; (ii) surface cover is important because it inhibits soil sealing; and (iii) ash temporarily prevents soil sealing and reduces post‐fire runoff and sediment yields.

Exactly dated tree-ring chronologies from ENSO-sensitive regions in subtropical North America and Indonesia together register the strongest ENSO signal yet detected in tree-ring data worldwide and have been used to reconstruct the winter Southern Oscillation index (SOI) from 1706 to 1977. This reconstruction explains 53% of the variance in the instrumental winter SOI during the boreal cool season (December–February) and was verified in the time, space, and frequency domains by comparisons with independent instrumental SOI and sea surface temperature (SST) data. The large-scale SST anomaly patterns associated with ENSO in the equatorial and North Pacific during the 1879–1977 calibration period are reproduced in detail by this reconstruction. Cross-spectral analyses indicate that the reconstruction reproduces over 70% of the instrumental winter SOI variance at periods between 3.5 and 5.6 yr, and over 88% in the 4-yr frequency band. Oscillatory modes of variance identified with singular spectrum analysis at ~3.5,4.0, and 5.8 yr in both the instrumental and reconstructed series exhibit regimelike behavior over the 272-yr reconstruction. The tree-ring estimates also suggest a statistically significant increase in the interannual variability of winter SOI, more frequent cold events, and a slightly stronger sea level pressure gradient across the equatorial Pacific from the mid–nineteenth to twentieth centuries. Some of the variability in this reconstruction must be associated with background climate influences affecting the ENSO teleconnection to subtropical North America and may not arise solely from equatorial ENSO forcing. However, there is some limited independent support for the nineteenth to twentieth century changes in tropical Pacific climate identified in this reconstruction and, if substantiated, it will have important implications to the low-frequency dynamics of ENSO.

Drought is the second major constraint to common bean ( Phaseolus vulgaris L) production after disease. This study examined yield under drought, yield potential, drought susceptibility index, harvest index, and geometric mean as potential indicators of drought resistant genotypes. The performance of two common bean populations, consisting of 78 and 95 recombinant inbred lines, was examined under moisture stress and nonstress regimes. Experiments were conducted at seven locations (1990–1994) in Michigan and Mexico to identify effective selection criteria for drought resistance. Two genotypes from each population yielded in the top 10% under both stress and nonstress conditions. Heritability estimates for yield in the Sierra/AC1028 population, based on 5 yr of data, ranged from 0.55 to 0.59 for stress and nonstress, respectively, and from 0.20 to 0.19 for stress and nonstress, respectively, in the Sierra/Lef‐2RB population. Heritability for plant biomass was 0.52 for stress and 0.55 for nonstress in the Sierra/AC1028 population and 0.15 under stress and 0.05 under nonstress in the Sierra/Lef‐2RB population. One‐hundred seed weight was the most highly heritable trait in both populations with heritability estimates of 0.80 for the Sierra/AC1028 population and 0.65 for the Sierra/Lef‐2RB population. The geometric mean of the two moisture regimes was the single strongest indicator of performance under stress and nonstress, and a breeding strategy that involves selection based first on the geometric mean, followed by selection based on yield under stress, was suggested as the most effective strategy to improve drought resistance in common bean.

Plant-associated microorganisms play an important role in agricultural production. Although various studies have shown that single microorganisms can exert beneficial effects on plants, it is increasingly evident that when a microbial consortium—two or more interacting microorganisms—is involved, additive or synergistic results can be expected. This occurs, in part, due to the fact that multiple species can perform a variety of tasks in an ecosystem like the rhizosphere. Therefore, the beneficial mechanisms of plant growth stimulation (i.e., enhanced nutrient availability, phytohormone modulation, biocontrol, biotic and abiotic stress tolerance) exerted by different microbial players within the rhizosphere, such as plant-growth-promoting bacteria (PGPB) and fungi (such as Trichoderma and Mycorrhizae), are reviewed. In addition, their interaction and beneficial activity are highlighted when they act as part of a consortium, mainly as mixtures of different species of PGPB, PGPB–Mycorrhizae, and PGPB–Trichoderma, under normal and diverse stress conditions. Finally, we propose the expansion of the use of different microbial consortia, as well as an increase in research on different mixtures of microorganisms that facilitate the best and most consistent results in the field.

One key advantage of eusociality is shared defense of the nest, brood, and stored food; nest defense plays an important role in the biology of eusocial bees. Recent studies on honey bees, Apis mellifera, have focused on the placement of defensive activity in the overall scheme of division of labor, showing that guard bees play a unique and important role in colony defense. Alarm pheromones function in integrating defensive responses; honey bee alarm pheromone is an excellent example of a multicomponent pheromonal blend. The genetic regulation of defensive behavior is now better understood from the mapping of quantitative trait loci (QTLs) associated with variation in defensiveness. Colony defense in other eusocial bees is less well understood, but enough information is available to provide interesting comparisons between A. mellifera and other species of Apis, as well as with allodapine, halictine, bombine, and meliponine bees. These comparative studies illustrate the wide variety of evolutionary solutions to problems in colony defense in the Apoidea.

Abstract Stem or black rust, caused by Puccinia graminis tritici , has historically caused severe losses to wheat ( Triticum aestivum ) production worldwide. Successful control of the disease for over three decades through the use of genetic resistance has resulted in a sharp decline in research activity in recent years. Detection and spread in East Africa of race TTKS, commonly known as Ug99, is of high significance as most wheat cultivars currently grown in its likely migration path, i.e. to North Africa through Arabian Peninsula and then to Middle East and Asia, are highly susceptible to this race and the environment is conducive to disease epidemics. Identifying/developing adapted resistant cultivars in a relatively short time and replacing the susceptible cultivars before rust migrates out of East Africa is the strategy to mitigate potential losses. Although several alien genes will provide resistance to this race, the long-term strategy should focus on rebuilding the 'Sr2-complex' (combination of slow rusting gene Sr2 with other unknown additive genes of similar nature) to achieve long-term durability. A Global Rust Initiative has been launched to monitor the further migration of this race, facilitate field testing in Kenya or Ethiopia of wheat cultivars and germplasm developed by wheat breeding programmes worldwide, understand the genetic basis of resistance especially the durable type, carry out targeted breeding to incorporate diverse resistance genes into key cultivars and germplasm, and enhance the capacity of national programmes. A few wheat genotypes that combine stem rust resistance with high yield potential and other necessary traits have been identified but need rigorous field testing to determine their adaptation in target areas.

ABSTRACT Leaf and stripe rusts, caused by Puccinia triticina and P. striiformis, respectively, are globally important fungal diseases of wheat that cause significant annual yield losses. A gene that confers slow rusting resistance to leaf rust, designated as Lr46, has recently been located on wheat chromosome 1B. The objectives of our study were to establish the precise genomic location of gene Lr46 using molecular approaches and to determine if there was an association of this locus with adult plant resistance to stripe rust. A population of 146 F(5) and F(6) lines produced from the cross of susceptible 'Avocet S' with resistant 'Pavon 76' was developed and classified for leaf rust and stripe rust severity for three seasons. Using patterns of segregation for the two diseases, we estimated that at least two genes with additive effects conferred resistance to leaf rust and three to four genes conferred resistance to stripe rust. Bulked segregant analysis and linkage mapping using amplified fragment length polymorphisms with the 'Avocet' x 'Pavon 76' population, F(3) progeny lines of a single chromosome recombinant line population from the cross 'Lalbahadur' x 'Lalbahadur (Pavon 1B)', and the International Triticeae Mapping Initiative population established the genomic location of Lr46 at the distal end of the long arm of wheat chromosome 1B. A gene that is closely linked to Lr46 and confers moderate levels of adult plant resistance to stripe rust is identified and designated as Yr29.

The synthesis of inorganic nanoparticles for diverse applications is an active research area that involves physical and chemical methods, which typically are expensive, involve hazardous chemical reagents, use complex equipment and synthesis conditions, and consume large amounts of time and energy. Thus, green synthesis methods have emerged as eco-friendly and easy alternatives for inorganic nanoparticle synthesis, particularly the use of plant-based extracts from fruit juice, leaves, seeds, peel, stem, barks, and roots, which act as reducing, capping, and stabilizing agents, contributing to the Sustainable Development Goals and circular economy principles. Therefore, diverse inorganic nanoparticles have been synthesized using plant-based extracts, including gold, silver, titanium dioxide, zinc, copper, platinum, zirconium, iron, selenium, magnesium, nickel, sulfur, cobalt, palladium, and indium nanoparticles, which exhibit different biological activities such as antioxidant, antimicrobial, dye degradation, cytotoxic, analgesic, sedative, wound-healing, skin protection, sensor development, and plant-growth-promoting effects. Therefore, this review summarizes the advantages and limitations of plant-based extracts as reducing, capping, and stabilizing agents for inorganic nanoparticle green synthesis.

Post-fire soil erosion is of considerable concern because of the potential decline in site productivity and adverse effects on downstream resources. For the Colorado Front Range there is a paucity of post-fire erosion data and a corresponding lack of predictive models. This study measured hillslope-scale sediment production rates and site characteristics for three wild and three prescribed fires over two summers and one winter using 48 sediment fences. Over 90% of the sediment was generated by summer convective storms. Sediment production rates from recent, high-severity wildfires were 0.2–1.0 kg m–2 year–1. Mean sediment production rates from areas recently burned at moderate and low severity were only 0.02 and 0.005 kg m–2 year–1, respectively. For a given severity, sediment production rates from prescribed fires were generally lower than from wildfires, but there was considerable variability between plots and within fire severity classes. Fire severity, percent bare soil, rainfall erosivity, soil water repellency and soil texture explained 77% of the variability in sediment production rates, while a two-parameter model using percentage bare soil and rainfall erosivity explained 62% of the variability. Model validation confirmed the usefulness of these empirical models. The improved understanding of post-fire erosion rates can help guide forest management and post-fire rehabilitation efforts.

A prominent theory states that animal phenotypes arise by evolutionary changes in gene regulation, but the extent to which this theory holds true for behavioral evolution is not known. Because "nature and nurture" are now understood to involve hereditary and environmental influences on gene expression, we studied whether environmental influences on a behavioral phenotype, i.e., aggression, could have evolved into inherited differences via changes in gene expression. Here, with microarray analysis of honey bees, we show that aggression-related genes with inherited patterns of brain expression are also environmentally regulated. There were expression differences in the brain for hundreds of genes between the highly aggressive Africanized honey bee compared with European honey bee (EHB) subspecies. Similar results were obtained for EHB in response to exposure to alarm pheromone (which provokes aggression) and when comparing old and young bees (aggressive tendencies increase with age). There was significant overlap of the gene lists generated from these three microarray experiments. Moreover, there was statistical enrichment of several of the same cis regulatory motifs in promoters of genes on all three gene lists. Aggression shows a remarkably robust brain molecular signature regardless of whether it occurs because of inherited, age-related, or environmental (social) factors. It appears that one element in the evolution of different degrees of aggressive behavior in honey bees involved changes in regulation of genes that mediate the response to alarm pheromone.