Search

Thirty sweetpotato (Ipomoea batatas var. batatas) genotypes were evaluated for yield, resistances to weevil or nematode pests, and consumer acceptance across three field trials planted at Pepe‘ekeo, Hawai‘i Island between 2017 to 2020. At harvest, storage roots were graded according to market standards, followed by scoring for damage by sweetpotato weevil (Cylas formicarius elegantulus), rough sweetpotato weevil (Blosyrus asellus), or nematodes; namely root-knot nematode (Meloidogyne spp.) or reniform nematode (Rotylenchus reniformis) in each market class. There were significant differences in marketable yields among accessions when data were analyzed statistically across all three field trials, as well as individually. ‘Regal’ (PI 566650) and ‘Sumor’ (PI 566657) were among the top three highest-yielding genotypes for Trials 1 and 2 (when no insecticides were applied to control weevils), and among the top six highest-yielding genotypes for the joint analysis across three trials. Significant differences among genotypes for combined sweetpotato weevil damage (incidence of sweetpotato weevil alone or incidence of both weevils together) were found in the joint analysis across three trials. ‘Regal’ was among the lowest seven genotypes for combined sweetpotato weevil damage, supporting earlier reports of its moderate resistance to this pest. In addition, two genotypes produced by the World Vegetable Center (Shanhua, Taiwan) (WT-320 and WT-108), were among the lowest genotypes for combined sweetpotato weevil damage, in agreement with earlier reports of their substantial resistance to this pest. Providing access to diverse germplasm will help farmers react to increasing pest pressure, while still allowing for high marketable yields. In addition, breeding and selection for pest resistance could be an important addition to integrated pest management of sweetpotato in Hawai‘i.

Abstract Although communicating research is a key part of public science, current graduate curricula in the agricultural sciences usually have a narrow focus on communication appropriate for presenting to scientific and academic audiences, such as in the form of the dreaded “seminar.” Yet the importance and impact of agriculture extends well beyond research communities, and communicating with other potential audiences is essential for realizing the full impact of research. Because public speaking is among the greatest fears for many people, it is critical to provide students with the tools needed to communicate effectively with diverse audiences, particularly as only a fraction of them will go on to give regular research seminars once they enter the professional world. Better communication can lead to more constructive engagement with the public as well as with policy‐makers, toward improved understanding of the science they are funding and from which they are benefiting. Purposeful instruction in public speaking should help alleviate the common anxieties that student presenters often experience. Here, we summarize general communication strategies that can be incorporated into any graduate agricultural science course to help address this need.

Abstract Domestication is an ongoing well‐described process. However, while many have studied the changes domestication causes in plant genetics, few have explored its impact on the portion of the geographic landscape in which the plants exist. Therefore, the goal of this study was to understand how the process of domestication changed the geographic space suitable for chile pepper (Capsicum annuum) in its center of origin (domestication). C. annuum is a major crop species globally whose center of domestication, Mexico, has been well‐studied. It provides a unique opportunity to explore the degree to which ranges of different domestication classes diverged and how these ranges might be altered by climate change. To this end, we created ecological niche models for four domestication classes (wild, semiwild, landrace, modern cultivar) based on present climate and future climate scenarios for 2050, 2070, and 2090. Considering present environment, we found substantial overlap in the geographic niches of all the domestication classes. Yet, environmental and geographic aspects of the current ranges did vary among classes. Wild and commercial varieties could grow in desert conditions, while landraces could not. With projections into the future, habitat was lost asymmetrically, with wild, semiwild, and landraces at greater risk of territorial declines than modern cultivars. Further, we identified areas where future suitability overlap between landraces and wilds is expected to be lost. While range expansion is widely associated with domestication, we found little support of a constant niche expansion (either in environmental or geographical space) throughout the domestication gradient in chile peppers in Mexico. Instead, particular domestication transitions resulted in loss, followed by capturing or recapturing environmental or geographic space. The differences in environmental characterization among domestication gradient classes and their future potential range shifts increase the need for conservation efforts to preserve landraces and semiwild genotypes.

Introduction: Genome-wide association studies (GWAS) have identified genetic markers for cattle production and reproduction traits. Several publications have reported Single Nucleotide Polymorphisms (SNPs) for carcass-related traits in cattle, but these studies were rarely conducted in pasture-finished beef cattle. Hawai’i, however, has a diverse climate, and 100% of its beef cattle are pasture-fed.Methods: Blood samples were collected from 400 cattle raised in Hawai’i islands at the commercial harvest facility. Genomic DNA was isolated, and 352 high-quality samples were genotyped using the Neogen GGP Bovine 100 K BeadChip. SNPs that did not meet the quality control standards were removed using PLINK 1.9, and 85 k high-quality SNPs from 351 cattle were used for association mapping with carcass weight using GAPIT (Version 3.0) in R 4.2. Four models were used for the GWAS analysis: General Linear Model (GLM), the Mixed Linear Model (MLM), the Fixed and Random Model Circulating Probability Unification (FarmCPU), the Bayesian-Information and Linkage-Disequilibrium Iteratively Nested Keyway (BLINK).Results and Discussion: Our results indicated that the two multi-locus models, FarmCPU and BLINK, outperformed single-locus models, GLM and MLM, in beef herds in this study. Specifically, five significant SNPs were identified using FarmCPU, while BLINK and GLM each identified the other three. Also, three of these eleven SNPs (“BTA-40510-no-rs”, “BovineHD1400006853”, and “BovineHD2100020346”) were shared by multiple models. The significant SNPs were mapped to genes such as EIF5, RGS20, TCEA1, LYPLA1, and MRPL15, which were previously reported to be associated with carcass-related traits, growth, and feed intake in several tropical cattle breeds. This confirms that the genes identified in this study could be candidate genes for carcass weight in pasture-fed beef cattle and can be selected for further breeding programs to improve the carcass yield and productivity of pasture-finished beef cattle in Hawai’i and beyond.

Abstract Food production strategies and patterns are being altered in response to climate change. Enhancing the adaptation of important food crops to novel climate regimes will be critical to maintaining world food supplies. Climate change is altering the suitability of production areas for crops such as potato (Solanum tuberosum L.) making future productivity, resilience, and sustainability of this crop dependent on breeding for climate adaptation, including through the introgression of novel traits from its wild relatives. To better understand the future production climate envelopes of potatoes, and the potential of its wild relatives to contribute to adaptation to these environments, we estimated the climate of potato in four future climate scenarios and overlapped the current climate of 72 wild relative species and potato with these future climates. We discovered a shift of up to 12.5% by potato from current to novel climate by 2070 and varying magnitudes of overlap by different wild relatives with potato, primarily driven by the extent of endemism. To address the threat of novel climate on potato production and with the wealth of data available for the agrobiodiversity in potato wild relatives, we systematically developed a prioritization value inspired by the logic of the breeder's equation for locating potentially beneficial species possessing local adaptability, climatic plasticity, and interspecific crossability. In doing so, 26 unique species by discrete climate combinations are found, highlighting the presence of unique species to use in adapting potato to changing local climates. Further, the 20 highest prioritized values belong to diploid species, enforcing the drive to shift into diploid breeding by the potato research community, where introgression of the local climate adaptability traits may be more streamlined.

Abstract Background World population is projected to reach 9–11 billion by 2050, raising concerns about food system security and sustainability. Modeling food systems are often a way to understand current and future dynamics. The most common model, first articulated by Malthus (Malthusian), shows population growth as an exponential function and food production as a linear function, concluding that human carrying capacity will be reached leading to mass starvation. Another prominent model was introduced by Boserup (Boserupian), which explains increases in food production as a function of population growth. Methodology Here, we explore which food systems dynamics exist at equilibrium and after perturbation. The model introduced explores food availability in an isolated village and then in a line of villages. The isolated village model includes three key parameters: maximum calorie production (a), food production resilience (b), and minimum calorie requirement per person (c). The multiple village model adds an additional parameter for trade. Results Isolated village populations are more resilient to famine than Malthusian theory predicts, suggesting that Malthus’ premise may be inaccurate. Predictably, across multiple villages increasing access and production reduce famine. However, under certain conditions large amounts of transport can lead to antagonist relationships leading to rapid changes in population. Conclusion Food systems under both production and access scenarios proved to be resilient to small perturbations, requiring a large catastrophe to induce mortality; this appeared to discount the Malthusian model. This model can create dynamics where different modes of famine relief apply, but here we see that a balanced approach of both access and production appears to be the most resilient to famine.

Taro (Colocasia esculenta) is a food staple widely cultivated in the humid tropics of Asia, Africa, Pacific and the Caribbean. One of the greatest threats to taro production is Taro Leaf Blight caused by the oomycete pathogen Phytophthora colocasiae. Here we describe a de novo taro genome assembly and use it to analyze sequence data from a Taro Leaf Blight resistant mapping population. The genome was assembled from linked-read sequences (10x Genomics; ∼60x coverage) and gap-filled and scaffolded with contigs assembled from Oxford Nanopore Technology long-reads and linkage map results. The haploid assembly was 2.45 Gb total, with a maximum contig length of 38 Mb and scaffold N50 of 317,420 bp. A comparison of family-level (Araceae) genome features reveals the repeat content of taro to be 82%, >3.5x greater than in great duckweed (Spirodela polyrhiza), 23%. Both genomes recovered a similar percent of Benchmarking Universal Single-copy Orthologs, 80% and 84%, based on a 3,236 gene database for monocot plants. A greater number of nucleotide-binding leucine-rich repeat disease resistance genes were present in genomes of taro than the duckweed, ∼391 vs. ∼70 (∼182 and ∼46 complete). The mapping population data revealed 16 major linkage groups with 520 markers, and 10 quantitative trait loci (QTL) significantly associated with Taro Leaf Blight disease resistance. The genome sequence of taro enhances our understanding of resistance to TLB, and provides markers that may accelerate breeding programs. This genome project may provide a template for developing genomic resources in other understudied plant species.

Understanding the factors driving ecological and evolutionary interactions of economically important plant species is important for agricultural sustainability. The geography of crop wild relatives, including wild potatoes (Solanum section Petota), have received attention; however, such information has not been analysed in combination with phylogenetic histories, genomic composition and reproductive systems to identify potential species for use in breeding for abiotic stress tolerance. We used a combination of ordinary least-squares (OLS) and phylogenetic generalized least-squares (PGLM) analyses to identify the discrete climate classes that make up the climate niche that wild potato species inhabit in the context of breeding system and ploidy. Self-incompatible diploid or self-compatible polyploid species significantly increase the number of discrete climate classes within a climate niche inhabited. This result was sustained when correcting for phylogenetic non-independence in the linear model. Our results support the idea that specific breeding system and ploidy combinations increase niche breadth through the decoupling of geographical range and niche diversity, and therefore, these species may be of particular interest for crop adaptation to a changing climate.

Adopting modern gene-editing technologies for trait improvement in agriculture requires important workflow developments, yet these developments are not often discussed. Using tropical crop systems as a case study, we describe a workflow broken down into discrete processes with specific steps and decision points that allow for the practical application of the CRISPR-Cas gene editing platform in a crop of interest. While we present the steps of developing genome-edited plants as sequential, in practice parts can be done in parallel, which are discussed in this perspective. The main processes include 1) understanding the genetic basis of the trait along with having the crop’s genome sequence, 2) testing and optimization of the editing reagents, development of efficient 3) tissue culture and 4) transformation methods, and 5) screening methods to identify edited events with commercial potential. Our goal in this perspective is to help any lab that wishes to implement this powerful, easy-to-use tool in their pipeline, thus aiming to democratize the technology.

Societal Impact Statement Plant breeding is crucial for improving agricultural crops for human use. However, an urgent rethink is needed to ensure the next generation of plant breeders have the necessary breadth of skills to provide ever more efficient, nutritious, profitable, and environmentally sustainable crops. Plant breeding is a multifaceted endeavor, which intersects with many other disciplines and professions. To help ensure that future plant breeding efforts are sustainable and relevant to the needs of society, it is vital that the interdisciplinary nature of the plant breeding profession is adequately reflected in student training and development. Summary Breeders need to have many faces to understand not only genetics but also environmental, social, and economic factors that are relevant for maintaining or improving crops for human use. In the United States, there is a long history of public involvement in agriculture and plant breeding. However, recent changes in the social systems underpinning public agriculture (i.e., funding structure) necessitate a rethinking of how agriculture education, specifically plant breeding education, should be facilitated. To provide viable plant breeding programs, it is necessary to explicitly acknowledge that breeding has been an interdisciplinary, long‐standing public endeavor to increase food system stability. Acknowledging this complexity has important pedagogical implications: the core of plant breeding resides in genetics, but the changing nature of this profession requires breeders to embrace a much broader training. Here, we suggest specific curricular objectives for plant breeders.

Turmeric (Curcuma longa) and related Curcuma species have been used traditionally in India, China, Hawaii, and other cultures for millennia. Today they are used around the world for spice, medicine, dye, and religious purposes. Recent biomedical studies have corroborated the long-known traditional medicinal values of turmeric and its constituent curcuminoid compounds, which have anti-inflammatory, antioxidant, and anticarcinogenic properties. As part of statewide research and extension efforts to support an expanding turmeric industry, we examined yield of 14 accessions across different climatic zones in Hawaii to observe and describe Genotype × Environmental influences. Fresh turmeric yield differed significantly among genotypes. The overall yields observed in this work ranged 11.3–57.22 t ha−1 and generally agree with those in the literature. Data from the different sites suggest that fertility and water management are able to mitigate moderate stress imposed by climate change within a certain range, but suboptimal temperatures associated with high elevation in the tropics (>1000 m) are an important driver of lower yields. This suggests that high yielding turmeric varieties may possess wide adaptability and may perform well across diverse environments. However, site-specific evaluations will still be necessary, particularly in environments outside turmeric’s environmental optima and in the presence of high pest pressure.

Plant breeding has been central to global increases in crop yields. Breeding deserves praise for helping to establish better food security, but also shares the responsibility of unintended consequences. Much work has been done describing alternative agricultural systems that seek to alleviate these externalities, however, breeding methods and breeding programs have largely not focused on these systems. Here we explore breeding and selection strategies that better align with these more diverse spatial and temporal agricultural systems.

The diversity observed among crop wild relatives (CWRs) and their ability to flourish in unfavorable and harsh environments have drawn the attention of plant scientists and breeders for many decades. However, it is also recognized that the benefit gained from using CWRs in breeding is a potential rose between thorns of detrimental genetic variation that is linked to the trait of interest. Despite the increased interest in CWRs, little attention was given so far to the statistical, analytical, and technical considerations that should guide the sampling design, the germplasm characterization, and later its implementation in breeding. Here, we review the entire process of sampling and identifying beneficial genetic variation in CWRs and the challenge of using it in breeding. The ability to detect beneficial genetic variation in CWRs is strongly affected by the sampling design which should be adjusted to the spatial and temporal variation of the target species, the trait of interest, and the analytical approach used. Moreover, linkage disequilibrium is a key factor that constrains the resolution of searching for beneficial alleles along the genome, and later, the ability to deplete linked deleterious genetic variation as a consequence of genetic drag. We also discuss how technological advances in genomics, phenomics, biotechnology, and data science can improve the ability to identify beneficial genetic variation in CWRs and to exploit it in strive for higher-yielding and sustainable crops.

Intensive cultivation of ‘uala (sweet potato) in the Leeward Kohala field system on Hawai’i Island supported substantial populations of Native Hawaiians prior to its abandonment in the 19th century. Productivity is influenced by the heterogeneity of the climate and biogeochemical soil characteristics across the substantial ecological gradient. Agricultural infrastructure and associated practices were developed to manage crop production eventuating from the variation in inter- and intra-annual rainfall. Mechanisms of sustaining soil nitrogen (N) are still unclear; however, a pronounced source of N is soil organic matter decomposition. This study investigated in situ the effects of indigenous Hawaiian mulching practices against two control treatments on soil moisture and temperature dynamics to facilitate N mineralization in soil mounds cultivated with ‘uala. Field experiments were set in two agricultural restoration plots with distinct climatic and soil characteristics. Data included soil moisture and temperature, soil and plant N, growth and development of ‘uala, and real-time weather data. Concurrently, N mineralization was also investigated under controlled conditions. All indigenous mulching treatments were found to significantly increase soil moisture, regulate temperature variation, and improve N availability compared to control. Differences in soil properties between treatments translated to significant differences in above-ground biomass. The data suggest that these differences would extend to tuber production, but the use of a long-gestation variety limited tuber production in the study. Increased temperatures in the controlled experiments were observed to increase inorganic N significantly, but less substantially than soil moisture. Indigenous practices in the region could have greatly mitigated plant stress due to moisture, temperature, and N availability, increasing productivity and reducing the variability of the Leeward Kohala Field System.

Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number of studies have shown that recently dried specimens can be used to yield ploidy data. Recent studies have started to explore whether high-throughput sequencing (HTS) data can be used to assess ploidy levels by analyzing allelic frequencies from single copy nuclear genes. Here, we compare different approaches using a range of yam (Dioscorea) tissues of varying ages, drying methods and quality, including herbarium tissue. Our aims were to: (1) explore the limits of flow cytometry in estimating ploidy level from dried samples, including herbarium vouchers collected between 1831 and 2011, and (2) optimize a HTS-based method to estimate ploidy by considering allelic frequencies from nuclear genes obtained using a target-capture method. We show that, although flow cytometry can be used to estimate ploidy levels from herbarium specimens collected up to fifteen years ago, success rate is low (5.9%). We validated our HTS-based estimates of ploidy using 260 genes by benchmarking with dried samples of species of known ploidy (Dioscorea alata, D. communis, and D. sylvatica). Subsequently, we successfully applied the method to the 85 herbarium samples analyzed with flow cytometry, and successfully provided results for 91.7% of them, comprising species across the phylogenetic tree of Dioscorea. We also explored the limits of using this HTS-based approach for identifying high ploidy levels in herbarium material and the effects of heterozygosity and sequence coverage. Overall, we demonstrated that ploidy diversity within and between species may be ascertained from historical collections, allowing the determination of polyploidization events from samples collected up to two centuries ago. This approach has the potential to provide insights into the drivers and dynamics of ploidy level changes during plant evolution and crop domestication.

Premise We developed a target enrichment panel for phylogenomic studies of Dioscorea, an economically important genus with incompletely resolved relationships. Methods Our bait panel comprises 260 low‐ to single‐copy nuclear genes targeted to work in Dioscorea, assessed here using a preliminary taxon sampling that includes both distantly and closely related taxa, including several yam crops and potential crop wild relatives. We applied coalescent‐based and maximum likelihood phylogenomic inference approaches to the pilot taxon set, incorporating new and published transcriptome data from additional species. Results The custom panel retrieved ~94% of targets and >80% of full gene length from 88% and 68% of samples, respectively. It has minimal gene overlap with existing panels designed for angiosperm‐wide studies and generally recovers longer and more variable targets. Pilot phylogenomic analyses consistently resolve most deep and recent relationships with strong support across analyses and point to revised relationships between the crop species D. alata and candidate crop wild relatives. Discussion Our customized panel reliably retrieves targeted loci from Dioscorea, is informative for resolving relationships in denser samplings, and is suitable for refining our understanding of the independent origins of cultivated yam species; the panel likely has broader promise for phylogenomic studies across Dioscoreales.

Natural populations across a species range demonstrate population structure owing to neutral processes such as localized origins of mutations and migration limitations. Selection also acts on a subset of loci, contributing to local adaptation. An understanding of the genetic basis of adaptation to local environmental conditions is a fundamental goal in basic biological research. When applied to crop wild relatives, this same research provides the opportunity to identify adaptive genetic variation that may be used to breed for crops better adapted to novel or changing environments. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses. The identification of potentially adaptive variants in this ex situ collection may permit a more targeted use of germplasm collections.

Small nonprotein-coding microRNAs (miRNAs) are present in most eukaryotes and are central effectors of RNA silencing-mediated mechanisms for gene expression regulation. In plants, DICER-LIKE1 (DCL1) is the founding member of a highly conserved family of RNase III-like endonucleases that function as core machinery proteins to process hairpin-like precursor transcripts into mature miRNAs, small regulatory RNAs, 21–22 nucleotides in length. Zinc finger nucleases (ZFNs) were used to generate single and double-mutants of putative soybean DCL1 homologs, DCL1a and DCL1b, to confirm their functional role(s) in the soybean miRNA pathway. Neither DCL1 single mutant, dcl1a or dcl1b plants, exhibited a pronounced morphological or molecular phenotype. However, the dcl1a/dcl1b double mutant expressed a strong morphological phenotype, characterized by reduced seed size and aborted seedling development, in addition to defective miRNA precursor transcript processing efficiency and deregulated miRNA target gene expression. Together, these findings indicate that the two soybean DCL1 paralogs, DCL1a and DCL1b, largely play functionally redundant roles in the miRNA pathway and are essential for normal plant development.

Global biodiversity hotspots are areas containing high levels of species richness, endemism and threat. Similarly, regions of agriculturally relevant diversity have been identified where many domesticated plants and animals originated, and co-occurred with their wild ancestors and relatives. The agro-biodiversity in these regions has, likewise, often been considered threatened. Biodiversity and agro-biodiversity hotspots partly overlap, but their geographic intricacies have rarely been investigated together. Here we review the history of these two concepts and explore their geographic relationship by analysing global distribution and human use data for all plants, and for major crops and associated wild relatives. We highlight a geographic continuum between agro-biodiversity hotspots that contain high richness in species that are intensively used and well known by humanity (i.e., major crops and most viewed species on Wikipedia) and biodiversity hotspots encompassing species that are less heavily used and documented (i.e., crop wild relatives and species lacking information on Wikipedia). Our contribution highlights the key considerations needed for further developing a unifying concept of agro-biodiversity hotspots that encompasses multiple facets of diversity (including genetic and phylogenetic) and the linkage with overall biodiversity. This integration will ultimately enhance our understanding of the geography of human-plant interactions and help guide the preservation of nature and its contributions to people.

Since the mid-20th century, crop breeding has driven unprecedented yield gains. Breeders generally select for broadly- and reliably-performing varieties that display little genotype-by-environment interaction (GxE). In contrast, ecological theory predicts that across environments that vary spatially or temporally, the most productive population will be a mixture of narrowly adapted specialists. We quantified patterns of broad and narrow adaptation in modern, commercial maize (Zea mays L.) hybrids planted across 216 site-years, from 1999-2018, for the University of Illinois yield trials. We found that location was the dominant source of yield variation (44.5%), and yearly weather was the smallest (1.7%), which suggested a benefit for reliable performance in narrow biophysical environments. Varieties displayed a large "home field advantage" when growing in the location of best performance relative to other varieties. Home field advantage accounted for 19% of GxE and provided a yield increase of 1.01 ± 0.04 Mg ∙ ha-1 (7.6% relative to mean yield), yet was both smaller than predicted by a null model and unchanged across time. This counterfactual suggests that commercial breeding programs have missed an opportunity to further increase yields by leveraging local adaptation. Public breeding programs may pursue this opportunity by releasing specialist varieties that perform reliably in narrow environments. As seed sources are increasingly privatized and consolidated, this alternate strategy may compliment private breeding to support global food security.

Interest in the development of organically grown vegetable crops has risen over the past decades due to consumer preferences. However, most crops that have desirable consumer traits have been bred in conventional growing conditions, and their transfer to an organic setting is challenging. Here, the organically grown Hawaiian pumpkin (Cucurbita moschata) accession ‘Shima’ was crossed with the conventionally grown Puerto Rican variety ‘Taina Dorada’ to develop a backcross (BC1) population, where ‘Shima’ was the recurrent parent. A total of 202 BC1 (‘Shima’ X F1) progenies were planted in a certified organic field, and twelve traits were evaluated. We used genotype-by-sequencing (GBS) to identify the Quantitative Trait Loci (QTL) associated with insect tolerance along with commercially desirable traits. A total of 1582 single nucleotide polymorphisms (SNPs) were identified, from which 711 SNPs were used to develop a genetic map and perform QTL mapping. Reads associated with significant QTLs were aligned to the publicly available Cucurbita moschata genome and identified several markers linked to genes that have been previously reported to be associated with that trait in other crop systems, such as melon (Cucumis melo L.). This research provides a resource for marker-assisted selection (MAS) efforts in Cucurbita moschata, as well as serving as a model study to improve cultivars that are transitioning from a conventional to an organic setting.

Changes in crop yield and production over time are driven by a combination of genetics, agronomics, and climate. Disentangling the role of these various influences helps us understand the capacity of agriculture to adapt to change. Here we explore the impact of climate variability on rice yield and production in the Philippines from 1987-2016 in both irrigated and rainfed production systems at various scales. Over this period, rice production is affected by variations in soil moisture, which are largely driven by the El Niño-Southern Oscillation (ENSO). We found that the climate impacts on rice production are strongly seasonally modulated and differ considerably by region. As expected, rainfed upland rice production systems are more sensitive to soil moisture variability than irrigated paddy rice. About 10% of the variance in rice production anomalies on the national level co-varies with soil moisture changes, which in turn are strongly negatively correlated with an index capturing ENSO variability. Our results show that while temperature variability is of limited importance in the Philippines today, future climate projections suggest that by the end of the century, temperatures might regularly exceed known limits to rice production if warming continues unabated. Therefore, skillful seasonal prediction will likely become increasingly crucial to provide the necessary information to guide agriculture management to mitigate the compounding impacts of soil moisture variability and temperature stress. Detailed case studies like this complement global yield studies and provide important local perspectives that can help in food policy decisions.

This study chronicles the ongoing process to domesticate an interspecific trigenomic tetraploid hybrid sunflower derived from a series of interspecific crosses between Helianthus annuus and Helianthus tuberosus. The goal of this process is to develop a perennial oilseed crop that can produce both high value vegetable oil and continuous ground-cover. Selection has focused on developing an ideotype with the domesticated morphology of H. annuus and the below-ground perennial features of H. tuberosus. The overarching challenge in the process of breeding and domesticating this interspecific perennial sunflower is overcoming obstacles associated with interploid meiosis in order to resolve a chromosomally stable hybrid population. As selection progresses through generations of intermating, there are improvements toward the desired ideotype, but selection efficiency is slowed by apparent antagonisms between annual- and perennial morphological targets and irregular meiosis which is especially problematic in a trigenomic tetraploid. This shows that keys toward perennial crop development through interspecific hybridization will be to capitalize on the abundant phenotypic variation within our population, achieve meiotic stability in order to maximize selection efficiency, and to break genetic correlations between annual and perennial traits.

Aeroponic cloning is a great strategy to maintain desired genotypes by generating a whole new plant from cuttings. While this propagation technique has been demonstrated for tomatoes (Solanum lycopersicum) and potatoes (Solanum tuberosum), no protocol has been developed for peppers (Capsicum spp.). The ability to clonally propagate different Capsicum holds promise for domestic and industrial growing operations since elite cultivars with desirable traits (e.g., high capsaicin levels, nutrient content, and striped fruit) can be perpetuated without the need of planning a nursery. We tested six Capsicum species for their feasibility of aeroponic cloning by stem cuttings. All domestic species were successfully regenerated under aeroponic conditions but not for Capsicum eximium, a wild species. Of the species analyzed, Capsicum annuum peppers had the fastest node formation (11.6 +/− 0.89 days, P ≤ 0.01) and obtained a larger volume of roots (P ≤ 0.01) after node formation as compared to C. baccatum, C. frutescens, and C. pubescens. This study presents a cost-effective strategy to clonally propagate peppers for personal, industrial, and conservation purposes.

Chile peppers, native to the Americas, have spread around the world and have been integrated into the diets of many cultures. Much like their heat content, nutritional content can vary dramatically between different pepper types. In this study, a diverse set of chile pepper types were examined for nutrient content. Some pepper types were found to have high levels of vitamin A, vitamin C, or folate. Correlations between nutrient content, species, cultivation status, or geographic region were limited. Varietal selection or plant breeding offer tools to augment nutrient content in peppers. Integration of nutrient rich pepper types into diets that already include peppers could help combat nutrient deficiencies by providing a significant portion of recommended daily nutrients.