- Efficiency of insect‐proof net tunnels in reducing virus‐related seed degeneration in sweet potato. “Seed” meaning vines. And yes, those tunnels work.
- Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana). Genetic differences between the two subspecies is maintained by adaptive divergence despite gene flow.
- Agronomic Performance and Nitrogen Fixation of Heirloom and Conventional Dry Bean Varieties Under Low-Nitrogen Field Conditions. Not much difference, which is actually interesting.
- Evolutionary Insights into the Nature of Plant Domestication. It’s a long process, in which natural selection and interspecific hybridization play an important part, involving many of the same genes across species.
- Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks. Add to the above? Ah no, only in bacteria so far.
- Screening African rice (Oryza glaberrima) for tolerance to abiotic stresses: III Flooding. From a collection of >2,000 to 11 better than Asian rice. You’re wondering about I and II, aren’t you?
- Understanding the factors influencing fall armyworm (Spodoptera frugiperda J.E. Smith) damage in African smallholder maize fields and quantifying its impact on yield. A case study in Eastern Zimbabwe. Differences among maize varieties, but weeding, tillage and intercropping also have an effect. Have yield losses been overestimated, though? Maybe.
- Natural selection contributed to immunological differences between hunter-gatherers and agriculturalists. But the evidence seems to be that the pathogen burden was higher for the hunter-gatherers, which goes counter to everything we’ve been taught by Jared Diamond.
- Increasing crop heterogeneity enhances multitrophic diversity across agricultural regions. More crops means more biodiversity in general.
- More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health. More microbes mean better plant growth.
- Science–graphic art partnerships to increase research impact. Free your inner artist.
- Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing. Four groups: pure wild type, admixed wild type, ancient landraces and modern landraces.
- The Relative Caloric Prices of Healthy and Unhealthy Foods Differ Systematically across Income Levels and Continents. …and at least partially explain differences in undernutrition and overweight in adults. Here’s the infographic.
- Household-level drivers of dietary diversity in transitioning agricultural systems: Evidence from the Greater Mekong Subregion. It’s complicated and context-specific, but dietary diversity seems to generally increase with agricultural “development,” i.e. market orientation, specialisation, and intensification. Somewhat surprising? I’ve lost track, frankly.
- Potential role of neglected and underutilized plant species in improving women’s empowerment and nutrition in areas of sub-Saharan Africa. So is increasing cultivation of orphan crops a driver or a consequence of agricultural development? See what I mean? Anyway, useful review.
A USDA legend retires
Marty Reisinger, who knows a thing or two about genebank documentation systems himself, has just sent in this appreciation of retiring USDA genebank database manager Quinn Sinnott. We all wish Quinn a long and happy retirement, and thank him for his important contribution to the field.
Quinn Sinnott, the database manager for GRIN, is retiring from the USDA Agricultural Research Service’s Database Management Unit (DBMU) on August 31, 2019.
Quinn is one of the founders and early builders of GRIN, having served the project since it was initiated in 1983. GRIN started as an ARS project funded through a cooperative agreement with the University of Maryland.
GRIN went live in late 1983 on a PR1ME minicomputer with only a few megabytes of memory and 300 MB disk drives. The drives were the size of a low filing cabinet. Backups were made on large 9-track tape reels; at one point, it took 15 tapes to back up the database. The software was coded in FORTRAN for a CODASYL database. There was no SQL query capability. Instead, there was a program called DISCOVER that could do queries. They would often take hours to complete.
During Quinn’s tenure, GRIN’s hardware and software evolved a great deal. New hardware was purchased in 1992 for approximately $500,000 after a lengthy procurement process. In late 1994, GRIN was moved to a relational Oracle database running on a Unix system. The entire system was rewritten to work with Oracle Forms and SQL. The GRIN hardware was originally housed in the USDA National Agriculture Library, but sometime in the mid-90’s it was moved to the attic of Building 003 on USDA’s Beltsville, Maryland campus.
In 2008, Crop Trust supported a project to rewrite the GRIN system so that it could be run on either a personal computer or network and be maintained by the world genebank community as open source software. The database and interfaces were designed to accommodate commercial and open-source programming tools and be database-flexible. The DBMU selected Microsoft SQL Server for the USDA National Plant Germplasm System’s database engine; Quinn was instrumental in ensuring that the robust GRIN schema and functionality could be emulated in the new GRIN-Global platform.
Quinn is among those who have made GRIN/GRIN-Global the highly regarded system that it is. Genebanks around the world have excellent, continually improving tools to manage their collections and data, thanks in part to his efforts over more than 35 years.
Quinn will continue to assist the National Germplasm Resources Laboratory as a volunteer and help with GRIN/GRIN-Global matters occasionally as needed. A tremendous thanks to Quinn for his outstanding 35 years of service to ARS, the National Plant Germplasm System, and the global genetic resource community.
Guide to a well trodden path
The International Seed Federation has a handy brief Guide to Genetic Resources online. It covers why plant genetic resources are important, and what arrangements are in place for access and benefit sharing1 — not surprisingly, perhaps, mainly from the point of view of crop breeders.
Breeders work mostly with modern varieties, the so-called “elite” genetic resources. Sometimes they look beyond modern varieties to develop a valuable attribute, such as resistance to new pests or diseases, nutritional content, or flavour. They might use nonelite varieties, such as landraces, heirlooms, or crop wild relatives, which come mostly from public or private gene banks.
The conservation of genetic resources is like having an insurance. By having a larger pool of genetic resources, plant breeders are more likely to find solutions that farmers and others need. This means that efforts to conserve genetic resources are critically important. These genetic resources may contain the traits that future generations will need.
There’s a page on genebanks, focusing on the international collections of CGIAR.
It’s ok as far as it goes, I guess, but I would have liked to see more on the role of national and regional genebanks, information sources such as Genesys and WIEWS, and traits beyond productivity.
- With a link to their Genetic Resources Information Tree. [↩]
Brainfood: Mexican maize landraces, Mediterranean wheat landraces, Grassland richness, RTBs, Gender and agrobiodiversity, Kenya pastoralists, Production and child mortality, Historical evaluation data, Drought & rice, Barley diversity, Restoration, Sweetpotato shape, Panama disease phenotyping, Solanum keys
- Single-gene resolution of locally adaptive genetic variation in Mexican maize. Let the gene editing begin.
- From landraces to improved cultivars: Assessment of genetic diversity and population structure of Mediterranean wheat using SNP markers. Landraces cluster geographically, modern varieties by breeding programme.
- Global evidence of positive biodiversity effects on spatial ecosystem stability in natural grasslands. Higher species richness increases productivity in low-productivity communities, decreases it in high-productivity.
- Understanding the consequences of changes in the production frontiers for roots, tubers and bananas. Forget marketing, focus research on productivity.
- Gendered agrobiodiversity management and adaptation to climate change: differentiated strategies in two marginal rural areas of India. Women exercise more public control over agrobiodiversity in the Himalayas than in the Indo-Gangetic Plain.
- Historical Ecologies of Pastoralist Overgrazing in Kenya: Long-Term Perspectives on Cause and Effect. Let pastoralists move around.
- Mortality impact of low annual crop yields in a subsistence farming population of Burkina Faso under the current and a 1.5°C warmer climate in 2100. Low production in any given year responsible for considerable child mortality, which is likely to double because of climate change. If nothing is done.
- Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection. Don’t throw any data away.
- Mapping drought-induced changes in rice area in India. 16% less rice area in a drought year compared to a normal year.
- Development of a Multi-parent Population for Genetic Mapping and Allele Discovery in Six-Row Barley. Asian material has flowering time variants found nowhere else.
- Ex situ collections and their potential for the restoration of extinct plants. There’s no excuse for not trying in situ.
- Assessing the remarkable morphological diversity and transcriptomic basis of leaf shape in Ipomoea batatas (sweetpotato). Mainly genetic, at least as currently measured.
- An Improved Phenotyping Protocol for Panama Disease in Banana. A single person can now inoculate 250 plants per hour.
- Dichotomous keys to the species of Solanum L. (Solanaceae) in continental Africa, Madagascar (incl. the Indian Ocean islands), Macaronesia and the Cape Verde Islands. Monumental.
Brainfood: Mineral history, Tomato nutrients, Tomato breeding, Phenotyping plants, Restoration genomics, Green Revolution, Banana B, SPAM2005, Ancient Chinese wheat, Late blight, Sorghum seed size, N & stability, African cannabis, Brazil wheat, Wild safflower
- Mineral nutrient composition of vegetables, fruits and grains: The context of reports of apparent historical declines. Apparent being the operative word. This is a couple of years old but always worth recycling. (There’s also this Politico piece from a couple of years back on the “nutrient collapse.”)
- Phenolic composition and antioxidant properties of ex-situ conserved tomato (Solanum lycopersicum L.) germplasm. But there’s always room for improvement.
- Genetic Diversity and Population Structure of Tomato (Solanum lycopersicum) Germplasm Developed by Texas A&M Breeding Programs. Plenty of diversity out there for it.
- Crop productivity as related to single-plant traits at key phenological stages in durum wheat. On isolated plants, only specific leaf weight and spike partitioning at anthesis were correlated with population yield.
- The potential of genomics for restoring ecosystems and biodiversity. From improved seed sourcing to gene editing for funky genotypes.
- Was the Green Revolution intended to maximise food production? No, apparently it was to encourage a move to commercial production in specific areas.
- Musa balbisiana genome reveals subgenome evolution and functional divergence. The starch synthesis pathway is more active than in the A-subgenome. There’s probably more, but that’s all I could understand.
- Pixelating crop production: Consequences of methodological choices. Crop prices and market access had little effect on the robustness of the SPAM2005 spatial production allocation model.
- Phylogenetic and population structural inference from genomic ancestry maintained in present‐day common wheat Chinese landraces. 3000 old wheat not dissimilar to current landraces in W China.
- Stacking three late blight resistance genes from wild species directly into African highland potato varieties confers complete field resistance to local blight races. But it’s GM so it doesn’t count, right?
- Genomic signatures of seed mass adaptation to global precipitation gradients in sorghum. Drought stress led to bigger grains.
- Nitrogen addition reduced ecosystem stability regardless of its impacts on plant diversity. Stability depends on more than just diversity. In grasslands.
- A brief agricultural history of cannabis in Africa, from prehistory to canna-colony. Decolonise the weed.
- Genetic Gain Over 30 Years of Spring Wheat Breeding in Brazil. 1.3% per year. Is it enough? Can it be sustained?
- The Use of Wild Relatives of Safflower to Increase Genetic Diversity for Fatty Acid Composition and Drought Tolerance. So transgressive.