Quinoa, potatoes, and llamas fueled emergent social complexity in the Lake Titicaca Basin of the Andes

Chromosome-level genome assemblies for two quinoa inbred lines from northern and southern highlands of Altiplano where quinoa originated

Quinoa is emerging as a key seed crop for global food security due to its ability to grow in marginal environments and its excellent nutritional properties. Because quinoa is partially allogamous, we have developed quinoa inbred lines necessary for molecular genetic analysis. Our comprehensive genomic analysis showed that the quinoa inbred lines fall into three genetic subpopulations: northern highland, southern highland, and lowland. Lowland and highland quinoa are the same species, but have very different genotypes and phenotypes. Lowland quinoa has relatively small grains and a darker grain color, and is widely tested and grown around the world. In contrast, the white, large-grained highland quinoa is grown in the Andean highlands, including the region where quinoa originated, and is exported worldwide as high-quality quinoa. Recently, we have shown that viral vectors can be used to regulate endogenous genes in quinoa, paving the way for functional genomics to reveal the diversity of quinoa. However, although a high-quality assembly has recently been reported for a lowland quinoa line, genomic resources of the quality required for functional genomics are not available for highland quinoa lines. Here we present high-quality chromosome-level genome assemblies for two highland inbred quinoa lines, J075 representing the northern highland line and J100 representing the southern highland line, using PacBio HiFi sequencing and dpMIG-seq. In addition, we demonstrate the importance of verifying and correcting reference-based scaffold assembly with other approaches such as linkage maps. The assembled genome sizes of J075 and J100 are 1.29 and 1.32 Gb, with contigs N50 of 66.3 and 12.6 Mb, and scaffold N50 of 71.2 and 70.6 Mb, respectively, comprising 18 pseudochromosomes. The repetitive sequences of J075 and J100 represent 72.6% and 71.5% of the genome, the majority of which are long terminal repeats, representing 44.0% and 42.7% of the genome, respectively. The de novo assembled genomes of J075 and J100 were predicted to contain 65,303 and 64,945 protein-coding genes, respectively. The high quality genomes of these highland quinoa lines will facilitate quinoa functional genomics research on quinoa and contribute to the identification of key genes involved in environmental adaptation and quinoa domestication.

South American Archaeological Isotopic Database, a regional-scale multi-isotope data compendium for research

The South American Archaeological Isotopic Database (SAAID) is a comprehensive open-access resource that aggregates all available bioarchaeological stable and radiogenic isotope measurements, encompassing data from human individuals, animals, and plants across South America. Resulting from a collaborative effort of scholars who work with stable isotopes in this region, SAAID contains 53,781 isotopic measurements across 24,507 entries from individuals/specimens spanning over 12,000 years. SAAID includes valuable contextual information on archaeological samples and respective sites, such as chronology, geographical region, biome, and spatial coordinates, biological details like estimated sex and age for human individuals, and taxonomic description for fauna and flora. SAAID is hosted at the PACHAMAMA community within the Pandora data platform and the CORA repository to facilitate easy access. Because of its rich data structure, SAAID is particularly well-suited for conducting spatiotemporal meta-analyses. It serves as a valuable tool for addressing a variety of research topics, including the spread, adoption, and consumption intensification of food items, paleo-environmental reconstruction, as well as the exploration of mobility patterns across extensive geographic regions.

Peruvian Amaranth (kiwicha) Accumulates Higher Levels of the Unsaturated Linoleic Acid

Grain amaranth (Amaranthus spp.) is an emerging crop rich in proteins and other valuable nutrients. It was domesticated twice, in Mexico and Peru. Although global trade is dominated by Mexican species of amaranth, Peruvian amaranth (A. caudatus, kiwicha) has remained neglected, although it harbours valuable traits. In the current study, we investigate the accumulation of polyunsaturated fatty acids, comparing four genotypes of A. caudatus with K432, a commercial variety deriving from the Mexican species A. hypochondriacus under the temperate environment of Southwest Germany. We show that the A. caudatus genotypes flowered later (only in late autumn), such that they were taller as compared to the Mexican hybrid but yielded fewer grains. The oil of kiwicha showed a significantly higher content of unsaturated fatty acids, especially of linoleic acid and α-linolenic acid compared to early flowering genotype K432. To gain insight into the molecular mechanisms behind these differences, we sequenced the genomes of the A. hypochondriacus × hybridus variety K432 and the Peruvian kiwicha genotype 8300 and identified the homologues for genes involved in the ω3 fatty-acid pathway and concurrent oxylipin metabolism, as well as of key factors for jasmonate signalling and cold acclimation. We followed the expression of these transcripts over three stages of seed development in all five genotypes. We find that transcripts for Δ6 desaturases are elevated in kiwicha, whereas in the Mexican hybrid, the concurrent lipoxygenase is more active, which is followed by the activation of jasmonate biosynthesis and signalling. The early accumulation of transcripts involved in cold-stress signalling reports that the Mexican hybrid experiences cold stress already early in autumn, whereas the kiwicha genotypes do not display indications for cold stress, except for the very final phase, when there were already freezing temperatures. We interpret the higher content of unsaturated fatty acids in the context of the different climatic conditions shaping domestication (tropical conditions in the case of Mexican amaranth, sharp cold snaps in the case of kiwicha) and suggest that kiwicha oil has high potential as functional food which can be developed further by tailoring genetic backgrounds, agricultural practice, and processing.

Holocene variations in Lake Titicaca water level and their implications for sociopolitical developments in the central Andes

Holocene climate in the high tropical Andes was characterized by both gradual and abrupt changes, which disrupted the hydrological cycle and impacted landscapes and societies. High-resolution paleoenvironmental records are essential to contextualize archaeological data and to evaluate the sociopolitical response of ancient societies to environmental variability. Middle-to-Late Holocene water levels in Lake Titicaca were reevaluated through a transfer function model based on measurements of organic carbon stable isotopes, combined with high-resolution profiles of other geochemical variables and paleoshoreline indicators. Our reconstruction indicates that following a prolonged low stand during the Middle Holocene (4000 to 2400 BCE), lake level rose rapidly ~15 m by 1800 BCE, and then increased another 3 to 6 m in a series of steps, attaining the highest values after ~1600 CE. The largest lake-level increases coincided with major sociopolitical changes reported by archaeologists. In particular, at the end of the Formative Period (500 CE), a major lake-level rise inundated large shoreline areas and forced populations to migrate to higher elevation, likely contributing to the emergence of the Tiwanaku culture.

Pre-Columbian cultivation of vegetatively propagated and fruit tree tropical crops in the Atacama Desert

South America is a megadiverse continent that witnessed the domestication, translocation and cultivation of various plant species from seemingly contrasting ecosystems. It was the recipient and supplier of crops brought to and from Mesoamerica (such as maize and cacao, respectively), and Polynesia to where the key staple crop sweet potato was exported. Not every instance of the trans-ecological expansion of cultivated plants (both domesticated and wild), however, resulted in successful farming. Here, we review the transregional circulation and introduction of five food tropical crops originated in the tropical and humid valleys of the eastern Andes—achira, cassava, ahipa, sweet potato, and pacay—to the hyper-arid coastal valleys of the Atacama Desert of northern Chile, where they have been found in early archeological sites. By means of an evaluation of the contexts of their deposition and supported by direct radiocarbon dating, stable isotopes analyses, and starch grain analysis, we evaluate different hypotheses for explaining their introduction and adaptation to the hyper-arid soils of northern Chile, by societal groups that after the introduction of cultigens still retained a strong dependence on marine hunting, gathering and fishing ways of life based on wide variety of marine coast resources. Many of the studied plants were part of a broader package of introduced goods and technological devices and procedures, linked to food, therapeutic medicine, social and ritual purposes that transformed previous hunter-gatherer social, economic, and ideological institutions. Based on archeological data, we discuss some of the possible socio-ecological processes involved in the development of agricultural landscapes including the adoption of tropical crops originated several hundred kilometers away from the Atacama Desert during the Late Holocene.

A rapid, simple, and reliable assay to authenticate Peruvian kiwicha (A. caudatus) for food applications

Amaranth has acquired great economic impact as functional food, with species originating from Mexico dominating global trade. In contrast, the Peruvian A. caudatus (kiwicha) has been vastly neglected, although it is endowed with very promising nutritive traits. Morphological plasticity and taxonomic ambiguities render authentication of Amaranth difficult, such that the identity of commercial samples is often unclear. To safeguard the authenticity of kiwicha and, thus, consumer safety, we characterised a germplasm collection of 84 Amaranth accessions on both, the morphological and the genetic level. We show that kiwicha can be delineated phenotypically from other species by its late flowering, taller posture, and lower grain yields. Instead, flower and seed color, often used as proxy for identity, do not qualify as taxonomic markers. Using the plastidic barcoding marker psbA-trnH igs we were able to identify a specific Single Nucleotide Polymorphism (SNP) that separated kiwicha from all other species of Amaranth. This allowed us to develop a sequencing-free authentication assay using an Amplified Refractory Mutation System (ARMS) strategy. As a result kiwicha in commercial samples can be authenticated by a single duplex-PCR yielding a diagnostic side band reporting A. caudatus against all other species of Amaranthus. This fingerprinting assay will help to develop the nutritive potential of kiwicha and to safeguard seed material for A. caudatus against adulteration by the far more prevalent species from Mexico.

Root Reinforcement Improved Performance, Productivity, and Grain Bioactive Quality of Field-Droughted Quinoa (Chenopodium quinoa)

Modern agriculture is facing multiple and complex challenges and has to produce more food and fiber to feed a growing population. Increasingly volatile weather and more extreme events such as droughts can reduce crop productivity. This implies the need for significant increases in production and the adoption of more efficient and sustainable production methods and adaptation to climate change. A new technological and environment-friendly management technique to improve the tolerance of quinoa grown to maturity is proposed using native microbial biostimulants (arbuscular mycorrhizal fungi; AMF) alone, in the consortium, or in combination with compost (Comp) as an organic matter source under two water treatments (normal irrigation and drought stress (DS)). Compared with controls, growth, grain yield, and all physiological traits under DS were significantly decreased while hydrogen peroxide, malondialdehyde, and antioxidative enzymatic functions were significantly increased. Under DS, biofertilizer application reverted physiological activities to normal levels and potentially strengthened quinoa's adaptability to water shortage as compared to untreated plants. The dual combination yielded a 97% improvement in grain dry weight. Moreover, the effectiveness of microbial and compost biostimulants as a biological tool improves grain quality and limits soil degradation under DS. Elemental concentrations, particularly macronutrients, antioxidant potential (1,1-diphenyl-2-picrylhydrazyl radical scavenging activity), and bioactive compounds (phenol and flavonoid content), were accumulated at higher levels in biofertilizer-treated quinoa grain than in untreated controls. The effects of AMF + Comp on post-harvest soil fertility traits were the most positive, with significant increases in total phosphorus (47%) and organic matter (200%) content under drought conditions. Taken together, our data demonstrate that drought stress strongly influences the physiological traits, yield, and quality of quinoa. Microbial and compost biostimulation could be an effective alternative to ensure greater recovery capability, thereby maintaining relatively high levels of grain production. Our study shows that aboveground stress responses in quinoa can be modulated by signals from the microbial/compost-treated root. Further, quinoa grains are generally of higher nutritive quality when amended and inoculated with AMF as compared to non-inoculated and compost-free plants.