Einkorn genomics sheds light on history of the oldest domesticated wheat

Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.

Climate risk to peanut cultivation in Brazil across different planting seasons

BACKGROUND

Peanuts are widely grown in Brazil because of their great importance in the domestic vegetable oil industry and the succession of sugarcane, soybean and maize crops, contributing to soil conservation and improvement in agricultural areas. Thus, the present study aimed to determine the zoning of peanuts' climatic risk by estimating the water requirement satisfaction index (WRSI) for the crop in Brazil. We used a historical series of data on average air temperature and rainfall between 1980 and 2016. Reference evapotranspiration was estimated using the method of Thornthwaite, and we subsequently calculated crop evapotranspiration and maximum evapotranspiration. Water balances for all stations were calculated using the method of Thornthwaite and Mather, with an available water capacity in the soil of 15, 30 and 45 mm. The definitions of suitable, unfit and restricted areas and the planting season were performed using the WRSI.

RESULTS

Brazil has low climatic risk areas for growing peanuts throughout the year, except for winter. The country reveals that 88.19%, 97.93%, 99.16% and 39.25% of its area is suitable for planting peanuts on planting dates in spring, summer, autumn and winter, respectively.

CONCLUSION

Brazil has a large part of the areas favorable to the planting of peanuts. The maximum availability of soil water at a depth of 15, 30 and 45 mm does not influence regions with respect to peanut growing in Brazil. The states of Piauí, Ceará and Bahia are the most unsuitable on the winter planting date, with an average WRSI of 0.22. © 2021 Society of Chemical Industry.

Genomic insights into the formation of human populations in East Asia

The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people1,2. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan.

Abandonment of pearl millet cropping and homogenization of its diversity over a 40 year period in Senegal

Cultivated diversity is considered an insurance against major climatic variability. However, since the 1980s, several studies have shown that climate variability and agricultural changes may already have locally eroded crop genetic diversity. We studied pearl millet diversity in Senegal through a comparison of pearl millet landraces collected 40 years apart. We found that more than 20% of villages visited in 1976 had stopped growing pearl millet. Despite this, its overall genetic diversity has been maintained but differentiation between early- and late-flowering accessions has been reduced. We also found stronger crop-to-wild gene flow than wild-to-crop gene flow and that wild-to-crop gene flow was weaker in 2016 than in 1976. In conclusion, our results highlight genetic homogenization in Senegal. This homogenization within cultivated pearl millet and between wild and cultivated forms is a key factor in genetic erosion and it is often overlooked. Improved assessment and conservation strategies are needed to promote and conserve both wild and cultivated pearl millet diversity.

Changes in rice yield and yield stability in China during the past six decades

BACKGROUND

Increasing rice yield and its stability are important to achieving the sustainability of rice production. Rice yields have increased substantially in China during recent decades, but information on the trend in yield stability has been limited. In this study, the trends in rice yield and rice yield stability from 1949 to 2015 were analysed in China's rice production.

RESULTS

The results showed that rice yields for all 16 provinces presented an increasing trend during the study period. The national annual rice yield gain was 86.0 kg ha^-1 during the last six decades, varying from 48.4 to 106.0 kg ha^-1 in different provinces and exhibiting linear, bilinear, or trilinear relationships. Remarkably, the annual yield increase was smaller in provinces dominated by double rice cropping systems than in the other provinces. Notably, rice yield stagnations have occurred in recent years at provincial and national levels. Absolute residuals over time showed slight increases in four of 16 provinces, indicating a reduction in yield stability in these four provinces. However, the relative yield residuals exhibited a clear trend towards increased yield stability for all 16 provinces. The rice yields of newer cultivars planted with improved crop management practices were consistently higher and more stable than with cultivars from the beginning of the study period.

CONCLUSION

This study revealed that rice yield in China has increased substantially, accompanied by improved stability over the last six decades. Given the spatial difference, this study emphasizes the priority of orienting long-term on-farm studies to investigate yield stability. © 2020 Society of Chemical Industry.

Agricultural intensification was associated with crop diversification in India (1947-2014)

Declines in agricultural biodiversity associated with modern farming practices may negatively affect the sustainability of agro-ecosystems, but formal knowledge of historical variation in spatio-temporal variation of agro-biodiversity is limited. We used time series of national (1947–2014) and district-level (1956–2008) crop distribution data for India to show that despite strong agricultural intensification after 1960, the average crop species diversity at the district level was stable, but increased at the country-level. While there was a decline in diversity in the major rice and wheat producing regions of northwestern India, associated with intensification of the production of these crops, diversity in western and southern India increased due to expansion of oilseeds and horticultural crops that replaced millet and sorghum. These opposite, but related, trends in crop-level diversity at the sub-national level partially canceled each other out at national level, but there nevertheless was a noticeable increase in overall crop diversity in India during this time period. Our results illustrate how patterns of change in crop diversity need to be considered at different levels of aggregation, and how a decrease in diversity associated with intensification and specialization in one area, may be associated with increased diversity elsewhere, and that support for intensive agriculture with relatively low crop diversity in some regions may be associated with an increase in crop diversity in other regions and at a higher level of aggregation.

Manuring practices in the first millennium AD in southern Sweden inferred from isotopic analysis of crop remains

This study uses crop stable nitrogen isotope analysis of charred grain to explore manuring practices in arable production at the affluent regional center Uppåkra and a set of smaller surrounding sites, dating to the first millennium AD in southern Sweden. The isotopic analysis focuses on hulled barley, the principle crop in the Scandinavian Iron Age, and the minor crops: bread wheat, emmer wheat, rye and oat, are included to compare manuring practices in cultivation of other crop species during this period. A field experiment was first conducted to establish relationships between manuring and δ15N values in modern grain from known growing conditions. The data formed an interpretive framework to reconstruct past agricultural practices and manuring intensity in the archaeological study area. Our results from the ancient grains have demonstrated that barley from the early phase in the study area (AD 0-200) varies widely in its δ15N values, reflecting mixed manuring regimes. In the following periods (AD 200-1000), isotopic values are relatively high overall, indicating systematic input of manure. In this paper, we explore whether the isotopic data that indicates sustained and high manuring levels could reflect the wealth of Uppåkra and its surrounding areas by showing prosperity also in its agricultural production, since intensive manuring would have required more resource and labor investments. The new crop nitrogen isotopic data shed light on the agricultural practices of a long-lived Iron Age center and its surrounding areas.

Genetic and phenotypic diversity in 2000 years old maize (Zea mays L.) samples from the Tarapacá region, Atacama Desert, Chile

The evolution of maize (Zea mays L.) is highly controversial given the discrepancies related to the phenotypic and genetic changes suffered by the species, the incidence of human groups and the times in which these changes occurred. Also, morphological and genetic traits of crops are difficult to evaluate in the absence of fossils macro-botanical remains. In contrast in the Tarapacá region (18–21° S), Atacama Desert of Chile, prehispanic settlements (ca. 2500–400 yr BP) displayed extensive maize agriculture. The presence of archaeological macro-botanical remains of maize provided a unique opportunity to study the evolution of this crop, covering a temporal sequence of at least 2000 years. Thus, in this study, we ask how the morphological and genetic diversity of maize has varied since its introduction during prehispanic times in the Tarapacá region. To answer this, we measured and compared morphological traits of size and shape between archaeological cobs and kernels and 95 ears from landraces. To established genetic diversity eight microsatellite markers (SSR) were analyzed in archaeological and modern kernels. Genetic diversity was estimated by allelic frequency rates, the average number of alleles per locus, observed heterozygosity (Ho) and expected heterozygosity (He). Differences between populations and genetic structure were estimated by fixation index F_ST and STRUCTURE analysis. Our results indicate significant phenotypic differences and genetic distance between archaeological maize and landraces. This result is suggestive of an introduction of new varieties or drastic selective changes in modern times in Tarapacá. Additionally, archaeological maize shows a low genetic diversity and a progressive increase in the size of ears and kernels. These results suggest a human selection during prehispanic times and establish that prehispanic farmers played an important role in maize development. They also provide new clues for understanding the evolutionary history of maize in hyperarid conditions.

SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination

BACKGROUND

Magna Graecia is the ancient name for the modern geopolitical region of South Italy extensively populated by Greek colonizers, shown by archeological and historical evidence to be the oldest wine growing region of Italy, crucial for the spread of specialized viticulture around Mediterranean shores. Here, the genetic diversity of Magna Graecia grape germplasm was assessed and its role in grapevine propagation around the Mediterranean basin was underlined.

RESULTS

A large collection of grapevines from Magna Graecia was compared with germplasm from Georgia to the Iberian Peninsula using the 18 K SNP array. A high level of genetic diversity of the analyzed germplasm was determined; clustering, structure analysis and DAPC (Discriminant Analysis of Principal Components) highlighted the genetic relationships among genotypes from South Italy and the Eastern Mediterranean (Greece). Gene flow from east (Georgia) to west (Iberian Peninsula) was identified throughout the large number of detected admixed samples. Pedigree analysis showed a complex and well-structured network of first degree relationships, where the cultivars from Magna Graecia were mainly involved.

CONCLUSIONS

This study provided evidence that Magna Graecia germplasm was shaped by historical events that occurred in the area due to the robust link between South Italian and Greek genotypes, as well as, by the availability of different thermal resources for cultivars growing in such different winegrowing areas. The uniqueness of this ampelographic platform was mainly an outcome of complex natural or human-driven crosses involving elite cultivars.

The Strawberry Tales: Size Matters

The history of the strawberry is one of ambitious kings and cunning spies, overseas adventures, and religious symbolism. Here, we will tell these stories, illustrated by relevant paintings and drawings, to give insight into the domestication of the strawberry. Furthermore, we will briefly discuss the complex strawberry genomes and aroma.

Impact of Farmland Change on Soybean Production Potential in Recent 40 Years: A Case Study in Western Jilin, China

During the last 40 years, the quantity and spatial patterns of farmland in Western Jilin have changed dramatically, which has had a great impact on soybean production potential. This study used one of the most advanced crop production potential models, the Global Agro-Ecological Zones model, to calculate the soybean production potential in Western Jilin based on meteorological, topography, soil and land use data, and analyzed the impact of farmland change on soybean production potential during 1975⁻2013. The main conclusions were the following: first, the total soybean production potential in Western Jilin in 2013 was 8.92 million tonnes, and the average soybean production potential was 1612 kg/ha. The production potential of eastern area was higher than the other areas of Western Jilin. Second, farmland change led to a growth of 3.30 million tonnes in soybean production potential between 1975 and 2000, and a decrease of 1.03 million tonnes between 2000 and 2013. Third, taking account of two situations of farmland change, the conversion between dryland and other categories, and the change of irrigation percentage led to the total soybean production potential in Western Jilin increased by 2.31 and only 0.28 million tonnes respectively between 1975 and 2000, and increased by 0.12 and 0.29 million tonnes respectively between 2000 and 2013. In general, the increase of soybean potential production was mainly due to grassland and woodland reclamation. The results of this study would be a good guideline for protecting safe baseline of farmland, managing land resources, and ensuring continuity and stability of soybean supply and food security.

On the origins and domestication of the olive: a review and perspectives

Background

Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully.

Scope

The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide.

Conclusion

The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.

Greater post-Neolithic wealth disparities in Eurasia than in North America and Mesoamerica

How wealth is distributed among households provides insight into the fundamental characters of societies and the opportunities they afford for social mobility. However, economic inequality has been hard to study in ancient societies for which we do not have written records, which adds to the challenge of placing current wealth disparities into a long-term perspective. Although various archaeological proxies for wealth, such as burial goods or exotic or expensive-to-manufacture goods in household assemblages, have been proposed, the first is not clearly connected with households, and the second is confounded by abandonment mode and other factors. As a result, numerous questions remain concerning the growth of wealth disparities, including their connection to the development of domesticated plants and animals and to increases in sociopolitical scale. Here we show that wealth disparities generally increased with the domestication of plants and animals and with increased sociopolitical scale, using Gini coefficients computed over the single consistent proxy of house-size distributions. However, unexpected differences in the responses of societies to these factors in North America and Mesoamerica, and in Eurasia, became evident after the end of the Neolithic period. We argue that the generally higher wealth disparities identified in post-Neolithic Eurasia were initially due to the greater availability of large mammals that could be domesticated, because they allowed more profitable agricultural extensification, and also eventually led to the development of a mounted warrior elite able to expand polities (political units that cohere via identity, ability to mobilize resources, or governance) to sizes that were not possible in North America and Mesoamerica before the arrival of Europeans. We anticipate that this analysis will stimulate other work to enlarge this sample to include societies in South America, Africa, South Asia and Oceania that were under-sampled or not included in this study.

Barley (Hordeum vulgare) in the Okhotsk culture (5th-10th century AD) of northern Japan and the role of cultivated plants in hunter-gatherer economies

This paper discusses archaeobotanical remains of naked barley recovered from the Okhotsk cultural layers of the Hamanaka 2 archaeological site on Rebun Island, northern Japan. Calibrated ages (68% confidence interval) of the directly dated barley remains suggest that the crop was used at the site ca. 440–890 cal yr AD. Together with the finds from the Oumu site (north-eastern Hokkaido Island), the recovered seed assemblage marks the oldest well-documented evidence for the use of barley in the Hokkaido Region. The archaeobotanical data together with the results of a detailed pollen analysis of contemporaneous sediment layers from the bottom of nearby Lake Kushu point to low-level food production, including cultivation of barley and possible management of wild plants that complemented a wide range of foods derived from hunting, fishing, and gathering. This qualifies the people of the Okhotsk culture as one element of the long-term and spatially broader Holocene hunter–gatherer cultural complex (including also Jomon, Epi-Jomon, Satsumon, and Ainu cultures) of the Japanese archipelago, which may be placed somewhere between the traditionally accepted boundaries between foraging and agriculture. To our knowledge, the archaeobotanical assemblages from the Hokkaido Okhotsk culture sites highlight the north-eastern limit of prehistoric barley dispersal. Seed morphological characteristics identify two different barley phenotypes in the Hokkaido Region. One compact type (naked barley) associated with the Okhotsk culture and a less compact type (hulled barley) associated with Early–Middle Satsumon culture sites. This supports earlier suggestions that the “Satsumon type” barley was likely propagated by the expansion of the Yayoi culture via south-western Japan, while the “Okhotsk type” spread from the continental Russian Far East region, across the Sea of Japan. After the two phenotypes were independently introduced to Hokkaido, the boundary between both barley domains possibly existed ca. 600–1000 cal yr AD across the island region. Despite a large body of studies and numerous theoretical and conceptual debates, the question of how to differentiate between hunter–gatherer and farming economies persists reflecting the wide range of dynamic subsistence strategies used by humans through the Holocene. Our current study contributes to the ongoing discussion of this important issue.

Composite Sickles and Cereal Harvesting Methods at 23,000-Years-Old Ohalo II, Israel

Use-wear analysis of five glossed flint blades found at Ohalo II, a 23,000-years-old fisher-hunter-gatherers’ camp on the shore of the Sea of Galilee, Northern Israel, provides the earliest evidence for the use of composite cereal harvesting tools. The wear traces indicate that tools were used for harvesting near-ripe semi-green wild cereals, shortly before grains are ripe and disperse naturally. The studied tools were not used intensively, and they reflect two harvesting modes: flint knives held by hand and inserts hafted in a handle. The finds shed new light on cereal harvesting techniques some 8,000 years before the Natufian and 12,000 years before the establishment of sedentary farming communities in the Near East. Furthermore, the new finds accord well with evidence for the earliest ever cereal cultivation at the site and the use of stone-made grinding implements.

Global nitrogen budgets in cereals: A 50-year assessment for maize, rice, and wheat production systems

Industrially produced N-fertilizer is essential to the production of cereals that supports current and projected human populations. We constructed a top-down global N budget for maize, rice, and wheat for a 50-year period (1961 to 2010). Cereals harvested a total of 1551 Tg of N, of which 48% was supplied through fertilizer-N and 4% came from net soil depletion. An estimated 48% (737 Tg) of crop N, equal to 29, 38, and 25 kg ha(-1) yr(-1) for maize, rice, and wheat, respectively, is contributed by sources other than fertilizer- or soil-N. Non-symbiotic N2 fixation appears to be the major source of this N, which is 370 Tg or 24% of total N in the crop, corresponding to 13, 22, and 13 kg ha(-1) yr(-1) for maize, rice, and wheat, respectively. Manure (217 Tg or 14%) and atmospheric deposition (96 Tg or 6%) are the other sources of N. Crop residues and seed contribute marginally. Our scaling-down approach to estimate the contribution of non-symbiotic N2 fixation is robust because it focuses on global quantities of N in sources and sinks that are easier to estimate, in contrast to estimating N losses per se, because losses are highly soil-, climate-, and crop-specific.

Farmers' Preference for Rice Traits: Insights from Farm Surveys in Central Luzon, Philippines, 1966-2012

Many modern rice varieties (MVs) have been released but only a few have been widely adopted by farmers. To understand farmers' preferences, we characterized MVs released in the Philippines from 1966 to 2013 and identified important characteristics of the varieties that were widely adopted in Central Luzon using farm surveys conducted in 1966-2012. We found that farmers adopt MVs that are high yielding, mature faster, and have long and slender grains, high milling recovery, and intermediate amylose content. The amylose content of adopted varieties has been declining, suggesting value in developing softer rice. To have a high potential for adoption, new MVs should have characteristics within the ranges of values observed for the adopted MVs. In addition, new MVs should have higher head rice recovery, less chalky grains, and better resistance to pests and diseases. Most MVs released in 2005-2013 compared poorly in these three traits. To reduce the risk of severe outbreaks, broad spectrum resistance should be incorporated into new MVs. This analysis of five decades of farm surveys provides insights into the varietal characteristics preferred by farmers which could contribute to the establishment of a product profile for developing improved MVs that are more targeted and, hence, would have high potential for adoption by farmers in Central Luzon and similar areas. We recommend a similar analysis be done in other major rice growing regions to aid the development of MVs that are more responsive to farmers' needs and preferences.

Experimental Barley Flour Production in 12,500-Year-Old Rock-Cut Mortars in Southwestern Asia

Experimental archaeology at a Natufian site in the Southern Levant documents for the first time the use of 12,500-year-old rock-cut mortars for producing wild barley flour, some 2,000 to 3,000 years before cereal cultivation. Our reconstruction involved processing wild barley on the prehistoric threshing floor, followed by use of the conical mortars (a common feature in Natufian sites), thereby demonstrating the efficient peeling and milling of hulled grains. This discovery complements nearly 80 years of investigations suggesting that the Natufians regularly harvested almost-ripe wild cereals using sickles hafted with flint blades. Sickles had been replicated in the past and tested in the field for harvesting cereals, thusly obtaining the characteristic sheen along the edge of the hafted flint blades as found in Natufian remnants. Here we report that Natufian wide and narrow conical mortars enabled the processing of wild barley for making the groats and fine flour that provided considerable quantities of nourishment. Dishes in the Early Natufian (15,000–13,500 CalBP) were groat meals and porridge and subsequently, in the Late Natufian (13,500–11,700 CalBP), we suggest that unleavened bread made from fine flour was added. These food preparing techniques widened the dietary breadth of the sedentary Natufian hunter-gatherers, paving the way to the emergence of farming communities, the hallmark of the Neolithic Revolution.

The Origin of Cultivation and Proto-Weeds, Long Before Neolithic Farming

Weeds are currently present in a wide range of ecosystems worldwide. Although the beginning of their evolution is largely unknown, researchers assumed that they developed in tandem with cultivation since the appearance of agricultural habitats some 12,000 years ago. These rapidly-evolving plants invaded the human disturbed areas and thrived in the new habitat. Here we present unprecedented new findings of the presence of “proto-weeds” and small-scale trial cultivation in Ohalo II, a 23,000-year-old hunter-gatherers' sedentary camp on the shore of the Sea of Galilee, Israel. We examined the plant remains retrieved from the site (ca. 150,000 specimens), placing particular emphasis on the search for evidence of plant cultivation by Ohalo II people and the presence of weed species. The archaeobotanically-rich plant assemblage demonstrates extensive human gathering of over 140 plant species and food preparation by grinding wild wheat and barley. Among these, we identified 13 well-known current weeds mixed with numerous seeds of wild emmer, barley, and oat. This collection provides the earliest evidence of a human-disturbed environment—at least 11 millennia before the onset of agriculture—that provided the conditions for the development of "proto-weeds", a prerequisite for weed evolution. Finally, we suggest that their presence indicates the earliest, small-scale attempt to cultivate wild cereals seen in the archaeological record.