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.

Early Holocene crop cultivation and landscape modification in Amazonia.

The onset of plant cultivation is one of the most important cultural transitions in human history1-4. Southwestern Amazonia has previously been proposed as an early centre of plant domestication, on the basis of molecular markers that show genetic similarities between domesticated plants and wild relatives4-6. However, the nature of the early human occupation of southwestern Amazonia, and the history of plant cultivation in this region, are poorly understood. Here we document the cultivation of squash (Cucurbita sp.) at about 10,250 calibrated years before present (cal. yr BP), manioc (Manihot sp.) at about 10,350 cal. yr BP and maize (Zea mays) at about 6,850 cal. yr BP, in the Llanos de Moxos (Bolivia). We show that, starting at around 10,850 cal. yr BP, inhabitants of this region began to create a landscape that ultimately comprised approximately 4,700 artificial forest islands within a treeless, seasonally flooded savannah. Our results confirm that the Llanos de Moxos is a hotspot for early plant cultivation and demonstrate that-ever since their arrival in Amazonia-humans have markedly altered the landscape, with lasting repercussions for habitat heterogeneity and species conservation.

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.

Major Outbreaks in the Nineteenth Century Shaped Grape Phylloxera Contemporary Genetic Structure in Europe.

Grape phylloxera is native to North America, where Vitis spp. acquired different mechanisms of resistance to leaf and root attack. Its appearance in European vineyards at the beginning of the 1860s, where the phylloxera-susceptible grapevine species V. vinifera L. is majorly cultivated, caused the devastation of a great number of vineyards, generating a deep crisis in the European wine production and trade industries. However, the origin and genetic structure of this pest across European vineyards still remain controversial and uncertain. Herein, we analysed the genetic structure of 1173 grape phylloxera individuals collected from 100 locations across eight European countries. Structure and phylogenetic analyses show that contemporary grape phylloxera populations in Europe are the result of at least two independent introductions from the native range that mirrors the historical records that also suggest two major outbreaks in Europe. The comparative analysis with samples from the native range trace back one of these two genetic groups to plants imported from the North East coast of North America, where the American species V. riparia and V. labrusca dominate. This study clarifies the level of genetic diversity of grape phylloxera in Europe and provides relevant information to resolve previous controversy about its origin.

Population structure in landrace barley (Hordeum vulgare L.) during the late 19th century crop failures in Fennoscandia.

Agricultural disasters and the subsequent need for supply of relief seed can be expected to influence the genetic composition of crop plant populations. The consequences of disasters and seed relief have, however, rarely been studied since specimens sampled before the events are seldomly available. A series of crop failures struck northern Fennoscandia (Norway, Sweden and Finland) during the second half of the 19th century. In order to assess population genetic dynamics of landrace barley (Hordeum vulgare), and consequences of crop failure and possible seed relief during this time period, we genotyped seeds from 16 historical accessions originating from two time periods spanning the period of repeated crop failure. Reliable identification of genetic structuring is highly dependent on sampling regimes and detecting fine-scale geographic or temporal differentiation requires large sample sizes. The robustness of the results under different sampling regimes was evaluated by analyzing subsets of the data and an artificially pooled dataset. The results led to the conclusion that six individuals per accession were insufficient for reliable detection of the observed genetic structure. We found that population structure among the data was best explained by collection year of accessions, rather than geographic origin. The correlation with collection year indicated a change in genetic composition of landrace barley in the area after repeated crop failures, likely a consequence of introgression of relief seed in local populations. Identical genotypes were found to be shared among some accessions, suggesting founder effects and local seed exchange along known routes for trade and cultural exchange.

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 FST 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.

Genomics of the origin and evolution of Citrus.

The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus.

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.

Hindcasting global population densities reveals forces enabling the origin of agriculture.

The development and spread of agriculture changed fundamental characteristics of human societies1-3. However, the degree to which environmental and social conditions enabled the origins of agriculture remains contested4-6. We test three hypothesized links between the environment, population density and the origins of plant and animal domestication, a prerequisite for agriculture: (1) domestication arose as environmental conditions improved and population densities increased7 (surplus hypothesis); (2) populations needed domestication to overcome deteriorating environmental conditions (necessity hypothesis)8,9; (3) factors promoting domestication were distinct in each location10 (regional uniqueness hypothesis). We overcome previous data limitations with a statistical model, in which environmental, geographic and cultural variables capture 77% of the variation in population density among 220 foraging societies worldwide. We use this model to hindcast potential population densities across the globe from 21,000 to 4,000 years before present. Despite the timing of domestication varying by thousands of years, we show that improving environmental conditions favoured higher local population densities during periods when domestication arose in every known agricultural origin centre. Our results uncover a common, global factor that facilitated one of humanity's most significant innovations and demonstrate that modelling ancestral demographic changes can illuminate major events deep in human history.