Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore.

Underrepresentation of Asian genomes has hindered population and medical genetics research on Asians, leading to population disparities in precision medicine. By whole-genome sequencing of 4,810 Singapore Chinese, Malays, and Indians, we found 98.3 million SNPs and small insertions or deletions, over half of which are novel. Population structure analysis demonstrated great representation of Asian genetic diversity by three ethnicities in Singapore and revealed a Malay-related novel ancestry component. Furthermore, demographic inference suggested that Malays split from Chinese ∼24,800 years ago and experienced significant admixture with East Asians ∼1,700 years ago, coinciding with the Austronesian expansion. Additionally, we identified 20 candidate loci for natural selection, 14 of which harbored robust associations with complex traits and diseases. Finally, we show that our data can substantially improve genotype imputation in diverse Asian and Oceanian populations. These results highlight the value of our data as a resource to empower human genetics discovery across broad geographic regions.

Concurrent Asian monsoon strengthening and early modern human dispersal to East Asia during the last interglacial.

The relationship between initial Homo sapiens dispersal from Africa to East Asia and the orbitally paced evolution of the Asian summer monsoon (ASM)-currently the largest monsoon system-remains underexplored due to lack of coordinated synthesis of both Asian paleoanthropological and paleoclimatic data. Here, we investigate orbital-scale ASM dynamics during the last 280 thousand years (kyr) and their likely influences on early H. sapiens dispersal to East Asia, through a unique integration of i) new centennial-resolution ASM records from the Chinese Loess Plateau, ii) model-based East Asian hydroclimatic reconstructions, iii) paleoanthropological data compilations, and iv) global H. sapiens habitat suitability simulations. Our combined proxy- and model-based reconstructions suggest that ASM precipitation responded to a combination of Northern Hemisphere ice volume, greenhouse gas, and regional summer insolation forcing, with cooccurring primary orbital cycles of ~100-kyr, 41-kyr, and ~20-kyr. Between ~125 and 70 kyr ago, summer monsoon rains and temperatures increased in vast areas across Asia. This episode coincides with the earliest H. sapiens fossil occurrence at multiple localities in East Asia. Following the transcontinental increase in simulated habitat suitability, we suggest that ASM strengthening together with Southeast African climate deterioration may have promoted the initial H. sapiens dispersal from their African homeland to remote East Asia during the last interglacial.

Understanding the Asian water tower requires a redesigned precipitation observation strategy.

The Asian water tower (AWT) serves as the source of 10 major Asian river systems and supports the lives of ~2 billion people. Obtaining reliable precipitation data over the AWT is a prerequisite for understanding the water cycle within this pivotal region. Here, we quantitatively reveal that the "observed" precipitation over the AWT is considerably underestimated in view of observational evidence from three water cycle components, namely, evapotranspiration, runoff, and accumulated snow. We found that three paradoxes appear if the so-called observed precipitation is corrected, namely, actual evapotranspiration exceeding precipitation, unrealistically high runoff coefficients, and accumulated snow water equivalent exceeding contemporaneous precipitation. We then explain the cause of precipitation underestimation from instrumental error caused by wind-induced gauge undercatch and the representativeness error caused by sparse-uneven gauge density and the complexity of local surface conditions. These findings require us to rethink previous results concerning the water cycle, prompting the study to discuss potential solutions.

Nationwide law enforcement impact on the pet bird trade in China.

Conservation enforcement is a direct strategy to combat illegal wildlife trade in open markets. Yet, its large-scale effectiveness has not been widely assessed due to the lack of extensive market data. Between August 2016 and June 2017, a national coordinated enforcement campaign led by the leading Chinese authority to combat illegal migratory bird trade coincided with the largest-ever pet bird market survey across China by voluntary birdwatchers before and after the enforcement, which served as a unique natural experiment. Across 73 markets from 22 Chinese provinces, the dataset contains 140,723 birds of 346 species from 48 families and recorded a drastic decline in bird abundance traded after enforcement. Notably, species protected under China's Wildlife Protection Law declined significantly, while commercially bred species increased, although responses to enforcement were spatially heterogeneous. Our model showed that the national protection level was the best predictor for the trend of traded species, even after accounting for confounding factors such as regional baseline enforcement pressure and wild native bird populations. However, the widely traded native songbirds were not offered adequate national protection. Future policies should consider the pet bird trade patterns, target key areas of trade, and develop a more systematic market survey design to monitor trade.

East Asian summer monsoon delivers large abundances of very-short-lived organic chlorine substances to the lower stratosphere.

Deep convection in the Asian summer monsoon is a significant transport process for lifting pollutants from the planetary boundary layer to the tropopause level. This process enables efficient injection into the stratosphere of reactive species such as chlorinated very-short-lived substances (Cl-VSLSs) that deplete ozone. Past studies of convective transport associated with the Asian summer monsoon have focused mostly on the south Asian summer monsoon. Airborne observations reported in this work identify the East Asian summer monsoon convection as an effective transport pathway that carried record-breaking levels of ozone-depleting Cl-VSLSs (mean organic chlorine from these VSLSs ~500 ppt) to the base of the stratosphere. These unique observations show total organic chlorine from VSLSs in the lower stratosphere over the Asian monsoon tropopause to be more than twice that previously reported over the tropical tropopause. Considering the recently observed increase in Cl-VSLS emissions and the ongoing strengthening of the East Asian summer monsoon under global warming, our results highlight that a reevaluation of the contribution of Cl-VSLS injection via the Asian monsoon to the total stratospheric chlorine budget is warranted.

Improved subseasonal prediction of South Asian monsoon rainfall using data-driven forecasts of oscillatory modes.

Predicting the temporal and spatial patterns of South Asian monsoon rainfall within a season is of critical importance due to its impact on agriculture, water availability, and flooding. The monsoon intraseasonal oscillation (MISO) is a robust northward-propagating mode that determines the active and break phases of the monsoon and much of the regional distribution of rainfall. However, dynamical atmospheric forecast models predict this mode poorly. Data-driven methods for MISO prediction have shown more skill, but only predict the portion of the rainfall corresponding to MISO rather than the full rainfall signal. Here, we combine state-of-the-art ensemble precipitation forecasts from a high-resolution atmospheric model with data-driven forecasts of MISO. The ensemble members of the detailed atmospheric model are projected onto a lower-dimensional subspace corresponding to the MISO dynamics and are then weighted according to their distance from the data-driven MISO forecast in this subspace. We thereby achieve improvements in rainfall forecasts over India, as well as the broader monsoon region, at 10- to 30-d lead times, an interval that is generally considered to be a predictability gap. The temporal correlation of rainfall forecasts is improved by up to 0.28 in this time range. Our results demonstrate the potential of leveraging the predictability of intraseasonal oscillations to improve extended-range forecasts; more generally, they point toward a future of combining dynamical and data-driven forecasts for Earth system prediction.

Black carbon aerosols over Indian Ocean have unique source fingerprint and optical characteristics during monsoon season.

Effects of aerosols such as black carbon (BC) on climate and buildup of the monsoon over the Indian Ocean are insufficiently quantified. Uncertain contributions from various natural and anthropogenic sources impede our understanding. Here, we use observations over 5 y of BC and its isotopes at a remote island observatory in northern Indian Ocean to constrain loadings and sources during little-studied monsoon season. Carbon-14 data show a highly variable yet largely fossil (65 ± 15%) source mixture. Combining carbon-14 with carbon-13 reveals the impact of African savanna burning, which occasionally approach 50% (48 ± 9%) of the total BC loadings. The BC mass-absorption cross-section for this regime is 7.6 ± 2.6 m2/g, with higher values during savanna fire input. Taken together, the combustion sources, longevity, and optical properties of BC aerosols over summertime Indian Ocean are different than the more-studied winter aerosol, with implications for chemical transport and climate model simulations of the Indian monsoon.

Mid-Pleistocene links between Asian dust, Tibetan glaciers, and Pacific iron fertilization.

Increasing Asian dust fluxes, associated with late Cenozoic cooling and intensified glaciations, are conventionally thought to drive iron fertilization of phytoplankton productivity in the North Pacific, contributing to ocean carbon storage and drawdown of atmospheric CO2. During the early Pleistocene glaciations, however, productivity remained low despite higher Asian dust fluxes, only displaying glacial stage increases after the mid-Pleistocene climate transition (~800 ka B.P.). We solve this paradox by analyzing an Asian dust sequence, spanning the last 3.6 My, from the Tarim Basin, identifying a major switch in the iron composition of the dust at ~800 ka, associated with expansion of Tibetan glaciers and enhanced production of freshly ground rock minerals. This compositional shift in the Asian dust was recorded synchronously in the downwind, deep sea sediments of the central North Pacific. The switch from desert dust, containing stable, highly oxidized iron, to glacial dust, richer in reactive reduced iron, coincided with increased populations of silica-producing phytoplankton in the equatorial North Pacific and increased primary productivity in more northerly locations, such as the South China Sea. We calculate that potentially bioavailable Fe2+ flux to the North Pacific was more than doubled after the switch to glacially- sourced dust. These findings indicate a positive feedback between Tibetan glaciations, glaciogenic production of dust with enhanced iron bioavailability, and changes in North Pacific iron fertilization. Notably, this strengthened link between climate and eolian dust coincided with the mid-Pleistocene transition to increased storage of C in the glacial North Pacific and more intense northern hemisphere glaciations.

Eccentricity-paced geomagnetic field and monsoon rainfall variations over the last 870 kyr.

Whether there are links between geomagnetic field and Earth's orbital parameters remains unclear. Synchronous reconstructions of parallel long-term quantitative geomagnetic field and climate change records are rare. Here, we present 10Be-derived changes of both geomagnetic field and Asian monsoon (AM) rainfall over the last 870 kyr from the Xifeng loess-paleosol sequence on the central Chinese Loess Plateau. The 10BeGM flux (a proxy for geomagnetic field-induced 10Be production rate) reveals 13 consecutive geomagnetic excursions in the Brunhes chron, which are synchronized with the global records, providing key time markers for Chinese loess-paleosol sequences. The 10Be-derived rainfall exhibits distinct ~100 kyr glacial-interglacial cycles, and superimposed precessional (~23 kyr) cycles that match with those in Chinese speleothem δ18O record. We find that changes in the geomagnetic field and AM rainfall share a common ~100 kyr cyclicity, implying a likely eccentricity modulation of both the geomagnetic field and climate.

El Niño-Southern Oscillation forcing on carbon and water cycling in a Bornean tropical rainforest.

Carbon dioxide and water vapor exchanges between tropical forest canopies and the atmosphere through photosynthesis, respiration, and evapotranspiration (ET) influence carbon and water cycling at the regional and global scales. Their inter- and intra-annual variations are sensitive to seasonal rhythms and longer-timescale tropical climatic events. In the present study, we assessed the El Niño-Southern Oscillation (ENSO) influence on ET and on the net ecosystem exchange (NEE), using eddy-covariance flux observations in a Bornean rainforest over a 10-y period (2010-2019) that included several El Niño and La Niña events. From flux model inversions, we inferred ecophysiological properties, notably the canopy stomatal conductance and "big-leaf" maximum carboxylation rate (Vcmax25_BL). Mean ET values were similar between ENSO phases (El Niño, La Niña, and neutral conditions). Conversely, the mean net ecosystem productivity was highest during La Niña events and lowest during El Niño events. Combining Shapley additive explanation calculations for nine controlling factors with a machine-learning algorithm, we determined that the primary factors for ET and NEE in the La Niña and neutral phases were incoming shortwave solar radiation and Vcmax25_BL, respectively, but that canopy stomatal conductance was the most significant factor for both ET and NEE in the El Niño phase. A combined stomatal-photosynthesis model approach further indicated that Vcmax25_BL differences between ENSO phases were the most significant controlling factor for canopy photosynthesis, emphasizing the strong need to account for ENSO-induced ecophysiological factor variations in model projections of the long-term carbon balance in Southeast Asian tropical rainforests.

Tectonic and orbital forcing of the South Asian monsoon in central Tibet during the late Oligocene.

The modern pattern of the Asian monsoon is thought to have formed around the Oligocene/Miocene transition and is generally attributed to Himalaya-Tibetan Plateau (H-TP) uplift. However, the timing of the ancient Asian monsoon over the TP and its response to astronomical forcing and TP uplift remains poorly known because of the paucity of well-dated high-resolution geological records from the TP interior. Here, we present a precession-scale cyclostratigraphic sedimentary section of 27.32 to 23.24 million years ago (Ma) during the late Oligocene epoch from the Nima Basin to show that the South Asian monsoon (SAM) had already advanced to the central TP (32°N) at least by 27.3 Ma, which is indicated by cyclic arid-humid fluctuations based on environmental magnetism proxies. A shift of lithology and astronomically orbital periods and amplified amplitude of proxy measurements as well as a hydroclimate transition around 25.8 Ma suggest that the SAM intensified at ~25.8 Ma and that the TP reached a paleoelevation threshold for enhancing the coupling between the uplifted plateau and the SAM. Orbital short eccentricity-paced precipitation variability is argued to be mainly driven by orbital eccentricity-modulated low-latitude summer insolation rather than glacial-interglacial Antarctic ice sheet fluctuations. The monsoon data from the TP interior provide key evidence to link the greatly enhanced tropical SAM at 25.8 Ma with TP uplift rather than global climate change and suggest that SAM's northward expansion to the boreal subtropics was dominated by a combination of tectonic and astronomical forcing at multiple timescales in the late Oligocene epoch.

Adaptive evolution of two distinct adaptive haplotypes of Neanderthal origin at the immunoglobulin heavy-chain locus in East Asian and European populations.

Immunoglobulins have a crucial role in humoral immunity. Two recent studies have reported a high-frequency Neanderthal-introgressed haplotype throughout Eurasia and a high-frequency Neanderthal-introgressed haplotype specific to southern East Asia at the immunoglobulin heavy-chain (IGH) gene locus on chromosome 14q32.33. Surprisingly, we found the previously reported high-frequency Neanderthal-introgressed haplotype does not exist throughout Eurasia. Instead, our study identified two distinct high-frequency haplotypes of putative Neanderthal origin in East Asia and Europe, although they shared introgressed alleles. Notably, the alleles of putative Neanderthal origin reduced the expression of IGHG1 and increased the expression of IGHG2 and IGHG3 in various tissues. These putatively introgressed alleles also affected the production of IgG1 upon antigen stimulation and increased the risk of systemic lupus erythematosus. Additionally, the greatest genetic differentiation across the whole genome between southern and northern East Asians was observed for the East Asian haplotype of putative Neanderthal origin. The frequency decreased from southern to northern East Asia and correlated positively with the genome-wide proportion of southern East Asian ancestry, indicating that this putative positive selection likely occurred in the common ancestor of southern East Asian populations before the admixture with northern East Asian populations.

Exploring Adaptive Phenotypes for the Human Calcium-Sensing Receptor Polymorphism R990G.

Rainforest hunter-gatherers from Southeast Asia are characterized by specific morphological features including a particularly dark skin color (D), short stature (S), woolly hair (W), and the presence of steatopygia (S)-fat accumulation localized in the hips (DSWS phenotype). Based on previous evidence in the Andamanese population, we first characterized signatures of adaptive natural selection around the calcium-sensing receptor gene in Southeast Asian rainforest groups presenting the DSWS phenotype and identified the R990G substitution (rs1042636) as a putative adaptive variant for experimental follow-up. Although the calcium-sensing receptor has a critical role in calcium homeostasis by directly regulating the parathyroid hormone secretion, it is expressed in different tissues and has been described to be involved in many biological functions. Previous works have also characterized the R990G substitution as an activating polymorphism of the calcium-sensing receptor associated with hypocalcemia. Therefore, we generated a knock-in mouse for this substitution and investigated organismal phenotypes that could have become adaptive in rainforest hunter-gatherers from Southeast Asia. Interestingly, we found that mouse homozygous for the derived allele show not only lower serum calcium concentration but also greater body weight and fat accumulation, probably because of enhanced preadipocyte differentiation and lipolysis impairment resulting from the calcium-sensing receptor activation mediated by R990G. We speculate that such differential features in humans could have facilitated the survival of hunter-gatherer groups during periods of nutritional stress in the challenging conditions of the Southeast Asian tropical rainforests.

Genomic and Phenotypic Adaptations of Rattus tanezumi to Cold Limit Its Further Northward Expansion and Range Overlap with R. norvegicus.

Global climate change has led to shifts in the distribution ranges of many terrestrial species, promoting their migration from lower altitudes or latitudes to higher ones. Meanwhile, successful invaders have developed genetic adaptations enabling the colonization of new environments. Over the past 40 years, Rattus tanezumi (RT) has expanded into northern China (Northwest and North China) from its southern origins. We studied the cold adaptation of RT and its potential for northward expansion by comparing it with sympatric Rattus norvegicus (RN), which is well adapted to cold regions. Through population genomic analysis, we revealed that the invading RT rats have split into three distinct populations: the North, Northwest, and Tibetan populations. The first two populations exhibited high genetic diversity, while the latter population showed remarkably low genetic diversity. These rats have developed various genetic adaptations to cold, arid, hypoxic, and high-UV conditions. Cold acclimation tests revealed divergent thermoregulation between RT and RN. Specifically, RT exhibited higher brown adipose tissue activity and metabolic rates than did RN. Transcriptome analysis highlighted changes in genes regulating triglyceride catabolic processes in RT, including Apoa1 and Apoa4, which were upregulated, under selection and associated with local adaptation. In contrast, RN showed changes in carbohydrate metabolism genes. Despite the cold adaptation of RT, we observed genotypic and phenotypic constraints that may limit its ability to cope with severe low temperatures farther north. Consequently, it is less likely that RT rats will invade and overlap with RN rats in farther northern regions.

Genotype imputation accuracy and the quality metrics of the minor ancestry in multi-ancestry reference panels.

Large-scale imputation reference panels are currently available and have contributed to efficient genome-wide association studies through genotype imputation. However, whether large-size multi-ancestry or small-size population-specific reference panels are the optimal choices for under-represented populations continues to be debated. We imputed genotypes of East Asian (180k Japanese) subjects using the Trans-Omics for Precision Medicine reference panel and found that the standard imputation quality metric (Rsq) overestimated dosage r2 (squared correlation between imputed dosage and true genotype) particularly in marginal-quality bins. Variance component analysis of Rsq revealed that the increased imputed-genotype certainty (dosages closer to 0, 1 or 2) caused upward bias, indicating some systemic bias in the imputation. Through systematic simulations using different template switching rates (θ value) in the hidden Markov model, we revealed that the lower θ value increased the imputed-genotype certainty and Rsq; however, dosage r2 was insensitive to the θ value, thereby causing a deviation. In simulated reference panels with different sizes and ancestral diversities, the θ value estimates from Minimac decreased with the size of a single ancestry and increased with the ancestral diversity. Thus, Rsq could be deviated from dosage r2 for a subpopulation in the multi-ancestry panel, and the deviation represents different imputed-dosage distributions. Finally, despite the impact of the θ value, distant ancestries in the reference panel contributed only a few additional variants passing a predefined Rsq threshold. We conclude that the θ value substantially impacts the imputed dosage and the imputation quality metric value.

Biotic colonization of subtropical East Asian caves through time.

Caves are home to unique and fragile biotas with high levels of endemism. However, little is known about how the biotic colonization of caves has developed over time, especially in caves from middle and low latitudes. Subtropical East Asia holds the world's largest karst landform with numerous ancient caves, which harbor a high diversity of cave-dwelling organisms and are regarded as a biodiversity hotspot. Here, we assess the temporal dynamics of biotic colonization of subtropical East Asian caves through a multi-taxon analysis with representatives of green plants, animals, and fungi. We then investigate the consequences of paleonviromental changes on the colonization dynamics of these caves in combination with reconstructions of vegetation, temperature, and precipitation. We discover that 88% of cave colonization events occurred after the Oligocene-Miocene boundary, and organisms from the surrounding forest were a major source for subtropical East Asian cave biodiversity. Biotic colonization of subtropical East Asian caves during the Neogene was subject to periods of acceleration and decrease, in conjunction with large-scale, seasonal climatic changes and evolution of local forests. This study highlights the long-term evolutionary interaction between surface and cave biotas; our climate-vegetation-relict model proposed for the subtropical East Asian cave biota may help explain the evolutionary origins of other mid-latitude subterranean biotas.

Mammalian diversification bursts and biotic turnovers are synchronous with Cenozoic geoclimatic events in Asia.

Asia's rich species diversity has been linked to its Cenozoic geodiversity, including active mountain building and dramatic climatic changes. However, prior studies on the diversification and assembly of Asian faunas have been derived mainly from analyses at taxonomic or geographic scales too limited to offer a comprehensive view of this complex region's biotic evolution. Here, using the class Mammalia, we built historical biogeographic models drawn on phylogenies of 1,543 species occurring across Asia to investigate how and when the mammal diversity in Asian regions and mountain hotspots was assembled. We explore the roles of in situ speciation, colonization, and vicariance and geoclimatic events to explain the buildup of Asia's regional mammal diversity through time. We found that southern Asia has served as the main cradle of Asia's mammal diversity. Present-day species richness in other regions is mainly derived from colonization, but by the Miocene, in situ speciation increased in importance. The high biodiversity present in the mountain hotspots (Himalayas and Hengduan) that flank the Qinghai-Tibetan plateau is a product of high colonization instead of in situ speciation, making them important centers of lineage accumulation. Overall, Neogene was marked by great diversification and migrations across Asia and surrounding continents but Paleogene environments already hosted rich mammal assemblages. Our study revealed that synchronous diversification bursts and biotic turnovers are temporally associated with tectonic events (mountain building, continental collisions) and drastic reorganization of climate (aridification of Asian interior, intensification of Asian monsoons, sea retreat) that took place throughout the Cenozoic in Asia.

The moral filter of patriotic prejudice: How Americans view Chinese in the COVID-19 era.

About one in six Asian Americans have fallen victim to anti-Asian racism during the COVID-19 pandemic [J. Lee, K. Ramakrishnan, aapidata.com/blog/discrimination-survey-2022/]. By examining anti-Asian racism in the United States primarily as a domestic issue, most prior studies have overlooked the connections between shifting US-China relations and Americans' prejudices against the Chinese in China and, by extension, East Asian Americans. This study investigates the patterns and perceptual bases of nationality-based prejudices against Chinese amid the COVID-19 pandemic in the United States. Our nationally representative online survey experiment reveals that Americans assess a hypothetical Chinese person in China as inferior in multiple social and psychological characteristics to an otherwise identical Japanese person in Japan or East Asian American. Furthermore, subjects who perceive China as more threatening to America's national interests assess Chinese more negatively, especially in terms of trustworthiness and morality, suggesting that perceived China threats propel Americans' negative stereotypes about Chinese. A contextual analysis further indicates that counties with a higher share of Trump voters in 2016 tend to perceive all East Asian-origin groups similarly as a racial outgroup. By contrast, residents in predominantly Democrat-voting counties tend to perceive Chinese in China more negatively relative to Asian Americans, despite broadly viewing East Asians more favorably. Overall, this study underscores the often-overlooked relationships between the prevailing anti-Asian sentiments in the United States and the US-China geopolitical tensions and America's domestic political polarization.

Longitudinal Transcriptomic, Proteomic, and Metabolomic Response of Citrus sinensis to Diaphorina citri Inoculation of Candidatus Liberibacter asiaticus.

Huanglongbing (HLB) is a fatal citrus disease that is currently threatening citrus varieties worldwide. One putative causative agent, Candidatus Liberibacter asiaticus (CLas), is vectored by Diaphorina citri, known as the Asian citrus psyllid (ACP). Understanding the details of CLas infection in HLB disease has been hindered by its Candidatus nature and the inability to confidently detect it in diseased trees during the asymptomatic stage. To identify early changes in citrus metabolism in response to inoculation of CLas using its natural psyllid vector, leaves from Madam Vinous sweet orange (Citrus sinensis (L.) Osbeck) trees were exposed to CLas-positive ACP or CLas-negative ACP and longitudinally analyzed using transcriptomics (RNA sequencing), proteomics (liquid chromatography-tandem mass spectrometry; data available in Dryad: 10.25338/B83H1Z), and metabolomics (proton nuclear magnetic resonance). At 4 weeks postexposure (wpe) to psyllids, the initial HLB plant response was primarily to the ACP and, to a lesser extent, the presence or absence of CLas. Additionally, analysis of 4, 8, 12, and 16 wpe identified 17 genes and one protein as consistently differentially expressed between leaves exposed to CLas-positive ACP versus CLas-negative ACP. This study informs identification of early detection molecular targets and contributes to a broader understanding of vector-transmitted plant pathogen interactions.

Spatially resolved gene regulatory networks in Asian rice (Oryza sativa cv. Nipponbare) leaves.

Transcriptome profiles in plants are heterogenous at every level of morphological organization. Even within organs, cells of the same type can have different patterns of gene expression depending on where they are positioned within tissues. This heterogeneity is associated with non-uniform distribution of biological processes within organs. The regulatory mechanisms that establish and sustain the spatial heterogeneity are unknown. Here, we identify regulatory modules that support functional specialization of different parts of Oryza sativa cv. Nipponbare leaves by leveraging transcriptome data, transcription factor binding motifs and global gene regulatory network prediction algorithms. We generated a global gene regulatory network in which we identified six regulatory modules that were active in different parts of the leaf. The regulatory modules were enriched for genes involved in spatially relevant biological processes, such as cell wall deposition, environmental sensing and photosynthesis. Strikingly, more than 86.9% of genes in the network were regulated by members of only five transcription factor families. We also generated targeted regulatory networks for the large MYB and bZIP/bHLH families to identify interactions that were masked in the global prediction. This analysis will provide a baseline for future single cell and array-based spatial transcriptome studies and for studying responses to environmental stress and demonstrates the extent to which seven coarse spatial transcriptome analysis can provide insight into the regulatory mechanisms supporting functional specialization within leaves.