The Impact of Climate on the Spread of Rice to North-Eastern China: A New Look at the Data from Shandong Province

Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis

Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress-tolerant varieties and genes that could limit future climate-changed-induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change-resilient phenotypes.

Positive selection and heat-response transcriptomes reveal adaptive features of the Brassicaceae desert model, Anastatica hierochuntica

Plant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat-tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts. We generated an A. hierochuntica reference transcriptome and identified extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat, and detecting positively selected genes in A. hierochuntica. The two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat 'stress-ready' state. Furthermore, the A. hierochuntica global transcriptome as well as heat-responsive orthologs, display a lower basal and higher heat-induced expression than in A. thaliana. Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV-B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod-insensitive, early-flowering phenotype. We suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle.

The importance of wild resources as a reflection of the resilience and changing nature of early agricultural systems in East Asia and Europe

We examine the changing importance of wild starch rich plant staples, predominantly tree nuts, in early agricultural societies in East Asia and Europe, focusing on Korea, Japan, and Britain. A comparative review highlights variations in the importance of wild plant staples compared to domesticated crops. The Korean Middle to Late Chulmun periods (c. 3,500–1,500 BC) was characterized by a high reliance on nuts alongside millet. This declines with the transition to rice agriculture, but remains significant during the Mumun period (c. 1,500–300 BC). In Japan, the arrival of rice and millets in the Yayoi Period (c. 1,000 BC−250 AD) saw continued evidence for high levels of reliance on wild resources, which declines only in the Kofun and early historical periods. In Early Neolithic Britain (c. 4,000–3,300 BC) cereal agriculture is accompanied by high evidence for wild plant foods. But during the Middle to Late Neolithic (3,300–c. 2,400/2,200 BC) cereals were abandoned on the mainland with hazelnuts becoming a prominent plant staple. Agriculture returned in the second half of the 3rd millennium BC, followed by a strong decline in wild plant food use during the Middle to Late Bronze Age (1,700–700 BC). Such patterns have previously been attributed to the slow adoption of farming by indigenous peoples, with a continued reliance on wild resources. In light of evidence demonstrating that the dispersal of agriculture was largely driven by a mixture of demic-diffusion and introgression of hunter-gatherers into agricultural groups, a reinterpretation of the role of wild foods is needed. It is argued that the relative importance of wild plant staples provides an indicator of the stability and dependability of agricultural and social systems. A heavy reliance on wild foods in early agricultural societies is tied to the slow adaptation of domesticated crops to new environments, where agricultural and social landscapes are yet to be firmly established, and social systems that could mitigate for poor harvests and storage were often absent. The retained lengthy persistence of wild plant staples in East Asian subsistence systems compared to the British Isles likely reflects differences in the ecological and labor demands for rice compared to Western Asiatic cereals.

Interspecific Hybridization Is an Important Driving Force for Origin and Diversification of Asian Cultivated Rice Oryza sativa L

As one of the most important crops, Asian cultivated rice has evolved into a complex group including several subgroups adapting various eco-climate-systems around the globe. Here, we pictured a comprehensive view of its original domestication, divergences, and the origin of different subgroups by integrating agriculture, archeology, genetics, nuclear, and cytoplasm genome results. Then, it was highlighted that interspecific hybridization-introgression has played important role in improving the genetic diversity and adaptation of Oryza sativa during its evolution process. Natural hybridization-introgression led to the origin of indica, aus, and basmatic subgroups, which adapted to changing cultivated environments, and produced feral weedy rice coexisting and competing with cultivars under production management. Artificial interspecific hybridization-introgression gained several breakthroughs in rice breeding, such as developing three-line hybrid rice, new rice for Africa (NERICA), and some important pest and disease resistance genes in rice genetic improvement, contributing to the stable increase of rice production to meet the expanding human population. We proposed a series to exploit the virtues of hybridization-introgression in the genetic improvement of Asian cultivated rice. But some key issues such as reproductive barriers especially hybrid sterility should be investigated further, which are conducive to gene exchange between cultivated rice and its relatives, and even is beneficial to exploiting interspecific hybrid vigor. New technologies help introduce favorable genes from distant wild species to Asian cultivated rice, such as transgenic and genome editing systems. Rising introgression lines in a wider range with multi-donor benefits allele mining, understanding genetic network of rice growth and development, yield formation, and environmental adaptation. Then, integration of new tools and interspecific hybridization can be a future direction to develop more usable breeding populations which can make Asian cultivated rice more resilient to the changing climate and world.

Sex-Biased Population Admixture Mediated Subsistence Strategy Transition of Heishuiguo People in Han Dynasty Hexi Corridor

The Hexi Corridor was an important arena for culture exchange and human migration between ancient China and Central and Western Asia. During the Han Dynasty (202 BCE–220 CE), subsistence strategy along the corridor shifted from pastoralism to a mixed pastoralist-agriculturalist economy. Yet the drivers of this transition remain poorly understood. In this study, we analyze the Y-chromosome and mtDNA of 31 Han Dynasty individuals from the Heishuiguo site, located in the center of the Hexi Corridor. A high-resolution analysis of 485 Y-SNPs and mitogenomes was performed, with the Heishuiguo population classified into Early Han and Late Han groups. It is revealed that (1) when dissecting genetic lineages, the Yellow River Basin origin haplogroups (i.e., Oα-M117, Oβ-F46, Oγ-IMS-JST002611, and O2-P164+, M134-) reached relatively high frequencies for the paternal gene pools, while haplogroups of north East Asian origin (e.g., D4 and D5) dominated on the maternal side; (2) in interpopulation comparison using PCA and Fst heatmap, the Heishuiguo population shifted from Southern-Northern Han cline to Northern-Northwestern Han/Hui cline with time, indicating genetic admixture between Yellow River immigrants and natives. By comparison, in maternal mtDNA views, the Heishuiguo population was closely clustered with certain Mongolic-speaking and Northwestern Han populations and exhibited genetic continuity through the Han Dynasty, which suggests that Heishuiguo females originated from local or neighboring regions. Therefore, a sex-biased admixture pattern is observed in the Heishuiguo population. Additionally, genetic contour maps also reveal the same male-dominated migration from the East to Hexi Corridor during the Han Dynasty. This is also consistent with historical records, especially excavated bamboo slips. Combining historical records, archeological findings, stable isotope analysis, and paleoenvironmental studies, our uniparental genetic investigation on the Heishuiguo population reveals how male-dominated migration accompanied with lifestyle adjustments brought by these eastern groups may be the main factor affecting the subsistence strategy transition along the Han Dynasty Hexi Corridor.

Ancient Starch Remains Reveal the Vegetal Diet of the Neolithic Late Dawenkou Culture in Jiangsu, East China

The Liangwangcheng site, located in Pizhou County, Xuzhou City, northern Jiangsu Province, is one of the most important Neolithic Dawenkou Culture archeological sites in the Haidai area of China’s eastern seaboard. In recent years, archaeobotanical studies in the Haidai area, mainly focusing on Shandong Province, have yielded fruitful results, while relatively few such studies have been undertaken in northern Jiangsu Province. Here, we report the results of dental residue analysis conducted on 31 individual human skulls unearthed from the Late Dawenkou Culture Liangwangcheng site. The starch granules extracted from these residue samples indicate that foxtail and broomcorn millet, rice, roots and tubers, and legumes comprised the vegetal diet of Liangwangcheng’s occupants. Evidence suggests that mixed rice–millet agriculture played a definite role, with the coexistence of gathering as an economic element. According to archaeobotanical evidence from surrounding cotemporaneous sites, the Late Neolithic human groups that lived in the lower Huang-Huai River drainage shared similar subsistence patterns. Our results provide new evidence for a more comprehensive understanding of plant resource utilization and agricultural development in northern Jiangsu during the Dawenkou period.

An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment

Rice production is shifting from transplanting seedlings to direct sowing of seeds. Following heavy rains, directly sown seeds may need to germinate under anaerobic environments, but most rice (Oryza sativa) genotypes cannot survive these conditions. To identify the genetic architecture of complex traits, we quantified percentage anaerobic germination (AG) in 2,700 (wet-season) and 1,500 (dry-season) sequenced rice genotypes and performed genome-wide association studies (GWAS) using 693,502 single nucleotide polymorphisms. This was followed by post-GWAS analysis with a generalized SNP-to-gene set analysis, meta-analysis, and network analysis. We determined that percentage AG is intermediate-to-high among indica subpopulations, and AG is a polygenic trait associated with transcription factors linked to ethylene responses or genes involved in metabolic processes that are known to be associated with AG. Our post-GWAS analysis identified several genes involved in a wide variety of metabolic processes. We subsequently performed functional analysis focused on the small RNA and methylation pathways. We selected CLASSY 1 (CLSY1), a gene involved in the RNA-directed DNA methylation (RdDm) pathway, for further analyses under AG and found several lines of evidence that CLSY1 influences AG. We propose that the RdDm pathway plays a role in rice responses to water status during germination and seedling establishment developmental stages.

Genomic history and ecology of the geographic spread of rice

Rice (Oryza sativa) is one of the world's most important food crops, and is comprised largely of japonica and indica subspecies. Here, we reconstruct the history of rice dispersal in Asia using whole-genome sequences of more than 1,400 landraces, coupled with geographic, environmental, archaeobotanical and paleoclimate data. Originating around 9,000 yr ago in the Yangtze Valley, rice diversified into temperate and tropical japonica rice during a global cooling event about 4,200 yr ago. Soon after, tropical japonica rice reached Southeast Asia, where it rapidly diversified, starting about 2,500 yr BP. The history of indica rice dispersal appears more complicated, moving into China around 2,000 yr BP. We also identify extrinsic factors that influence genome diversity, with temperature being a leading abiotic factor. Reconstructing the dispersal history of rice and its climatic correlates may help identify genetic adaptations associated with the spread of a key domesticated species.

Raising girls and boys in early China: Stable isotope data reveal sex differences in weaning and childhood diets during the eastern Zhou era

Objectives

Using stable isotope analysis of incremental dentin segments, we reconstruct breastfeeding, weaning, and childhood dietary patterns of Eastern Zhou period (771–221 BC) individuals from the Central Plains of China. Previous isotopic research on the Eastern Zhou demonstrated dietary difference between male and female diets in adulthood via bone collagen analysis. To understand the development of gendered dietary patterns we must examine the early life period. We aim to identify the timing of the weaning process, whether childhood diets were the same as adulthood diets, and if there were differences between the diets of boys and girls during childhood.

Materials and Methods

We present incremental dentin and bone collagen δ¹³C and δ¹⁵N isotope data from 23 individuals from two Eastern Zhou archaeological sites (Xiyasi 西亚斯and Changxinyuan 畅馨苑).

Results

Weaning was completed between ages 2.5 and 4 years. Females were weaned slightly earlier than males. Early childhood diets show significant incorporation of C₃ foods, such as wheat and soybean, for almost all children, while later adulthood diets indicate greater incorporation of C₄ foods (millets), particularly for males.

Discussion

Childhood diets included greater amounts of C₃ foods than expected, suggesting that grains such as wheat may have been adopted in these communities as foods for children. Nevertheless, dietary differentiation between females and males began in childhood, with boys eating more millets (C₄ foods) than girls. The findings suggest that feeding children was a significant aspect of socialization and cultural gendering of individuals in ancient China.

Sedentism and plant cultivation in northeast China emerged during affluent conditions

The reasons and processes that led hunter-gatherers to transition into a sedentary and agricultural way of life are a fundamental unresolved question of human history. Here we present results of excavations of two single-occupation early Neolithic sites (dated to 7.9 and 7.4 ka) and two high-resolution archaeological surveys in northeast China, which capture the earliest stages of sedentism and millet cultivation in the second oldest center of domestication in the Old World. The transition to sedentism coincided with a significant transition to wetter conditions in north China, at 8.1-7.9 ka. We suggest that these wetter conditions were an empirical precondition that facilitated the complex transitional process to sedentism and eventually millet domestication in north China. Interestingly, sedentism and plant domestication followed different trajectories. The sedentary way of life and cultural norms evolved rapidly, within a few hundred years, we find complex sedentary villages inhabiting the landscape. However, the process of plant domestication, progressed slowly over several millennia. Our earliest evidence for the beginning of the domestication process appear in the context of an already complex sedentary village (late Xinglongwa culture), a half millennia after the onset of cultivation, and even in this phase domesticated plants and animals were rare, suggesting that the transition to domesticated (sensu stricto) plants in affluent areas might have not played a substantial role in the transition to sedentary societies.

A northern Chinese origin of Austronesian agriculture: new evidence on traditional Formosan cereals

BACKGROUND

Genetic data for traditional Taiwanese (Formosan) agriculture is essential for tracing the origins on the East Asian mainland of the Austronesian language family, whose homeland is generally placed in Taiwan. Three main models for the origins of the Taiwanese Neolithic have been proposed: origins in coastal north China (Shandong); in coastal central China (Yangtze Valley), and in coastal south China. A combination of linguistic and agricultural evidence helps resolve this controversial issue.

RESULTS

We report on botanically informed linguistic fieldwork of the agricultural vocabulary of Formosan aborigines, which converges with earlier findings in archaeology, genetics and historical linguistics to assign a lesser role for rice than was earlier thought, and a more important one for the millets. We next present the results of an investigation of domestication genes in a collection of traditional rice landraces maintained by the Formosan aborigines over a hundred years ago. The genes controlling awn length, shattering, caryopsis color, plant and panicle shapes contain the same mutated sequences as modern rice varieties everywhere else in the world, arguing against an independent domestication in south China or Taiwan. Early and traditional Formosan agriculture was based on foxtail millet, broomcorn millet and rice. We trace this suite of cereals to northeastern China in the period 6000-5000 BCE and argue, following earlier proposals, that the precursors of the Austronesians, expanded south along the coast from Shandong after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE. This expansion introduced to Taiwan a mixed farming, fishing and intertidal foraging subsistence strategy; domesticated foxtail millet, broomcorn millet and japonica rice; a belief in the sacredness of foxtail millet; ritual ablation of the upper incisors in adolescents of both sexes; domesticated dogs; and a technological package including inter alia houses, nautical technology, and loom weaving.

CONCLUSION

We suggest that the pre-Austronesians expanded south along the coast from that region after c. 5000 BCE to reach northwest Taiwan in the second half of the 4th millennium BCE.

Twenty-first century approaches to ancient problems: Climate and society

By documenting how humans adapted to changes in their environment that are often much greater than those experienced in the instrumental record, archaeology provides our only deep-time laboratory for highlighting the circumstances under which humans managed or failed to find to adaptive solutions to changing climate, not just over a few generations but over the longue durée Patterning between climate-mediated environmental change and change in human societies has, however, been murky because of low spatial and temporal resolution in available datasets, and because of failure to model the effects of climate change on local resources important to human societies. In this paper we review recent advances in computational modeling that, in conjunction with improving data, address these limitations. These advances include network analysis, niche and species distribution modeling, and agent-based modeling. These studies demonstrate the utility of deep-time modeling for calibrating our understanding of how climate is influencing societies today and may in the future.

Tracing the locality of prisoners and workers at the Mausoleum of Qin Shi Huang: First Emperor of China (259-210 BC)

The mausoleum complex of the First Emperor of China, Qin Shi Huang (259-210 BC), is one of the most famous and important archaeological sites in China, yet questions remain as to how it was constructed and by whom. Here we present isotopic results of individuals from the Liyi (n = 146) and Shanren sites (n = 14), both associated with the mausoleum complex. Those buried at Liyi represent the local workers/inhabitants of the Qin population, and the δ(13)C (-8.7 ± 1.5%) and δ(15)N (10.3 ± 0.7%) values indicate that they consumed predominately millet and/or domestic animals fed millet. In contrast, the Shanren individuals were prisoners forced to construct the mausoleum (found buried haphazardly in a mass grave and some in iron leg shackles), and their δ(13)C (-15.4 ± 2.9%) and δ(15)N (8.0 ± 0.6%) results indicate a more mixed C3/C4 diet, with possibly less domestic animals and more wild game protein consumed. This pattern of decreased millet consumption is also characteristic of archaeological sites from southern China, and possible evidence the Shanren prisoners originated from this region (possibly the ancient Chu state located in modern day Hubei Province and parts of Hunan and Anhui Provinces). Further, this finding is in agreement with historical sources and is supported by previous ancient DNA evidence that the mausoleum workers had diverse origins, with many genetically related to southern Chinese groups.

VT, Devi SJSR, Mangrauthia SK, Voleti SR, Sarla N. Field level evaluation of rice introgression lines for heat tolerance and validation of markers linked to spikelet fertility

Rice lines derived from wild species and mutants can serve as a good resource for favorable alleles for heat tolerance. In all, 48 stable lines including 17 KMR3/O. rufipogon introgression lines (KMR3 ILs), 15 Swarna/O. nivara ILs (Swarna ILs) along with their parents, Nagina 22 (N22) and its 4 EMS induced mutants and 7 varieties were evaluated for heat tolerance under irrigated conditions under field in two seasons, wet season 2012 using poly cover house method and dry season 2013 using late sown method. Spikelet fertility (SF), yield per plant (YP) and heat susceptibility index (HSI) for these two traits were considered as criteria to assess heat tolerance compared to control. Four KMR3 ILs and eight Swarna ILs were identified as heat tolerant based on SF and YP and their HSIs in both wet and dry seasons. S-65 and S-70 showed low SF and high YP consistently in response to heat in both seasons. We provide evidence that SF alone may not be the best criterion to assess heat tolerance and including YP is important as lines with low SF but high YP and vice versa were identified under heat stress. Out of 49 SSR markers linked to spikelet fertility, 18 were validated for five traits. RM229 in wet season and RM430 and RM210 in dry season were significantly associated with both SF and its HSI under heat stress. RM430 was also significantly associated with both YP and its HSI in dry season. Thirty two candidate genes were identified close to nine markers associated with traits under heat stress.