A northern Chinese origin of Austronesian agriculture: new evidence on traditional Formosan cereals.
ABSTRACT: 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.
Project description:Although broomcorn and foxtail millet are among the earliest staple crop domesticates, their spread and impacts on demography remain controversial, mainly because of the use of indirect evidence. Bayesian modeling applied to a dataset of new and published radiocarbon dates derived from domesticated millet grains suggests that after their initial cultivation in the crescent around the Bohai Sea ca. 5800 BCE, the crops spread discontinuously across eastern Asia. Our findings on the spread of millet that intensified during the fourth millennium BCE coincide with published dates of the expansion of the Sino-Tibetan languages from the Yellow River basin. In northern China, the spread of millet-based agriculture supported a quasi-exponential population growth from 6000 to 2000 BCE. While growth continued in northeastern China after 2000 BCE, the Upper/Middle Yellow River experienced decline. We propose that this pattern of regional divergence is mainly the result of internal and external anthropogenic factors.
Project description:We have collated and reviewed published records of the genera Panicum and Setaria (Poaceae), including the domesticated millets Panicum miliaceum L. (broomcorn millet) and Setaria italica (L.) P. Beauv. (foxtail millet) in pre-5000 cal b.c. sites across the Old World. Details of these sites, which span China, central-eastern Europe including the Caucasus, Iran, Syria and Egypt, are presented with associated calibrated radiocarbon dates. Forty-one sites have records of Panicum (P. miliaceum, P. cf. miliaceum, Panicum sp., Panicum type, P. capillare (?) and P. turgidum) and 33 of Setaria (S. italica, S. viridis, S. viridis/verticillata, Setaria sp., Setaria type). We identify problems of taphonomy, identification criteria and reporting, and inference of domesticated/wild and crop/weed status of finds. Both broomcorn and foxtail millet occur in northern China prior to 5000 cal b.c.; P. miliaceum occurs contemporaneously in Europe, but its significance is unclear. Further work is needed to resolve the above issues before the status of these taxa in this period can be fully evaluated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00334-008-0187-1) contains supplementary material, which is available to authorized users.
Project description:Broomcorn millet (Panicum miliaceum L.) has strong tolerance to abiotic stresses, and is probably one of the oldest crops, with its earliest cultivation that dated back to ca. ~10,000 years. We report here its genome assembly through a combination of PacBio sequencing, BioNano, and Hi-C (in vivo) mapping. The 18 super scaffolds cover ~95.6% of the estimated genome (~887.8?Mb). There are 63,671 protein-coding genes annotated in this tetraploid genome. About ~86.2% of the syntenic genes in foxtail millet have two homologous copies in broomcorn millet, indicating rare gene loss after tetraploidization in broomcorn millet. Phylogenetic analysis reveals that broomcorn millet and foxtail millet diverged around ~13.1 Million years ago (Mya), while the lineage specific tetraploidization of broomcorn millet may be happened within ~5.91 million years. The genome is not only beneficial for the genome assisted breeding of broomcorn millet, but also an important resource for other Panicum species.
Project description:It is generally understood that foxtail millet and broomcorn millet were initially domesticated in Northern China where they eventually became the dominant plant food crops. The rarity of older archaeological sites and archaeobotanical work in the region, however, renders both the origins of these plants and their processes of domestication poorly understood. Here we present ancient starch grain assemblages recovered from cultural deposits, including carbonized residues adhering to an early pottery sherd as well as grinding stone tools excavated from the sites of Nanzhuangtou (11.5-11.0 cal kyBP) and Donghulin (11.0-9.5 cal kyBP) in the North China Plain. Our data extend the record of millet use in China by nearly 1,000 y, and the record of foxtail millet in the region by at least two millennia. The patterning of starch residues within the samples allow for the formulation of the hypothesis that foxtail millets were cultivated for an extended period of two millennia, during which this crop plant appears to have been undergoing domestication. Future research in the region will help clarify the processes in place.
Project description:An assemblage of charred plant remains collected from 26 sites in the Yiluo valley of North China as part of an archaeological survey spans the period from the sixth millennium to 1300 calibrated calendrical years (cal) B.C. The plant remains document a long sequence of crops, weeds, and other plants in the country. The results also demonstrate the effectiveness of sediment sampling as part of an archaeological survey. Ten accelerator mass spectrometer (AMS) radiocarbon dates on crop remains inform an assessment of the sequence of agricultural development in the region. Foxtail millet (Setaria italica subsp. italica) was grown during the Early Neolithic period and was the principal crop for at least four millennia. Broomcorn millet (Panicum miliaceum) was significantly less important throughout the sequence. Rice (Oryza sativa) was introduced by 3000 cal B.C. but apparently was not an important local crop. Wheat became a significant crop between 1600 and 1300 cal B.C. The weed flora diversified through time and were dominated by annual grasses, some of which were probably fodder for domesticated animals. The North China farming tradition that emphasized dry crops (millets, wheat, and legumes) with some rice appears to have been established at the latest by the Early Shang (Erligang; 1600-1300 B.C.) period.
Project description:Foxtail millet is considered a 'smart food' because of nutrient richness and resilience to environments. A diversity panel of 92 foxtail millet landraces preserved by Taiwan indigenous peoples containing amylose content (AC) in the range of 0.7% to 16.9% exhibited diverse physiochemical properties revealed by a rapid viscosity analyzer (RVA). AC was significantly correlated with 5 RVA parameters, and some RVA parameters were also highly correlated with one another. In comparison to rice, foxtail millet contained less starch (65.9-73.1%) and no significant difference in totals of resistant starch (RS), slowly digestible starch (SDS), hydrolysis index (HI), and expected glycemic index (eGI) according to in vitro digestibility assays of raw flour with similar AC. RS was significantly positively correlated with AC and four RVA parameters, cold paste viscosity (CPV), setback viscosity (SBV), peak time (PeT), and pasting temperature (PaT), implying that suitable food processing to alter physicochemical properties of foxtail millet might mitigate hyperglycemia. This investigation of pasting properties and digestibility of diverse foxtail millet germplasm revealed much variation and showed potential for multi-dimensional utilizations in daily staple food and food industries.
Project description:Foxtail millet (Setaria italica) originated in China and is generally cultivated in arid and barren soil. Through long-term harsh environmental selection, foxtail millet has acquired significant drought resistance. However, the molecular mechanism of foxtail millet drought resistance is still unknown. Here, we identified a drought-induced R2R3-MYB transcription factor SiMYB56 in foxtail millet. Overexpression of SiMYB56 significantly enhances tolerance to drought stress in transgenic rice plants at both the vegetative and the reproductive stage and has no adverse effect on its normal growth. Compared with wild-type controls, SiMYB56-overexpressing rice plants had lower MDA content and higher lignin content under drought conditions. Quantitative real-time PCR and Transcriptional activity assays demonstrated that SiMYB56 could activate expression of lignin biosynthesis genes under drought conditions. Also, we found that overexpression of SiMYB56 can led to ABA accumulation in the seeds transgenic rice plants. Further experiments showed that Overexpression of SiMYB56 can upregulate the expression of ABA synthesis and response related genes under drought conditions. In conclusion, SiMYB56 may enhance the drought resistance of transgenic rice plants by regulating lignin biosynthesis and ABA signaling pathway, making SiMYB56 a candidate gene for drought resistance improvement in gramineous crops.
Project description:Foxtail millet (Setaria italica), which originated in China, has a strong tolerance to low nutrition stresses. However, the mechanism of foxtail millet tolerance to low-nitrogen stress is still unknown. In this study, the transcriptome of foxtail millet under low-nitrogen stress was systematically analyzed. Expression of 1891 genes was altered, including 1318 up-regulated genes and 573 down-regulated genes. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed that 3% of these genes were involved in membrane transport and 5% were involved in redox processes. There were 74 total transcription factor (TF) genes in the DEGs (differentially expressed genes), and MYB-like transcription factors accounted for one-third (25) of the TF genes. We systematically analyzed the characteristics, expression patterns, chromosome locations, and protein structures of 25 MYB-like genes. The analysis of gene function showed that Arabidopsis and rice overexpressing SiMYB3 had better root development than WT under low-nitrogen stress. Moreover, EMSA results showed that SiMYB3 protein could specifically bind MYB elements in the promoter region of TAR2, an auxin synthesis related gene and MYB3-TAR2 regulate pair conserved in rice and foxtail millet. These results suggested that SiMYB3 can regulate root development by regulating plant root auxin synthesis under low-nitrogen conditions.
Project description:A Taiwan origin for the expansion of the Austronesian languages and their speakers is well supported by linguistic and archaeological evidence. However, human genetic evidence is more controversial. Until now, there had been no ancient skeletal evidence of a potential Austronesian-speaking ancestor prior to the Taiwan Neolithic ~6,000 years ago, and genetic studies have largely ignored the role of genetic diversity within Taiwan as well as the origins of Formosans. We address these issues via analysis of a complete mitochondrial DNA genome sequence of an ~8,000-year-old skeleton from Liang Island (located between China and Taiwan) and 550 mtDNA genome sequences from 8 aboriginal (highland) Formosan and 4 other Taiwanese groups. We show that the Liangdao Man mtDNA sequence is closest to Formosans, provides a link to southern China, and has the most ancestral haplogroup E sequence found among extant Austronesian speakers. Bayesian phylogenetic analysis allows us to reconstruct a history of early Austronesians arriving in Taiwan in the north ~6,000 years ago, spreading rapidly to the south, and leaving Taiwan ~4,000 years ago to spread throughout Island Southeast Asia, Madagascar, and Oceania.
Project description:BACKGROUND: Foxtail millet (Setaria italica (L.) P. Beauv.), one of the most ancient domesticated crops, is becoming a model system for studying biofuel crops and comparative genomics in the grasses. However, knowledge on the level of genetic diversity and linkage disequilibrium (LD) is very limited in this crop and its wild ancestor, green foxtail (Setaria viridis (L.) P. Beauv.). Such information would help us to understand the domestication process of cultivated species and will allow further research in these species, including association mapping and identification of agricultural significant genes involved in domestication. RESULTS: In this study, we surveyed DNA sequence for nine loci across 50 accessions of cultivated foxtail millet and 34 of its wild progenitor. We found a low level of genetic diversity in wild green foxtail (? = 0.0059), ? means Watterson's estimator of ?. Despite of a 55% loss of its wild diversity, foxtail millet still harbored a considerable level of diversity (? = 0.0027) when compared to rice and sorghum (? = 0.0024 and 0.0034, respectively). The level of LD in the domesticated foxtail millet extends to 1 kb, while it decayed rapidly to a negligible level within 150 bp in wild green foxtail. Using coalescent simulation, we estimated the bottleneck severity at k = 0.6095 when ?/? = 1. These results indicated that the domestication bottleneck of foxtail millet was more severe than that of maize but slightly less pronounced than that of rice. CONCLUSIONS: The results in this study establish a general framework for the domestication history of foxtail millet. The low level of genetic diversity and the increased level of LD in foxtail millet are mainly caused by a population bottleneck, although gene flow from foxtail millet to green foxtail is another factor that may have shaped the pattern of genetic diversity of these two related gene pools. The knowledge provided in this study will benefit future population based studies in foxtail millet.