Rice origins and cultural history

Seed development, especially the relevant regulatory mechanism and genetic network are of fundamental scientific interest. Seed development consists of the development of embryo and endosperm; and endosperm development of rice (model species of monocots) is closely related to grain yield and quality. Recent genetic studies, together with other approaches, including transcriptome and proteomics analysis, high-throughput sequencing (RNA-seq, ChIP-seq), revealed the crucial roles of genetic and epigenetic controls in rice endosperm development. Here we summarize and update the genetic networks involved in the regulation of endosperm initiation, cell cycle regulation, aleurone layer specification, starch synthesis, storage protein accumulation and endosperm size, and the interactions between embryo and endosperm.

Flowering time (i.e., heading date in crops) is an important ecological trait that determines growing seasons and regional adaptability of plants to specific natural environments. Rice (Oryza sativa L.) is a short-day plant that originated in the tropics. Increasing evidence suggests that the northward expansion of cultivated rice was accompanied by human selection of the heading date under noninductive long-day (LD) conditions. We report here the molecular cloning and characterization of DTH2 (for Days to heading on chromosome 2), a minor-effect quantitative trait locus that promotes heading under LD conditions. We show that DTH2 encodes a CONSTANS-like protein that promotes heading by inducing the florigen genes Heading date 3a and RICE FLOWERING LOCUS T 1, and it acts independently of the known floral integrators Heading date 1 and Early heading date 1. Moreover, association analysis and transgenic experiments identified two functional nucleotide polymorphisms in DTH2 that correlated with early heading and increased reproductive fitness under natural LD conditions in northern Asia. Our combined population genetics and network analyses suggest that DTH2 likely represents a target of human selection for adaptation to LD conditions during rice domestication and/or improvement, demonstrating an important role of minor-effect quantitative trait loci in crop adaptation and breeding.

Systematical descriptions of phytoliths from rice species in East Asia are scarce. In order to investigate the relationship among diversity of phytolith morphology, taxonomy and genome, comparative research on phytolith morphology of the wild and domesticated rice species is first performed on the basis of statistics and cluster analysis. All morphological parameters were measured at 500× magnification using a Zeiss light microscope. 3-D plots and cluster analysis are performed by SPSS 10.0 software. The leaves and inflorescences of domesticated and wild rice contain a great diversity of phytolith types including long cells, short cells, bulliform cells, hair cells, irregular epidermal cells, mesophyll and vascular tissues. Comparative research on phytolith morphology demonstrates that most overlap occurs among long cells, short cells, bulliform cells, hair cells and vascular tissues at the species level. Rondels, crosses, long cells, hair cells, parallepipedal bulliform cells, tracheid and vascular tissue exhibit no taxonomical value. Complex saddles and irregular epidermal phytoliths might be diagnostic to the rice species that had not been described before. Further comparative research on the morphological features of three phytolith types from the wild and domesticated rice species has confirmed that double-peaked glume cells measurements can separate domesticated Oryza species from wild ones successfully. Hierarchical cluster analysis on all morphological parameters of bilobates, cuneiform bulliform cells and double-peaked glume cells strongly demonstrates that phytolith assemblage appears to be under genetic control and therefore reflect taxonomical significance. The results are significant for plant physiology, rice cultivation and environmental archaeology.

Convergent phenotypic evolution may or may not be associated with convergent genotypic evolution. Agricultural weeds have repeatedly been selected for weed-adaptive traits such as rapid growth, increased seed dispersal and dormancy, thus providing an ideal system for the study of convergent evolution. Here, we identify QTL underlying weedy traits and compare their genetic architecture to assess the potential for convergent genetic evolution in two distinct populations of weedy rice. F2 offspring from crosses between an indica cultivar and two individuals from genetically differentiated U.S. weedy rice populations were used to map QTL for four quantitative (heading date, seed shattering, plant height and growth rate) and two qualitative traits. We identified QTL on nine of the twelve rice chromosomes, yet most QTL locations do not overlap between the two populations. Shared QTL among weed groups were only seen for heading date, a trait for which weedy groups have diverged from their cultivated ancestors and from each other. Sharing of some QTL with wild rice also suggests a possible role in weed evolution for genes under selection during domestication. The lack of overlapping QTL for the remaining traits suggests that, despite a close evolutionary relationship, weedy rice groups have adapted to the same agricultural environment through different genetic mechanisms.

As a weed of rice paddy fields, weedy rice has spread worldwide. In northern China, the expansion of weedy rice has been rapid over the past two decades. Its evolutionary history and adaptive mechanisms are poorly understood.Evolutionary relationships between northern weedy rice and rice cultivars were analyzed using presumed neutral markers sampled across the rice genome. Genes involved in rice domestication were evaluated for their potential roles in weedy rice adaptation. Seed longevity, a critical trait of weedy rice, was examined in an F2 population derived from a cross between weedy rice and a rice cultivar to evaluate weedy rice adaptation and the potential effect of candidate genes.Weedy rice in northern China was not derived directly from closely related wild Oryza species or from the introgression of indicasubspecies. Introgression with local cultivars, coupled with selection that maintained weedy identity, shaped the evolution of weedy rice in northern China.

Rice can be cultivated in a range of arable systems, including upland rainfed, lowland rainfed or irrigated, flooded or décrue, and deep water cultivation. These agricultural regimes represent ecosystems controlled to large degree by agricultural practices, and can be shown to produce different weed flora assemblages. In order to reconstruct early rice cultivation systems it is necessary to better establish how ancient rice farming practices may be seen using archaeobotanical data. This paper focuses on using modern analogue phytolith assemblages of associated crop weeds found within cultivation regimes, as well as in wild rice stands (unplanted stands of Oryza nivara or O. rufipogon), as a means of interpreting archaeobotanical assemblages. Rice weeds and sediment samples have been recorded and collected from a range of arable systems and wild stands in India. The husks, leaves and culms of associated weeds were processed for phytolith reference samples, and sediment samples were processed for phytoliths in order to establish patterns identifiable to specific systems. The preliminary results of the phytolith analysis of samples from these modern fields demonstrate that phytolith assemblage statistics show correlation with variation in rice cultivation systems on the basis of differences in environmental conditions and regimes, with wetness being one major factor. Analysis of phytoliths from archaeological samples from contrasting systems in Neolithic China and India demonstrate how this method can be applied to separate archaeological regions and periods based on inferred differences in past agricultural practices, identifying wet cultivation systems in China, dry millet-dominated agriculture of north China and rainfed/dry rice in Neolithic India.

Improvement of rice eating quality is an important objective in current breeding programs. In this study, 130 rice accessions of diverse origin were genotyped using 170 SSR markers to identify marker–trait associations with physicochemical traits on eating quality. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r 2value for all intrachromosomal loci pairs was 0.0940. LD between linked markers decreased with distance. Marker–trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). In total, 101 marker–trait associations (p < 0.05) were identified using 52 different SSR markers covering 12 chromosomes. The results suggest that association mapping in rice is a viable alternative to quantitative trait loci mapping, and detection of new marker–trait associations associated with rice eating quality will also provide important information for marker-assisted breeding and functional analysis of rice grain quality.

During the diversification of cultivated rice after domestication, rice was grown in diverse geographic regions using genetic variations attributed to the combination of alleles in loci for adaptability to various environmental conditions. To elucidate the key gene for adaptation in rice cultivars to the northern limit of rice cultivation, we conducted genetic analyses of heading date using extremely early-heading cultivars. The Hd5 gene controlling heading date (flowering time) generated variations in heading date among cultivars adapted to Hokkaido, where is the northernmost region of Japan and one of the northern limits of rice cultivation in the world. The association of the Hd5 genotype with heading date and genetical analysis clearly showed that the loss-of-function Hd5 has an important role in exhibiting earlier heading among a local population in Hokkaido. Distinct distribution of the loss-of-function Hd5 revealed that this mutation event of the 19-bp deletion occurred in a local landrace Bouzu and that this mutation may have been selected as an early-heading variety in rice breeding programs in Hokkaido in the early 1900s. The loss-of-function Hd5 was then introduced into the rice variety Fanny from France and contributed to its extremely early heading under the presence of functional Ghd7. These results demonstrated that Hd5 plays roles not only in generating early heading in variations of heading date among a local population in Hokkaido, but also in extremely early heading for adaptation to northern limits of rice cultivation

Systematic archaeobotanical work at Xihe site recovered 8000 years old rice and other plant remains. Cultural context analyses of the plant and animal remains indicated Xihe people relied mainly on fishing–hunting–gathering as their subsistence. As the largest amount and higher concentration of plant remains, rice might contribute much to plant food resource at the settlement. Even though it is too early to demonstrate the nature of the rice remains (whether it is wild, cultivated or domesticated), the case that discovery of Xihe rice has undoubtedly provided new evidence for our understanding of rice exploitation subsistence at about 8000 years ago in East China.

Indica is not only an important rice subspecies widely planted in Asia and the rest of the world, but it is also the genetic background of the majority of hybrid varieties in China. Studies on genetic structure and genetic diversity in indica germplasm resources are important for the classification and utilization of cultivated rice in China. Using a genetically representative core collection comprising 1482 Chinese indica landraces, we analysed the genetic structure, geographic differentiation and diversity. Model-based structure analysis of varieties within three ecotypes revealed nine eco-geographical types partially accordant with certain ecological zones in China. Differentiation of eco-geographical types was attributed to local ecological adaption and physical isolation. These groups may be useful for developing heterotic groups of indica. To facilitate the identification of different ecotypes and eco-geographical types, we identified characteristic SSR alleles of each ecotype and eco-geographical type and a rapid index of discrimination based on characteristic alleles. The characteristic alleles and rapid discrimination index may guide development of heterotic groups, and selection of hybrid parents

Dorian has been awarded a NERC Research Grant of over £700,000 for a 3-year project, working with Andrew Bevan, new research staff and collaborative project partners to investigate the evolution of rice systems from China to Southeast Asia....

His previous NERC-funded research project on 'The identification of arable rice systems in prehistory' has consolidated our understanding of early rice agricultural development in the Yangtze and in India.