Solving the mystery of Obake rice in Africa: population structure analyses of Oryza longistaminata reveal three genetic groups and evidence of both recent and ancient introgression with O. sativa.

The undomesticated rice relative Oryza longistaminata is a valuable genetic resource for the improvement of the domesticated Asian rice, Oryza sativa. To facilitate the conservation, management, and use of O. longistaminata germplasm, we sought to quantify the population structure and diversity of this species across its geographic range, which includes most of sub-Saharan Africa, and to determine phylogenetic relationships to other AA-genome species of rice present in Africa, including the prevalence of interspecific hybridization between O. longistaminata and O. sativa. Though past plant breeding efforts to introgress genes from O. longistaminata have improved biotic stress resistance, ratooning ability, and yield in O. sativa, progress has been limited by substantial breeding barriers. Nevertheless, despite the strong breeding barriers observed by plant breeders who have attempted this interspecific cross, there have been multiple reports of spontaneous hybrids of O. sativa and O. longistaminata (aka "Obake") obtained from natural populations in Africa. However, the frequency and extent of such natural introgressions and their effect on the evolution of O. longistaminata had not been previously investigated. We studied 190 O. longistaminata accessions, primarily from the International Rice Research Institute genebank collection, along with 309 O. sativa, 25 Oryza barthii, and 83 Oryza glaberrima control outgroups, and 17 control interspecific O. sativa/O. longistaminata hybrids. We analyzed the materials using 178,651 single-nucleotide polymorphisms (SNPs) and seven plastid microsatellite markers. This study identified three genetic subpopulations of O. longistaminata, which correspond geographically to Northwestern Africa, Pan-Africa, and Southern Africa. We confirmed that O. longistaminata is, perhaps counterintuitively, more closely related to the Asian species, O. sativa, than the African species O. barthii and O. glaberrima. We identified 19 recent spontaneous interspecific hybrid individuals between O. sativa and O. longistaminata in the germplasm sampled. Notably, the recent introgression between O. sativa and O. longistaminata has been bidirectional. Moreover, low levels of O. sativa alleles admixed in many predominantly O. longistaminata accessions suggest that introgression also occurred in the distant past, but only in Southern Africa.

Brown Rice, a Diet Rich in Health Promoting Properties.

As a staple food crop rice caters to the energy needs of more than 4 billion people around the globe. Since the 1980s, rice breeding focused on breeding for superior grain quality with good texture, taste, palatability and aroma. The recent rise in double burden nutrition challenges suggests that there is a pressing need to focus on incorporating nutritional traits also in rice breeding efforts. The present rice based diet contains nutritional gaps mainly due to the milling process which removes health promoting compounds present in rice bran. Therefore, less milled or brown rice consumption is highly recommended to achieve nutrition sustainability. Brown rice contains relatively higher amounts of dietary fibre, moderate amount of proteins, unsaturated lipids, micronutrients and several bioactive compounds. Some landraces consumed as brown rice have low glycemic index properties; hence they might be helpful to counter the growing type II diabetes. Colored rice varieties with red or purple pericarps are known to possess high levels of bioactive compounds such as cyanidin-3-glucoside, various flavanoids and γ-oryzanol. Germinated brown rice has more potential health benefits, for example, 10-fold of γ-aminobutyric acid than milled rice. For future nutritional intervention, we recommend further explorations into the nutritional value of brown rice as well as to modify the endosperm for enhanced nutrition without altering the texture to ensure consumer acceptance.

Rice SNP-seek database update: new SNPs, indels, and queries.

We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Web-service calls were implemented to access most data. These features enable seamless querying of SNP-Seek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org.

Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice.

BACKGROUND: Understanding population structure of the wild progenitor of Asian cultivated rice (O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing (113,739 SNPs) and for chloroplast variation using Sanger sequencing (25 polymorphic sites). RESULTS: Six wild subpopulations were identified, with 25 % of accessions classified as admixed. Three of the wild groups were genetically and geographically closely related to the O. sativa subpopulations, indica, aus and japonica, and carried O. sativa introgressions; the other three wild groups were genetically divergent, had unique chloroplast haplotypes, and were located at the geographical extremes of the species range. The genetic subpopulations were significantly correlated (r 2 = 0.562) with traditional species designations, O. rufipogon (perennial) and O. nivara (annual), differentiated based on morphology and life history. A wild diversity panel of 95 purified (inbred) accessions was developed for future genetic studies. CONCLUSIONS: Our results suggest that the cultivated aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wild relative, and indica to an admixed population of diverse annual and perennial wild ancestors. Gene flow between ORSC and O. sativa is common in regions where rice is cultivated, threatening the identity and diversity of wild ORSC populations. The three geographically isolated ORSC populations harbor variation rarely seen in cultivated rice and provide a unique window into the genetic composition of ancient rice subpopulations.

Plant Genetic Resources: Needs, Rights, and Opportunities.

Technological advances allow us to tap into genetic resources to address food and nutritional security in the face of population growth, urbanization, climate change, and environmental degradation. It is vital, particularly for developing countries, to ensure that the policy framework regulating access and use of genetic resources keeps pace with technological developments.

Identification of stable QTLs causing chalk in rice grains in nine environments.

KEY MESSAGE: A novel QTL cluster for chalkiness on Chr04 was identified using single environment analysis and joint mapping across 9 environments in Asia and South American. QTL NILs showed that each had a significant effect on chalk. Chalk in rice grains leads to a significant loss in the proportion of marketable grains in a harvested crop, leading to a significant financial loss to rice farmers and traders. To identify the genetic basis of chalkiness, two sets of recombinant inbred lines (RILs) derived from reciprocal crosses between Lemont and Teqing were used to find stable QTLs for chalkiness. The RILs were grown in seven locations in Asia and Latin American and in two controlled environments in phytotrons. A total of 32 (21) and 46 (22) QTLs for DEC and PGWC, most of them explaining more than 10% of phenotypic variation, were detected based on single environment analysis in T/L (L/T) population, respectively. Seven (2) and 7 (3) QTLs for DEC and PGWC were identified in the T/L (L/T) population using joined analysis across all environments, respectively. Six major QTLs clusters were found on five chromosomes: 1, 2, 4, 5 and 11. The biggest cluster at id4007289-RM252 on Chr04 was a novelty, including 16 and 4 QTLs detected by single environment analysis and joint mapping across all environments, respectively. The detected digenic epistatic QTLs explained up to 13% of phenotypic variation, suggesting that epistasis play an important role in the genetic control of chalkiness in rice. QTL NILs showed that each QTL cluster had a significant effect on chalk. These chromosomal regions could be targets for MAS, fine mapping and map-based cloning for low chalkiness breeding.

SNP-Seek database of SNPs derived from 3000 rice genomes.

We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome. The SNPs and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/), which consists of Oracle database having a total number of rows with SNP genotypes close to 60 billion (20 M SNPs × 3 K rice lines) and web interface for convenient querying. The database allows quick retrieving of SNP alleles for all varieties in a given genome region, finding different alleles from predefined varieties and querying basic passport and morphological phenotypic information about sequenced rice lines. SNPs can be visualized together with the gene structures in JBrowse genome browser. Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.

Within-population variation in localized and integrated responses of Trifolium repens to biotically patchy environments.

Genets of Trifolium repens (white clover) were collected from three patches of old permanent pasture dominated by Agrostis capillaris, Holcus lanatus or Lolium perenne. Plants derived from the genets were grown with plants of one grass species present on one side of each T. repens, and a different grass species on the other side, in all combinations of two of the three grasses. Different modules (a node with its associated internode, leaf, and axillary bud) on the same clover plant responded independently to the microenvironment provided by their own neighbouring grasses. In contrast, all apical meristems on the plant reacted similarly, showing a unified response and integrating the effects of the different microenvironments experienced by the whole clover plant. This is consistent with what is known both physiologically about the nutrition of meristems and modules, and ecologically about the exploratory growth habit of the species. Averaged over all associated grasses, there was no significant variation in the final dry weight of the different clover genets but these differed in their growth habit response to different grasses. In response to Agrostis as a neighbour, each meristem of T. repens rapidly produced many small modules. New modules were produced more slowly and were larger when Holcus or Lolium was the neighbour. The same pattern of differences occurred among clovers sampled from different backgrounds. Either genetic differences paralleled plastic responses, or plastic changes in phenotype that developed in response to different neighbours in the field persisted in the greenhouse. Plants taken from backgrounds of different grass species showed different responses to growing with those grass species. The differences were manifest primarily in a "positive leading diagonal" effect of Holcus or not-Holcus. They were the result primarily of differences in the dry weight per module and the probability of development of the axillary bud into a branch. This confirms earlier results, and implicates the central importance of branching as a means of local response to the microenvironment.