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Grain size is one of the most important components of grain yield and selecting large seeds has been a main target during plant domestication. Surprisingly, the grain of African cultivated rice ( Oryza glaberrima Steud.) typically is smaller than that of its progenitor, Oryza barthii . Here we report the cloning and characterization of a quantitative trait locus, GL4 , controlling the grain length on chromosome 4 in African rice, which regulates longitudinal cell elongation of the outer and inner glumes. Interestingly, GL4 also controls the seed shattering phenotype like its orthologue SH4 gene in Asian rice. Our data show that a single-nucleotide polymorphism (SNP) mutation in the GL4 gene resulted in a premature stop codon and led to small seeds and loss of seed shattering during African rice domestication. These results provide new insights into diverse domestication practices in African rice, and also pave the way for enhancing crop yield to meeting the challenge of cereal demand in West Africa. The reason why African cultivated rice has smaller grains than its wild progenitor has remained puzzling. Now, scientists find that the selection of a single-nucleotide polymorphism mutation in the GL4 gene during African rice domestication causes loss of seed shattering and smaller seeds.

Iron (Fe) toxicity is a major constraint in lowland rice. Because of its higher rusticity and adaptability to adverse soil conditions, the African rice Oryza glaberrima constitutes a new potential source of genes for rice improvement. This study aimed at mapping quantitative trait loci (QTLs) for resistance to Fe toxicity. A set of 220 BC 3 DH lines derived from the backcross O. sativa (Caiapo)/ O. glaberrima (MG12)// O. sativa (Caiapo) was tested in hydroponics in the presence or absence of Fe 2+ (0 or 250 mg L −1 ). The experiment was repeated twice independently in time. In each repetition, each line was repeated three times under each Fe 2+ condition. A total of 28 QTLs were detected in 18 distinct chromosomal regions for 11 morphological and physiological traits. The single and joint composite interval mappings confirmed the interest of region RM5-RM246 on chromosome 1. Several QTLs were detected in new regions, including five QTLs and one joint QTL on chromosome 5, and one QTL on chromosome 10. Interestingly, the favorable allele for all these seven new QTLs were provided by the O. glaberrima cultivar MG12, i.e. the lesser investigated species. These QTLs corresponded to leaf bronzing index, dry weights, Fe concentration in the root-plaque system and stomatal conductance. Our results suggest that resistance mechanisms to Fe toxicity may differ between both cultivated rices and confirmed the possible interest of O. glaberrima as a source of new alleles for QTL detection and introgression in the perspective of improving rice resistance to Fe toxicity.

A feed trial was carried out to evaluate potential unconventional feed resources such as Trichanthera gigantica and moruga hill rice (Oryza glaberrima) as a partial supplementation to the diet of adult male agoutis (Dasyprocta leporina). Supplemental feeding of the agouti will decrease feeding cost to produce this animal and aid in sustainable agricultural practices. Male agoutis were used as this physiological state was the easiest to attain as well as male animals are generally used for meat production. The trial consisted of 16 male agoutis that were allocated into four dietary treatments using a completely randomized experimental design. Four diet treatments were used in the experiment; treatment 1 (T1) was the positive control which consisted of rabbit ration whilst treatment 2 (T2) to 4 (T4) had different ratios of O. glaberrima, Trichanthera gigantica and Rabbit Ration. The feeding trial had 8-week duration. T2 consisted of 5% T. gigantica, 35% O. glaberrima supplemented for rabbit ration. T3 had 10% T. gigantica and 40% O. glaberrima supplemented for rabbit ration. T4 consisted of 15% Trichanthera and 45% O. glaberrima supplemented for rabbit ration in the diet. Proximate analysis showed that Dry Matter (DM) and Ash was highest in T4 and lowest in T2. Whilst ether extract (EE) and crude protein (CP) were highest in T2 and lowest in T4. Crude fiber (CF) was highest in T3 and lowest in T2. The weights of the agoutis at the start of the experiment (2595 g–2971 g) were not significantly different to their final weight (2469–2762 g) (p > 0.05). There was a significant difference seen between treatments groups and weeks of the experiment (p < 0.05). There was no significant difference in the interactions between treatment and weeks (p > 0.05). T1 and T2 were not significantly different (p > 0.05) with respect to average daily gain (−0.98 g/d, −1.61 g/d) and weight loss (55 g, 90 g). T2 can be used as an alternative feed source than rabbit ration (control diet) for adult male agoutis. As the final body mass of the male agoutis did not change with the inclusion of 40% Trichanthera and Moruga hill rice, this substitution can be used to maintain male agoutis before slaughter. However, higher amounts of supplements may be detrimental to this animal.

Rice breeding and crop research predominantly emphasize adaptation to ecological conditions. Based on qualitative and quantitative research conducted between 2000 and 2012 we show how ecological factors, combined with socioeconomic variables, cultural norms and values, shape the use and development of local technologies related to the cultivation of African rice (Oryza glaberrima Steud.) in seven West African countries (Ghana, Guinea, Guinea-Bissau, Senegal, Sierra Leone, The Gambia and Togo). In this region the role of African rice is diverse across ethnic groups. Findings suggest that farmers, through various pathways, are active in the development of promising new varieties based on genetic resources of Asian rice, African rice, or both, as well as in the adoption of modern varieties. These findings require further research into interactions among ecological, genetic, socioeconomic and cultural factors within farmers’ innovation systems and recognition of emergent knowledge and technologies resulting from such interactions.

Oryza glaberrima has mostly been used as a source to improve stress resistance of Oryza sativa. Improvement of this species could be an approach to use its adaptability to local environments in Africa such as multiple resistance to several indigenous constraints. The yield of O. glaberrima was inferior to that of O. sativa under favorable growth conditions but not under unfavorable conditions. Moreover, spikelet number before grain shattering was no less in O. glaberrima than in O. sativa at any fertilizer input levels, suggesting that the yield potential of O. glaberrima is as high as that of O. sativa. Inferior yield of O. glaberrima reported in favorable environments could result from grain shattering enhanced by such growth environments where higher incidence of lodging, which is another undesirable character of O. glaberrima, can occur. Regarding characteristics associated to yield generation, O. glaberrima seemed to possess: higher dry matter production and greater leaf area than O. sativa at least until heading; a lower photosynthetic rate per leaf area but a higher rate against the same leaf nitrogen content in a low content range; higher responsiveness of dry matter, leaf area and leaf photosynthesis to increases in nitrogen inputs; lower water-use efficiency on dry matter accumulation and gas exchange bases; faster progress of leaf senescence during maturity; and faster completion of grain filling during maturity than O. sativa.

Domestication of crops based on artificial selection has contributed numerous beneficial traits for agriculture. Wild characteristics such as red pericarp and seed shattering were lost in both Asian (Oryza sativa) and African (Oryza glaberrima) cultivated rice species as a result of human selection on common genes. Awnedness, in contrast, is a trait that has been lost in both cultivated species due to selection on different sets of genes. In a previous report, we revealed that at least three loci regulate awn development in rice; however, the molecular mechanism underlying awnlessness remains unknown. Here we isolate and characterize a previously unidentified EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family member named REGULATOR OF AWN ELONGATION 2 (RAE2) and identify one of its requisite processing enzymes, SUBTILISIN-LIKE PROTEASE 1 (SLP1). The RAE2 precursor is specifically cleaved by SLP1 in the rice spikelet, where the mature RAE2 peptide subsequently induces awn elongation. Analysis of RAE2 sequence diversity identified a highly variable GC-rich region harboring multiple independent mutations underlying protein-length variation that disrupt the function of the RAE2 protein and condition the awnless phenotype in Asian rice. Cultivated African rice, on the other hand, retained the functional RAE2 allele despite its awnless phenotype. Our findings illuminate the molecular function of RAE2 in awn development and shed light on the independent domestication histories of Asian and African cultivated rice.

Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara , Oryza glaberrima , Oryza barthii , Oryza glumaepatula , and Oryza meridionalis . Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm. Significance Asian rice ( Oryza sativa ) is among the world’s most important crops. The genus Oryza has become a model for the study of plant genome structure, function, and evolution. We have undertaken de novo, full-genome sequence analysis of five diploid AA-genome species that are closely related to O. sativa . These species are native to quite different environments, representing four continents, thus exhibiting very different adaptations. Our studies identify specific genetic changes, in both gene copy number and the degree of diversifying natural selection, that indicate specific genes responsible for these adaptations, particularly in genes related to defense against pathogens and reproductive diversification. This genome discovery and comparative analysis provide a powerful tool for future Oryza study and rice improvement.

There are two species of cultivated rice in the world—Oryza sativa L. from Asia and Oryza glaberrima Steud. from Africa. The former was domesticated from the wild progenitor Oryza rufipogon Griff. and the latter from the African wild rice species Oryza barthii A. Shiv. The first known center of rice cultivation in China generated the O. sativa subspecies japonica. The indica subspecies arose from the second center of domestication in the Ganges River plains of India. Variants of domesticated lines and the continuous hybridization between cultivated varieties and the wild progenitor(s) resulted in weedy rice types. Some weedy types resemble the wild ancestor, but the majority of weedy rices today bear close resemblance to cultivated rice. Weedy rice accompanies rice culture and has increased in occurrence with the global shift in rice establishment from transplanting to direct-seeded or dry-drill-seeded rice. Weedy rice (Oryza spp.) is the most difficult weed to control in rice, causing as much as 90% yield loss or abandonment of severely infested fields. The gene flow continuum between cultivar and weedy rice or wild relative, crop de-domestication, and regionalized adaptation have resulted in a myriad of weedy rice types. The complex lineage of weedy rice has resulted in confusion of weedy rice nomenclature. Two names are generally used for weedy rice—Oryza sativa L. and Oryza sativa f. spontanea. Genomic data show that O. sativa L. applies to weedy rice populations derived from cultivated O. sativa, whereas O. sativa f. spontanea applies only to weedy types that primarily descended from O. rufipogon. Neither of these names applies to African weedy rice, which is of African wild rice or O. glaberrima lineage. Therefore, unless the lineage of the weedy population in question is known, the proper name to use is the generalized name Oryza spp.

Two species of rice have been independently domesticated from different ancestral wild species in Asia and Africa. Comparison of mutations that underlie phenotypic and physiological alterations associated with domestication traits in these species gives insights into the domestication history of rice in both regions. Asian cultivated rice, Oryza sativa, and African cultivated rice, Oryza glaberrima, have been modified and improved for common traits beneficial for humans, including erect plant architecture, nonshattering seeds, nonpigmented pericarp, and lack of awns. Independent mutations in orthologous genes associated with these traits have been documented in the two cultivated species. Contrary to this prevailing model, selection for awnlessness targeted different genes in O. sativa and O. glaberrima. We identify Regulator of Awn Elongation 3 (RAE3) a gene that encodes an E3 ubiquitin ligase and is responsible for the awnless phenotype only in O. glaberrima. A 48-bp deletion may disrupt the substrate recognition domain in RAE3 and diminish awn elongation. Sequencing analysis demonstrated low nucleotide diversity in a ~600-kb region around the derived rae3 allele on chromosome 6 in O. glaberrima compared with its wild progenitor. Identification of RAE3 sheds light on the molecular mechanism underlying awn development and provides an example of how selection on different genes can confer the same domestication phenotype in Asian and African rice.

Summary African cultivated rice (Oryza glaberrima Steud.) was domesticated from its wild progenitor species (Oryza barthii) about 3000 years ago. Seed shattering is one of the main constraints on grain production in African cultivated rice, which causes severe grain losses during harvest. By contrast, Asian cultivated rice (Oryza sativa) displays greater resistance to seed shattering, allowing higher grain production. A better understanding in regulation of seed shattering would help to improve harvesting efficiency in African cultivated rice. Here, we report the map‐based cloning and characterization of OgSH11, a MYB transcription factor controlling seed shattering in O. glaberrima. OgSH11 represses the expression of lignin biosynthesis genes and lignin deposition by binding to the promoter of GH2. We successfully developed a new O. glaberrima material showing significantly reduced seed shattering by knockout of SH11 in O. glaberrima using CRISPR‐Cas9 mediated approach. Identification of SH11 not only supplies a new target for seed shattering improvement in African cultivated rice, but also provides new insights into the molecular mechanism of abscission layer development.