Genetics and phylogenetics of rice domestication

Natural Variation of PH8 Allele Improves Architecture and Cold Tolerance in Rice

Empirical breeding efforts targeting cold tolerance and ideal plant architecture have significantly improved yield and facilitated the geographic expansion of japonica rice cultivation. However, the genetic drivers and underlying molecular mechanisms of these traits remain insufficiently understood. Here, we identify Plant Height 8 (PH8) as a key gene regulating both plant stature and cold stress response in rice. Genome wide association analysis (GWAS), supported by functional validation, shows that loss of PH8 reduces plant height without affecting other agronomic traits. Notably, we found that PH8 also negatively regulates cold tolerance. A prevalent haplotype, PH8Hap.0, exhibits reduced PH8 expression due to natural variation in its promoter region, resulting in shorter plants and enhanced cold tolerance. Selective sweep and geographic distribution analyses indicate that PH8Hap.0 originated in high-latitude regions and underwent strong directional selection during modern japonica improvement. Functional assays demonstrate that PH8 enhances cold tolerance via improved reactive oxygen species (ROS) scavenging by repressing APX2, an antioxidant gene involved in ROS detoxification. Our findings reveal PH8 as a dual regulator of plant architecture and cold stress adaptation, and highlight PH8Hap.0 as a historically selected allele that contributed to the climatic adaptation and geographical expansion of japonica rice.

Differentiation of genome-wide DNA methylation between japonica and indica rice

Rice (Oryza sativa L.) subspecies japonica and indica show distinct morphological and genetic differentiation. However, the differences in the genome-wide DNA methylation and its effects on gene expression and metabolic levels between japonica and indica rice remain unclear. In this study, we investigated the genome-wide DNA methylation, transcriptomes and metabolomes of 12 representative japonica and indica rice accessions, to reveal the differentiation between rice subspecies. We detected 83 327 differentially methylated regions (DMRs) and 14 903 DMR-associated genes between two subspecies. Indica rice showed significantly lower levels of the CG, CHG, and CHH methylation compared with japonica rice. Subsequently, we identified 5596 differentially expressed genes between the two subspecies, predominantly enriched in pathways related to carbohydrate and amino acid metabolism. By integrating DNA methylation with transcriptomic data, a significant correlation was established between methylation patterns and the expression level of key agronomic genes in rice. Furthermore, multi-omics analyses reveal that carbohydrate metabolism pathways, especially the tricarboxylic acid (TCA) cycle metabolites, are remarkable differentiation between rice subspecies. These results provide a foundation for future studies in rice domestication and genetic improvement.

Phenological and morphological variations of Oryza rufipogon and O. nivara in Sri Lanka and their evolutionary implications

Phenological and morphological variation are widely viewed as a pivotal driver of ecological adaptation and speciation. Here, we investigate variation patterns of flowering phenology and morphological traits within and between O. rufipogon and O. nivara populations in Sri Lanka by incorporating the in situ observation in natural habitats and manipulative experiments in the common gardens. First, we observed varying degrees of phenological variation under different temporal and spatial conditions, suggesting that flowering phenology of two Oryza species varied depending on both environments and management practices. Particularly, the Sri Lankan O. nivara exhibits high plasticity in flowering phenology, implying that O. nivara might not be an annual in the strict sense. Second, the observation that flowering time of the two species overlapped suggests that the primary factor to maintain the species divergence in Sri Lanka may not be flowering time but rather environments. Third, our selection analysis suggests that interspecific divergence in the traits related to reproduction and habitat preference is adaptive and most likely driven by natural selection. Together, our case study on the Sri Lankan O. rufipogon and O. nivara enhances the understanding of the roles of phenotypic plasticity and environmental factors in the processes of adaptation and speciation.

Genetic dissection of a reduced seed-shattering trait acquired in rice domestication

Asian rice (Oryza sativa L.) was domesticated from wild rice (O. rufipogon Griff.). During rice domestication, the wild characteristic of seed-shattering behaviour was suppressed, enabling an efficient harvest with increased yield. Rice, a stable food for humans, is one of the most important crops consumed by billions of people, especially in Asian countries. With advances in molecular genetic studies, genes or loci involved in reduced seed shattering via the inhibition of abscission layer formation have been identified. The mutations alone showed no inhibitory effect on abscission layer formation in the wild rice O. rufipogon, but their combination enabled a stepwise change in the degree of seed shattering, which may be associated with advances in harvesting tools. In the early stages of rice domestication, the closed panicle formation and slight inhibition of the abscission layer resulted in complementary effects that increased harvesting efficiency. Furthermore, common and distinct loci were found to contribute to reduced seed shattering in groups of rice cultivars, indicating that mutations at seed-shattering loci are important information for tracing the process of rice domestication.

Fumarate reductase drives methane emissions in the genus Oryza through differential regulation of the rhizospheric ecosystem

The emergence of waterlogged Oryza species ∼15Mya (million years ago) supplied an anoxic warm bed for methane-producing microorganisms, and methane emissions have hence accompanied the entire evolutionary history of the genus Oryza. However, to date no study has addressed how methane emission has been altered during Oryza evolution. In this paper we used a diverse collection of wild and cultivated Oryza species to study the relation between Oryza evolution and methane emissions. Phylogenetic analyses and methane detection identified a co-evolutionary pattern between Oryza and methane emissions, mediated by the diversity of the rhizospheric ecosystems arising from different oxygen levels. Fumarate was identified as an oxygen substitute used to retain the electron transport/energy production in the anoxic rice root, and the contribution of fumarate reductase to Oryza evolution and methane emissions has also been assessed. We confirmed the between-species patterns using genetic dissection of the traits in a cross between a low and high methane-emitting species. Our findings provide novel insights on the evolutionary processes of rice paddy methane emissions: the evolution of wild rice produces different Oryza species with divergent rhizospheric ecosystem attributing to the different oxygen levels and fumarate reductase activities, methane emissions are comprehensively assessed by the rhizospheric environment of diversity Oryza species and result in a co-evolution pattern.

OsKASI-2 is required for the regulation of unsaturation levels of membrane lipids and chilling tolerance in rice

Chilling stress has seriously limited the global production and geographical distribution of rice. However, the molecular mechanisms associated with plant responses to chilling stress are less known. In this study, we revealed a member of β-ketoacyl-ACP synthase I family (KASI), OsKASI-2 which confers chilling tolerance in rice. OsKASI-2 encodes a chloroplast-localized KASI enzyme mainly expressed in the leaves and anthers of rice and strongly induced by chilling stress. Disruption of OsKASI-2 led to decreased KAS enzymatic activity and the levels of unsaturated fatty acids, which impairs degree of unsaturation of membrane lipids, thus increased sensitivity to chilling stress in rice. However, the overexpression of OsKASI-2 significantly improved the chilling tolerance ability in rice. In addition, OsKASI-2 may regulate ROS metabolism in response to chilling stress. Natural variation of OsKASI-2 might result in difference in chilling tolerance between indica and japonica accessions, and Hap1 of OsKASI-2 confers chilling tolerance in rice. Taken together, we suggest OsKASI-2 is critical for regulating degree of unsaturation of membrane lipids and ROS accumulation for maintenance of membrane structural homeostasis under chilling stress, and provide a potential target gene for improving chilling tolerance of rice.

MORN motif-containing protein OsMORN1 and OsMORN2 are crucial for rice pollen viability and cold tolerance

The pollen viability directly affects the pollination process and the ultimate grain yield of rice. Here, we identified that the MORN motif-containing proteins, OsMORN1 and OsMORN2, had a crucial role in maintaining pollen fertility. Compared with the wild type (WT), the pollen viability of the osmorn1 and osmorn2 mutants was reduced, and pollen germination was abnormal, resulting in significantly lower spikelet fertility, seed-setting rate, and grain yield per plant. Further investigation revealed that OsMORN1 was localized to the Golgi apparatus and lipid droplets. Lipids associated with pollen viability underwent alterations in osmorn mutants, such as the diacylglyceride (18:3_18:3) was 5.1-fold higher and digalactosyldiacylglycerol (18:2_18:2) was 5.2-fold lower in osmorn1, while the triacylglycerol (TG) (16:0_18:2_18:3) was 8.3-fold higher and TG (16:0_18:1_18:3) was 8.5-fold lower in osmorn2 than those in WT. Furthermore, the OsMORN1/2 was found to be associated with rice cold tolerance, as osmorn1 and osmorn2 mutants were more sensitive to chilling stress than WT. The mutants displayed increased hydrogen peroxide accumulation, reduced antioxidant enzyme activities, elevated malondialdehyde content, and a significantly decreased seedling survival rate. Lipidomics analysis revealed distinct alterations in lipids under low temperature, highlighting significant changes in TG (18:2_18:3_18:3) and TG (18:4_18:2_18:2) in osmorn1, TG (16:0_18:2_18:2) and PI (17:2_18:3) in osmorn2 compared to the WT. Therefore, it suggested that OsMORN1 and OsMORN2 regulate both pollen viability and cold tolerance through maintaining lipid homeostasis.

A major gene for chilling tolerance variation in Indica rice codes for a kinase OsCTK1 that phosphorylates multiple substrates under cold

Rice is susceptible to chilling stress. Identifying chilling tolerance genes and their mechanisms are key to improve rice performance. Here, we performed a genome-wide association study to identify regulatory genes for chilling tolerance in rice. One major gene for chilling tolerance variation in Indica rice was identified as a casein kinase gene OsCTK1. Its function and natural variation are investigated at the physiological and molecular level by its mutants and transgenic plants. Potential substrates of OsCTK1 were identified by phosphoproteomic analysis, protein-protein interaction assay, in vitro kinase assay, and mutant characterization. OsCTK1 positively regulates rice chilling tolerance. Three of its putative substrates, acidic ribosomal protein OsP3B, cyclic nucleotide-gated ion channel OsCNGC9, and dual-specific mitogen-activated protein kinase phosphatase OsMKP1, are each involved in chilling tolerance. In addition, a natural OsCTK1 chilling-tolerant (CT) variant exhibited a higher kinase activity and conferred greater chilling tolerance compared with a chilling-sensitive (CS) variant. The CT variant is more prevalent in CT accessions and is distributed more frequently in higher latitude compared with the CS variant. This study thus enables a better understanding of chilling tolerance mechanisms and provides gene variants for genetic improvement of chilling tolerance in rice.

Genetic architecture of ecological divergence between Oryza rufipogon and Oryza nivara

Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding.

A mitochondrial pentatricopeptide repeat protein enhances cold tolerance by modulating mitochondrial superoxide in rice

Cold stress affects rice growth and productivity. Defects in the plastid-localized pseudouridine synthase OsPUS1 affect chloroplast ribosome biogenesis, leading to low-temperature albino seedlings and accumulation of reactive oxygen species (ROS). Here, we report an ospus1-1 suppressor, sop10. SOP10 encodes a mitochondria-localized pentatricopeptide repeat protein. Mutations in SOP10 impair intron splicing of the nad4 and nad5 transcripts and decrease RNA editing efficiency of the nad2, nad6, and rps4 transcripts, resulting in deficiencies in mitochondrial complex I, thus decrease ROS generation and rescuing the albino phenotype. Overexpression of different compartment-localized superoxide dismutases (SOD) genes in ospus1-1 reverses the ROS over-accumulation and albino phenotypes to various degrees, with Mn-SOD reversing the best. Mutation of SOP10 in indica rice varieties enhances cold tolerance with lower ROS levels. We find that the mitochondrial superoxide plays a key role in rice cold responses, and identify a mitochondrial superoxide modulating factor, informing efforts to improve rice cold tolerance.

Differentiation of Morphological Traits and Genome-Wide Expression Patterns between Rice Subspecies Indica and Japonica

Changes in gene expression patterns can lead to the variation of morphological traits. This phenomenon is particularly evident in recent evolution events such as crop domestication and responses to environmental stress, where alterations in expression levels can efficiently give rise to domesticated syndromes and adaptive phenotypes. Rice (Oryza sativa L.), one of the world's most crucial cereal crops, comprises two morphologically distinct subspecies, Indica and Japonica. To investigate the morphological divergence between these two rice subspecies, this study planted a total of 315 landrace individuals of both Indica and Japonica under identical cultivation conditions. Out of the 16 quantitative traits measured in this study, 12 exhibited significant differences between the subspecies. To determine the genetic divergence between Indica and Japonica at the whole-genome sequence level, we constructed a phylogenetic tree using a resequencing dataset encompassing 95 rice landrace accessions. The samples formed two major groups that neatly corresponded to the two subspecies, Indica and Japonica. Furthermore, neighbor-joining (NJ) trees based on the expression quantity of effectively expressed genes (EEGs) across five different tissues categorized 12 representative samples into two major clades aligning with the two subspecies. These results imply that divergence in genome-wide expression levels undergoes stabilizing selection under non-stressful conditions, with evolutionary trends in expression levels mirroring sequence variation levels. This study further supports the pivotal role of changes in genome-wide expression regulation in the divergence of the two rice subspecies, Indica and Japonica.

Multiple domestications of Asian rice

The origin of domesticated Asian rice (Oryza sativa L.) has been controversial for more than half a century. The debates have focused on two leading hypotheses: a single domestication event in China or multiple domestication events in geographically separate areas. These two hypotheses differ in their predicted history of genes/alleles selected during domestication. Here we amassed a dataset of 1,578 resequenced genomes, including an expanded sample of wild rice from throughout its geographic range. We identified 993 selected genes that generated phylogenetic trees on which japonica and indica formed a monophyletic group, suggesting that the domestication alleles of these genes originated only once in either japonica or indica. Importantly, the domestication alleles of most selected genes (~80%) stemmed from wild rice in China, but the domestication alleles of a substantial minority of selected genes (~20%) originated from wild rice in South and Southeast Asia, demonstrating separate domestication events of Asian rice.

Overexpression of OsPIN9 Impairs Chilling Tolerance via Disturbing ROS Homeostasis in Rice

The auxin efflux transporter PIN-FORMED (PIN) family is one of the major protein families that facilitates polar auxin transport in plants. Here, we report that overexpression of OsPIN9 leads to altered plant architecture and chilling tolerance in rice. The expression profile analysis indicated that OsPIN9 was gradually suppressed by chilling stress. The shoot height and adventitious root number of OsPIN9-overexpressing (OE) plants were significantly reduced at the seedling stage. The roots of OE plants were more tolerant to N-1-naphthylphthalamic acid (NPA) treatment than WT plants, indicating the disturbance of auxin homeostasis in OE lines. The chilling tolerance assay showed that the survival rate of OE plants was markedly lower than that of wild-type (WT) plants. Consistently, more dead cells, increased electrolyte leakage, and increased malondialdehyde (MDA) content were observed in OE plants compared to those in WT plants under chilling conditions. Notably, OE plants accumulated more hydrogen peroxide (H2O2) and less superoxide anion radicals (O2-) than WT plants under chilling conditions. In contrast, catalase (CAT) and superoxide dismutase (SOD) activities in OE lines decreased significantly compared to those in WT plants at the early chilling stage, implying that the impaired chilling tolerance of transgenic plants is probably attributed to the sharp induction of H2O2 and the delayed induction of antioxidant enzyme activities at this stage. In addition, several OsRboh genes, which play a crucial role in ROS production under abiotic stress, showed an obvious increase after chilling stress in OE plants compared to that in WT plants, which probably at least in part contributes to the production of ROS under chilling stress in OE plants. Together, our results reveal that OsPIN9 plays a vital role in regulating plant architecture and, more importantly, is involved in regulating rice chilling tolerance by influencing auxin and ROS homeostasis.

Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of Indica Rice

Cold stress significantly constrains the growth, development, productivity, and distribution of rice, particularly the indica cultivar, known for its susceptibility to cold, limiting its cultivation to specific regions. This study investigated the genes associated with cold responsiveness in the roots of two indica cultivars, SQSL (cold-tolerant) and XZX45 (cold-susceptible), through transcriptome dynamics analysis during the seedling stage. The analysis identified 8144 and 6427 differentially expressed genes (DEGs) in XZX45 and SQSL, respectively. Among these DEGs, 4672 (G2) were shared by both cultivars, while 3472 DEGs (G1) were specific to XZX45, and 1755 DEGs (G3) were specific to SQSL. Additionally, 572 differentially expressed transcription factors (TFs) from 48 TF families, including WRKY, NAC, bHLH, ERF, bZIP, MYB, C2H2, and GRAS, were identified. Gene Ontology (GO) enrichment analysis revealed significant enrichment of DEGs in the G3 group, particularly in the "response to cold" category, highlighting the crucial role of these specific genes in response to cold stress in SQSL. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated pronounced enrichment of DEGs in the G3 group in metabolic pathways such as "Pyruvate metabolism", "Glycolysis/Gluconeogenesis", and "Starch and sucrose metabolism", contributing to cold tolerance mechanisms in SQSL. Overall, this study provides comprehensive insights into the molecular mechanisms underlying cold responses in the indica cultivar, informing future genetic improvement strategies to enhance cold tolerance in susceptible indica rice cultivars.

Mutations, sex, and genetic diversity: New arguments for partially directed evolution

A review of the theories of the existence of sexes, genetic diversity, and the distribution of mutations among organisms shows that all these concepts are not a product of random evolution and cannot be explained within the framework of Darwinism. Most mutations are the result of the genome acting on itself. This is an organized process that is implemented very differently in different species, in different places in the genome. Because of the fact that it is not random, this process must be directed and regulated, albeit with complex and not fully understood laws. This means that an additional reason must be included in order to model such mutations during evolution. The assumption of directionality must not only be explicitly included in evolutionary theory but must also occupy a central place in it. In this study an updated model of partially directed evolution is constructed, which is capable of qualitatively explaining the indicated features of evolution. Experiments are described that can confirm or disprove the proposed model.

bHLH57 confers chilling tolerance and grain yield improvement in rice

Chilling stress has become a major limiting factor that reduces crop productivity worldwide. In this study, we identified a new gene bHLH57, whose product enhances chilling tolerance in rice at diverse developmental stages. bHLH57 was mainly expressed in leaves and anthers, and its protein was targeted to the nucleus. Overexpression of bHLH57 enhanced chilling tolerance by increasing trehalose synthesis, whereas its mutants by CRISPR/Cas9-mediated mutagenesis were more sensitive to chilling and had reduced trehalose. Meanwhile, bHLH57 may regulate ROS metabolism and CBFs/DREBs- dependent pathways in response to chilling stress. In addition, the overexpression of bHLH57 resulted in increased grain yield under normal and chilling conditions, however, the disruption of bHLH57 displayed decreased grain size and seed setting rate, thus reduced grain yield. Phylogenetic and nucleotide diversity analyses suggested that bHLH57 is relatively conserved in monocotyledons, and may be selected during indica populations adaptation. Taken together, we have identified a new bHLH regulator involved rice chilling tolerance and grain yield, and provide a potential target gene for improving chilling tolerance and grain yield of rice.

Trait specific marker-based characterization and population structure analysis in rice (Oryza sativa L.) germplasm of Kashmir Himalayas

BACKGROUND

Rice is a key food grain contributor to the global food grain basket and is considered the main food crop in India with a large number of varieties released every year. SSR markers have proven to be an excellent tool for studying genetic diversity. As a result, the present study was done to characterize and assess genetic diversity as well as population structural aspects.

METHODS AND RESULTS

Fifty genotypes of rice were characterized using 40 SSR markers to assess the genetic diversity and genetic relationship. A total of 114 alleles were amplified with an average of 2.85 alleles per locus. The Polymorphism Information Content (PIC) values varied from 0.30 (RM162) to 0.58 (RM413) with an average of 0.44. Gene diversity was in the range of 0.35 (RM162) to 0.66 (RM413), with an average value of 0.52, while heterozygosity ranged from 0.18 (RM27) to 0.74 (RM55), with an average of 0.39. The population structure revealed a narrow genetic base with only three major subpopulations. Analysis of molecular variance revealed that 74% of the variation was attributed within individuals, 23% was among individuals, and 3% was among populations. Pairwise Fst value of population A & B is 0.024, population B & C is 0.120 and population A & C is 0.115. Dendrogram grouped the genotypes into three clusters with wide variation among the accessions.

CONCLUSION

Genotyping combined with phylogeny and population structure analysis proved to be a powerful method for characterizing germplasm in this study. There is significant gene flow within populations, as well as the presence of different combinations of alleles, and that allelic exchange rates within the populations are higher than among the populations. Assessing the genetic diversity among individual genotypes within populations is quite useful in selecting candidate parents for future breeding programs to improve the target traits in rice for the Himalayan region.

COG2 negatively regulates chilling tolerance through cell wall components altered in rice

Chilling-tolerant QTL gene COG2 encoded an extensin and repressed chilling tolerance by affecting the compositions of cell wall. Rice as a major crop is susceptible to chilling stress. Chilling tolerance is a complex trait controlled by multiple quantitative trait loci (QTLs). Here, we identify a QTL gene, COG2, that negatively regulates cold tolerance at seedling stage in rice. COG2 overexpression transgenic plants are sensitive to cold, whereas knockout transgenic lines enhance chilling tolerance. Natural variation analysis shows that Hap1 is a specific haplotype in japonica/Geng rice and correlates with chilling tolerance. The SNP1 in COG2 promoter is a specific divergency and leads to the difference in the expression level of COG2 between japonica/Geng and indica/Xian cultivars. COG2 encodes a cell wall-localized extensin and affects the compositions of cell wall, including pectin and cellulose, to defense the chilling stress. The results extend the understanding of the adaptation to the environment and provide an editing target for molecular design breeding of cold tolerance in rice.

Dual Domestication, Diversity, and Differential Introgression in Old World Cotton Diploids

Domestication in the cotton genus is remarkable in that it has occurred independently four different times at two different ploidy levels. Relatively little is known about genome evolution and domestication in the cultivated diploid species Gossypium herbaceum and Gossypium arboreum, due to the absence of wild representatives for the latter species, their ancient domestication, and their joint history of human-mediated dispersal and interspecific gene flow. Using in-depth resequencing of a broad sampling from both species, we provide support for their independent domestication, as opposed to a progenitor-derivative relationship, showing that diversity (mean π = 6 × 10-3) within species is similar, and that divergence between species is modest (FST = 0.413). Individual accessions were homozygous for ancestral single-nucleotide polymorphisms at over half of variable sites, while fixed, derived sites were at modest frequencies. Notably, two chromosomes with a paucity of fixed, derived sites (i.e., chromosomes 7 and 10) were also strongly implicated as having experienced high levels of introgression. Collectively, these data demonstrate variable permeability to introgression among chromosomes, which we propose is due to divergent selection under domestication and/or the phenomenon of F2 breakdown in interspecific crosses. Our analyses provide insight into the evolutionary forces that shape diversity and divergence in the diploid cultivated species and establish a foundation for understanding the contribution of introgression and/or strong parallel selection to the extensive morphological similarities shared between species.

WRKY53 negatively regulates rice cold tolerance at the booting stage by fine-tuning anther gibberellin levels

Cold tolerance at the booting (CTB) stage is a major factor limiting rice (Oryza sativa L.) productivity and geographical distribution. A few cold-tolerance genes have been identified, but they either need to be overexpressed to result in CTB or cause yield penalties, limiting their utility for breeding. Here, we characterize the function of the cold-induced transcription factor WRKY53 in rice. The wrky53 mutant displays increased CTB, as determined by higher seed setting. Low temperature is associated with lower gibberellin (GA) contents in anthers in the wild type but not in the wrky53 mutant, which accumulates slightly more GA in its anthers. WRKY53 directly binds to the promoters of GA biosynthesis genes and transcriptionally represses them in anthers. In addition, we uncover a possible mechanism by which GA regulates male fertility: SLENDER RICE1 (SLR1) interacts with and sequesters two critical transcription factors for tapetum development, UNDEVELOPED TAPETUM1 (UDT1), and TAPETUM DEGENERATION RETARDATION (TDR), and GA alleviates the sequestration by SLR1, thus allowing UDT1 and TDR to activate transcription. Finally, knocking out WRKY53 in diverse varieties increases cold tolerance without a yield penalty, leading to a higher yield in rice subjected to cold stress. Together, these findings provide a target for improving CTB in rice.

Multiple Facets of Nitrogen: From Atmospheric Gas to Indispensable Agricultural Input

Nitrogen (N) is a gas and the fifth most abundant element naturally found in the atmosphere. N's role in agriculture and plant metabolism has been widely investigated for decades, and extensive information regarding this subject is available. However, the advent of sequencing technology and the advances in plant biotechnology, coupled with the growing interest in functional genomics-related studies and the various environmental challenges, have paved novel paths to rediscovering the fundamentals of N and its dynamics in physiological and biological processes, as well as biochemical reactions under both normal and stress conditions. This work provides a comprehensive review on multiple facets of N and N-containing compounds in plants disseminated in the literature to better appreciate N in its multiple dimensions. Here, some of the ancient but fundamental aspects of N are revived and the advances in our understanding of N in the metabolism of plants is portrayed. It is established that N is indispensable for achieving high plant productivity and fitness. However, the use of N-rich fertilizers in relatively higher amounts negatively affects the environment. Therefore, a paradigm shift is important to shape to the future use of N-rich fertilizers in crop production and their contribution to the current global greenhouse gases (GHGs) budget would help tackle current global environmental challenges toward a sustainable agriculture.

CRISPR/Cas9-mediated mutation in auxin efflux carrier OsPIN9 confers chilling tolerance by modulating reactive oxygen species homeostasis in rice

Phytohormone auxin plays a vital role in plant development and responses to environmental stresses. The spatial and temporal distribution of auxin mainly relies on the polar distribution of the PIN-FORMED (PIN) auxin efflux carriers. In this study, we dissected the functions of OsPIN9, a monocot-specific auxin efflux carrier gene, in modulating chilling tolerance in rice. The results showed that OsPIN9 expression was dramatically and rapidly suppressed by chilling stress (4°C) in rice seedlings. The homozygous ospin9 mutants were generated by CRISPR/Cas9 technology and employed for further research. ospin9 mutant roots and shoots were less sensitive to 1-naphthaleneacetic acid (NAA) and N-1-naphthylphthalamic acid (NPA), indicating the disturbance of auxin homeostasis in the ospin9 mutants. The chilling tolerance assay showed that ospin9 mutants were more tolerant to chilling stress than wild-type (WT) plants, as evidenced by increased survival rate, decreased membrane permeability, and reduced lipid peroxidation. However, the expression of well-known C-REPEAT BINDING FACTOR (CBF)/DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 1 (DREB)-dependent transcriptional regulatory pathway and Ca²⁺ signaling genes was significantly induced only under normal conditions, implying that defense responses in ospin9 mutants have probably been triggered in advance under normal conditions. Histochemical staining of reactive oxygen species (ROS) by 3'3-diaminobenzidine (DAB) and nitroblue tetrazolium (NBT) showed that ospin9 mutants accumulated more ROS than WT at the early stage of chilling stress, while less ROS was observed at the later stage of chilling treatment in ospin9 mutants. Consistently, antioxidant enzyme activity, including catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD), improved significantly during the early chilling treatments, while was kept similar to WT at the later stage of chilling treatment, implying that the enhanced chilling tolerance of ospin9 mutants is mainly attributed to the earlier induction of ROS and the improved ROS scavenging ability at the subsequent stages of chilling treatment. In summary, our results strongly suggest that the OsPIN9 gene regulates chilling tolerance by modulating ROS homeostasis in rice.

The Fits and Starts of Indian Rice Domestication: How the Movement of Rice Across Northwest India Impacted Domestication Pathways and Agricultural Stories

Rice is currently the staple food for over 3.5 billion people and is arguably the most important crop exploited by humans. Understanding how we came to the point where a single crop dominates the lives of almost half of the Earth’s population has major significance for our future, even more so given the climatic instability we face today, as rice is a cereal that is dependent on water to an extreme degree. In this study, the nature of early rice agriculture in South Asia is explored, looking at how this critical crop may have begun to be exploited, cultivated, and then brought under agricultural regimes during the long span between c.6500 and 1500 BC. There is now clear evidence for early Holocene cultivation of rice in the Middle Gangetic plains of northern India, but there is still considerable debate about the timing of when this cultivation began and whether it involved domestication of rice. By 3200 BC, however, rice agriculture was present outside the Ganges in the Indus Civilization. The data show accelerated domestication in the Indus environment and agricultural systems that played a part in later hybridization with the arrival of Chinese rice. Understanding how this move from its place of origin to a new environment may have become entangled in the domestication pathways of South Asia rice prior to the arrival of Chinese rice c.1500 BC are important to the overall rice story, as they play into modern concerns relating to biodiversity and different ways of growing and watering rice.

Genomic Survey of PEBP Gene Family in Rice: Identification, Phylogenetic Analysis, and Expression Profiles in Organs and under Abiotic Stresses

Phosphatidylethanolamine-binding-protein (PEBP) domain-containing proteins play important roles in multiple developmental processes of plants; however, functions of few members in the PEBP gene family have been elucidated in rice and other crops. In this study, we found that twenty OsPEBPs genes identified in rice are not evenly distributed on the chromosomes. Four colinear pairs are identified, suggesting the duplication of OsPEBPs during evolution. The OsPEBPs are classified into six subgroups by phylogenetic analysis. The structure of all the OsPEBP genes and encoded proteins are similar. The 262 PEBP domain-containing proteins from crops are divided into six groups. The number of colinear pairs varies between rice and other crops. More than thirty cis-acting elements in the promoter region of OsPEBPs are discovered. Expression profiles of OsPEBP genes are differential. Most of the OsPEBPs expression can be regulated by NaCl, ABA, JA, and light, indicating that OsPEBPs may be involved in the control of the response to the environmental signals. These results lay sound foundation to further explore their functions in development of rice and crops.

Low-temperature stress affects reactive oxygen species, osmotic adjustment substances, and antioxidants in rice (Oryza sativa L.) at the reproductive stage

The sensitivity of rice to low-temperature stress (LTS), especially at the reproductive stage, is a primary factor of rice yield fluctuation in cold cultivate region. Here, the changes of reactive oxygen species (ROS), osmotic adjustment substances, and antioxidants in different tissues were analyzed during rice growing under low temperatures (LT) at the reproductive stage. Results showed that LTS increases the levels of proline (Pro), soluble protein (SP), glutathione (GSH), superoxidase (SOD), and ascorbate peroxidase (APX) in LJ25 (LTS-resistant) and LJ11 (LTS-sensitive). The activities of catalase (CAT) and peroxidase (POD) were significantly increased in LJ25 but decreased in LJ11 under LTS, while an opposite trend in ROS and malondialdehyde (MDA) was observed in both varieties. Moreover, most physicochemical properties were higher in flag leaves and panicles compared with those in leaf sheaths. The expression patterns of OsCOIN, OsCATC, OsMAP1, OsPOX1, and OsAPX were the same with phenotypic changes in Pro and the enzymes encoded by them, confirming the accuracy of the physicochemical analysis. Therefore, only CAT and POD increased more in LJ25, suggesting they could be the key factors used for LT-tolerant breeding of rice in cold regions.

NILs of Cold Tolerant Japonica Cultivar Exhibited New QTLs for Mineral Elements in Rice

Chilling stress at booting stage can cause floret deterioration and sterility by limiting the supply of food chain and the accumulation of essential mineral elements resulting in reduction of yield and grain quality attributes in rice. Genomic selection of chilling tolerant rice with reference to the accumulation of mineral elements will have great potential to cope with malnutrition and food security in times of climate change. Therefore, a study was conducted to explore the genomic determinants of cold tolerance and mineral elements content in near-isogenic lines (NILs) of japonica rice subjected to chilling stress at flowering stage. Detailed morphological analysis followed by quantitative analysis of 17 mineral elements revealed that the content of phosphorus (P, 3,253 mg/kg) and potassium (K, 2,485 mg/kg) were highest while strontium (Sr, 0.26 mg/kg) and boron (B, 0.34 mg/kg) were lowest among the mineral elements. The correlation analysis revealed extremely positive correlation of phosphorus (P) and copper (Cu) with most of the cold tolerance traits. Among all the effective ear and the second leaf length correlation was significant with half of the mineral elements. As a result of comparative analysis, some QTLs (qBRCC-1, qBRCIC-2, qBRZC-6, qBRCHC-6, qBRMC-6, qBRCIC-6a, qBRCIC-6b, qBRCHC-6, and qBRMC-6) identified for calcium (Ca), zinc (Zn), chromium (Cr) and magnesium (Mg) on chromosome number 1, 2, and 6 while, a novel QTL (qBCPC-1) was identified on chromosome number 1 for P element only. These findings provided bases for the identification of candidate genes involved in mineral accumulation and cold tolerance in rice at booting stage.

Stepwise selection of natural variations at CTB2 and CTB4a improves cold adaptation during domestication of japonica rice

The improvement of cold adaptation has contributed to the increased growing area of rice. Standing variation and de novo mutation are distinct natural sources of beneficial alleles in plant adaptation. However, the genetic mechanisms and evolutionary patterns underlying these sources in a single population during crop domestication remain elusive. Here we cloned the CTB2 gene, encoding a UDP-glucose sterol glucosyltransferase, for cold tolerance in rice at the booting stage. A single standing variation (I408V) in the conserved UDPGT domain of CTB2 originated from Chinese Oryza rufipogon and contributed to the cold adaptation of Oryza sativa ssp. japonica. CTB2 is located in a 56.8 kb region, including the previously reported gene CTB4a in which de novo mutation arose c. 3200 yr BP in Yunnan province, China, conferring cold tolerance. Standing variation of CTB2 and de novo mutation of CTB4a underwent stepwise selection to facilitate cold adaptation to expand rice cultivation from high-altitude to high-latitude regions. These results provide an example of stepwise selection on two kinds of variation and describe a new molecular mechanism of cold adaptation in japonica rice.

Advances in Genomics Approaches Shed Light on Crop Domestication

Crop domestication occurred ~10,000–12,000 years ago when humans shifted from a hunter–gatherer to an agrarian society. Crops were domesticated by selecting the traits in wild plant species that were suitable for human use. Research is crucial to elucidate the mechanisms and processes involved in modern crop improvement and breeding. Recent advances in genomics have revolutionized our understanding of crop domestication. In this review, we summarized cutting-edge crop domestication research by presenting its (1) methodologies, (2) current status, (3) applications, and (4) perspectives. Advanced genomics approaches have clarified crop domestication processes and mechanisms, and supported crop improvement.

Homoploid F1 hybrids and segmental allotetraploids of japonica and indica rice subspecies show similar and enhanced tolerance to nitrogen deficiency than parental lines

It remains unclear whether the merger of two divergent genomes by hybridization at the homoploid level or coupled with whole-genome duplication (WGD; allopolyploidy) can result in plants having better tolerance to stress conditions. In this study, we compared phenotypic performance and gene expression in the two diploid subspecies of rice (Oryza sativa subsp. japonica and indica), their reciprocal F1 hybrids, and in segmental allotetraploids under normal and nitrogen (N)-deficient conditions. We found that F1 hybrids and tetraploids showed higher and similar levels of tolerance to N deficiency than either parent. In parallel, total expression levels of 18 relevant functional genes were less perturbed by N deficiency in the F1 hybrids and tetraploids than in the parents. This was consistent with stable intrinsic partitioning of allelic/homoeologous expression defined by parental legacy in the homoploid F1 hybrids/tetraploids between the two conditions. The results suggest that genetic additivity at both the homoploid and allopolyploidy level might lead to similar beneficial phenotypic responses to nitrogen stress compared with the parents. The lack of synergistic responses to N limitation concomitant with WGD, relative to that exhibited by F1 hybrids, adds new empirical evidence in support of the emerging hypothesis that hybridization by itself can play a significant role in plant adaptive evolution in times of stress.

Molecular and genetic dissection of the USDA rice mini-core collection using high-density SNP markers

Molecular tools and knowledge of crop germplasm are vital for their effective utilization. In this study, we developed 40,866 high-quality and well distributed SNPs for a rice mini-core collection (RMC) developed by the United States Department of Agriculture (USDA). The high-quality SNPs clustered the USDA-RMC into five subpopulations (Ind, indica; Aus, aus; Afr, African rice; TeJ, temperate japonica; TrJ, tropical japonica) and one admixture (Adm). This classification was further confirmed by phylogenetic and principal component analyses. The rice ARO (aromatic) subpopulation of previous studies was re-assigned with Adm and the WD (wild-type) subpopulation was re-defined to the Afr subpopulation because most of its accessions are African cultivated rice. The Aus and Ind subpopulations had a substantially wider genetic variation than the TrJ and TeJ subpopulations. The genetic diversities were much larger between the Ind or Aus subpopulation and the TrJ or TeJ subpopulation than between the Afr subpopulation and the Ind, Aus, TrJ or TeJ subpopulation. Comparative agronomic trait analysis between the subpopulations also supported the genetic structure and variation of the RMC, and suggested the existence of extensive variation in the genes controlling agronomic traits among them. Furthermore, analysis of ancestral membership of the RMC accessions revealed that reproductive barrier or wide incompatibility existed between the Indica and Japonica groups, while gene flow occurred between them. These results provide high-quality SNPs and knowledge of genetic structure and diversity of the USDA-RMC necessary for enhanced rice research and breeding.

The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes

The plastid is an essential organelle in autotrophic plant cells, descending from free-living cyanobacteria and acquired by early eukaryotic cells through endosymbiosis roughly one billion years ago. It contained a streamlined genome (plastome) that is uniparentally inherited and non-recombinant, which makes it an ideal tool for resolving the origin and diversity of plant species and populations. In the present study, a large dataset was amassed by de novo assembling plastomes from 295 common wild rice (Oryza rufipogon Griff.) and 1135 Asian cultivated rice (Oryza sativa L.) accessions, supplemented with 34 plastomes from other Oryza species. From this dataset, the phylogenetic relationships and biogeographic history of O. rufipogon and O. sativa were reconstructed. Our results revealed two major maternal lineages across the two species, which further diverged into nine well supported genetic clusters. Among them, the Or-wj-I/II/III and Or-wi-I/II genetic clusters were shared with cultivated (percentage for each cluster ranging 54.9%∼99.3%) and wild rice accessions. Molecular dating, phylogeographic analyses and reconstruction of population historical dynamics indicated an earlier origin of the Or-wj-I/II genetic clusters from East Asian with at least two population expansions, and later origins of other genetic clusters from multiple regions with one or more population expansions. These results supported a single origin of japonica rice (mainly in Or-wj-I/II) and multiple origins of indica rice (in all five clusters) for the history of rice domestication. The massive plastomic data set presented here provides an important resource for understanding the history and evolution of rice domestication as well as a genomic resources for use in future breeding and conservation efforts.

Differentiation, evolution and utilization of natural alleles for cold adaptability at the reproductive stage in rice

Genetic studies on cold tolerance at the reproductive stage in rice could lead to significant reductions in yield losses. However, knowledge about the genetic basis and adaptive differentiation, as well as the evolution and utilization of the underlying natural alleles, remains limited. Here, 580 rice accessions in two association panels were used to perform genome-wide association study, and 156 loci associated with cold tolerance at the reproductive stage were identified. Os01g0923600 and Os01g0923800 were identified as promising candidate genes in qCTB1t, a major associated locus. Through population genetic analyses, 22 and 29 divergent regions controlling cold adaptive differentiation inter-subspecies (Xian/Indica and Geng/Japonica) and intra-Geng, respectively, were identified. Joint analyses of four cloned cold-tolerance genes showed that they had different origins and utilizations under various climatic conditions. bZIP73 and OsAPX1 differentiating inter-subspecies evolved directly from wild rice, whereas the novel mutations CTB4a and Ctb1 arose in Geng during adaptation to colder climates. The cold-tolerant Geng accessions have undergone stronger selection under colder climate conditions than other accessions during the domestication and breeding processes. Additive effects of dominant allelic variants of four identified genes have been important in adaptation to cold in modern rice varieties. Therefore, this study provides valuable information for further gene discovery and pyramiding breeding to improve cold tolerance at the reproductive stage in rice.

Natural Genetic Resources from Diverse Plants to Improve Abiotic Stress Tolerance in Plants

The current agricultural system is biased for the yield increase at the cost of biodiversity. However, due to the loss of precious genetic diversity during domestication and artificial selection, modern cultivars have lost the adaptability to cope with unfavorable environments. There are many reports on variations such as single nucleotide polymorphisms (SNPs) and indels in the stress-tolerant gene alleles that are associated with higher stress tolerance in wild progenitors, natural accessions, and extremophiles in comparison with domesticated crops or model plants. Therefore, to gain a better understanding of stress-tolerant traits in naturally stress-resistant plants, more comparative studies between the modern crops/model plants and crop progenitors/natural accessions/extremophiles are required. In this review, we discussed and summarized recent progress on natural variations associated with enhanced abiotic stress tolerance in various plants. By applying the recent biotechniques such as the CRISPR/Cas9 gene editing tool, natural genetic resources (i.e., stress-tolerant gene alleles) from diverse plants could be introduced to the modern crop in a non-genetically modified way to improve stress-tolerant traits.

Divergence in flowering time is a major component contributing to reproductive isolation between two wild rice species (Oryza rufipogon and O. nivara)

It is of critical importance for our understanding of speciation process to determine the forms of reproductive isolation and their relative importance in species divergence. Oryza nivara and O. rufipogon are direct ancestors of Asian cultivated rice and a progenitor-daughter species pair. Investigating the reproductive isolation between them provides insights into plant speciation and helps understanding of the rice domestication. Here, we quantitatively measured the major components of reproductive isolation between the two species based on common garden and crossing experiments for three pairs of sympatric populations in Nepal, Cambodia and Laos. We revealed significant differences in the flowering times between species pairs, with O. nivara flowering much earlier than O. rufipogon. A very weak reduction in seed set but no reduction in F1 viability and fertility were detected for the crosses between species relative to those within species. Moreover, we detected asymmetrical compatibility between species and found that emasculation significantly decreased pollination success in O. nivara but not in O. rufipogon. Our study demonstrates that the divergence between O. nivara and O. rufipogon is maintained almost entirely by the difference in flowering times and suggests that differential flowering times contribute to both habitat preferences and reproductive isolation between species.

A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice

Oryza rufipogon Griff. is a wild progenitor of the Asian cultivated rice Oryza sativa. To better understand the genomic diversity of the wild rice, high-quality reference genomes of O. rufipogon populations are needed, which also facilitate utilization of the wild genetic resources in rice breeding. In this study, we generated a chromosome-level genome assembly of O. rufipogon using a combination of short-read sequencing, single-molecule sequencing, BioNano and Hi-C platforms. The genome sequence (399.8 Mb) was assembled into 46 scaffolds on the 12 chromosomes, with contig N50 and scaffold N50 of 13.2 Mb and 20.3 Mb, respectively. The genome contains 36,520 protein-coding genes, and 49.37% of the genome consists of repetitive elements. The genome has strong synteny with those of the O. sativa subspecies indica and japonica, but containing some large structural variations. Evolutionary analysis unveiled the polyphyletic origins of O. sativa, in which the japonica and indica genome formations involved different divergent O. rufipogon (including O. nivara) lineages, accompanied by introgression of genomic regions between japonica and indica. This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O. sativa subspecies, and valuable information for basic research and rice breeding.

OsTMF attenuates cold tolerance by affecting cell wall properties in rice

Plant cell wall composition and structure can be modified as plants adapt to environmental stresses; however, the underlying regulatory mechanisms remain elusive. Here, we report that OsTMF, a homologue of the human TATA modulatory factor (TMF) in rice (Oryza sativa) and highly conserved in plants, negatively regulates cold tolerance through modification of cell wall properties. Cold stress increased the expression of OsTMF and accumulation of OsTMF in the nucleus, where OsTMF acts as a transcription activator and modulates the expression of genes involved in pectin degradation (OsBURP16), cellulose biosynthesis (OsCesA4 and OsCesA9), and cell wall structural maintenance (genes encoding proline-rich proteins and peroxidases). OsTMF directly activated the expression of OsBURP16, OsCesA4, and OsCesA9 through binding to the TATA cis-elements in their promoters. Under cold stress conditions, OsTMF negatively regulated pectin content and peroxidase activity and positively regulated cellulose content, causing corresponding alterations to cell wall properties, all of which collectively contribute to the negative effect of OsTMF on cold tolerance. Our findings unravel a previously unreported molecular mechanism of a conserved plant TMF protein in the regulation of cell wall changes under cold stress.

Global analysis of differentially expressed genes between two Japonica rice varieties induced by low temperature during the booting stage by RNA-Seq

As one of the abiotic stresses, low temperature severely threatens rice production during its entire growth period, especially during the booting stage. In the present study, transcriptome analysis was performed comparing Longjing (LJ) 25 (chilling-tolerant) and LJ 11 (chilling-sensitive) rice varieties to identify genes associated with chilling tolerance in rice spikelets. A total of 23 845 expressed genes and 13 205 differentially expressed genes (DEGs) were identified, respectively. Gene ontology (GO) enrichment analyses revealed 'response to cold' (containing 180 DEGs) as the only category enriched in both varieties during the entire cold treatment period. Through MapMan analysis, we identified nine and six DEGs related to the Calvin cycle and antioxidant enzymes, respectively, including OsRBCS3, OsRBCS2, OsRBCS4, OsAPX2 and OsCATC, that under chilling stress were markedly downregulated in LJ11 compared with LJ25. Furthermore, we predicted their protein-protein interaction (PPI) network and identified nine hub genes (the threshold of co-expressed gene number ≥ 11) in Cytoscape, including three RuBisCO-related genes with 14 co-expressed genes. Under chilling stress, antioxidant enzyme activities (peroxidase (POD) and catalase (CAT)) were downregulated in LJ11 compared with LJ25. However, the content of malondialdehyde (MDA) was higher in LJ11 compared with LJ25. Collectively, our findings identify low temperature responsive genes that can be effectively used as candidate genes for molecular breeding programmes to increase the chilling tolerance of rice.

Genome-wide identification and phylogenetic analysis of rice FTIP gene family

FT-INTERACTING PROTEIN (FTIP) gene family in rice are the members of multiple C2 domain and transmembrane region proteins (MCTPs). There are many homologs of OsFTIPs in plants; however, the bioinformatics of them remains unclear. In the studies, 13 OsFTIP genes are identified in rice. OsFTIPs are unevenly located in 12 chromosomes. The OsFTIPs are phylogenetically divided into three clades. Cis-elements respond to abiotic stress, light, and hormones are found in the promoter region of OsFTIPs which are induced by the stimuli. All OsFTIPs are expressed with different profiles. Syntenic analysis of 128 OsFTIPs and FTIP-like homologs reveals that various number of gene pairs are identified between rice and other species. The 128 FTIP-like homologs are divided into six groups which fall into three classes. Ten motifs are shared by most OsFTIPs and their homologs. The studies provide a theoretical basis for further elucidating the functions of OsFTIP gene family.

Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice (Oryza sativa L.)

Basmati is considered a unique varietal group of rice (Oryza sativa L.) because of its aroma and superior grain quality. Previous genetic analyses of rice showed that most of the Basmati varieties are classified into the aromatic group. Despite various efforts, genomic relationship of Basmati rice with other varietal groups and genomic variation in Basmati rice are yet to be understood. In the present study, we resequenced the whole genome of three traditional Basmati varieties at a coverage of more than 25X using Illumina HiSeq2500 and mapped the obtained sequences to the reference genome sequences of Nipponbare (japonica rice), Kasalath (aus rice), and Zhenshan 97 (indica rice). Comparison of these sequences revealed common single nucleotide polymorphisms (SNPs) in the genic regions of three Basmati varieties. Analysis of these SNPs revealed that Basmati varieties showed fewer sequence variations compared with the aus group than with the japonica and indica groups. Gene ontology (GO) enrichment analysis indicated that SNPs were present in genes with various biological, molecular, and cellular functions. Additionally, functional annotation of the Basmati mutated gene cluster shared by Nipponbare, Kasalath, and Zhenshan 97 was found to be associated with the metabolic process involved in the cellular aromatic compound, suggesting that aroma is an important specific genomic feature of Basmati varieties. Furthermore, 30 traditional Basmati varieties were classified into three different groups, aromatic (22 varieties), aus (four varieties), and indica (four varieties), based on genome-wide SNPs. All 22 aromatic Basmati varieties harbored the fragrant-inducing Badh2 allele. We also performed comparative analysis of 13 key agronomic and grain quality traits of Basmati rice and other rice varieties. Three traits including length-to-width ratio of grain (L/W ratio), panicle length (PL), and amylose content (AC) showed significant (P < 0.05 and P < 0.01) differences between the aromatic and indica/aus groups. Comparative analysis of genome structure, based on genome sequence variation and GO analysis, revealed that the Basmati genome was derived mostly from the aus and japonica groups. Overall, whole-genome sequence data and genetic diversity information obtained in this study will serve as an important resource for molecular breeding and genetic analysis of Basmati varieties.

Genome-wide analyses reveal the role of noncoding variation in complex traits during rice domestication

Genomes carry millions of noncoding variants, and identifying the tiny fraction with functional consequences is a major challenge for genomics. We assessed the role of selection on long noncoding RNAs (lncRNAs) for domestication-related changes in rice grains. Among 3363 lncRNA transcripts identified in early developing panicles, 95% of those with differential expression (329 lncRNAs) between Oryza sativa ssp. japonica and wild rice were significantly down-regulated in the domestication event. Joint genome and transcriptome analyses reveal that directional selection on lncRNAs altered the expression of energy metabolism genes during domestication. Transgenic experiments and population analyses with three focal lncRNAs illustrate that selection on these loci led to increased starch content and grain weight. Together, our findings indicate that genome-wide selection for lncRNA down-regulation was an important mechanism for the emergence of rice domestication traits.

Signatures of differential selection in chloroplast genome between japonica and indica

BACKGROUND

The domestication process of Asian rice (Oryza sativa L.) is complicated. It's well established that Oryza rufipogon is the ancestor of Asian rice, although the number of domestication events still controversial. Recently, numerous types of studies based on rice nuclear genome have been conducted, but the results are quite different. Chloroplasts (cp) are also part of the rice genome and have a conserved cyclic structure that is valuable for plant genetics and evolutionary studies. Therefore, we conducted chloroplast-based studies, aiming to provide more evidence for the domestication of Asian rice.

RESULTS

A total of 1389 variants were detected from the chloroplast genomes of 412 accessions obtained through the world. Oryza sativa L. ssp. japonica exhibited slightly less diversity (π) than Oryza sativa L. indica and wild rice. The fixation index values (F_ST) revealed that indica and japonica exhibited farther genetic distances compared with wild rice. Across cp genome, Tajima's D test demonstrated that different selection sites occurred in Asian rice. Principal component analyses (PCA) and multidimensional scaling (MDS) clearly classify the Asian rice into different groups. Furthermore, introgression patterns identified that indica and japonica shared no introgression events in cp level, and phylogenetic studies showed cultivated rice were well separated from different type of wild rice.

CONCLUSIONS

Here, we focus on the domestication of Asian rice (indica and japonica). Diversity and phylogenetic analyses revealed some selection characteristics in the chloroplast genome that potentially occurred in different Asian rice during the domestication. The results shown that Asian rice had been domesticated at least twice. In additional, japonica may experience a strong positive selection or bottleneck event during the domestication.

Evidence for selection events during domestication by extensive mitochondrial genome analysis between japonica and indica in cultivated rice

The history of the domestication of rice is controversial, as it remains unknown whether domestication processes occurred once or multiple times. To date, genetic architecture and phylogenetic studies based on the rice nuclear genome have been extensively studied, but the results are quite different. Here, we found interesting results for different selections in Oryza sativa based on comprehensive studies of the rice mitochondrial (mt) genome. In detail, 412 rice germplasms were collected from around the world for variant architecture studies. A total of 10632 variants were detected in the mt genome, including 7277 SNPs and 3355 InDels. Selection signal (πw/πc) indicated that the selection sites in Oryza sativa L. ssp. japonica were different from those of Oryza sativa L. indica rice. The fixation index (FST) was higher between indica and japonica than between indica and wild rice. Moreover, haplotype and phylogenetic analyses also revealed indica clusters and japonica clusters that were well separated from wild rice. As mentioned above, our studies indicate that the selection sites of the indica type were different from those of the japonica type. This means that indica and japonica have experienced different domestication processes. We also found that japonica may have experienced a bottleneck event during domestication.

Parallel Speciation of Wild Rice Associated with Habitat Shifts

The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a “magic” trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.

The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis

Here, we review recent progress in genetic and genomic studies of the diversity of Oryza species. In recent years, unlocking the genetic diversity of Oryza species has provided insights into the genomics of rice domestication, heterosis, and complex traits. Genome sequencing and analysis of numerous wild rice (Oryza rufipogon) and Asian cultivated rice (Oryza sativa) accessions have enabled the identification of genome-wide signatures of rice domestication and the unlocking of the origin of Asian cultivated rice. Moreover, similar studies on genome variations of African rice (Oryza glaberrima) cultivars and their closely related wild progenitor Oryza barthii accessions have provided strong evidence to support a theory of independent domestication in African rice. Integrated genomic approaches have efficiently investigated many heterotic loci in hybrid rice underlying yield heterosis advantages and revealed the genomic architecture of rice heterosis. We conclude that in-depth unlocking of genetic variations among Oryza species will further enhance rice breeding.

Origin of the Aromatic Group of Cultivated Rice (Oryza sativa L.) Traced to the Indian Subcontinent

The aromatic group of Asian cultivated rice is a distinct population with considerable genetic diversity on the Indian subcontinent and includes the popular Basmati types characterized by pleasant fragrance. Genetic and phenotypic associations with other cultivated groups are ambiguous, obscuring the origin of the aromatic population. From analysis of genome-wide diversity among over 1,000 wild and cultivated rice accessions, we show that aromatic rice originated in the Indian subcontinent from hybridization between a local wild population and examples of domesticated japonica that had spread to the region from their own center of origin in East Asia. Most present-day aromatic accessions have inherited their cytoplasm along with 29-47% of their nuclear genome from the local Indian rice. We infer that the admixture occurred 4,000-2,400 years ago, soon after japonica rice reached the region. We identify aus as the original crop of the Indian subcontinent, indica and japonica as later arrivals, and aromatic a specific product of local agriculture. These results prompt a reappraisal of our understanding of the emergence and development of rice agriculture in the Indian subcontinent.

Mining Beneficial Genes for Aluminum Tolerance Within a Core Collection of Rice Landraces Through Genome-Wide Association Mapping With High Density SNPs From Specific-Locus Amplified Fragment Sequencing

Trivalent Aluminum (Al³⁺) in acidic soils is harmful to root growth and significantly reduce crop yields. Therefore, mining beneficial genes for Al tolerance is valuable for rice production. The objective of this research is to identify some beneficial genes for Al tolerance from rice landraces with high density SNP set from SLAF-seq (Specific-Locus Amplified Fragment sequencing). A total of 67,511 SNPs were obtained from SLAF-seq and used for genome-wide association study (GWAS) for Al tolerance with the 150 accessions of rice landraces in the Ting's rice core collection. The results showed that rice landraces in the Ting's rice core collection possessed a wide-range of variation for Al tolerance, measured by relative root elongation (RRE). With the mixed linear models, GWAS identified a total of 25 associations between SNPs and Al tolerant trait with p < 0.001 and false discovery rate (FDR) <10%. The explained percentage by quantitative trait locus (QTL) to phenotypic variation was from 7.27 to 13.31%. Five of twenty five QTLs identified in this study were co-localized with the previously cloned genes or previously identified QTLs related to Al tolerance or root growth/development. These results indicated that landraces are important sources for Al tolerance in rice and the mapping results could provide important information to breed Al tolerant rice cultivars through marker-assisted selection.

Population genetics and evolutionary history of the wild rice species Oryza rufipogon and O. nivara in Sri Lanka

Genetic diversity and population genetic structure of the wild rice species Oryza rufipogon and O. nivara in Sri Lanka were studied using 33 microsatellite markers. A total of 315 individuals of 11 natural populations collected from the wet, intermediate, and dry zones of the country were used in the study. We found a moderate to high level of genetic diversity at the population level, with the polymorphic loci (P) ranging from 60.6% to 100% (average 81.8%) and the expected heterozygosity (H E) varying from 0.294 to 0.481 (average 0.369). A significant genetic differentiation between species and strong genetic structure within species were also observed. Based on species distribution modeling, we detected the dynamics of the preferred habitats for the two species in Sri Lanka and demonstrated that both O. rufipogon and O. nivara populations have expanded substantially since the last internal glacial. In addition, we showed that the geographical distribution of the two species corresponded to the climate zones and identified a few of key environmental variables that contribute to the distribution of the two species, implying the potential mechanism for ecological adaptation of these two species in Sri Lanka. These studies provided important insights into the population genetics and evolution of these wild species in Sri Lanka and are of great significance to the in situ conservation and utilization of these wild resources in genetic improvement of rice.

Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice

Improving the yield by modifying plant architecture was a key step during crop domestication. Here, we show that a 110-kb deletion on the short arm of chromosome 7 in Asian cultivated rice (Oryza sativa), which is closely linked to the previously identified PROSTRATE GROWTH 1 (PROG1) gene, harbors a tandem repeat of seven zinc-finger genes. Three of these genes regulate the plant architecture, suggesting that the deletion also promoted the critical transition from the prostrate growth and low yield of wild rice (O. rufipogon) to the erect growth and high yield of Asian cultivated rice. We refer to this locus as RICE PLANT ARCHITECTURE DOMESTICATION (RPAD). Further, a similar but independent 113-kb deletion is detected at the RPAD locus in African cultivated rice. These results indicate that the deletions, eliminating a tandem repeat of zinc-finger genes, may have been involved in the parallel domestication of plant architecture in Asian and African rice.

Plant architecture transition is one of the great consequences during rice domestication. Here, the authors find that chromosomal deletions linked to the previously known PROG1 gene also participate in plant architecture domestication in both Asian and African cultivated rice.