OsMADS17 simultaneously increases grain number and grain weight in rice.

During the processes of rice domestication and improvement, a trade-off effect between grain number and grain weight was a major obstacle for increasing yield. Here, we identify a critical gene COG1, encoding the transcription factor OsMADS17, with a 65-bp deletion in the 5' untranslated region (5' UTR) presented in cultivated rice increasing grain number and grain weight simultaneously through decreasing mRNA translation efficiency. OsMADS17 controls grain yield by regulating multiple genes and that the interaction with one of them, OsAP2-39, has been characterized. Besides, the expression of OsMADS17 is regulated by OsMADS1 directly. It indicates that OsMADS1-OsMADS17-OsAP2-39 participates in the regulatory network controlling grain yield, and downregulation of OsMADS17 or OsAP2-39 expression can further improve grain yield by simultaneously increasing grain number and grain weight. Our findings provide insights into understanding the molecular basis co-regulating rice yield-related traits, and offer a strategy for breeding higher-yielding rice varieties.

Polyamine oxidase 3 is involved in salt tolerance at the germination stage in rice.

Soil salinity inhibits seed germination and reduces seedling survival rate, resulting in significant yield reductions in crops. Here, we report the identification of a polyamine oxidase, OsPAO3, conferring salt tolerance at the germination stage in rice (Oryza sativa L.), through map-based cloning approach. OsPAO3 is up-regulated under salt stress at the germination stage and highly expressed in various organs. Overexpression of OsPAO3 increases activity of polyamine oxidases, enhancing the polyamine content in seed coleoptiles. Increased polyamine may lead to the enhance of the activity of ROS-scavenging enzymes to eliminate over-accumulated H2O2 and to reduce Na+ content in seed coleoptiles to maintain ion homeostasis and weaken Na+ damage. These changes resulted in stronger salt tolerance at the germination stage in rice. Our findings not only provide a unique gene for breeding new salt-tolerant rice cultivars but also help to elucidate the mechanism of salt tolerance in rice.

Identification of quantitative trait loci for important agronomic traits using chromosome segment substitution lines from a japonica × indica cross in rice.

Asian cultivated rice (Oryza sativa L.) has two subspecies, indica and japonica, which display clear differences in yield-related traits and environmental adaptation. Here, we developed a set of chromosome segment substitution lines (CSSLs) from an advanced backcross between japonica variety C418, as the recipient, and indica variety IR24, as the donor. Through evaluating the genotypes and phenotypes of 181 CSSLs, a total of 85 quantitative trait loci (QTLs) for 14 yield-related traits were detected, with individual QTLs explaining from 6.2 to 42.9% of the phenotypic variation. Moreover, twenty-six of these QTLs could be detected in the two trial sites (Beijing and Hainan). Among these loci, the QTLs for flag leaf width and effective tiller number, qFLW4.2 and qETN4.2, were delimited to an approximately 256-kb interval on chromosome 4. Through a comparison of nucleotide sequences and expression levels in "C418" and the CSSL CR31 containing qFLW4.2 and qETN4.2, we found that the NAL1 (LOC_Os04g52479) gene was the candidate gene for qFLW4.2 and qETN4.2. Our results show that CSSLs are powerful tools for identifying and fine-mapping QTLs, while the novel QTLs identified in this study will also provide new genetic resources for rice improvement. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01343-3.

Genome-Wide Identification of Miniature Inverted-Repeat Transposable Elements by Targeted High-Throughput Sequencing.

Miniature inverted-repeat transposable elements (MITEs) are a subset of short, non-autonomous class II transposable elements and also a major source of eukaryotic genomic variation. Therefore, genome-wide identification of MITE insertions can help to shed light on their copy number variation and genome insertion features. Here, we present a protocol for targeted MITE identification and genotyping by high-throughput sequencing. By introducing genome-wide detection of the rice mJing MITE as an example, we describe DNA extraction, DNA fragmentation, targeted DNA fragment enrichment, library construction for high-throughput sequencing, and sequence analysis.

Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding.

Crop domestication has fundamentally altered the course of human history, causing a shift from hunter-gatherer to agricultural societies and stimulating the rise of modern civilization. A greater understanding of crop domestication would provide a theoretical basis for how we could improve current crops and develop new crops to deal with environmental challenges in a sustainable manner. Here, we provide a comprehensive summary of the similarities and differences in the domestication processes of maize and rice, two major staple food crops that feed the world. We propose that maize and rice might have evolved distinct genetic solutions toward domestication. Maize and rice domestication appears to be associated with distinct regulatory and evolutionary mechanisms. Rice domestication tended to select de novo, loss-of-function, coding variation, while maize domestication more frequently favored standing, gain-of-function, regulatory variation. At the gene network level, distinct genetic paths were used to acquire convergent phenotypes in maize and rice domestication, during which different central genes were utilized, orthologous genes played different evolutionary roles, and unique genes or regulatory modules were acquired for establishing new traits. Finally, we discuss how the knowledge gained from past domestication processes, together with emerging technologies, could be exploited to improve modern crop breeding and domesticate new crops to meet increasing human demands.

TAC4 controls tiller angle by regulating the endogenous auxin content and distribution in rice.

Tiller angle, an important component of plant architecture, greatly influences the grain yield of rice (Oryza sativa L.). Here, we identified Tiller Angle Control 4 (TAC4) as a novel regulator of rice tiller angle. TAC4 encodes a plant-specific, highly conserved nuclear protein. The loss of TAC4 function leads to a significant increase in the tiller angle. TAC4 can regulate rice shoot gravitropism by increasing the indole acetic acid content and affecting the auxin distribution. A sequence analysis revealed that TAC4 has undergone a bottleneck and become fixed in indica cultivars during domestication and improvement. Our findings facilitate an increased understanding of the regulatory mechanisms of tiller angle and also provide a potential gene resource for the improvement of rice plant architecture.

Natural polymorphisms in a pair of NSP2 homoeologs can cause loss of nodulation in peanut.

Microbial symbiosis in legumes is achieved through nitrogen-fixing root nodules, and these are important for sustainable agriculture. The molecular mechanisms underlying development of root nodules in polyploid legume crops are largely understudied. Through map-based cloning and QTL-seq approaches, we identified a pair of homoeologous GRAS transcription factor genes, Nodulation Signaling Pathway 2 (AhNSP2-B07 or Nb) and AhNSP2-A08 (Na), controlling nodulation in cultivated peanut (Arachis hypogaea L.), an allotetraploid legume crop, which exhibited non-Mendelian and Mendelian inheritance, respectively. The segregation of nodulation in the progeny of Nananbnb genotypes followed a 3:1 Mendelian ratio, in contrast to the 5:3~1:1 non-Mendelian ratio for nanaNbnb genotypes. Additionally, a much higher frequency of the nb allele (13%) than the na allele (4%) exists in the peanut germplasm collection, suggesting that Nb is less essential than Na in nodule organogenesis. Our findings reveal the genetic basis of naturally occurred non-nodulating peanut plants, which can be potentially used for nitrogen fixation improvement in peanut. Furthermore, the results have implications for and provide insights into the evolution of homoeologous genes in allopolyploid species.

HIGH-TILLERING AND DWARF 12 modulates photosynthesis and plant architecture by affecting carotenoid biosynthesis in rice.

Photosynthesis and plant architecture are important factors influencing grain yield in rice (Oryza sativa L.). Here, we identified a high-tillering and dwarf 12 (htd12) mutant and analyzed the effects of the HTD12 mutation on these important factors. HTD12 encodes a 15-cis-ζ-carotene isomerase (Z-ISO) belonging to the nitrite and nitric oxide reductase U (NnrU) protein family, as revealed by positional mapping and transformation experiments. Sequence analysis showed that a single nucleotide transition from guanine (G) to adenine (A) in the 3' acceptor site between the first intron and second exon of HTD12 alters its mRNA splicing in htd12 plants, resulting in a 49-amino acid deletion that affects carotenoid biosynthesis and photosynthesis. In addition, compared with the wild type, htd12 had significantly lower concentrations of ent-2'-epi-5-deoxystrigol (epi-5DS), a native strigolactone, in both roots and root exudates, resulting in an obvious increase in tiller number and decrease in plant height. These findings indicate that HTD12, the rice homolog of Z-ISO, regulates chloroplast development and photosynthesis by functioning in carotenoid biosynthesis, and modulates plant architecture by affecting strigolactone concentrations.

Whole-genome de novo assemblies reveal extensive structural variations and dynamic organelle-to-nucleus DNA transfers in African and Asian rice.

Asian cultivated rice (Oryza sativa) and African cultivated rice (Oryza glaberrima) originated from the wild rice species Oryza rufipogon and Oryza barthii, respectively. The genomes of both cultivated species have undergone profound changes during domestication. Whole-genome de novo assemblies of O. barthii, O. glaberrima, O. rufipogon and Oryza nivara, produced using PacBio single-molecule real-time (SMRT) and next-generation sequencing (NGS) technologies, showed that Gypsy-like retrotransposons are the major contributors to genome size variation in African and Asian rice. Through the detection of genome-wide structural variations (SVs), we observed that besides 28 shared SV hot spots, another 67 hot spots existed in either the Asian or African rice genomes. Based on gene annotation information of the SVs, we established that organelle-to-nucleus DNA transfers resulted in numerous SVs that participated in the nuclear genome divergence of rice species and subspecies. We detected 52 giant nuclear integrants of organelle DNA (NORGs, defined as >10 kb) in six Oryza AA genomes. In addition, we developed an effective method to genotype giant NORGs, based on genome assembly, and first showed the dynamic change in the distribution of giant NORGs in rice natural population. Interestingly, 16 highly differentiated giant NORGs tended to accumulate in natural populations of Asian rice from higher latitude regions, grown at lower temperatures and light intensities. Our study provides new insight into the genome divergence of African and Asian rice, and establishes that organelle-to-nucleus DNA transfers, as potentially powerful contributors to environmental adaptation during rice evolution, play a major role in producing SVs in rice genomes.

A common wild rice-derived BOC1 allele reduces callus browning in indica rice transformation.

Callus browning, a common trait derived from the indica rice cultivar (Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 (BOC1) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession (Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1, which consequently improves the genetic transformation efficiency. The presence of a Tourist-like miniature inverted-repeat transposable element (Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation.

Control of locomotor speed, arousal, and hippocampal theta rhythms by the nucleus incertus.

Navigation requires not only the execution of locomotor programs but also high arousal and real-time retrieval of spatial memory that is often associated with hippocampal theta oscillations. However, the neural circuits for coordinately controlling these important processes remain to be fully dissected. Here we show that the activity of the neuromedin B (NMB) neurons in the nucleus incertus (NI) is tightly correlated with mouse locomotor speed, arousal level, and hippocampal theta power. These processes are reversibly suppressed by optogenetic inhibition and rapidly promoted by optogenetic stimulation of NI NMB neurons. These neurons form reciprocal connections with several subcortical areas associated with arousal, theta oscillation, and premotor processing. Their projections to multiple downstream stations regulate locomotion and hippocampal theta, with the projection to the medial septum being particularly important for promoting arousal. Therefore, NI NMB neurons functionally impact the neural circuit for navigation control according to particular brains states.

Identification of microRNAs responding to cold stress in Dongxiang common wild rice.

Low temperature is a vital effector of rice at different growth stages. MicroRNAs (miRNAs) play important roles in responding to abiotic and biotic stresses. Here, we confirmed the cold tolerance of Dongxiang common wild rice and explored the miRNAs differentially expressed under cold stress using genome-wide small RNA sequencing. In total, 16 miRNAs, nine upregulated and seven downregulated by cold stress, were characterized in Dongxiang common wild rice, and their target genes were predicted. Additionally, an AgriGO analysis of the target genes revealed that they were enriched in several terms related to cold-stress tolerance, suggesting a complex response mechanism, involving miRNAs, to cold stress in Dongxiang common wild rice.

Natural Variations at TIG1 Encoding a TCP Transcription Factor Contribute to Plant Architecture Domestication in Rice.

The modification of plant architecture is a crucial target in rice domestication and modern genetic improvement. Although several genes regulating rice plant architecture have been characterized, the molecular mechanisms underlying rice plant architecture domestication remain largely unclear. Here we show that the inclined tiller growth in wild rice is controlled by a single dominant gene, TILLER INCLINED GROWTH 1 (TIG1), which is located on chromosome 8 and encodes a TCP transcriptional activator. TIG1 is primarily expressed in the adaxial side of the tiller base, promotes cell elongation, and enlarges the tiller angle in wild rice. Variations in the TIG1 promoter of indica cultivars (tig1 allele) resulted in decreased expression of TIG1 in the adaxial side of tiller base and reduced cell length and tiller angle, leading to the transition from inclined tiller growth in wild rice to erect tiller growth during rice domestication. TIG1 positively regulates the expression of EXPA3, EXPB5, and SAUR39 to promote cell elongation and increase the tiller angle. Selective sweep analysis revealed that the tig1 allele was selected in indica cultivars by human beings. The cloning and characterization of TIG1 supports a new scenario of plant architecture evolution in rice.

ESA1 Is Involved in Embryo Sac Abortion in Interspecific Hybrid Progeny of Rice.

The emergence of sterile individuals in the hybrid backcross progeny of wild and cultivated rice limits the use of wild rice alleles for improving cultivated rice, but the molecular mechanisms underlying this sterility remain unclear. Here, we identified the semisterile introgression line YIL42, derived from a cross between the indica rice variety Teqing (Oryza sativa) and Oryza rufipogon accession YJCWR (Yuanjiang common wild rice), which exhibits semisterility. Using positional cloning, we isolated EMBRYO SAC ABORTION 1 (ESA1), which encodes a nuclear-membrane localized protein containing an armadillo repeat domain. A mutation in ESA1 at position 1819 (T1819C) converts a stop codon into an Arg (R) codon, causing delayed termination of protein translation. Analysis of transgenic lines indicated that the difference in ESA1 protein structure between O. rufipogon-derived ESA1 and Teqing-derived esa1 affects female gamete abortion during early mitosis. Fertility investigation and expression analysis indicated that the interaction between ESA1 T1819 and unknown gene(s) of Teqing affects spikelet fertility of the hybrid backcross progeny. The ESA1 T1819 allele is present in O. rufipogon but absent in O. sativa, suggesting that variation in ESA1 may be associated with interspecific hybrid incompatibility between wild and cultivated rice. Our findings provide insight into the molecular mechanism underlying female sterility, which is useful for improving the panicle seed setting rate of rice and for developing a strategy to overcome interspecific hybrid sterility between cultivated rice and wild rice.

Identification of an active miniature inverted-repeat transposable element mJing in rice.

Miniature inverted-repeat transposable elements (MITEs) are structurally homogeneous non-autonomous DNA transposons with high copy numbers that play important roles in genome evolution and diversification. Here, we analyzed the rice high-tillering dwarf (htd) mutant in an advanced backcross population between cultivated and wild rice, and identified an active MITE named miniature Jing (mJing). The mJing element belongs to the PIF/Harbinger superfamily. japonica rice var. Nipponbare and indica var. 93-11 harbor 72 and 79 mJing family members, respectively, have undergone multiple rounds of amplification bursts during the evolution of Asian cultivated rice (Oryza sativa L.). A heterologous transposition experiment in Arabidopsis thaliana indicated that the autonomous element Jing is likely to have provides the transposase needed for mJing mobilization. We identified 297 mJing insertion sites and their presence/absence polymorphism among 71 rice samples through targeted high-throughput sequencing. The results showed that the copy number of mJing varies dramatically among Asian cultivated rice (O. sativa), its wild ancestor (O. rufipogon), and African cultivated rice (O. glaberrima) and that some mJing insertions are subject to directional selection. These findings suggest that the amplification and removal of mJing elements have played an important role in rice genome evolution and species diversification.

The APETALA2-Like Transcription Factor SUPERNUMERARY BRACT Controls Rice Seed Shattering and Seed Size.

The elimination of seed shattering was a crucial event during crop domestication. Improving and fine-tuning the regulation of this process will further enhance grain yield by avoiding seed losses during crop production. In this work, we identified the loss-of-shattering mutant suppression of shattering1 (ssh1) through a screen of mutagenized wild rice (Oryza rufipogon) introgression lines with naturally high shattering. Using the MutMap approach and transformation experiments, we isolated a genetic factor for seed shattering, SSH1, which is an allele of SUPERNUMERARY BRACT (SNB), a gene encoding a plant-specific APETALA2-like transcription factor. A C-to-A point mutation in the ninth intron of SNB altered the splicing of its messenger RNA, causing the reduced shattering of the ssh1 mutant by altering the development of the abscission layer and vascular bundle at the junction between the seed and the pedicel. Our data suggest that SNB positively regulates the expression of two rice REPLUMLESS orthologs, qSH1 and SH5 In addition, the ssh1 mutant had larger seeds and a higher grain weight, resulting from its increased elongation of the glume longitudinal cells. The further identification of favorable SNB alleles will be valuable for improving rice seed shattering and grain yield using molecular breeding strategies.

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.

Variation in the regulatory region of FZP causes increases in secondary inflorescence branching and grain yield in rice domestication.

Inflorescence branching is a key agronomic trait determining rice yield. The primary branch of the ancestral wild rice (Oryza rufipogon Griff.) bears few grains, due to minimal secondary branching. By contrast, Oryza sativa cultivars have been selected to produce large panicles with more secondary branches. Here we showed that the CONTROL OF SECONDARY BRANCH 1 (COS1) gene, which is identical to FRIZZY PANICLE (FZP), plays an important role in the key transition from few secondary branches in wild rice to more secondary branches in domesticated rice cultivars. A 4-bp tandem repeat deletion approximately 2.7 kb upstream of FZP may affect the binding activities of auxin response factors to the FZP promoter, decrease the expression level of FZP and significantly enhance the number of secondary branches and grain yield in cultivated rice. Functional analyses showed that NARROW LEAF 1 (NAL1), a trypsin-like serine and cysteine protease, interacted with FZP and promoted its degradation. Consistently, downregulating FZP expression or upregulating NAL1 expression in the commercial cultivar Zhonghua 17 increased the number of secondary branches per panicle, grain number per panicle and grain yield per plant. Our findings not only provide insights into the molecular mechanism of increasing grain number and yield during rice domestication, but also offer favorable genes for improving the grain yield of rice.

Genetic control of seed shattering during African rice domestication.

Domestication represents a unique opportunity to study the evolutionary process. The elimination of seed dispersal traits was a key step in the evolution of cereal crops under domestication. Here, we show that ObSH3, a YABBY transcription factor, is required for the development of the seed abscission layer. Moreover, selecting a genomic segment deletion containing SH3 resulted in the loss of seed dispersal in populations of African cultivated rice (Oryza glaberrima Steud.). Functional characterization of SH3 and SH4 (another gene controlling seed shattering on chromosome 4) revealed that multiple genes can lead to a spectrum of non-shattering phenotypes, affecting other traits such as ease of threshing that may be important to tune across different agroecologies and postharvest practices. The molecular evolution analyses of SH3 and SH4 in a panel of 93 landraces provided unprecedented geographical detail of the domestication history of African rice, tracing multiple dispersals from a core heartland and introgression from local wild rice. The cloning of ObSH3 not only provides new insights into a critical crop domestication process but also adds to the body of knowledge on the molecular mechanism of seed dispersal.

NOG1 increases grain production in rice.

During rice domestication and improvement, increasing grain yield to meet human needs was the primary objective. Rice grain yield is a quantitative trait determined by multiple genes, but the molecular basis for increased grain yield is still unclear. Here, we show that NUMBER OF GRAINS 1 (NOG1), which encodes an enoyl-CoA hydratase/isomerase, increases the grain yield of rice by enhancing grain number per panicle without a negative effect on the number of panicles per plant or grain weight. NOG1 can significantly increase the grain yield of commercial high-yield varieties: introduction of NOG1 increases the grain yield by 25.8% in the NOG1-deficient rice cultivar Zhonghua 17, and overexpression of NOG1 can further increase the grain yield by 19.5% in the NOG1-containing variety Teqing. Interestingly, NOG1 plays a prominent role in increasing grain number, but does not change heading date or seed-setting rate. Our findings suggest that NOG1 could be used to increase rice production.