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Selection for yield during B. rapa breeding may have unintended consequences for other traits, such as flavour. LYH-type (light yellow head) Chinese cabbage (Brassica rapa ssp. pekinensis) and wucai (Brassica rapa L. ssp. chinensis var. rosularis) varieties are becoming popular because of their unique flavour and yellow leaves. However, the molecular mechanism underlying the interplay for these traits remains unknown. We conducted a fine mapping and genome-wide exploration analysis of the leaf yellowing of LYH and wucai, including transgenic plants, to identify causal genes. We identified that BrHISN2, a rate-limiting enzyme in histidine biosynthesis, causes leaf yellowing by destroying LYH chloroplasts. Normal growing Brhisn2 mutant plants became etiolated and senesced at the cotyledon-seedling stage. Sequence variations in the promoter confers cold-dependent expression on BrHISN2, probably resulting in leaf yellowing in LYH and wucai. Insertions of two DRE cis elements and the subsequent recruitment of two CBF2 proteins by the DREs to the promoter provided the cold-induced expression plasticity of BrHISN2 in plants. Both LYH and wucai are farmed in the fall, in which the temperature gradually decreases, therefore the CBF2-BrHISN2 module probably maximises the benefits of gene-environment interaction for breeding. We determined the mechanistic connections of chlorophyll synthesis and the growth-flavour trade-off in these B. rapa varieties.

Leaf curling is an essential prerequisite for the formation of leafy heads in Chinese cabbage. However, the part or tissue that determines leaf curvature remains largely unclear. In this study, we first introduced the auxin-responsive marker DR5::GUS into the Chinese cabbage genome and visualized its expression during the farming season. We demonstrated that auxin response is adaxially/abaxially distributed in leaf veins. Together with the fact that leaf veins occupy considerable proportions of the Chinese cabbage leaf, we propose that leaf veins play a crucial supporting role as a framework for heading. Then, by combining analyses of QTL mapping and a time-course transcriptome from heading Chinese cabbage and non-heading pak choi during the farming season, we identified the auxin-related gene BrPIN5 as a strong candidate for leafy head formation. PIN5 displays an adaxial/abaxial expression pattern in leaf veins, similar to that of DR5::GUS, revealing an involvement of BrPIN5 in leafy head development. The association of BrPIN5 function with heading was further confirmed by its haplo-specificity to heading individuals in both a natural population and two segregating populations. We thus conclude that the adaxial/abaxial patterning of auxin and auxin genes in leaf veins functions in the formation of the leafy head in Chinese cabbage.

Carotenoid esterification plays indispensable roles in preventing degradation and maintaining the stability of carotenoids. Although the carotenoid biosynthetic pathway has been well characterized, the molecular mechanisms underlying carotenoid esterification, especially in floral organs, remain poorly understood. In this study, we identified a natural mutant flowering Chinese cabbage (Caixin, Brassica rapa L. subsp. chinensis var. parachinensis) with visually distinguishable pale-yellow petals controlled by a single recessive gene. Transmission electron microscopy (TEM) demonstrated that the chromoplasts in the yellow petals were surrounded by more fully developed plastoglobules compared to the pale-yellow mutant. Carotenoid analyses further revealed that, compared to the pale-yellow petals, the yellow petals contained high levels of esterified carotenoids, including lutein caprate, violaxanthin dilaurate, violaxanthin-myristate-laurate, 5,6epoxy-luttein dilaurate, lutein dilaurate, and lutein laurate. Based on bulked segregation analysis and fine mapping, we subsequently identified the critical role of a phytyl ester synthase 2 protein (PALE YELLOW PETAL, BrPYP) in regulating carotenoid pigmentation in flowering Chinese cabbage petals. Compared to the yellow wild-type, a 1,148 bp deletion was identified in the promoter region of BrPYP in the pale-yellow mutant, resulting in down-regulated expression. Transgenic Arabidopsis plants harboring beta-glucuronidase (GUS) driven by yellow (BrPYPY::GUS) and pale-yellow type (BrPYPPY::GUS) promoters were subsequently constructed, revealing stronger expression of BrPYPY::GUS both in the leaves and petals. Furthermore, virus-induced gene silencing of BrPYP significantly altered petal color from yellow to pale yellow. These findings demonstrate the molecular mechanism of carotenoid esterification, suggesting a role of phytyl ester synthase in carotenoid biosynthesis of flowering Chinese cabbage.

Polyploidization or whole-genome duplication (WGD) is a well-known speciation and adaptation mechanism in angiosperms, while subgenome dominance is a crucial phenomenon in allopolyploids, established following polyploidization. The dominant subgenomes contribute more to genome evolution and homoeolog expression bias, both of which confer advantages for short-term phenotypic adaptation and long-term domestication. In this review, we firstly summarize the probable mechanistic basis for subgenome dominance, including the effects of genetic [transposon, genetic incompatibility, and homoeologous exchange (HE)], epigenetic (DNA methylation and histone modification), and developmental and environmental factors on this evolutionary process. We then move to Brassica rapa, a typical allopolyploid with subgenome dominance. Polyploidization provides the B. rapa genome not only with the genomic plasticity for adapting to changeable environments, but also an abundant genetic basis for morphological variation, making it a representative species for subgenome dominance studies. According to the ‘two-step theory’, B. rapa experienced genome fractionation twice during WGD, in which most of the genes responding to the environmental cues and phytohormones were over-retained, enhancing subgenome dominance and consequent adaption. More than this, the pangenome of 18 B. rapa accessions with different morphotypes recently constructed provides further evidence to reveal the impacts of polyploidization and subgenome dominance on intraspecific diversification in B. rapa. Above and beyond the fundamental understanding of WGD and subgenome dominance in B. rapa and other plants, however, it remains elusive why subgenome dominance has tissue- and spatiotemporal-specific features and could shuffle between homoeologous regions of different subgenomes by environments in allopolyploids. We lastly propose acceleration of the combined application of resynthesized allopolyploids, omics technology, and genome editing tools to deepen mechanistic investigations of subgenome dominance, both genetic and epigenetic, in a variety of species and environments. We believe that the implications of genomic and genetic basis of a variety of ecologically, evolutionarily, and agriculturally interesting traits coupled with subgenome dominance will be uncovered and aid in making new discoveries and crop breeding.

Carotenoids were synthesized in the plant cells involved in photosynthesis and photo-protection. In humans, carotenoids are essential as dietary antioxidants and vitamin A precursors. Brassica crops are the major sources of nutritionally important dietary carotenoids. Recent studies have unraveled the major genetic components in the carotenoid metabolic pathway in Brassica, including the identification of key factors that directly participate or regulate carotenoid biosynthesis. However, recent genetic advances and the complexity of the mechanism and regulation of Brassica carotenoid accumulation have not been reviewed. Herein, we reviewed the recent progress regarding Brassica carotenoids from the perspective of forward genetics, discussed biotechnological implications and provided new perspectives on how to transfer the knowledge of carotenoid research in Brassica to the crop breeding process.

Purple heading Chinese cabbage has become popular in recent years due to its attractive color and health benefits. However, purple varieties remain rare, and the regulation mechanism of anthocyanin accumulation in Chinese cabbage is still largely unknown. By introducing the purple color trait from Brassica juncea, a new purple heading Chinese cabbage cultivar (18M-245) was generated with deep purple leaves at both the seedling and adult stages. Anthocyanin accumulation in 18M-245 increased when grown at low temperatures. FISH and genotyping results showed that the purple trait was caused by an alien chromosome addition line derived from the Brassica B genome. The LDOX coding gene BjuB014115 from the addition line was highly expressed in 18M-245, consistent with the results of anthocyanin accumulation. Meanwhile, several MYB and bHLH transcriptional factors from the Brassica A genome were found to directly bind to the promoter of BjuB014115, suggesting that interactions between the Brassica A and B genomes are involved in the regulatory network of anthocyanin biosynthesis in Chinese cabbage. Our results provide new insights into the regulation mechanism of anthocyanin biosynthesis in purple heading Chinese cabbage.

The wall-associated kinase (WAK) gene family, a subfamily of the receptor-like kinase (RLK) gene family, is associated with the cell wall in plants, and has vital functions in cell expansion, pathogen resistance, and heavy metal stress tolerance because of their roles of the extracellular environment sensors to trigger intracellular signals in Arabidopsis. In the present study, 96 Chinese cabbage (Brassica rapa ssp. pekinensis) BrWAK gene family members were identified from the B. rapa genome using a reiterative database search and manual confirmation. The protein domain characterization, gene structure analysis, and phylogenetic analysis of the BrWAKs classified them into three gene groups. Comparative genomic analysis between WAK genes from Chinese cabbage and Arabidopsis revealed that the BrWAK genes have undergone the gene expansion and deletion events during evolution. Furthermore, the conserved motifs in the kinase domains of the WAK proteins and eukaryotic protein kinase family proteins were compared and some non-RD kinase proteins among the BrWAKs were identified. Ultimately, expression analysis of BrWAK genes in six tissues and under various stress conditions revealed that some tissue-specific WAK genes might function in callus cell growth and reproduction process; Bra012273, Bra016426, Bra016427, and Bra025882 might be involved in downy mildew resistance and high humidity stress; Bra012273, Bra025882, and Bra025883 might be responded to drought and heat stress. Taken together, this research was identified and classified the WAK gene family in Chinese cabbage and provided valuable resources to explore the potential roles of BrWAK genes in plant development and stress responses.

Heading date is one of the most important traits in rice and regulated by multiple genes. Common wild rice is the ancestor of Asian cultivated rice and harbours abundant genetic diversity. To use wild rice resource in rice breeding, a set of 154 introgression lines (ILs) covering 93% of the genome of Jinghong common wild rice was constructed in the background 'Teqing', using 208 simple sequence repeat markers evenly distributed on 12 chromosomes. Among the ILs, the line JIL64 displayed late heading independent of photoperiod. Genetic analysis using the two F₂ populations crossed ''Teqing'/JIL64 and JIL64/'Teqing' revealed that late flowering was controlled by a recessive gene on chromosome 8 (designated early heading date 8, ehd8), and ehd8 was fine mapped to the 50‐kb region flanked by markers RM22221 and 64Indel4. Sequencing and qRT‐PCR demonstrated that LOC_Os08g01410 and LOC_Os08g01420 were deleted in JIL64 and may be associated with the late heading of Jinghong common wild rice. These findings lay a practical foundation for characterizing ehd8, and the ILs help to mine genes from Jinghong common wild rice.

Brassica downy mildew, a severe disease caused by Hyaloperonospora brassicae, can cause enormous economic losses in Chinese cabbage (Brassica rapa L. ssp. pekinensis) production. Although some research has been reported recently concerning the underlying resistance to this disease, no studies have identified or characterized long noncoding RNAs involved in this defense response. In this study, using high-throughput RNA sequencing, we analyzed the disease-responding mRNAs and long noncoding RNAs in two resistant lines (T12–19 and 12–85) and one susceptible line (91–112). Clustering and Gene Ontology analysis of differentially expressed genes (DEGs) showed that more DEGs were involved in the defense response in the two resistant lines than in the susceptible line. Different expression patterns and proposed functions of differentially expressed long noncoding RNAs among T12–19, 12–85, and 91–112 indicated that each has a distinct disease response mechanism. There were significantly more cis- and trans-functional long noncoding RNAs in the resistant lines than in the susceptible line, and the genes regulated by these RNAs mostly participated in the disease defense response. Furthermore, we identified a candidate resistance-related long noncoding RNA, MSTRG.19915, which is a long noncoding natural antisense transcript of a MAPK gene, BrMAPK15. Via an agroinfiltration-mediated transient overexpression system and virus-induced gene silencing technology, BrMAPK15 was indicated to have a greater ability to defend against pathogens. MSTRG.19915-silenced seedlings showed enhanced resistance to downy mildew, probably because of the upregulated expression of BrMAPK15. This research identified and characterized long noncoding RNAs involved in resistance to downy mildew, laying a foundation for future in-depth studies of disease resistance mechanisms in Chinese cabbage.

Heterosis is a complex phenomenon in which hybrids show better phenotypic characteristics than their parents do. Chinese cabbage (Brassica rapaL. spp.pekinensis) is a popular leafy crop species, hybrids of which are widely used in commercial production; however, the molecular basis of heterosis for biomass of Chinese cabbage is poorly understood. We characterized heterosis in a Chinese cabbage F1hybrid cultivar and its parental lines from the seedling stage to the heading stage; marked heterosis of leaf weight and biomass yield were observed. Small RNA sequencing revealed 63 and 50 differentially expressed microRNAs (DEMs) at the seedling and early-heading stages, respectively. The expression levels of the majority of miRNA clusters in the F1hybrid were lower than the mid-parent values (MPVs). Using degradome sequencing, we identified 1,819 miRNA target genes. Gene ontology (GO) analyses demonstrated that the target genes of the MPV-DEMs and low parental expression level dominance (ELD) miRNAs were significantly enriched in leaf morphogenesis, leaf development, and leaf shaping. Transcriptome analysis revealed that the expression levels of photosynthesis and chlorophyll synthesis-related MPV-DEGs (differentially expressed genes) were significantly different in the F1hybrid compared to the parental lines, resulting in increased photosynthesis capacity and chlorophyll content in the former. Furthermore, expression of genes known to regulate leaf development was also observed at the seedling stage. Arabidopsis plants overexpressingBrGRF4.2and bra-miR396 presented increased and decreased leaf sizes, respectively. These results provide new insight into the regulation of target genes and miRNA expression patterns in leaf size and heterosis for biomass ofB. rapa.

Flowering is an important trait in Chinese cabbage, because premature flowering reduces yield and quality of the harvested products. Water deficit, caused by drought or other environmental conditions, induces early flowering. Drought resistance involves global reprogramming of transcription, hormone signaling, and chromatin modification. We show that a histone H4 protein, BrHIS4.A04, physically interacts with a homeodomain protein BrVIN3.1, which was selected during the domestication of late-bolting Chinese cabbage. Over-expression of BrHIS4.A04 resulted in premature flowering under normal growth conditions, but prevented further premature bolting in response to drought. We show that the expression of key abscisic acid (ABA) signaling genes, and also photoperiodic flowering genes was attenuated in BrHIS4.A04-overexpressing (BrHIS4.A04OE) plants under drought conditions. Furthermore, the relative change in H4-acetylation at these gene loci was reduced in BrHIS4.A04OE plants. We suggest that BrHIS4.A04 prevents premature bolting by attenuating the expression of photoperiodic flowering genes under drought conditions, through the ABA signaling pathway. Since BrHIS4.A04OE plants displayed no phenotype related to vegetative or reproductive development under laboratory-induced drought conditions, our findings contribute to the potential fine-tuning of flowering time in crops through genetic engineering without any growth penalty, although more data are necessary under field drought conditions.

GRAS proteins belong to a plant-specific transcription factor family and play roles in diverse physiological processes and environmental signals. In this study, we identified and characterized a GRAS transcription factor gene in Brassica rapa, BrLAS, an ortholog of Arabidopsis AtLAS. BrLAS was primarily expressed in the roots and axillary meristems, and localized exclusively in the nucleus of B. rapa protoplast cells. qRT-PCR analysis indicated that BrLAS was upregulated by exogenous abscisic acid (ABA) and abiotic stress treatment [polyethylene glycol (PEG), NaCl, and H2O2]. BrLAS-overexpressing Arabidopsis plants exhibited pleiotropic characteristics, including morphological changes, delayed bolting and flowering time, reduced fertility and delayed senescence. Transgenic plants also displayed significantly enhanced drought resistance with decreased accumulation of ROS and increased antioxidant enzyme activity under drought treatment compared with the wild-type. Increased sensitivity to exogenous ABA was also observed in the transgenic plants. qRT-PCR analysis further showed that expression of several genes involved in stress responses and associated with leaf senescence were also modified. These findings suggest that BrLAS encodes a stress-responsive GRASs transcription factor that positively regulates drought stress tolerance, suggesting a role in breeding programs aimed at improving drought tolerance in plants.

Downy mildew, caused by Hyaloperonospora parasitica, is a major disease of Brassica rapa that causes large economic losses in many B. rapa-growing regions of the world. The genotype used in this study was based on a double haploid population derived from a cross between the Chinese cabbage line BY and a European turnip line MM, susceptible and resistant to downy mildew, respectively. We initially located a locus Br-DM04 for downy mildew resistance in a region about 2.7 Mb on chromosome A04, which accounts for 22.3% of the phenotypic variation. Using a large F2 mapping population (1156 individuals) we further mapped Br-DM04 within a 160 kb region, containing 17 genes encoding proteins. Based on sequence annotations for these genes, four candidate genes related to disease resistance, BrLRR1, BrLRR2, BrRLP47, and BrRLP48 were identified. Overexpression of both BrRLP47 and BrRLP48 using a transient expression system significantly enhanced the downy mildew resistance of the susceptible line BY. But only the leaves infiltrated with RNAi construct of BrRLP48 could significantly reduce the disease resistance in resistant line MM. Furthermore, promoter sequence analysis showed that one salicylic acid (SA) and two jasmonic acid-responsive transcript elements were found in BrRLP48 from the resistant line, but not in the susceptible one. Real-time PCR analysis showed that the expression level of BrRLP48 was significantly induced by inoculation with downy mildew or SA treatment in the resistant line MM. Based on these findings, we concluded that BrRLP48 was involved in disease resistant response and the disease-inducible expression of BrRLP48 contributed to the downy mildew resistance. These findings led to a new understanding of the mechanisms of resistance and lay the foundation for marker-assisted selection to improve downy mildew resistance in Brassica rapa.

Chinese cabbage is the most consumed leafy crop in East Asian countries. However, premature bolting induced by continuous low temperatures severely decreases the yield and quality of the Chinese cabbage, and therefore restricts its planting season and geographic distribution. In the past 40 years, spring Chinese cabbage with strong winterness has been selected to meet the market demand. Here, we report a genome variation map of Chinese cabbage generated from the resequencing data of 194 geographically diverse accessions of three ecotypes. In-depth analyses of the selection sweeps and genome-wide patterns revealed that spring Chinese cabbage was selected from a specific population of autumn Chinese cabbage around the area of Shandong peninsula in northern China. We identified 23 genomic loci that underwent intensive selection, and further demonstrated by gene expression and haplotype analyses that the incorporation of elite alleles of VERNALISATION INSENTIVE 3.1 (BrVIN3.1) and FLOWER LOCUS C 1 (BrFLC1) is a determinant genetic source of variation during selection. Moreover, we showed that the quantitative response of BrVIN3.1 to cold due to the sequence variations in the cis elements of the BrVIN3.1 promoter significantly contributes to bolting-time variation in Chinese cabbage. Collectively, our study provides valuable insights into the genetic basis of spring Chinese cabbage selection and will facilitate the breeding of bolting-resistant varieties by molecular-marker-assisted selection, transgenic or gene editing approaches.

The calcium-dependent protein kinase OsCPK4 has been demonstrated to play important roles in salt and drought tolerance, plant growth, and development in rice (Oryza sativa). However, little is known about molecular mechanisms underlying OsCPK4 function in rice immunity. In this study, we demonstrated that the generation of oxidative burst and pathogenesis-related gene expression triggered by microbe-associated molecular patterns were significantly enhanced in the oscpk4 mutants. These mutant lines are more resistant to bacterial blight and fungal blast diseases than the wild-type plants, indicating that OsCPK4 negatively regulates innate immunity in rice. OsCPK4 was further identified to interact with a receptor-like cytoplasmic kinase OsRLCK176. OsRLCK176 accumulation is negatively regulated by OsCPK4. Interestingly, the kinase-dead OsCPK4 promotes OsRLCK176 degradation more strongly than the wild-type protein. OsCPK4 and OsRLCK176 mutually phosphorylate each other and form a feedback loop. Moreover, the kinase activity and phosphorylation of OsCPK4 and OsRLCK176 contribute to the stability of OsRLCK176. These findings indicate that the kinase-inactive OsCPK4 promotes OsRLCK176 degradation and restricts plant defenses, whereas the activation of OsCPK4-OsRLCK176 phosphorylation circuit invalidates the OsRLCK176 degradation machinery, thus enhancing plant immunity. Collectively, the study proposes a novel defense buffering mechanism mediated by OsCPK4, which fine-tunes microbe-associated molecular pattern-triggered immunity in rice.

Grain size and shape are important determinants of grain weight and yield in rice. Here, we report a new major quantitative trait locus (QTL), qTGW3, that controls grain size and weight in rice. This locus, qTGW3, encodes OsSK41 (also known as OsGSK5), a member of the GLYCOGEN SYNTHASE KINASE 3/SHAGGY-like family. Rice near-isogenic lines carrying the loss-of-function allele of OsSK41 have increased grain length and weight. We demonstrate that OsSK41 interacts with and phosphorylates AUXIN RESPONSE FACTOR 4 (OsARF4). Co-expression of OsSK41 with OsARF4 increases the accumulation of OsARF4 in rice protoplasts. Loss of function of OsARF4 results in larger rice grains. RNA-sequencing analysis suggests that OsARF4 and OsSK41 repress the expression of a common set of downstream genes, including some auxin-responsive genes, during rice grain development. The loss-of-function form of OsSK41 at qTGW3 represents a rare allele that has not been extensively utilized in rice breeding. Suppression of OsSK41 function by either targeted gene editing or QTL pyramiding enhances rice grain size and weight. Thus, our study reveals the important role of OsSK41 in rice grain development and provides new candidate genes for genetic improvement of grain yield in rice and perhaps in other cereal crops.

A thorough understanding of the genetic basis of rice grain traits is critical for the improvement of rice (Oryza sativa L.) varieties. In this study, we generated an F₂ population by crossing the large-grain japonica cultivar CW23 with Peiai 64 (PA64), an elite indica small-grain cultivar. Using QTL analysis, 17 QTLs for five grain traits were detected on four different chromosomes. Eight of the QTLs were newly-identified in this study. In particular, qGL3-1, a newly-identified grain length QTL with the highest LOD value and largest phenotypic variation, was fine-mapped to the 17 kb region of chromosome 3. A serine/threonine protein phosphatase gene encoding a repeat domain containing two Kelch motifs was identified as the unique candidate gene corresponding to this QTL. A comparison of PA64 and CW23 sequences revealed a single nucleotide substitution (C→A) at position 1092 in exon 10, resulting in replacement of Asp (D) in PA64 with Glu (E) in CW23 for the 364(th) amino acid. This variation is located at the D position of the conserved sequence motif AVLDT of the Kelch repeat. Genetic analysis of a near-isogenic line (NIL) for qGL3-1 revealed that the allele qGL3-1 from CW23 has an additive or partly dominant effect, and is suitable for use in molecular marker-assisted selection.

Many rice breeding programs have currently reached yield plateaus as a result of limited genetic variability in parental strains. Dongxiang common wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and serves as an important gene pool for the genetic improvement of rice cultivars. In this study, heterotic loci (HLs) associated with six yield-related traits were identified in wild and cultivated rice and investigated using a set of 265 introgression lines (ILs) of O. rufipogon Griff. in the background of the Indica high-yielding cultivar Guichao 2 (O. sativa L.). Forty-two HLs were detected by a single point analysis of mid-parent heterosis values from test cross F(1) offspring, and 30 (71.5%) of these HLs showed significantly positive effects, consistent with the superiority shown by the F(1) test cross population in the six yield-related traits under study. Genetic mapping of hsp11, a locus responsible for the number of spikelets per panicle, confirmed the utility of these HLs. The results indicate that favorable HLs capable of improving agronomic traits are available. The identification of HLs between wild rice and cultivated rice could lead to a new strategy for the application of heterosis in rice breeding.

A dwarf mutant, designated LB4D, was obtained among the progeny of backcrosses to a wild rice introgression line. Genetic analysis of LB4D indicated that the dwarf phenotype was controlled by a single semidominant dwarfing gene, which was named LB4D. The mutants were categorized as dn-type dwarf mutants according to the pattern of internode reduction. In addition, gibberellin (GA) response tests showed that LB4D plants were neither deficient nor insensitive to GA. This study found that tiller formation by LB4D plants was decreased by 40% compared with the wild type, in contrast to other dominant dwarf mutants that have been identified, indicating that a different dwarfing mechanism might be involved in the LB4D dominant mutant. The reduction of plant height in F(1) plants ranged from 27.9% to 38.1% in different genetic backgrounds, showing that LB4D exerted a stronger dominant dwarfing effect. Using large F(2) and F(3) populations derived from a cross between heterozygous LB4D and the japonica cultivar Nipponbare, the LB4D gene was localized to a 46 kb region between the markers Indel 4 and Indel G on the short arm of chromosome 11, and four predicted genes were identified as candidates in the target region.

Common wild rice (Oryza rufipogon Griff.) is an important genetic reservoir for rice improvement. We investigated a quantitative trait locus (QTL), qGP5-1, which is related to plant height, leaf size and panicle architecture, using a set of introgression lines of O. rufipogon in the background of the Indica cultivar Guichao2 (Oryza sativa L.). We cloned and characterized qGP5-1 and confirmed that the newly identified gene OsEBS (enhancing biomass and spikelet number) increased plant height, leaf size and spikelet number per panicle, leading to an increase in total grain yield per plant. Our results showed that the increased size of vegetative organs in OsEBS-expressed plants was enormously caused by increasing cell number. Sequence alignment showed that OsEBS protein contains a region with high similarity to the N-terminal conserved ATPase domain of Hsp70, but it lacks the C-terminal regions of the peptide-binding domain and the C-terminal lid. More results indicated that OsEBS gene did not have typical characteristics of Hsp70 in this study. Furthermore, Arabidopsis (Arabidopsis thaliana) transformed with OsEBS showed a similar phenotype to OsEBS-transgenic rice, indicating a conserved function of OsEBS among plant species. Together, we report the cloning and characterization of OsEBS, a new QTL that controls rice biomass and spikelet number, through map-based cloning, and it may have utility in improving grain yield in rice.