Indica Cultivars Research Articles

DS1/OsEMF1 interacts with OsARF11 to control rice architecture by regulation of brassinosteroid signaling

BackgroundPlant height and leaf angle are important determinants of yield in rice (Oryza sativa L.). Genes involved in regulating plant height and leaf angle were identified in previous studies; however, there are many remaining unknown factors that affect rice architecture.ResultsIn this study, we characterized a dwarf mutant named ds1 with small grain size and decreased leaf angle,selected from an irradiated population of ssp. japonica variety Nanjing35. The ds1 mutant also showed abnormal floral organs. ds1 plants were insensitive to BL treatment and expression of genes related to BR signaling was changed. An F2 population from a cross between ds1 and indica cultivar 93–11 was used to fine map DS1 and to map-based clone the DS1 allele, which encoded an EMF1-like protein that acted as a transcriptional regulator. DS1 was constitutively expressed in various tissues, and especially highly expressed in young leaves, panicles and seeds. We showed that the DS1 protein interacted with auxin response factor 11 (OsARF11), a major transcriptional regulator of plant height and leaf angle, to co-regulate D61/OsBRI1 expression. These findings provide novel insights into understanding the molecular mechanisms by which DS1 integrates auxin and brassinosteroid signaling in rice.ConclusionThe DS1 gene encoded an EMF1-like protein in rice. The ds1 mutation altered the expression of genes related to BR signaling, and ds1 was insensitive to BL treatment. DS1 interacts with OsARF11 to co-regulate OsBRI1 expression.

Variations in grain cadmium and arsenic concentrations and screening for stable low-accumulating rice cultivars from multi-environment trials

In order to help mitigate widespread cadmium (Cd) and arsenic (As) co-contamination in paddy soils in China, screening and breeding of low-accumulating rice (Oryza sativa L.) cultivars (excluders) have been widely adopted. However, the performance of rice cultivars for grain Cd and As accumulation may vary in different growing environments. The inability to identify stable low-accumulating cultivars has largely hindered their application. In this study, 51 rice cultivars were evaluated at four Cd- and As-contaminated paddy sites in two crop seasons in northern Guangdong Province, China. The aim was to investigate the effects of cultivar, environment and their interactions in determining grain Cd and As concentrations, and so to identify stable low-accumulating cultivars. Results showed that environment effects dominated the Cd and As concentrations in rice grains, explaining 87% of the total variations. The crop season played a vital role; compared to early season, grain Cd levels increased and As levels lowered significantly in late season. Large variations in grain Cd, total As, inorganic As concentrations and the percentage of inorganic As were observed between different cultivars. Conventional japonica cultivars exhibited lower Cd levels but higher As levels in the grains than did indica cultivars. The cultivar × environment interaction (CEI) was significant, and its importance was comparable to the cultivar effect. By measuring and interpreting such an interaction, stable Cd and As excluder cultivars were identified based upon the yield, grain Cd and As levels as well as the stabilities of cultivars across the trial environments. Two stable Cd and As co-excluders were found among the hybrid indica cultivars. These results demonstrated that the variations in grain Cd and As concentrations could mainly be attributed to the environment effects and cultivar selection practices should include the analysis of CEI to identify stable low-accumulating rice cultivars.

Identification of QTLs associated with cadmium concentration in rice grains

Cadmium (Cd) contamination in rice has been a hot topic of research because of its potential risk to human health. In this study, a double haploid (DH) population derived from Zhongjiazao 17 (YK17) (an early-season indica cultivar)×D50 (a tropical japonica cultivar) was used to identify quantitative trait loci (QTLs) associated with Cd concentration in brown rice (CCBR) and Cd concentration in milled rice (CCMR). Continuous and wide variation for CCBR and CCMR were observed among the DH population. Correlation analysis revealed a positive and highly significant correlation between the two traits. A total of 18 QTLs for CCBR and 14 QTLs for CCMR were identified in five different pot and field trials. Two pairs of QTLs for CCBR (qCCBR2-1 and qCCBR2-2, qCCBR9-1 and qCCBR9-2) and one pair of QTLs for CCMR (qCCMR5-1 and qCCMR5-2) were detected in multiple trials. The alleles increasing CCBR at the qCCBR2-1/qCCBR2-2 and qCCBR9-1/qCCBR9-2 QTLs were contributed by YK17 and D50, respectively, whereas the D50 allele at the qCCMR5-1/qCCMR5-2 QTLs increased CCMR. Eight pairs of QTLs for CCBR and CCMR, qCCBR2-2 and qCCMR2-2, qCCBR3 and qCCMR3, qCCBR4-2 and qCCMR4-1, qCCBR4-3 and qCCMR4-2, qCCBR4-4 and qCCMR4-3, qCCBR5 and qCCMR5-2, qCCBR7 and qCCMR7, and qCCBR11-1 and qCCMR11-2, co-localized on chromosomes 2, 3, 4, 5, 7, and 11, respectively. For all of these QTL pairs, except qCCBR5/qCCMR5-2, the additive effects came from YK17. In addition, four CCMR QTLs showing significant additive×environment interaction and two pairs of CCMR QTLs with bi-allelic epistatic interactions were identified. The results of this study could facilitate marker-assisted selection of breeding rice varieties with low Cd accumulation in grain.

Abscisic acid biosynthesis under water stress: anomalous behavior of the 9-cis-epoxycarotenoid dioxygenase1 (NCED1) gene in rice

The gene NCED1 encodes 9-cis-epoxycarotenoid dioxygenase, which catalyzes oxidative cleavage of 9-cis-epoxycarotenoids neoxanthin and violaxanthin to xanthoxin, a key step in the biosynthesis of abscisic acid (ABA) in higher plants. In the present study, the complete NCED1 of 1 917 bp was cloned and characterized from rice (Oryza sativa L. cv. N22) as no earlier reports were available for its characterization from the indica cultivar. The NCED1 had no intron and encoded a protein of 639 amino acids with a predicted molecular mass of 68.62 kD and pI of 6.07. The aliphatic index and grand average of hydropathicity were found to be 77.04 and -0.148, respectively. Multiple alignment analysis revealed that the sequence shared a high identity with the Oryza sativa japonica group (100 %) followed by Triticum aestivum (90 %), Hordeum vulgare (90 %), and Zea mays (89 %). The enzyme had a RPE65 domain of 476 amino acid residues. The RPE65 domain requires Fe(II) as a cofactor coordinated with 4 histidine residues and 3 glutamic acid residues. The phylogenic tree shows that NCED1 of japonica rice and NCED1 of indica rice were in the same group. They might have been evolved from a common ancestor. Analysis with a PSORT III tool shows that NCED is a chloroplastic protein. The real-time quantitative PCR and RNA-sequencing studies show that the expression of NCED1 was progressively reduced with increasing water stress, and a negative correlation between expression of OsNCED1 and severity of stress was established. Further, NCED1 expression negatively correlated with ABA accumulation under water stress whereas in some other species, its expression increased along with ABA accumulation. This might be due to feedback inhibition of the ABA biosynthesis in rice.

Genetic analysis and fine-mapping of a new rice mutant, white and lesion mimic leaf1

Rice (Oryza sativa L.) leaf color mutants are excellent models for studying chlorophyll biosynthesis and chloroplast development. In this study, we isolated a stable genetic white and lesion mimic leaf1 (wlml1) mutant from an ethyl methanesulfonate (EMS)-mutagenized population of the indica cultivar TN1. Compared with wild-type TN1, the wlml1 mutant had lower contents of chlorophyll and carotenoids, altered chloroplast ultrastructure, and altered regulation of genes associated with chlorophyll metabolism and chloroplast development. In addition, lesions formed on the leaves of wlml1 plants grown at 20 °C and genes related to disease resistance and antioxidant functions were up-regulated; by contrast, the mutant phenotype was partially suppressed at 28 °C. These findings indicated that WLML1 might play a role in chlorophyll metabolism and chloroplast development, as well as in biotic and abiotic stress responses. Genetic analysis showed that WLML1 was controlled by a recessive nuclear gene, and map-based cloning delimited WLML1 to a 159.7-kb region on chromosome 4 that includes 30 putative open reading frames. Based on these findings, the wlml1 mutant will be a good genetic material for further studies on chlorophyll metabolism and stress responses in rice.

Fine mapping and identification of a novel locus qGL12.2 control grain length in wild rice (Oryza rufipogon Griff.).

A wild rice QTL qGL12.2 for grain length was fine mapped to an 82-kb interval in chromosome 12 containing six candidate genes and none was reported previously. Grain length is an important trait for yield and commercial value in rice. Wild rice seeds have a very slender shape and have many desirable genes that have been lost in cultivated rice during domestication. In this study, we identified a quantitative trait locus, qGL12.2, which controls grain length in wild rice. First, a wild rice chromosome segment substitution line, CSSL41, was selected that has longer glume and grains than does the Oryza sativa indica cultivar, 9311. Next, an F2 population was constructed from a cross between CSSL41 and 9311. Using the next-generation sequencing combined with bulked-segregant analysis and F3 recombinants analysis, qGL12.2 was finally fine mapped to an 82-kb interval in chromosome 12. Six candidate genes were found, and no reported grain length genes were found in this interval. Using scanning electron microscopy, we found that CSSL41 cells are significantly longer than those of 9311, but there is no difference in cell widths. These data suggest that qGL12.2 is a novel gene that controls grain cell length in wild rice. Our study provides a new genetic resource for rice breeding and a starting point for functional characterization of the wild rice GL gene.

Temperature-dependent QTLs in indica alleles for improving grain quality in rice: increased prominence of QTLs responsible for reduced chalkiness under high-temperature conditions

Quantitative trait loci (QTLs) for the apparent quality of brown rice under high temperatures during ripening were analyzed using chromosomal segment substitution lines. Segments from the indica cultivar Habataki were substituted into a japonica cultivar with a Sasanishiki background. We found the following two QTLs for increasing grain quality in the Habataki allele on chromosome 3: (1) qTW3-2, located near the marker RM14702, decreased the percentage of total white immature (TWI) grains, and (2) qRG3-2, located near RM3766, increased the percentage of regular grains. The effects of these two QTLs were more obvious under high-temperature ripening conditions; hence, these loci are considered QTLs not only for reducing TWI grains but also for increasing high-temperature tolerance. Additionally, we found two QTLs, i.e., qTW3-1 and qRG3-1, responsible for reduced grain quality near RM14314 on chromosome 3. Although the QTL for narrow grains in the Habataki allele qNG3 was genetically linked to qTW3-2, the effect was only slightly significant, and the length/width ratio of qNG3-carrying grains was within the range observed in widely grown japonica cultivars. Incorporating the Habataki region, including qRG3-2 and qTW3-2 but not qTW3-1 and qRG3-1, in addition to previously reported grain quality QTLs in breeding japonica cultivars will improve high-temperature tolerance and grain quality.

The Brown Midrib Leaf (bml) Mutation in Rice (Oryza sativa L.) Causes Premature Leaf Senescence and the Induction of Defense Responses.

Isolating and characterizing mutants with altered senescence phenotypes is one of the ways to understand the molecular basis of leaf aging. Using ethyl methane sulfonate mutagenesis, a new rice (Oryza sativa) mutant, brown midrib leaf (bml), was isolated from the indica cultivar ‘Zhenong34’. The bml mutants had brown midribs in their leaves and initiated senescence prematurely, at the onset of heading. The mutants had abnormal cells with degraded chloroplasts and contained less chlorophyll compared to the wild type (WT). The bml mutant showed excessive accumulation of reactive oxygen species (ROS), increased activities of superoxide dismutase, catalase, and malondialdehyde, upregulation of senescence-induced STAY-GREEN genes and senescence-related transcription factors, and down regulation of photosynthesis-related genes. The levels of abscisic acid (ABA) and jasmonic acid (JA) were increased in bml with the upregulation of some ABA and JA biosynthetic genes. In pathogen response, bml demonstrated higher resistance against Xanthomonas oryzae pv. oryzae and upregulation of four pathogenesis-related genes compared to the WT. A genetic study confirmed that the bml trait was caused by a single recessive nuclear gene (BML). A map-based cloning using insertion/deletion markers confirmed that BML was located in the 57.32kb interval between the L5IS7 and L5IS11 markers on the short arm of chromosome 5. A sequence analysis of the candidate region identified a 1 bp substitution (G to A) in the 5′-UTR (+98) of bml. BML is a candidate gene associated with leaf senescence, ROS regulation, and disease response, also involved in hormone signaling in rice. Therefore, this gene might be useful in marker-assisted backcrossing/gene editing to improve rice cultivars.

Minor-effect QTL for heading date detected in crosses between indica rice cultivar Teqing and near isogenic lines of IR24

Identification of quantitative trait loci (QTL) having small effects on heading date (HD) is important for fine-tuning flowering time in rice (Oryza sativa L.). In this study, minor-effect QTL for HD were identified using five segregating rice populations, including a recombinant inbred line population derived from crosses between indica cultivar Teqing and near isogenic lines of IR24, and four populations derived from residual heterozygotes identified in the original population. HD data from these populations were obtained in multiple years or at two locations with different photoperiods. A total of 11 QTL were detected; they had small additive effects ranging from 0.21 to 1.63days. The QTL were all detected in different populations, locations and/or years, having consistent allelic effects across experiments and a stable magnitude across years at the same location. These QTL, and other minor-effect QTL that have been cloned or fine-mapped, generally do not have strong photoperiod sensitivity, and thus can be used in a wide range of eco-geographical conditions. Seven of the 11 QTL were different from those that have been cloned or fine-mapped, providing new candidates for gene cloning and marker-assisted breeding. Allelic effects of QTL corresponding to those that had been cloned or fine-mapped, were much smaller in this study than previously reported. The results supported the assumption that qualitative and quantitative genes may be different alleles at the same loci, suggesting that it may be promising to identify minor-effect QTL from major heading date genes/QTL that have been cloned.

Rice gene, BBH/Lsi1, regulates the color of rice hull by reducing the absorption and deposition of silicon and accumulating excess flavonoid

The color of grain hull is one of the remarkable traits which can be easily identified after heading, especially at the mature stage. In present study, a discoloration hull mutant named black–brown hull (bbh), was obtained from an indica cultivar Zhenong 34 by mutagenesis with ethyl methane sulfonate (EMS). The hull color of bbh mutant initially appeared black–brown on the 15th day and became completely black–brown on the 30th day after heading. The root of bbh was shorter than that of WT during the whole growth period. Furthermore, the total flavonoids content in the hulls and the silicon deposition in the leaves of bbh were both remarkably higher than WT. The results of map-based cloning indicated that the mutant trait of bbh was controlled by a single recessive nuclear gene, which was located on the long arm of chromosome 2 with a physical distance of 64.9 kb. The comparison of gDNA sequence between bbh and WT showed that there was a substitution from T to C (+ 2360) in the third exon of LOC_Os02g51110. BBH was an allelic gene of Lsi1, which encoded a water channel protein (aquaporin) involving in silicon uptake. The expression levels of the genes related to silicon absorption, transportation and distribution were detected to be up- or down-regulated at different stages in bbh root. Moreover, the transcripts of structural enzymatic genes involved in flavonoid biosynthesis in hulls also had apparent differences between WT and bbh mutant. Above all, the results revealed that BBH/Lsi1 was responsible to the black–brown hull by reducing the absorption and deposition of silicon and accumulating overmuch flavonoid.

Introgression of a functional epigenetic OsSPL14WFP allele into elite indica rice genomes greatly improved panicle traits and grain yield

Rice yield potential has been stagnant since the Green Revolution in the late 1960s, especially in tropical rice cultivars. We evaluated the effect of two major genes that regulate grain number, Gn1a/OsCKX2 and IPA1/WFP/OsSPL14, in elite indica cultivar backgrounds. The yield-positive Gn1a-type 3 and OsSPL14WFP alleles were introgressed respectively through marker-assisted selection (MAS). The grain numbers per panicle (GNPP) were compared between the recipient allele and the donor allele groups using segregating plants in BC3F2 and BC3F3 generations. There was no significant difference in GNPP between the two Gn1a alleles, suggesting that the Gn1a-type 3 allele was not effective in indica cultivars. However, the OsSPL14WFP allele dramatically increased GNPP by 10.6–59.3% in all four different backgrounds across cropping seasons and generations, indicating that this allele provides strong genetic gain to elite indica cultivars. Eventually, five high-yielding breeding lines were bred using the OsSPL14WFP allele by MAS with a conventional breeding approach that showed increased grain yield by 28.4–83.5% (7.87–12.89 t/ha) vis-à-vis the recipient cultivars and exhibited higher yield (~64.7%) than the top-yielding check cultivar, IRRI 156 (7.82 t/ha). We demonstrated a strong possibility to increase the genetic yield potential of indica rice varieties through allele mining and its application.

Supplementation with ferromanganese oxide–impregnated biochar composite reduces cadmium uptake by indica rice (Oryza sativa L.)

Abstract The use of a ferromanganese oxide biochar composite (FMBC) to reduce cadmium (Cd) uptake in an indica cultivar of rice (Oryza sativa L.) was investigated by a pot experiment. Application of 0.5–2.0% FMBC or biochar to rice plants in pots improved the dry weight of the rice roots, stems, leaves, and grains in soils contaminated with either high or low levels of Cd. Compared with the biochar treatment, the FMBC treatment significantly reduced Cd accumulation in different parts of the rice plant (P

High-resolution genetic mapping of a novel brown planthopper resistance locus, Bph34 in Oryza sativa L. X Oryza nivara (Sharma & Shastry) derived interspecific F2 population.

A BPH-resistant locus designated as Bph34 identified in Oryza nivara acc. IRGC104646 on long arm of chromosome 4 using high-resolution mapping with 50K SNP chip. BPH resistance contributed by locus showed dominant inheritance in F2 and F3. The Bph34 locus is 91kb in size and contains 11 candidate genes. In addition to SNP markers, SSR markers, RM16994 and RM17007 co-segregated with the BPH resistance. These two SSR markers can facilitate marker-assisted transfer of the Bph34 locus into elite rice cultivars in all labs. Brown planthopper (BPH, Nilaparvata lugen Stål) is one of the most destructive insects of rice (Oryza sativa L.) causing significant yield losses annually. Exploiting host plant resistance to BPH and incorporating resistant genes in susceptible commercial cultivars is economical and environmentally friendly approach to manage this pest. Here, we report high-resolution mapping of a novel genetic locus for resistance to BPH, designated as Bph34 on long arm of rice chromosome 4. The locus was mapped using an interspecific F2 population derived from a cross between susceptible indica cultivar PR122 and BPH-resistant wild species, O. nivara acc. IRGC104646. Inheritance studies performed using F2 and F2:3 populations revealed the presence of single dominant gene. Construction of high-density linkage map using 50K SNP chip (OsSNPnks) followed by QTL mapping identified single major locus at 28.8 LOD score between SNP markers, AX-95952039 and AX-95921548. The major locus contributing resistance to BPH designated as Bph34 and explained 68.3% of total phenotypic variance. The Bph34 locus is 91Kb in size on Nipponbare reference genome-IRGSP-1.0 and contains 11 candidate genes. In addition to associated SNP markers, two SSR markers, RM16994 and RM17007, also co-segregated with the Bph34 which can be used efficiently for markers assisted transfer into elite rice cultivars across the labs.

Effect of Lactic Acid on α-Amylase Activity and Phytic Acid Content in Germination of Rice (<i>Oryza sativa</i> L.)

Lactic acid has known as a one of compounds to cause cellular harm in waterlogged tissue through the process of cytoplasmic acidosis. The effects of lactic acid on α-amylase activity and phytic acid content using an assay for high phosphate in germination stage of rice were evaluated. It is showed that lactic acid inhibited rice germination at every treated dose. The reduction of α-amylase content attributed to lactic acid at 24 h after germination of rice seeds was observed. The analysis of phosphate concentration at 48 h after treatment noted that although the content of phytic acid was reduced in Japonica varieties, but in contrast its amount was enhanced in Indica cultivars. The findings highlighted the positive effects of lactic acid on α-amylase activity and phytic acid content and suggested that this compound may play a potent role as a germinated regulator in rice.

Estimates of rice lodging using indices derived from UAV visible and thermal infrared images

Rice lodging not only causes difficulty in harvest operations, but also drastically reduces yield. Rice lodging assessment contributes greatly to rice plantation and crop field management. In this study, we collected visible and thermal infrared images with an unmanned aerial vehicle. Then, based on hybrid image analysis and field investigation, we established a comprehensive rice lodging recognition model using a particle swarm optimization and support vector machine algorithm. The results showed that color and texture features were different between lodged and non-lodged rice plants. Moreover, the temperature was distinct between lodging and non-lodging areas, with lodged rice having higher canopy temperature. The developed model based on the visible and thermal infrared images was validated using different Indica and Japonica rice cultivars. The model had a false positives rate and false negatives rate of less than 10%, and estimated lodging rate with an R2 greater than 0.9. These results indicated that combination of visible and thermal infrared images feature significantly increased the rice lodging recognition accuracy. The developed model can be used to monitor rice lodging and estimate the lodging rate.

A near-isogenic rice line carrying a QTL for larger leaf inclination angle yields heavier biomass and grain

Manipulating plant architecture is a promising strategy for further improving rice production. The canopy extinction coefficient (k), the most important parameter of canopy architecture, represents the characteristics of light penetration into the canopy, and is determined mainly by the leaf inclination angle. With its erect leaves, the high-yielding indica cultivar ‘Takanari’ has a smaller k during ripening than the elite japonica cultivar ‘Koshihikari’. Using chromosome segment substitution lines derived from a cross between ‘Takanari’ and ‘Koshihikari’, we previously detected a quantitative trait locus (QTL) for leaf inclination angle on a chromosome 3. Here, we tested a near-isogenic line (NIL-3) carrying the ‘Takanari’ allele of a QTL for larger leaf inclination angle on chromosome 3, qLIA3, in the ‘Koshihikari’ genetic background for the effects of qLIA3 on k, dry matter production, and grain yield. NIL-3 had leaves with a larger inclination angle from the full heading through ripening stages and a smaller k at the ripening stage than ‘Koshihikari’. There were no differences in plant height, panicle size, heading date, leaf area index, or individual leaf photosynthesis between NIL-3 and ‘Koshihikari’. Biomass at harvest was significantly greater in NIL-3 than in ‘Koshihikari’ owing to a higher net assimilation rate during ripening, resulting in a higher grain yield. qLIA3 might incorporate a promising gene for improving rice production.

Effect of Lactic Acid on α-Amylase Activity and Phytic Acid Content in Germination of Rice (<i>Oryza sativa</i> L.)

Lactic acid has known as a one of compounds to cause cellular harm in waterlogged tissue through the process of cytoplasmic acidosis. The effects of lactic acid on α-amylase activity and phytic acid content using an assay for high phosphate in germination stage of rice were evaluated. It is showed that lactic acid inhibited rice germination at every treated dose. The reduction of α-amylase content attributed to lactic acid at 24 h after germination of rice seeds was observed. The analysis of phosphate concentration at 48 h after treatment noted that although the content of phytic acid was reduced in Japonica varieties, but in contrast its amount was enhanced in Indica cultivars. The findings highlighted the positive effects of lactic acid on α-amylase activity and phytic acid content and suggested that this compound may play a potent role as a germinated regulator in rice.

Comparative transcriptome analysis reveals molecular response to salinity stress of salt-tolerant and sensitive genotypes of indica rice at seedling stage

Abiotic stresses, such as salinity, greatly threaten the growth and productivity of plants. Rice (Oryza sativa L.) is one of the most important food crops, as well as a monocot model for genomic research. To obtain a global view of the molecular response to salinity stress, we conducted a leaf transcriptome analysis on rice seedlings. Two cultivars of rice subspecies indica, including the salt-tolerant genotype Xian156 and the salt-sensitive genotype IR28, were used in the present study. Eighteen RNA libraries were obtained from these two genotypes at three timepoints (0 h, 48 h and 72 h) after applying salinity stress. We obtained the reference-guided assembly of the rice transcriptome, which resulted in 1,375 novel genes, including 1,371 annotated genes. A comparative analysis between genotypes and time points showed 5,273 differentially expressed genes (DEGs), of which 286 DEGs were only found in the tolerant genotype. The Disease resistance response protein 206 and TIFY 10 A were differentially expressed, which were validated by quantitative real-time PCR. The differentially expressed genes identified through the mRNA transcriptome, along with the structure, provide a revealing insight into rice molecular response to salinity stress and underlie the salinity tolerance mechanism between genotypes.

Characterisation of a novel quantitative trait locus, GN4-1, for grain number and yield in rice (Oryza sativa L.).

A novel QTL for grain number, GN4-1, was identified and fine-mapped to an~190-kb region on the long arm of rice chromosome 4. Rice grain yield is primarily determined by three components: number of panicles per plant, grain number per panicle and grain weight. Among these traits, grain number per panicle is the major contributor to grain yield formation and is a crucial trait for yield improvement. In this study, we identified a major quantitative trait locus (QTL) responsible for rice grain number on chromosome 4, designated GN4-1 (a QTL for Grain Number on chromosome 4), using advanced segregating populations derived from the crosses between an elite indica cultivar 'Zhonghui 8006' (ZH8006) and a japonica rice 'Wuyunjing 8' (WYJ8). GN4-1 was delimited to an~190-kb region on chromosome 4. The genetic effect of GN4-1 was estimated using a pair of near-isogenic lines. The GN4-1 gene from WYJ8 promoted accumulation of cytokinins in the inflorescence and increased grain number per panicle by~17%. More importantly, introduction of the WYJ8 GN4-1 gene into ZH8006 increased grain yield by~14.3 and~11.5% in the experimental plots in 2014 and 2015, respectively. In addition, GN4-1 promoted thickening of the culm and may enhance resistance to lodging. These results demonstrate that GN4-1 is a potentially valuable gene for improvement of yield and lodging resistance in rice breeding.

A novel QTL associated with rice canopy temperature difference affects stomatal conductance and leaf photosynthesis.

Canopy temperature can be a good indicator of stomatal conductance. To understand the genetic basis of phenotypic differences in stomatal conductance between average and high-yielding rice (Oryza sativa L.) cultivars, we conducted a quantitative trait locus (QTL) analysis of canopy temperature. We developed reciprocal series of backcross inbred lines (BC1F6) derived from a cross between the average-yielding japonica cultivar ‘Koshihikari’ and the high-yielding indica cultivar ‘Takanari’. A stable QTL, qCTd11 (QTL for canopy temperature difference on chromosome 11) on the short arm of chromosome 11, accounted for 10.4 and 19.8% of the total phenotypic variance in the two lines; the ‘Takanari’ allele decreased the canopy temperature difference value. A chromosome segment substitution line carrying the Takanari qCTd11 showed a greater reduction in canopy temperature than ‘Koshihikari’, and had higher stomatal conductance and photosynthetic rate. These results suggest that qCTd11 is not only involved in canopy temperature, but is also involved in both stomatal conductance and photosynthetic rate.