Improving Plant Architecture Research Articles

The Genetic Architecture of Barley Plant Stature.

Plant stature in temperate cereals is predominantly controlled by tillering and plant height as complex agronomic traits, representing important determinants of grain yield. This study was designed to reveal the genetic basis of tillering at five developmental stages and plant height at harvest in 218 worldwide spring barley (Hordeum vulgare L.) accessions under greenhouse conditions. The accessions were structured based on row-type classes [two- vs. six-rowed] and photoperiod response [photoperiod-sensitive (Ppd-H1) vs. reduced photoperiod sensitivity (ppd-H1)]. Phenotypic analyses of both factors revealed profound between group effects on tiller development. To further verify the row-type effect on the studied traits, Six-rowed spike 1 (vrs1) mutants and their two-rowed progenitors were examined for tiller number per plant and plant height. Here, wild-type (Vrs1) plants were significantly taller and had more tillers than mutants suggesting a negative pleiotropic effect of this row-type locus on both traits. Our genome-wide association scans further revealed highly significant associations, thereby establishing a link between the genetic control of row-type, heading time, tillering, and plant height. We further show that associations for tillering and plant height are co-localized with chromosomal segments harboring known plant stature-related phytohormone and sugar-related genes. This work demonstrates the feasibility of the GWAS approach for identifying putative candidate genes for improving plant architecture.

Characterization and fine mapping of osh15(t), a novel dwarf mutant gene in rice (Oryza sativa L.)

Plant height is one of the most important agronomic traits of plant architecture, and also affects grain yield in rice. In this study, we obtained a novel dwarf rice mutant of japonica variety Shennong9816, designated Shennong9816d. Compared with wild-type, the Shennong9816d plant height was significantly reduced, and the tiller number significantly increased. Additionally, the mutant yield component, and the number of large and small vascular bundles were significantly decreased compared with wild-type. Genetic analysis indicated that the Shennong9816d dwarf phenotype was controlled by a recessive nuclear gene, while the plant was shown to be sensitive to gibberellic acid. Using a large F2 population derived from a cross between Shennong9816d and the indica rice variety Habataki, the osh15(t) gene was fine mapped between RM20891 and RM20898, within a physical distance of 73.78 kb. Sequencing analysis showed that Shennong9816d carries a 1 bp mutation and a 30 bp insertion in the OSH15 region. These results suggest that osh15(t) is a novel allelic mutant originally derived from japonica variety Shennong9816, which may be useful for introducing the semi-dwarf phenotype to improve plant architecture in rice breeding practice.

Characterizing Variation of Branch Angle and Genome-Wide Association Mapping in Rapeseed (Brassica napus L.).

Changes in the rapeseed branch angle alter plant architecture, allowing more efficient light capture as planting density increases. In this study, a natural population of rapeseed was grown in three environments and evaluated for branch angle trait to characterize their phenotypic patterns and genotype with a 60K Brassica Infinium SNP array. Significant phenotypic variation was observed from 20 to 70°. As a result, 25 significant quantitative trait loci (QTL) associated with branch angle were identified on chromosomes A2, A3, A7, C3, C5, and C7 by the MLM model in TASSEL 4.0. Orthologs of the functional candidate genes involved in branch angle were identified. Among the key QTL, the peak SNPs were close to the key orthologous genes BnaA.Lazy1 and BnaC.Lazy1 on A3 and C3 homologous genome blocks. With the exception of Lazy (LA) orthologous genes, SQUMOSA PROMOTER BINDING PROTEIN LIKE 14 (SPL14) and an auxin-responsive GRETCHEN HAGEN 3 (GH3) genes from Arabidopsis thaliana were identified close to two clusters of SNPs on the A7 and C7 chromosomes. These findings on multiple novel loci and candidate genes of branch angle will be useful for further understanding and genetic improvement of plant architecture in rapeseed.

ClRTL1 Encodes a Chinese Fir RNase III-Like Protein Involved in Regulating Shoot Branching.

Identification of genes controlling shoot branching is crucial for improving plant architecture and increasing crop yield or biomass. A branching mutant of Chinese fir named “Dugansha” (Cunninghamia lanceolata var. dugan.) has been isolated in our laboratory. We chose the cDNA-AFLP technique and an effective strategy to screen genes that potentially regulate shoot branching in Chinese fir using this mutant. An RNase III-like1 cDNA fragment named ClRTL1 was identified as a potential positive regulator. To investigate the function of ClRTL1 in regulating shoot branching, we cloned the full-length cDNA sequence from C. lanceolata (Lamb.) Hook, deduced its secondary structure and function, and overexpressed the coding sequence in Arabidopsis. The ClRTL1 cDNA is 1045 bp and comprises an open reading frame of 705 bp. It encodes a protein of 235 amino acids. The deduced secondary structure of the ClRTL1 indicates that it is a mini-RNase III-like protein. The expression analysis and phenotypes of 35S: ClRTL1 in A. thaliana implies that ClRTL1 plays a role in promoting shoot branching in Chinese fir.

Genetic modification of Rosa pinna (Clerodendrum philippinum Schauer) with gai mutant gene for improved plant architecture

Rosa pinna ( Clerodendrum philippinum Schaue r), is a shrub with attractive and fragrant flowers. However, the tall and spread architecture and high leaf to flower ratio hinder its use as an ornamental plant. Hence, changing the level of acceptance of C. philippinum by incorporating a dwarfing gene to the plant is considered useful. A study was conducted to find a suitable regeneration medium and ultimately to modify the plant architecture through transformation of the gibberellic acid inhibitor (gai) mutant dwarfing gene by particle bombardment. Effects of different concentrations of thidiazuron (TDZ:Nphenyl N’ 1,2,3-thidiazol-5-yl urea) on callus initiation and regeneration of shoots and the effects of micro career flying distance in gene transformation of C. philippinum were investigated. The regenerated shoots were first cultured on hormone free MS medium and transferred to a MS medium with 0.5 mg/L in dole butyric acid for rooting after four weeks. The shortest duration for callus initiation, the largest callus volume (28 days after establishment) and the highest number of shoots (75 days after establishment) were observed in 1.5 mg/L TDZ in the MS medium. Results of transferring the gai mutant gene to in vitro leaves of C. philippinum revealed that both the shortest time duration and the highest plant regeneration were at 9 cm micro-carrier flying distance. Leaf tissues of regenerated plants, which carry the gai mutant gene, positively responded for the beta-glucuronidase (GUS) assay. The regenerated shoots were rooted and successfully acclimatized. Tropical Agricultural Research Vol. 25 (1): 27-37 (2013)

OsPIN5b modulates rice (Oryza sativa) plant architecture and yield by changing auxin homeostasis, transport and distribution.

Plant architecture attributes such as tillering, plant height and panicle size are important agronomic traits that determine rice (Oryza sativa) productivity. Here, we report that altered auxin content, transport and distribution affect these traits, and hence rice yield. Overexpression of the auxin efflux carrier-like gene OsPIN5b causes pleiotropic effects, mainly reducing plant height, leaf and tiller number, shoot and root biomass, seed-setting rate, panicle length and yield parameters. Conversely, reduced expression of OsPIN5b results in higher tiller number, more vigorous root system, longer panicles and increased yield. We show that OsPIN5b is an endoplasmic reticulum (ER) -localized protein that participates in auxin homeostasis, transport and distribution invivo. This work describes an example of an auxin-related gene where modulating its expression can simultaneously improve plant architecture and yield potential in rice, and reveals an important effect of hormonal signaling on these traits.

PAY1 improves plant architecture and enhances grain yield in rice.

SummaryPlant architecture, a complex of the important agronomic traits that determine grain yield, is a primary target of artificial selection of rice domestication and improvement. Some important genes affecting plant architecture and grain yield have been isolated and characterized in recent decades; however, their underlying mechanism remains to be elucidated. Here, we report genetic identification and functional analysis of the PLANT ARCHITECTURE AND YIELD 1 (PAY1) gene in rice, which affects plant architecture and grain yield in rice. Transgenic plants over‐expressing PAY1 had twice the number of grains per panicle and consequently produced nearly 38% more grain yield per plant than control plants. Mechanistically, PAY1 could improve plant architecture via affecting polar auxin transport activity and altering endogenous indole‐3‐acetic acid distribution. Furthermore, introgression of PAY1 into elite rice cultivars, using marker‐assisted background selection, dramatically increased grain yield compared with the recipient parents. Overall, these results demonstrated that PAY1 could be a new beneficial genetic resource for shaping ideal plant architecture and breeding high‐yielding rice varieties.

Promoting flowering, lateral shoot outgrowth, leaf development, and flower abscission in tobacco plants overexpressing cotton FLOWERING LOCUS T (FT)-like gene GhFT1.

FLOWERING LOCUS T (FT) encodes a mobile signal protein, recognized as major component of florigen, which has a central position in regulating flowering, and also plays important roles in various physiological aspects. A mode is recently emerging for the balance of indeterminate and determinate growth, which is controlled by the ratio of FT-like and TERMINAL FLOWER 1 (TFL1)-like gene activities, and has a strong influence on the floral transition and plant architecture. Orthologs of GhFT1 was previously isolated and characterized from Gossypium hirsutum. We demonstrated that ectopic overexpression of GhFT1 in tobacco, other than promoting flowering, promoted lateral shoot outgrowth at the base, induced more axillary bud at the axillae of rosette leaves, altered leaf morphology, increased chlorophyll content, had higher rate of photosynthesis and caused flowers abscission. Analysis of gene expression suggested that flower identity genes were significantly upregulated in transgenic plants. Further analysis of tobacco FT paralogs indicated that NtFT4, acting as flower inducer, was upregulated, whereas NtFT2 and NtFT3 as flower inhibitors were upregulated in transgenic plants under long-day conditions, but downregulated under short-day conditions. Our data suggests that sufficient level of transgenic cotton FT might disturb the balance of the endogenous tobacco FT paralogs of inducers and repressors and resulted in altered phenotype in transgenic tobacco, emphasizing the expanding roles of FT in regulating shoot architecture by advancing determine growth. Manipulating the ratio for indeterminate and determinate growth factors throughout FT-like and TFL1-like gene activity holds promise to improve plant architecture and enhance crop yield.

Shaping plant architecture.

Plants exhibit phenotypical plasticity. Their general body plan is genetically determined, but plant architecture and branching patterns are variable and can be adjusted to the prevailing environmental conditions. The modular design of the plant facilitates such morphological adaptations. The prerequisite for the formation of a branch is the initiation of an axillary meristem. Here, we review the current knowledge about this process. After its establishment, the meristem can develop into a bud which can either become dormant or grow out and form a branch. Many endogenous factors, such as photoassimilate availability, and exogenous factors like nutrient availability or shading, have to be integrated in the decision whether a branch is formed. The underlying regulatory network is complex and involves phytohormones and transcription factors. The hormone auxin is derived from the shoot apex and inhibits bud outgrowth indirectly in a process termed apical dominance. Strigolactones appear to modulate apical dominance by modification of auxin fluxes. Furthermore, the transcription factor BRANCHED1 plays a central role. The exact interplay of all these factors still remains obscure and there are alternative models. We discuss recent findings in the field along with the major models. Plant architecture is economically significant because it affects important traits of crop and ornamental plants, as well as trees cultivated in forestry or on short rotation coppices. As a consequence, plant architecture has been modified during plant domestication. Research revealed that only few key genes have been the target of selection during plant domestication and in breeding programs. Here, we discuss such findings on the basis of various examples. Architectural ideotypes that provide advantages for crop plant management and yield are described. We also outline the potential of breeding and biotechnological approaches to further modify and improve plant architecture for economic needs.

Genetic control of the leaf angle and leaf orientation value as revealed by ultra-high density maps in three connected maize populations.

Plant architecture is a key factor for high productivity maize because ideal plant architecture with an erect leaf angle and optimum leaf orientation value allow for more efficient light capture during photosynthesis and better wind circulation under dense planting conditions. To extend our understanding of the genetic mechanisms involved in leaf-related traits, three connected recombination inbred line (RIL) populations including 538 RILs were genotyped by genotyping-by-sequencing (GBS) method and phenotyped for the leaf angle and related traits in six environments. We conducted single population quantitative trait locus (QTL) mapping and joint linkage analysis based on high-density recombination bin maps constructed from GBS genotype data. A total of 45 QTLs with phenotypic effects ranging from 1.2% to 29.2% were detected for four leaf architecture traits by using joint linkage mapping across the three populations. All the QTLs identified for each trait could explain approximately 60% of the phenotypic variance. Four QTLs were located on small genomic regions where candidate genes were found. Genomic predictions from a genomic best linear unbiased prediction (GBLUP) model explained 45±9% to 68±8% of the variation in the remaining RILs for the four traits. These results extend our understanding of the genetics of leaf traits and can be used in genomic prediction to accelerate plant architecture improvement.

Comprehensive analysis of CCCH-type zinc finger family genes facilitates functional gene discovery and reflects recent allopolyploidization event in tetraploid switchgrass.

BackgroundIn recent years, dozens of Arabidopsis and rice CCCH-type zinc finger genes have been functionally studied, many of which confer important traits, such as abiotic and biotic stress tolerance, delayed leaf senescence and improved plant architecture. Switchgrass (Panicum virgatum) is an important bioenergy crop. Identification of agronomically important genes and/or loci is an important step for switchgrass molecular breeding. Annotating switchgrass CCCH genes using translational genomics methods will help further the goal of understanding switchgrass genetics and creating improved varieties.ResultsTaking advantage of the publicly-available switchgrass genomic and transcriptomic databases, we carried out a comprehensive analysis of switchgrass CCCH genes (PvC3Hs). A total of 103 PvC3Hs were identified and divided into 21 clades according to phylogenetic analysis. Genes in the same clade shared similar gene structure and conserved motifs. Chromosomal location analysis showed that most of the duplicated PvC3H gene pairs are in homeologous chromosomes. Evolution analysis of 19 selected PvC3H pairs showed that 42.1% of them were under diversifying selection. Expression atlas of the 103 PvC3Hs in 21 different organs, tissues and developmental stages revealed genes with higher expression levels in lignified cells, vascular cells, or reproductive tissues/organs, suggesting the potential function of these genes in development. We also found that eight PvC3Hs in Clade-XIV were orthologous to ABA- or stress- responsive CCCH genes in Arabidopsis and rice with functions annotated. Promoter and qRT-PCR analyses of Clade-XIV PvC3Hs showed that these eight genes were all responsive to ABA and various stresses.ConclusionsGenome-wide analysis of PvC3Hs confirmed the recent allopolyploidization event of tetraploid switchgrass from two closely-related diploid progenitors. The short time window after the polyploidization event allowed the existence of a large number of PvC3H genes with a high positive selection pressure onto them. The homeologous pairs of PvC3Hs may contribute to the heterosis of switchgrass and its wide adaptation in different ecological niches. Phylogenetic and gene expression analyses provide informative clues for discovering PvC3H genes in some functional categories. Particularly, eight PvC3Hs in Clade-XIV were found involved in stress responses. This information provides a foundation for functional studies of these genes in the future.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1328-4) contains supplementary material, which is available to authorized users.

Alteration of osa-miR156e expression affects rice plant architecture and strigolactones (SLs) pathway.

Overexpressing osa--miR156e in rice produced a bushy mutant and osa--miR156e regulation of tillering may do this through the strigolactones (SLs) pathway. Appropriate downregulation of osa--miR156 expression contributed to the improvement of plant architecture. Tillering is one of the main determinants for rice architecture and yield. In this study, a bushy mutant of rice was identified with increased tiller number, reduced plant height, prolonged heading date, low seed setting, and small panicle size due to a T-DNA insertion which essentially elevated the expression of osa-miR156e. Transgenic plants with constitutive expression of osa-miR156e also had the bushy phenotype, which showed osa-miR156 may control apical dominance and tiller outgrowth via regulating the strigolactones signaling pathway. Furthermore, the extent of impaired morphology was correlated with the expression level of osa-miR156e. In an attempt to genetically improve rice architecture, ectopic expression of osa-miR156e under the GAL4-UAS system or OsTB1 promoter was conducted. According to agronomic trait analysis, pTB1:osa-miR156e transgenic plants significantly improved the grain yield per plant compared to plants overexpressing osa-miR156e, even though the yield was still inferior to the wild type, making it a very interesting albeit negative result. Our results suggested that osa-miR156 could serve as a potential tool for modifying rice plant architecture through genetic manipulation of the osa-miR156 expression level.

Potential of hypocotyl diameter in family selection aiming at plant architecture improvement of common bean.

Cultivars of common bean with more erect plant architecture and greater tolerance to degree of lodging are required by producers. Thus, to evaluate the potential of hypocotyl diameter (HD) in family selection for plant architecture improvement of common bean, the HDs of 32 F2 plants were measured in 3 distinct populations, and the characteristics related to plant architecture were analyzed in their progenies. Ninety-six F2:3 families and 4 controls were evaluated in a randomized block design, with 3 replications, analyzing plant architecture grade, HD, and grain yield during the winter 2010 and drought 2011 seasons. We found that the correlation between the HD of F2 plants and traits related to plant architecture of F2:3 progenies were of low magnitude compared to the estimates for correlations considering the parents, indicating a high environmental influence on HD in bean plants. There was a predominance of additive genetic effects on the determination of hypocotyl diameter, which showed higher precision and accuracy compared to plant architecture grade. Thus, this characteristic can be used to select progenies in plant architecture improvement of common beans; however, selection must be based on the means of at least 39 plants in the plot, according to the results of repeatability analysis.

Identification and overexpression of gibberellin 2-oxidase (GA2ox) in switchgrass (Panicum virgatum L.) for improved plant architecture and reduced biomass recalcitrance.

Gibberellin 2-oxidases (GA2oxs) are a group of 2-oxoglutarate-dependent dioxygenases that catalyse the deactivation of bioactive GA or its precursors through 2β-hydroxylation reaction. In this study, putatively novel switchgrass C20 GA2ox genes were identified with the aim of genetically engineering switchgrass for improved architecture and reduced biomass recalcitrance for biofuel. Three C20 GA2ox genes showed differential regulation patterns among tissues including roots, seedlings and reproductive parts. Using a transgenic approach, we showed that overexpression of two C20 GA2ox genes, that is PvGA2ox5 and PvGA2ox9, resulted in characteristic GA-deficient phenotypes with dark-green leaves and modified plant architecture. The changes in plant morphology appeared to be associated with GA2ox transcript abundance. Exogenous application of GA rescued the GA-deficient phenotypes in transgenic lines. Transgenic semi-dwarf lines displayed increased tillering and reduced lignin content, and the syringyl/guaiacyl lignin monomer ratio accompanied by the reduced expression of lignin biosynthetic genes compared to nontransgenic plants. A moderate increase in the level of glucose release in these transgenic lines might be attributed to reduced biomass recalcitrance as a result of reduced lignin content and lignin composition. Our results suggest that overexpression of GA2ox genes in switchgrass is a feasible strategy to improve plant architecture and reduce biomass recalcitrance for biofuel.

The auxin response factor, OsARF19, controls rice leaf angles through positively regulating OsGH3-5 and OsBRI1.

Auxin and brassinosteroid (BR) are important phytohormones for controlling lamina inclination implicated in plant architecture and grain yield. But the molecular mechanism of auxin and BR crosstalk for regulating lamina inclination remains unknown. Auxin response factors (ARFs) control various aspects of plant growth and development. We here report that OsARF19-overexpression rice lines show an enlarged lamina inclination due to increase of its adaxial cell division. OsARF19 is expressed in various organs including lamina joint and strongly induced by auxin and BR. Chromatin immunoprecipitation (ChIP) and yeast one-hybrid assays demonstrate that OsARF19 binds to the promoter of OsGH3-5 and brassinosteroid insensitive 1 (OsBRI1) directing their expression. OsGH3-5-overexpression lines show a similar phenotype as OsARF19-O1. Free auxin contents in the lamina joint of OsGH3-5-O1 or OsARF19-O1 are reduced. OsGH3-5 is localized at the endoplasmic retieulum (ER) matching reduction of the free auxin contents in OsGH3-5-O1. osarf19-TDNA and osgh3-5-Tos17 mutants without erected leaves show a function redundancy with other members of their gene family. OsARF19-overexpression lines are sensitive to exogenous BR treatment and alter the expressions of genes related to BR signalling. These findings provide novel insights into auxin and BR signalling, and might have significant implications for improving plant architecture of monocot crops.

Fine mapping and candidate gene analysis of a major QTL for panicle structure in rice.

Key message A gene not only control tiller and plant height, but also regulate panicle structure by QTL dissection in rice. An ideal panicle structure is important for improvement of plant architecture and rice yield. In this study, using recombinant inbred lines (RILs) of PA64s and 93-11, we identified a quantitative trait locus (QTL), designated qPPB3 for primary panicle branch number. With a BC3F2 population derived from a backcross between a resequenced RIL carrying PA64s allele and 93-11, qPPB3 was fine mapped to a 34.6-kb genomic region. Gene prediction analysis identified four putative genes, among which Os03g0203200, a previously reported gene for plant height and tiller number, Dwarf 88 (D88)/Dwarf 14 (D14), had three nucleotide substitutions in 93-11 compared with PA64s. The T to G substitution resulted in one amino acid change from valine in 93-11 to glycine in PA64s. Real-time PCR analysis showed expression level of D88 was higher in 93-11 than PA64s. The expression of APO1 and IPA1 increased, while GN1a and DST decreased in 93-11 compared with PA64s. Therefore, D88/D14 is not only a key regulator for branching, but also affects panicle structure.Electronic supplementary materialThe online version of this article (doi:10.1007/s00299-014-1661-0) contains supplementary material, which is available to authorized users.

The ZmCLA4 gene in the qLA4-1 QTL controls leaf angle in maize (Zea mays L.).

Maize architecture is a major contributing factor to their high level of productivity. Maize varieties with an erect-leaf-angle (LA) phenotype, which increases light harvesting for photosynthesis and grain-filling, have elevated grain yields. Although a large body of information is available on the map positions of quantitative trait loci (QTL) for LA, little is known about the molecular mechanism of these QTL. In this study, the ZmCLA4 gene, which is responsible for the qLA4-1 QTL associated with LA, was identified and isolated by fine mapping and positional cloning. The ZmCLA4 gene is an orthologue of LAZY1 in rice and Arabidopsis. Sequence analysis revealed two SNPs and two indel sites in ZmCLA4 between the D132 and D132-NIL inbred maize lines. Association analysis showed that C/T/mutation667 and CA/indel965 were strongly associated with LA. Subcellular localization verified the functions of a predicted transmembrane domain and a nuclear localization signal in ZmCLA4. Transgenic maize plants with a down-regulated ZmCLA4 RNAi construct and transgenic rice plants over-expressing ZmCLA4 confirmed that the ZmCLA4 gene located in the qLA4 QTL regulated LA. The allelic variants of ZmCLA4 in the D132 and D132-NIL lines exhibited significant differences in leaf angle. ZmCLA4 transcript accumulation was higher in D132-NIL than in D132 during all the developmental stages and was negatively correlated with LA. The gravitropic response was increased and cell shape and number at the leaf and stem junctions were altered in D132-NIL relative to D132. These findings suggest that ZmCLA4 plays a negative role in the control of maize LA through the alteration of mRNA accumulation, leading to altered shoot gravitropism and cell development. The cloning of the gene responsible for the qLA4-1 QTL provides information on the molecular mechanisms of LA in maize and an opportunity for the improvement of plant architecture with regard to LA through maize breeding.

Isolation and Characterization of the Brassinosteroid Receptor Gene (GmBRI1) from Glycine max

Brassinosteroids (BRs) constitute a group of steroidal phytohormones that contribute to a wide range of plant growth and development functions. The genetic modulation of BR receptor genes, which play major roles in the BR signaling pathway, can create semi-dwarf plants that have great advantages in crop production. In this study, a brassinosteroid insensitive gene homologous with AtBRI1 and other BRIs was isolated from Glycine max and designated as GmBRI1. A bioinformatic analysis revealed that GmBRI1 shares a conserved kinase domain and 25 tandem leucine-rich repeats (LRRs) that are characteristic of a BR receptor for BR reception and reaction and bear a striking similarity in protein tertiary structure to AtBRI1. GmBRI1 transcripts were more abundant in soybean hypocotyls and could be upregulated in response to exogenous BR treatment. The transformation of GmBRI1 into the Arabidopsis dwarf mutant bri1-5 restored the phenotype, especially regarding pod size and plant height. Additionally, this complementation is a consequence of a restored BR signaling pathway demonstrated in the light/dark analysis, root inhibition assay and BR-response gene expression. Therefore, GmBRI1 functions as a BR receptor to alter BR-mediated signaling and is valuable for improving plant architecture and enhancing the yield of soybean.

Quantitative trait locus mapping and candidate gene analysis for plant architecture traits using whole genome re-sequencing in rice.

Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 F7 recombinant in-bred lines (RILs) from a cross of japonica rice line ‘SNUSG1’ and indica rice line ‘Milyang23’. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.

NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars.

Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13-36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica-growing regions such as South and Southeast Asia.