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Lodging resistance in rice is a complex trait determined by culm morphological and culm physical strength traits, and these traits are a major determinant of yield. We made a detailed analysis of various component traits with the aim of deriving optimized parameters for measuring culm strength. Genotyping by sequencing (GBS)-based genome-wide association study (GWAS) was employed among 181 genotypes for dissecting the genetic control of culm strength traits. The VanRaden kinship algorithm using 6,822 filtered single-nucleotide polymorphisms (SNPs) revealed the presence of two sub-groups within the association panel with kinship values concentrated at<0.5 level, indicating greater diversity among the genotypes. A wide range of phenotypic variation and high heritability for culm strength and yield traits were observed over two seasons, as reflected in best linear unbiased prediction (BLUP) estimates. The multi-locus model for GWAS resulted in the identification of 15 highly significant associations (p< 0.0001) for culm strength traits. Two novel major effect marker-trait associations (MTAs) for section modulus and bending stress were identified on chromosomes 2 and 12 with a phenotypic variance of 21.87% and 10.14%, respectively. Other MTAs were also noted in the vicinity of previously reported putative candidate genes for lodging resistance, providing an opportunity for further research on the biochemical basis of culm strength. The quantitative trait locus (QTL) hotspot identified on chromosome 12 with the synergistic association for culm strength trait (section modulus, bending stress, and internode breaking weight) and grain number can be considered a novel genomic region that can serve a dual purpose of enhancing culm strength and grain yield. Elite donors in the indica background with beneficial alleles of the identified major QTLs could be a valuable resource with greater significance in practical plant breeding programs focusing on improving lodging resistance in rice. [ABSTRACT FROM AUTHOR]

Lodging resistance in rice is a complex trait determined by culm morphological and culm physical strength traits, and these traits are a major determinant of yield. We made a detailed analysis of various component traits with the aim of deriving optimized parameters for measuring culm strength. Genotyping by sequencing (GBS)-based genome-wide association study (GWAS) was employed among 181 genotypes for dissecting the genetic control of culm strength traits. The VanRaden kinship algorithm using 6,822 filtered single-nucleotide polymorphisms (SNPs) revealed the presence of two sub-groups within the association panel with kinship values concentrated at

Lodging is one of the major abiotic stresses, affecting the total crop yield and quality. The improved lodging resistance and its component traits potentially reduce the yield losses. The section modulus (SM), bending moment at breaking (M), pushing resistance (PR), and coefficient of lodging resistance (cLr) are the key elements to estimate the lodging resistance. Understanding the genetic architecture of lodging resistance-related traits will help to improve the culm strength and overall yield potential. In this study, a natural population of 795 globally diverse genotypes was further divided into two (indica and japonica) subpopulations and was used to evaluate the lodging resistance and culm strength-related traits. Significant diversity was observed among the studied traits. We carried out the genome-wide association evaluation of four lodging resistance traits with 3.3 million deep resolution single-nucleotide polymorphic (SNP) markers. The general linear model (GLM) and compressed mixed linear model (MLM) were used for the whole population and two subpopulation genome-wide association studies (GWAS), and a 1000-time permutation test was performed to remove the false positives. A total of 375 nonredundant QTLs were observed for four culm strength traits on 12 chromosomes of the rice genome. Then, 33 pleiotropic loci governing more than one trait were mined. A total of 4031 annotated genes were detected within the candidate genomic region of 33 pleiotropic loci. The functional annotations and metabolic pathway enrichment analysis showed cellular localization and transmembrane transport as the top gene ontological terms. The in silico and in vitro expression analyses were conducted to validate the three candidate genes in a pleiotropic QTL on chromosome 7. It validated OsFBA2 as a candidate gene to contribute to lodging resistance in rice. The haplotype analysis for the candidate gene revealed a significant functional variation in the promoter region. Validation and introgression of alleles that are beneficial to induce culm strength may be used in rice breeding for lodging resistance. [ABSTRACT FROM AUTHOR]

Lodging resistance is one of the vital traits in improving the yield and sustainability of production in rice (Oryza sativa L.). A quantitative trait loci (QTL), SCM2 for enhancing the culm strength and increased spikelet number has been reported. In the present study, a diverse collection of 150 accessions from the rice 3K-RG panel were assembled and evaluated for the STRONG CULM2 locus. All the accessions under study showed a normal phenotypic distribution for culm diameter and the allelic diversity analysis for SCM2 resulted in four INDEL’s and 17 SNP’s in both coding and non-coding regions of the genome. Haplotype analysis grouped the entire population into three significant haplotype groups with 114 accessions in H1, 19 accessions in H2 and 17 accessions in H3. Haplotypes were formed using two significant SNP sites viz., 27480778 and 27481339. Dunnett’s test disclosed a significant variation between H1-H2 and H1-H3 haplotypes. Phenotypic evaluation for culm diameter in all the three haplotype groups revealed that the genotypes BR IRGA and PERUNEL in H1, CICA 9 and MOSHI in H2 and KITRANA in H3 possess a maximum culm diameter. H2 and H3 were found to be superior to H1 hence can be utilized for lodging resistance in further breeding programs.

Lodging is one of the major abiotic stresses, affecting the total crop yield and quality. The improved lodging resistance and its component traits potentially reduce the yield losses. The section modulus (SM), bending moment at breaking (M), pushing resistance (PR), and coefficient of lodging resistance (cLr) are the key elements to estimate the lodging resistance. Understanding the genetic architecture of lodging resistance–related traits will help to improve the culm strength and overall yield potential. In this study, a natural population of 795 globally diverse genotypes was further divided into two (indica and japonica) subpopulations and was used to evaluate the lodging resistance and culm strength–related traits. Significant diversity was observed among the studied traits. We carried out the genome-wide association evaluation of four lodging resistance traits with 3.3 million deep resolution single-nucleotide polymorphic (SNP) markers. The general linear model (GLM) and compressed mixed linear model (MLM) were used for the whole population and two subpopulation genome-wide association studies (GWAS), and a 1000-time permutation test was performed to remove the false positives. A total of 375 nonredundant QTLs were observed for four culm strength traits on 12 chromosomes of the rice genome. Then, 33 pleiotropic loci governing more than one trait were mined. A total of 4031 annotated genes were detected within the candidate genomic region of 33 pleiotropic loci. The functional annotations and metabolic pathway enrichment analysis showed cellular localization and transmembrane transport as the top gene ontological terms. The in silico and in vitro expression analyses were conducted to validate the three candidate genes in a pleiotropic QTL on chromosome 7. It validated OsFBA2 as a candidate gene to contribute to lodging resistance in rice. The haplotype analysis for the candidate gene revealed a significant functional variation in the promoter region. Validation and introgression of alleles that are beneficial to induce culm strength may be used in rice breeding for lodging resistance.

Significant achievements have been made in breeding programs for the heavy‐panicle‐type (HPT) rice (Oryza sativa) in Southwest China. The HPT varieties now exhibit excellent lodging resistance, allowing them to overcome the greater pressures caused by heavy panicles. However, the genetic mechanism of this lodging resistance remains elusive. Here, we isolated a major quantitative trait locus, Panicle Neck Diameter 1 (PND1), and identified the causal gene as GRAIN NUMBER 1A/CYTOKININ OXIDASE 2 (Gn1A/OsCKX2). The null gn1a allele from rice line R498 (gn1aR498) improved lodging resistance through increasing the culm diameter and promoting crown root development. Loss‐of‐function of Gn1a/OsCKX2 led to cytokinin accumulation in the crown root tip and accelerated the development of adventitious roots. Gene pyramiding between the null gn1aR498 allele with two gain‐of‐function alleles, STRONG CULM 2 (SCM2) and SCM3, further improved lodging resistance. Moreover, Gn1a/OsCKX2 had minimal influence on overall rice quality. Our research thus highlights the distinct genetic components of lodging resistance of HPT varieties and provides a strategy for tailor‐made crop improvement of both yield and lodging resistance in rice. [ABSTRACT FROM AUTHOR]

We compared the effects of four seeding rates, 60, 100, 140, and 180 seeds m−2, on yield, lodging resistance and culm strength using two Japanese wheat cultivars Ayahikari and Iwainodaichi. With the decreasing seeding rate, maximum tiller number decreased, percentage of productive culms increased and spike number m−2 decreased, and the spikelet number per spike, percentage of fertile spikelets, grain number per spikelet and grain number per spike increased. Consequently, grain yield was not significantly affected. Lodging was not observed, but the lodging index was significantly affected by the seeding rate and was the highest in the plots sown at 180 seeds m−2. The bending moment at the breaking point and flexural rigidity of the basal internode with leaf sheaths were highest in the plots sown at 60 seeds m−2. In conclusion, the culm strength and stem lodging resistance increased with decreasing seeding rate. Section modulus and bending stress, which constitute the bending moment at the breaking point, and the moment of inertia area and Young’s modulus, which represent the flexural rigidity, were highest in plots sown at 60 seeds m−2. Therefore, the seeding rate was considered to influence the culm morphology and functions of the cell wall components. The effects of the seeding rate on culm characteristics and lodging resistance did not differ between the two cultivars, and ‘Ayahikari’ had consistently stronger culms than ‘Iwainodaichi’. We suggest that low seeding rates method would be suitable for heavily fertilized cultivation for both cultivar with high and low culm strength. Abbreviations AMeDAS: the automated meteorological data acquisition system; HSD: honestly significant difference

New plant type core set comprising indica and tropical japonica accessions along with checks were evaluated for yield and culm strength related traits and characterized with gene specific markers viz., Gn1a, DEP1, Ghd7, SPL14, GS5, TGW6 and SCM2. Analysis of variance revealed significant differences as well as presence of variability among the genotypes for all the traits. Seven genotypes (IRGC25510, IRGC1742, Haorei machang, Azhoghi, Thangmoi, BPT5204 and Swarnadhan) do not possess similar allele as that of the assessed genes based on combined analysis for all the traits and genes. Of them, four genotypes IRGC1742, Azhoghi, BPT5204 and Swarnadhan possess ideal trait combination (90–100 days to 50% flowering, 100–120 cm plant height, grain number of > 200, 11–15 productive tillers) but with weak culm can be ideal sources for identification of new genes for yield attributing traits and direct introgression of SCM2. Based on single trait-gene analysis, nine trait wise donors with high value for the trait (also with desirable plant type) but without similar allele of the corresponding gene were identified. One genotype IRGC7486 with high grain number (300), four genotypes (IRGC50448, IRGC43741, IRGC15147 and IRGC39111) with strong culm (1195–2655 g.f), three genotypes viz., IRGC15147, IRGC39111 and IRGC10658 with high panicle weight and one genotype Solumpiket with high 1000-grain weight and high panicle weight can be considered for identification of novel gene(s) for respective traits. [ABSTRACT FROM AUTHOR]

Summary: Lodging reduces grain yield in cereal crops. Understanding the genetic basis of lodging resistance (LR) benefits LR breeding. In the study, 524 accessions from a rice germplasm collection and 193 recombinant inbred lines were phenotyped for 17 LR‐related traits. Height and culm strength (the magnitude of applied force necessary to break the culm) were two major factors affecting LR. We conducted genome‐wide association study (GWAS) and identified 127 LR‐associated loci. Significant phenotypic correlations between culm‐strength traits and yield‐related traits were observed. To reveal the genetic relationship between them, we conducted GWAS of culm‐strength traits with adding yield‐related trait as a covariate and detected 63 loci linking culm strength and yield. As a proof, a near‐isogenic line for an association locus on chromosome 7 showed enhanced LR and yield. Strikingly, 58 additional loci were identified in the covariate‐added GWAS. Several LR‐associated loci had undergone divergent selection. Linkage analysis supported the GWAS results. We propose that introgression of alleles beneficial for both culm strength and panicle weight without negative effects on panicle number or pyramiding high‐yielding alleles and lodging‐resistant alleles without effects on yield can be employed for the post‐Green‐Revolution breeding. [ABSTRACT FROM AUTHOR]

We compared the effects of four seeding rates, 60, 100, 140, and 180 seeds m−2, on yield, lodging resistance and culm strength using two Japanese wheat cultivars Ayahikari and Iwainodaichi. With the decreasing seeding rate, maximum tiller number decreased, percentage of productive culms increased and spike number m−2 decreased, and the spikelet number per spike, percentage of fertile spikelets, grain number per spikelet and grain number per spike increased. Consequently, grain yield was not significantly affected. Lodging was not observed, but the lodging index was significantly affected by the seeding rate and was the highest in the plots sown at 180 seeds m−2. The bending moment at the breaking point and flexural rigidity of the basal internode with leaf sheaths were highest in the plots sown at 60 seeds m−2. In conclusion, the culm strength and stem lodging resistance increased with decreasing seeding rate. Section modulus and bending stress, which constitute the bending moment at the breaking point, and the moment of inertia area and Young's modulus, which represent the flexural rigidity, were highest in plots sown at 60 seeds m−2. Therefore, the seeding rate was considered to influence the culm morphology and functions of the cell wall components. The effects of the seeding rate on culm characteristics and lodging resistance did not differ between the two cultivars, and 'Ayahikari' had consistently stronger culms than 'Iwainodaichi'. We suggest that low seeding rates method would be suitable for heavily fertilized cultivation for both cultivar with high and low culm strength. AMeDAS: the automated meteorological data acquisition system; HSD: honestly significant difference [ABSTRACT FROM AUTHOR]

This study was conducted to characterize new plant type (NPT) traits among 650 genetically diverse rice genotypes of tropical japonica and indica and to establish an initial core set for NPT traits. Analysis of variance revealed highly significant differences among the genotypes for all the traits assessed except flag length and width and leaf angles. Dendrogram categorized the genotypes into five distinct duration groups. Genotypes viz., Pumphamah, IRGC5097, IRGC37015, IRGC43741, IRGC50448, IRGC53089, IRGC39111, IRGC18021, Haorei Machang, IRGC44069, IRGC8269, Thangmoi, IRGC33130 and IRGC29772 were identified as possessing strong culm. Long panicles with a length of more than 35 cm were found in IRGC8269, IRGC9147, IRGC14694, IRGC19642, IRGC27435, IRGC39111, IRGC31051, IRGC26011and IRGC25892. Ideal leaf angle of NPT genotypes of 5°, 10° and 20° of flag leaf, 1st and 2nd leaves was not found in any genotype but with a combination of 5°, 10° and 10° was observed in IRGC63102 and IRGC66644. NPT flag leaf length and width of 50 and 2 cm, respectively, was seen in 'Kemenya Kepeu' and 'IRGC29772'. High grain number of more than 350 was observed in IRGC53089, IRGC31063 and Azhoghi. A total of 72 genotypes were found with a combination of one or more ideal plant type traits of which, hierarchical cluster analysis based on genetic distances selected 32 as NPT core set. This core set will serve as an ideal genetic resource for breeding programs aimed at NPT development. [ABSTRACT FROM AUTHOR]

High tropospheric ozone concentrations reduce rice yield and grain quality, which imposes a serious threat to food security in Asia. This study aimed at determining the effect of ozone on rice lodging, an unpredictable constraint for achieving high yield and good quality in rice production under climate change. Two rice cultivars with different ozone sensitivity were exposed to ozone concentration of 80 ppb (8 h per day) and control conditions (13 ppb) in natural-light fumigation chambers from tillering to maturity. The pushing resistance of intact plants and the lodging-related culm traits were examined. Ozone exposure significantly decreased the in-situ pushing resistance of intact plant or single culm in the ozone-sensitive cultivar YD6, but had no effects in the ozone-tolerant cultivar WYJ27. Ozone reduced breaking resistance and bending moment to a similar magnitude, resulting in no change of lodging index when averaged across all rice basal internodes. In general, WYJ27 was less responsive to ozone than YD6. Negative ozone effects on lodging-related culm traits of YD6 included reductions in the internode dry weight as well as the dry weight per unit internode length, decreases in internode diameter, cross section area and culm wall thickness of basal internodes, and reduced concentrations of soluble sugar and starch. Correlation analysis indicated that ozone-induced decrease in culm strength of YD6 was mainly attributed to the thinner internodes and the smaller culm density due to less nonstructural carbohydrate deposition. The ozone-sensitivity of YD6 was confirmed by its high yield reduction of 25 %, caused by an 11 % decrease in spikelet number per panicle and a 10 % decrease in fulfilled grain weight. The results suggested that rice ozone sensitivity in yield was in consistent with that in stem strength, which could result in no change of lodging index under greenhouse conditions. The realistic lodging susceptibility of these cultivars in response to ozone pollution in open paddy fields, where rice was often subjected to wind and rain during ripening stage, needs further investigation. [Display omitted] • Lodging-related traits differed between an indica cultivar and a japonica cultivar. • Ozone exposure during rice growth decreased stem strength of the indica cultivar YD6. • Ozone-induced stem strength reduction related to thinner internodes and lower culm density. • Decreases in nonstructural carbohydrates content by ozone led to smaller culm density. [ABSTRACT FROM AUTHOR]

To understand the lodging behavior in kodo millet (Paspalum scrobiculatum L.) at morphological, biochemical, and molecular levels, 22 germplasm accessions selected based on previous trials were characterized for culm strength-related morphological traits such as pulling force, culm weight per unit length, culm diameter, recovery angle after bending and degree of lodging, and biochemical traits such as cellulose, hemicellulose, and lignin content of the culm. Correlation among traits and path analysis with degree of lodging showed that only lignin content per unit length of the culm had a very high negative effect on degree of lodging, followed by culm diameter, which means that higher the lignin content and culm diameter, the lesser will be the degree of lodging. Hence, it was concluded that any improvement for lodging resistance in kodo millet can be achieved through improving the lignin content (mg/cm of the dry culm) and culm diameter. Gene expression studies in kodo millet for FLEXIBLE CULM 1 (FC1), a gene implicated in lignin biosynthetic pathway and lodging resistance in rice, suggests the role of FC1 gene ortholog in lignin accumulation in kodo millet as well. Accordingly, the highest gene expression was recorded in strong culm line “Adari” a land race and the lowest expression in “Aamo 10,” a weak culm line. [ABSTRACT FROM AUTHOR]