Vigor Of Rice Research Articles

A seed-specific DNA-binding with One Finger transcription factor, RPBF, positively regulates galactinol synthase to maintain seed vigour in rice.

Seed vigour and longevity are intricate yet indispensable physiological traits for agricultural crops, as they play a crucial role in facilitating the successful emergence of seedlings and exert a substantial influence on crop productivity. Transcriptional regulation plays an important role in seed development, maturation, and desiccation tolerance, which are important attributes for seed vigour and longevity. Here, we have investigated the regulatory role of the seed-specific DNA binding with the One Finger (DOF) transcription factor and the RPBF (Rice P-box Binding Factor) in seed vigour. RPBF modulates the transcription of galactinol synthase and improves seed vigour. The promoter region of Galactinol synthase (GolS)-encoding genes from different species was enriched with DOF binding sites, and the expression levels of both RPBF and OsGolS were found to enhance during seed development. Furthermore, direct interaction of RPBF with OsGolS promoter has been demonstrated through multiple approaches: yeast one-hybrid (Y1H) assays, in planta promoter-GUS assays, dual luciferase assay, and in silico molecular docking. To assess functionality, Agrobacterium-mediated genetic transformation of rice was performed to generate the RNAi lines with reduced RPBF expression. In these RNAi lines, a reduction in both galactinol and raffinose content was observed. Since galactinol and raffinose are known contributors to seed vigour, the T2-transgenic lines were assessed for vigour and viability. For this, RNAi seeds were subjected to accelerated ageing by exposing them to high relative humidity and temperature, followed by scoring the germination and viability potential. Tetrazolium and seed germination assay revealed that the RNAi seeds were more sensitive to ageing compared to their wild-type and vector control counterparts. Collectively, this is the first report demonstrating that the DOF transcription factor RPBF controls the seed vigour through transcriptional regulation of galactinol synthase.

Proline Priming Enhances Seed Vigour and Biochemical Attributes of Rice (Oryza sativa L.) during Germination.

Seed vigour is a desirable trait especially for direct seeded rice (DSR) cultivation. Seeds with high vigour could improve seed germination, support seedlings in competing with weeds for water and nutrients, and improving seedling establishment throughout the early stages of crop growth. The success of DSR system which account for more 25% of world cultivation areas is highly dependent on the seed vigour and seedling establishment. Seed priming is a promising technique to improve seed vigour. Proline is an amino acid that has been well studied for its roles in plants under different environmental stress conditions. Nevertheless, the effect of proline as a seed priming agent in improving seed vigour in rice remain elusive. In this research, the effect of 24 h of proline priming at various concentrations (0 mM, 1 mM, 2 mM, 10 mM and 20 mM) on rice seed vigour, amylase activity, and total soluble sugar (TSS) content of a Malaysia indica rice variety, MR269 was investigated. Results showed that seeds primed with lower concentration of proline (0 mM, 1 mM and 2 mM) had better germination responses while priming at high concentrations (10 mM and 20 mM) reduced seed germination. Among the concentration tested, priming with 1 mM proline enhanced seed vigour with significantly higher germination percentage (GP), germination rate index (GRI) and seedling vigour index (SVI). In addition, proline primed seeds also exhibited increased amylase activity and TSS content as compared to unprimed seeds. However, priming seed with 20 mM proline was detrimental to the seed vigour and seedling growth whereby lower GP, GRI and SVI and higher mean germination time (MGT) were observed. In short, this study shows that proline could be a potential seed priming agent to improve seed vigour in rice.

Effect of Imbibition Phase-Based Low Water Potential Seed Priming on Seedling Vigour in Rice (Oryza sativa L.)

Effect of Imbibition Phase-Based Low Water Potential Seed Priming on Seedling Vigour in Rice (Oryza sativa L.)

The Function of SD1 on Shoot Length and its Pyramiding Effect on Shoot Length and Plant Height in Rice (Oryza sativa L.)

Strong seedling vigor is imperative to achieve stable seedling establishment and enhance the competitiveness against weeds in rice direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor in rice, but few genes for SL have been cloned so far. In the previous study, we identified two tightly linked and stably expressed QTLs for SL, qSL-1f and qSL-1d by genome-wide association study, and cloned the causal gene (LOC_Os01g68500) underlying qSL-1f. In the present study, we identify LOC_Os01g66100 (i.e. the semidwarf gene SD1), a well-known gene controlling plant height (PH) at the adult-plant stage, as the causal gene underlying qSL-1d through gene-based haplotype analysis and knockout transgenic verification. By measuring the phenotypes (SL and PH) of various haplotypes of the two genes and their knockout lines, we found SD1 and LOC_ Os01g68500 controlled both SL and PH, and worked in the same direction, which provided the directly genetic evidence for a positive correlation between SL and PH combined with the analysis of SL and PH in the diverse natural population. Moreover, the knockout transgenic experiments suggested that SD1 had a greater effect on PH compared with LOC_ Os01g68500, but no significant difference in the effect on SL. Further investigation of the pyramiding effects of SD1 and LOC_Os01g68500 based on their haplotype combinations suggested that SD1 may play a dominant role in controlling SL and PH when the two genes coexist. In this study, the effect of SD1 on SL at the seedling stage is validated. In total, two causal genes, SD1 and LOC_ Os01g68500, for SL are cloned in our studies, which controlled both SL and PH, and the suitable haplotypes of SD1 and LOC_ Os01g68500 are beneficial to achieve the desired SL and PH in different rice breeding objectives. These results provide a new clue to develop rice varieties for direct seeding and provide new genetic resources for molecular breeding of rice with suitable PH and strong seedling vigor.

Genetic Variability of Floral and Agronomic Characteristics that Influence Outcrossing Rate Percentage of Cytoplasmic Male Sterile Rice

Developing high-yielding hybrid rice varieties is much needed to ensure food security to meet the requirement of the increasing population across the world. Cytoplasmic male genetic sterility system is a valuable technology for the exploitation of heterosis and production of high-yielding hybrid rice with better grain quality. Large-scale commercial exploitation of hybrid vigor in rice largely depends on the availability of good CMS (Cytoplasmic Male Sterile) lines. A total of eighteen traits of five CMS lines of rice were evaluated to study the variability and correlation between floral and other yield-contributing traits with outcrossing rate using Randomized Complete Block Design with three replications. High significant variation was observed among the genotypes for all the studied traits. High GCV (Genotypic Coefficient of Variance) and PCV (phenotypic Coefficient of Variance) coupled with high heritability and high genetic advance in percent of mean were observed for number of panicles per plant, filled grain, flag leaf breadth, stigma length and breadth, filament length and outcrossing rate which indicated the broad genetic base, less environmental influence, and these traits are under the control of additive gene action. character association and path analysis indicated that number of grains per panicle, filled grains per panicle, stigma length, and breadth possessed both positive significant correlation and positive direct effects on outcrossing rate therefore, selection for the traits mentioned above will certainly bring in the improvement of the outcrossing percentage of the lines, which in turn enhances the seed quantity of the hybrid.

Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice.

Highly seed vigor (SV) is essential for rice direct seeding (DS). Understanding the genetic mechanism of SV-related traits could contribute to increasing the efficiency of DS. However, only a few genes responsible for SV have been determined in rice, and the regulatory network of SV remains obscure. In this study, the seed germination rate (GR), seedling shoot length (SL), and shoot fresh weight (FW) related to SV traits were measured, and a genome-wide association study (GWAS) was conducted to detect high-quality loci responsible for SV using a panel of 346 diverse accessions. A total of 51 significant SNPs were identified and arranged into six quantitative trait locus (QTL) regions, including one (qGR1-1), two (qSL1-1, qSL1-2), and three (qFW1-1, qFW4-1, and qFW7-1) QTLs associated with GR, SL, and FW respectively, which were further validated using chromosome segment substitution lines (CSSLs). Integrating gene expression, gene annotation, and haplotype analysis, we found 21 strong candidate genes significantly associated with SV. In addition, the SV-related functions of LOC_Os01g11270 and LOC_Os01g55240 were further verified by corresponding CRISPR/Cas9 gene-edited mutants. Thus, these results provide clues for elucidating the genetic basis of SV control. The candidate genes or QTLs would be helpful for improving DS by molecular marker-assisted selection (MAS) breeding in rice.

Unraveling the genomic regions controlling the seed vigour index, root growth parameters and germination per cent in rice.

High seed vigour ensures good quality seed and higher productivity. Early seedling growth parameters indicate seed vigour in rice. Seed vigour via physiological growth parameters is a complex trait controlled by many quantitative trait loci. A panel was prepared representing a population of 274 rice landraces by including genotypes from all the phenotypic groups of sixseedling stage physiological parameters including germination % for association mapping. Wide variations for the six studiedtraits were observed in the population. The population was classified into 3 genetic groups. Fixation indices indicated the presence of linkage disequilibrium in the population. The population was classified into subpopulations and each subpopulation showed correspondence with the 6 physiological traits. A total of 5 reported QTLs viz., qGP8.1 for germination % (GP); qSVII2.1, qSVII6.1 and qSVII6.2 for seed vigour index II (SVII), and qRSR11.1 for root-shoot ratio (RSR) were validated in this mapping population. In addition, 13 QTLs regulating the physiological parameters such as qSVI 11.1 for seed vigour index I; qSVI11.1 and qSVI12.1 for seed vigour index II; qRRG10.1, qRRG8.1, qRRG8.2, qRRG6.1 and qRRG4.1 for rate of root growth (RRG); qRSR2.1, qRSR3.1 and qRSR5.1 for root-shoot ratio (RSR) while qGP6.2 and qGP6.3 for germination %were identified. Additionally, co-localization or co-inheritance of QTLs, qGP8.1 and qSVI8.1 for GP and SVI-1; qGP6.2 and qRRG6.1 for GP and RRG, and qSVI11.1 and qRSR11.1 for SVI and RSR were detected. The QTLs identified in this study will be useful for improvement of seed vigour trait in rice.

Degradome sequencing reveals an integrative miRNA-mediated gene interaction network regulating rice seed vigor

BackgroundIt is well known that seed vigor is essential for agricultural production and rice (Oryza sativa L.) is one of the most important crops in the world. Though we previously reported that miR164c regulates rice seed vigor, but whether and how other miRNAs cooperate with miR164c to regulate seed vigor is still unknown.ResultsBased on degradome data of six RNA samples isolated from seeds of the wild-type (WT) indica rice cultivar ‘Kasalath’ as well as two modified lines in ‘Kasalath’ background (miR164c-silenced line [MIM164c] and miR164c overexpression line [OE164c]), which were subjected to either no aging treatment or an 8-day artificial aging treatment, 1247 different target transcripts potentially cleaved by 421 miRNAs were identified. The miRNA target genes were functionally annotated via GO and KEGG enrichment analyses. By STRING database assay, a miRNA-mediated gene interaction network regulating seed vigor in rice was revealed, which comprised at least four interconnected pathways: the miR5075-mediated oxidoreductase related pathway, the plant hormone related pathway, the miR164e related pathway, and the previously reported RPS27AA related pathway. Knockout and overexpression of the target gene Os02g0817500 of miR5075 decreased and enhanced seed vigor, respectively. By Y2H assay, the proteins encoded by five seed vigor-related genes, Os08g0295100, Os07g0633100, REFA1, OsPER1 and OsGAPC3, were identified to interact with Os02g0817500.ConclusionsmiRNAs cooperate to regulate seed vigor in rice via an integrative gene interaction network comprising miRNA target genes and other functional genes. The result provided a basis for fully understanding the molecular mechanisms of seed vigor regulation.

OsHIPL1, a hedgehog-interacting protein-like 1 protein, increases seed vigour in rice.

SummaryThe cultivation of rice varieties with high seed vigour is vital for the direct seeding of rice, and the molecular basis of regulation of seed vigour remains elusive. Here, we cloned a new gene OsHIPL1, which encodes hedgehog‐interacting protein‐like 1 protein as a causal gene of the major QTL qSV3 for rice seed vigour. OsHIPL1 was mainly localized in the plasma membrane and nucleus. RNA sequencing (RNA‐seq) revealed that the ABA‐related genes were involved in the OsHIPL1 regulation of seed vigour in rice. The higher levels of endogenous ABA were measured in germinating seeds of OsHIPL1 mutants and NIL‐qsv3 line compared to IR26 plants, with two up‐regulated ABA biosynthesis genes (OsZEP and OsNCED4) and one down‐regulated ABA catabolism gene OsABA8ox3. The expression of abscisic acid‐insensitive 3 (OsABI3), OsABI4 and OsABI5 was significantly up‐regulated in germinating seeds of OsHIPL1 mutants and NIL‐qsv3 line compared to IR26 plants. These results indicate that the regulation of seed vigour of OsHIPL1 may be through modulating endogenous ABA levels and altering OsABIs expression during seed germination in rice. Meanwhile, we found that OsHIPL1 interacted with the aquaporin OsPIP1;1, then affected water uptake to promote rice seed germination. Based on analysis of single‐nucleotide polymorphism data of rice accessions, we identified a Hap1 haplotype of OsHIPL1 that was positively correlated with seed germination. Our findings showed novel insights into the molecular mechanism of OsHIPL1 on seed vigour.

A multiomic study uncovers a bZIP23-PER1A–mediated detoxification pathway to enhance seed vigor in rice

Seed vigor in crops is important in terms of improving grain quality and germplasm conservation; however, little is known about its regulatory mechanisms through the encoded proteome and gene network. Comparative analyses of transcriptome (RNA sequencing [RNA-seq]) and broadly targeted metabolic profiling of two subspecific rice cultivars with distinct seed vigor during accelerated aging revealed various biological pathways and metabolic processes as key influences explaining trait differences. RNA-seq coexpression regulatory network analyses identified several transcription factors, including bZIP23 and bZIP42, that act as nodes in the gene network. Importantly, transgenic seeds of overexpression of bZIP23 enhanced seed vigor, whereas its gene knockout reduced seed vigor, suggesting that the protein it encodes functions as a positive regulator. Similarly, overexpression and knockout of PER1A that encodes a key player in the detoxification pathway enhanced and decreased seed vigor, respectively. We further demonstrated a direct interaction of the PER1A promoter with bZIP23 in seeds, which activates the expression of PER1A, and the genetic evidence suggested that bZIP23 most likely functions in a common pathway with and acts upstream of PER1A to modulate seed vigor. In addition, the control of seed vigor by the bZIP23-PER1A module was connected with that of the abscisic acid signaling pathway. Collectively, we revealed the genetic architecture of variation in seed vigor and uncovered the bZIP23-PER1A-mediated detoxification pathway that enhances the trait in rice.

Genome-wide association study reveals that the cupin domain protein OsCDP3.10 regulates seed vigour in rice.

SummarySeed vigour is an imperative trait for the direct seeding of rice. In this study, we examined the genetic regulation of seedling percentage at the early germination using a genome‐wide association study in rice. One major quantitative trait loci qSP3 for seedling percentage was identified, and the candidate gene was validated as qSP3, encoding a cupin domain protein OsCDP3.10 for the synthesis of 52 kDa globulin. Disruption of this gene in Oscdp3.10 mutants reduced the seed vigour, including the germination potential and seedling percentage, at the early germination in rice. The lacking accumulation of 52 kDa globulin was observed in the mature grains of the Oscdp3.10 mutants. The significantly lower amino acid contents were observed in the mature grains and the early germinating seeds of the Oscdp3.10 mutants compared with those of wild‐type. Rice OsCDP3.10 regulated seed vigour mainly via modulating the amino acids e.g. Met, Glu, His, and Tyr that contribute to hydrogen peroxide (H2O2) accumulation in the germinating seeds. These results provide important insights into the application of seed priming with the amino acids and the selection of OsCDP3.10 to improve seed vigour in rice.

Genetic structure and molecular markers-trait association for physiological traits related to seed vigour in rice

Good quality seed is an important factor for a good crop and harvest. Vigour is the key performing trait of quality seed. Many physiological traits influence seed vigour in rice. Association of molecular markers with eleven physiological traits were investigated in a representative population. A representative population was constituted by including genotypes from all the phenotypic groups of the 11 physiological traits from the shortlisted population of 120 genotypes. The genotypic accessions with rich in multiple physiological traits were identified from the representative population. STRUCTURE, GenAlEx and Darwin software were used to classify the population. Generalized Linear Model (GLM) and Mixed Linear Models (MLM) were used in the marker-trait association analysis using the TASSEL software. Wide variations among the genotypic accessions were observed for the physiological traits estimated from the panel population. Linkage disequilibrium was detected for the 11 physiological traits in the panel population. STRUCTURE software classified the population into two genetic structure groups. Higher values of gene diversity and polymorphic information content (PIC) were estimated from the population based on genotyping using 50 simple sequence repeat markers. Genotypes present within groups and sub-groups showed similarity for their physiological traits. Strong association of the markers with physiological parameters namely RM167 for seed vigour index-I; RM7364 and RM235 for seed vigour index-II; RM440, RM223 for seedling dry weight; RM 256,RM25181, RM6547, RM328, RM201 for rate of root growth; RM 20, RM13335, RM216 for rate of shoot growth while RM20A and RM201 for absolute growth rate were detected by both GLM and MLM analyses. Markers detected in this association analysis may be potential use for future seed vigour improvement in rice.

Genome‐wide association study for traits related to seedling vigor in rice

AbstractSeedling vigor is a desirable trait in direct‐seeded rice (Oryza sativa L.) to improve plant establishment and enhance weed competition. In this study, a genome‐wide association study (GWAS) on seedling vigor traits was performed on a rice panel of 244 accessions consisting of the five major rice subpopulations (aromatic, aus, tropical japonica, temperate japonica, and indica) using the 7K SNP Cornell‐IR LD Rice Array. A total of seven seedling vigor‐related traits were evaluated under controlled conditions in a growth chamber. All traits had a normal distribution with a wide range of phenotypic variation with CV between 27.6 and 43.9%, except for seedling dry weight, which had a CV of 11.4%. We identified 43 GWAS‐quantitative trait locus (QTL) regions associated with different seedling vigor traits, of which 19 QTL regions were near previously identified genes or QTL regions. These findings confirmed 19 previous QTL and identified 24 potential novel QTL targets for marker‐assisted breeding programs. Additionally, superior donors with high seedling vigor were identified and can be used for rice crop improvement in direct‐seeded systems.

A genome-wide association study reveals that the 2-oxoglutarate/malate translocator mediates seed vigor in rice.

Seed vigor is an important trait for the direct seeding of rice (Oryza sativa L.). In this study, we examined the genetic architecture of variation in the germination rate using a diverse panel of rice accessions. Four quantitative trait loci for germination rate were identified using a genome-wide association study during early germination. One candidate gene, encoding the 2-oxoglutarate/malate translocator (OsOMT), was validated for qGR11. Disruption of this gene (Osomt mutants) reduced seed vigor, including seed germination and seedling growth, in rice. Functional analysis revealed that OsOMT influences seed vigor mainly by modulating amino acid levels and glycolysis and tricarboxylic acid cycle processes. The levels of most amino acids, including the Glu family (Glu, Pro, Arg, and GABA), Asp family (Asp, Thr, Lys, Ile, and Met), Ser family (Ser, Gly, and Cys), and others (His, Ala, Leu, and Val), were significantly reduced in the mature grains and the early germinating seeds of Osomt mutants compared to wild type (WT). The glucose and soluble sugar contents, as well as adenosine triphosphate levels, were significantly decreased in germinating seeds of Osomt mutants compared to WT. These results provide important insights into the role of OsOMT in seed vigor in rice.

Advances in the Identification of Quantitative Trait Loci and Genes Involved in Seed Vigor in Rice.

Seed vigor is a complex trait, including the seed germination, seedling emergence, and growth, as well as seed storability and stress tolerance, which is important for direct seeding in rice. Seed vigor is established during seed development, and its level is decreased during seed storage. Seed vigor is influenced by genetic and environmental factors during seed development, storage, and germination stages. A lot of factors, such as nutrient reserves, seed dying, seed dormancy, seed deterioration, stress conditions, and seed treatments, will influence seed vigor during seed development to germination stages. This review highlights the current advances on the identification of quantitative trait loci (QTLs) and regulatory genes involved in seed vigor at seed development, storage, and germination stages in rice. These identified QTLs and regulatory genes will contribute to the improvement of seed vigor by breeding, biotechnological, and treatment approaches.

The Rice Small Auxin-Up RNA Gene OsSAUR33 Regulates Seed Vigor via Sugar Pathway during Early Seed Germination.

Seed vigor affects seed germination and seedling emergence, and therefore is an important agronomic trait in rice. Small auxin-up RNAs (SAURs) function in a range of developmental processes, but their role in seed vigor remains unclear. Here, we observed that disruption of OsSAUR33 resulted in reduced germination rates and low seed uniformity in early germination. Expression of OsSAUR33 was higher in mature grains and early germinating seeds. RNA-seq analysis revealed that OsSAUR33 modulated seed vigor by affecting the mobilization of stored reserves during germination. Disruption of OsSAUR33 increased the soluble sugar content in dry mature grains and seeds during early germination. OsSAUR33 interacted with the sucrose non-fermenting-1-related protein kinase OsSnRK1A, a regulator of the sugar signaling pathway, which influences the expression of sugar signaling-related genes during germination. Disruption of OsSAUR33 increased sugar-sensitive phenotypes in early germination, suggesting OsSAUR33 likely affects seed vigor through the sugar pathway. One elite haplotype of OsSAUR33 associated with higher seed vigor was identified mainly in indica accessions. This study provides insight into the effects of OsSAUR33 on seed vigor in rice.

Genetic yield improvement forecast and water-limited productivity of significant agricultural crops

In the next 4 decades, when growth of this segment, feed, and biofuel feedstock is expected to stabilize, improve crop yields under potential (Yp) as well as water scarcity (Yw) conditions will be important to enhancing food security. To meet predicted demand in 2050, the three main cereal crops (cereals, maize, and rice) will require 1.16-1.31% yearly increase in Yp and Yw. They may fall much more if current absolute yield increase rates continue steady, or if recent indicators of agricultural production halting in certain parts of the world become widespread. There are a variety of methods for increasing Yp and Yw genetic improvement rates, including photosynthetic genetic engineering, above-ground awareness and high design, and boosting root levels of water uptake. Because time is limited, the time scales required to progress potentially advantageous features to field prototype system, farmer-ready cultivars, and widespread farmer adoption are given special attention. The value of molecular breeding methods as tools for improving fundamental and complicated genetic features is highlighted. Only a small percentage of useful features are integrated into the breeding process, and information is not widely shared between research teams. Increasing financing for targeted research, as well as identifying and removing or decreasing roadblocks at different stages of the concept to farmer-ready cultivar chain, might help to accelerate the exploitation of these prospects. Possible genetic advances in Yp or Yw, such as using hybrid vigor in rice or genetically engineering photosynthesis, are unlikely to alter this prognosis. No amount of optimism can hide the reality that without sustained investment in genetic improvement and breeding aids, unfulfilled demand for grains in 2050 will be much higher.

Elucidation of the miR164c-Guided Gene/Protein Interaction Network Controlling Seed Vigor in Rice.

MicroRNAs (miRNAs) play important roles in various aspects of plant physiology and metabolism. The expression level of miR164c is negatively correlated with seed vigor in rice (Oryza sativa L.); however, the mechanism of seed vigor regulation by miR164c remains unknown. Anti-aging capacity is an important indicator of seed vigor. Here, we report an miR164c-guided gene/protein interaction network that regulates the anti-aging ability of rice seeds. Seeds of the wild-type (WT) rice cultivar “Kasalath” and its transgenic derivatives, miR164c-silenced line (MIM164c) and miR164c overexpression line (OE164c), with significant differences in anti-aging capacity, showed significant differences in gene and protein expression levels. The differentially expressed genes (DEGs) or proteins were significantly enriched in six metabolic functional categories related to seed vigor, including “stress response,” “protein processing in endoplasmic reticulum (ER),” “embryo development,” “serine-type endopeptidase inhibitor,” “energy metabolism,” and “other.” Differences in the expression levels of genes or proteins related to energy metabolism, serine endopeptidase, and stress response in seeds under normal storage conditions may be associated with anti-aging capacity. The results of gene/protein interaction analyses suggest that miR164c first targets PSK5, and the PSK5 protein then interacts with the ubiquitin-associated gene RPS27AA, which simultaneously impacts the genes/proteins in the six above-mentioned functional categories. Expression levels of some of the key genes and proteins in the interaction network were verified by real-time fluorescence quantitative PCR (RT-qPCR) and multiple reaction monitoring mass spectrometry (MRM-MS), respectively. Thus, the present study provides new insights into the miRNA-mediated gene and protein interaction network that regulates seed vigor.

Non-destructive phenotyping for early seedling vigor in direct-seeded rice

BackgroundEarly seedling vigor is an essential trait of direct-seeded rice. It helps the seedlings to compete with weeds for water and nutrient availability, and contributes to better seedling establishment during the initial phase of crop growth. Seedling vigor is a complex trait, and phenotyping by a destructive method limits the improvement of this trait through traditional breeding. Hence, a non-invasive, rapid, and precise image-based phenotyping technique is developed to increase the possibility to improve early seedling vigor through breeding in rice and other field crops.ResultsTo establish and assess the methodology using free-source software, early seedling vigor was estimated from images captured with a digital SLR camera in a non-destructive way. Here, the legitimacy and strength of the method have been proved through screening seven diverse rice cultivars varying for early seedling vigor. In the regression analysis, whole-plant area (WPA) estimated by destructive-flatbed scanner (WPAs) and non-destructive imaging (WPAi) approaches was strongly related (R2 > 83%) and suggested that WPAi can be adapted in place of destructive methods to estimate seedling vigor. In addition, this study has identified a set of new geometric traits (convex hull and top view area) for screening breeding lines for early seedling vigor in rice, which decreased the time by 80% and halved the cost of labor in data observation.ConclusionsThe method demonstrated here is affordable and easy to establish as a phenotypic platform. It is suitable for most glasshouses/net houses for characterizing genotypes to understand the plasticity of shoots under a given environment at the seedling stage. The methodology explained in this experiment has been proven to be practical and suggested as a technique for researchers involved in direct-seeded rice. Consequently, it will help in the simultaneous screening of genotypes in large numbers, the identification of donors, and in gaining information on the genetic basis of the trait to design a breeding program for direct-seeded rice.

Association of molecular markers with physio-biochemical traits related to seed vigour in rice.

Eighteen physio-biochemical traits influencing seed vigour were studied for their association with molecular markers using a mini core set constituted from 120 germplasm lines. High genetic variation was detected in the parameters namely chlrophyll a, Chlrophyll b, total chlorophyll, carotenoids, total anthocyanin content, gamma-oryzanols, total phenolics content,superoxide dismutase, catalase, guaicol peroxidase, total soluble sugar, total protein, seed vigour index -I and seed vigour index -II. Strong positive correlation of seed vigour index II was observed with amylose content, total anthocyanin content, catalase, total phenolic content and total flavonoid content while a negative association was observed for gamma-oryzanol content. High gene diversity (0.7169) and informative markers value (0.6789) were estimated from the investigation. Three genetic structure groups were observed in the panel population and genotypes were grouped in the subpopulations based on the seed vigour trait. Differences in the fixation indices of the three sub populations indicated existence of linkage disequilibrium in the studied panel population. Association of the traits namely total flavonoids, superoxide dismutase, catalase, chlorophyll a, Chlorophyll b, total chlorophyll, carotenoids, starch, amylose, total anthocyanin, gamma-oryzanol, total phenolics with the molecular markers were detected by Generalized Linear Model and Mixed Linear Model showing > 0.10 R2 value. Association of the trait, total flavonoids with marker RM7364 located on chromosome 8 reported in earlier study was validated in this investigation. The validated markers and the novel markers detected showing higher R2 value will be useful for improvement of seed vigour in rice.