Early Seedling Vigour Research Articles

Genome Wide Association Analysis for Uniform Coleoptiles Emergence and Early Seedling Growth in Rice

Early seedling vigour (ESV) is a complex trait in rice. Detection of QTLs/genes controlling these traits can help us in enhancing the yield potential in rice varieties. Association mapping is a technique based on the principle of linkage disequilibrium that is used to find genes or quantitative trait loci (QTL) underlying the complex traits. In this study of haplotype breeding 281 rice genotypes were taken. ANOVA analysis showed P- value for traits and genotypes was found significant. Similarly, P-value for interaction between the traits and genotypes was also found to be highly significant (1.8663*10-208). Further, mean germination data positively correlated with mean shoot length, mean leaf number, mean culm diameter, mean shoot dry weight, and mean shoot area of 21st day among the 281 genotypes. Among the 281 number of genotypes, 111 genotypes are found to be in PCA1 and 170 genotypes are found to be in PCA2 based on the phenotypic analysis. PCA1 component constituted 29.93% and PCA2 constituted the 13.68% of total variation in the analysis. Besides, whole genome phylogenetic analysis showed three major groups of which Group 1 consists of 215 genotypes, group 2 consists of 38 genotypes and group 3 consists of 28 genotypes respectively. Especially, both the subgroups II and III comprised of the unique genotypes from the indica and aus subpopulations of rice. In this analysis, 16 significant associations (LOD Score >7) for different traits were identified using the three different models (MLM, farmCPU, and blink) for GWAS studies Especially, one major QTL was identified for the mean coleoptiles’ emergence for 10 DAS on 11th chromosome (18983591) which explained 49% of the phenotypic variance. Additionally, another major QTL contributing to the shoot length variation of 29.75% was identified in the Chr02 (32954393) for shoot length trait on 28 DAS. A candidate gene namely Os02g0778400 UMP/CMP kinase A/adenylate kinase (LOC_Os02g53790) was located in the significant SNP region of the GWAS analysis. Further characterization of this gene would assist in elucidation of the mechanism regulating the early seedling length in rice under direct seeded rice.

Unlocking the genetic potential of Indian rice germplasm across different environments for early seedling vigour

Unlocking the genetic potential of Indian rice germplasm across different environments for early seedling vigour

Integrated Application of Silicic and Humic Acid Seed Priming for Enhanced Germination and Yield of Lentil (Lens culinaris L.)

Background: Lentil is second most important nutritionally dense pulse crop of India due to its ability to fix nitrogen, helps to maintain soil fertility and increase yield of other crops grown in rotations. Seed priming is a good innovative technology for improvement of emergence and plant stand under various stress conditions and also could enhance various defense mechanisms in seeds against biotic and abiotic stresses. The present study aimed to examine the effect of seed priming with silicic acid (3 mM @18 hr), humic acid (600 ppm @18 hr) and combination of humic and silicic acid (100 ppm + 1 mM @ 16 hr), that may reduce harmful effect of stress at seedling stage and improve early seedling vigor. Methods: In this field-laboratory investigation during 2022-2023, seed quality and yield quality attributing parameters i.e. germination percentage, seed vigor index-I and II, total chlorophyll, emergence percentage, final plant stand, final plant stand emergence, plant height, secondary branches, tertiary branches, number of pod per plant, average number of pod per plant, pod cluster, seed yield per plot and yield per plot were recorded in both laboratory and field conditions. Result: The results demonstrated a positive effect of seed priming on seed quality parameters against the stress. The highest seed quality and yield quality attributing parameter was recorded in treatment (T5) combination of humic and silicic acid as compare to control. The chemical priming with combination of humic and silicic acid was found to be most effective treatment to enhance plant stand establishment against stress.

Seed traits and recruitment interact with habitats to generate patterns of local adaptation in a perennial grass.

A fundamental challenge in the field of ecology involves understanding the adaptive traits and life history stages regulating the population dynamics of species across diverse habitats. Seed traits and early seedling vigor are thought to be key functional traits in plants, with important consequences for recruitment, establishment, and population persistence. However, little is known about how diverse seed traits interact with seed and microsite availability to impact plant populations. Here, we performed a factorial experiment involving seed addition and surface soil disturbance to explore the combined effects of seed and site availability using genotypes characterized by varying seed mass and dormancy traits. Additionally, we included hybrids that exhibited recombined seed trait relationships compared with natural genotypes, allowing us to assess the impact of specific seed traits on establishment across different sites. We detected a significant three-way interaction between seed addition, site conditions, and soil surface disturbance, influencing both seedling establishment and adult recruitment in Panicum hallii, a perennial grass found in coastal mesic (lowland) and inland xeric (upland) habitats. This establishment/recruitment pattern suggests that mesic and xeric establishment at foreign sites is constrained by the interplay of seed and site limitations. Notably, soil surface disturbance facilitated establishment and recruitment of the xeric genotype while limiting the mesic genotype across all sites. Our results highlight the importance of seed size and dormancy as key factors impacting seedling establishment and adult recruitment, suggesting a potential interactive relationship between these traits.

Photosynthetically active radiation is required for seedling growth promotion by volcanic dacitic tuff breccia (Azomite).

A plant's growth and development are shaped by its genome and the capacity to negotiate its environment for access to light, water, and nutrients. There is a vital need to understand the interactions between the plant, its physical environment, and the fertilizers used in agriculture. In this study, a commercially available volcanic ash fertilizer, Azomite®, characterized as dacitic (rhyolitic) tuff breccia, was tested for its effect on promoting early seedling vigor. Early growth and photomorphogenesis processes are well studied in Arabidopsis. Seedling assays under different light conditions were used to dissect the underlying mechanisms involved. These assays are well established and can be translated to agriculturally important crop plants. The volcanic ash fertilizer was tested at different concentrations on seedlings grown on basic media lacking sucrose either in continuous darkness (Dc), continuous Red (Rc), Far-Red (FRc), or White Light (WLc). Micronutrients in the volcanic ash significantly increased seedling growth under Rc and WLc, but not under Dc and FRc, indicating that photosynthetically active radiation was required for the observed growth increase. Furthermore, red-light photoreceptor mutant, phyB-9, lacked the growth response, and higher amount of fertilizer reduced growth in all conditions tested. These data suggest that light triggers the ability of the seedling to utilize micronutrients in volcanic ash in a dose-dependent manner. The methods described here can be used to establish mechanisms of activity of various nutrient inputs and, coupled with whole-genome expression profiling, can lead to better insights into optimizing nutrient field applications to improve crop production.

Divergence Studies for Early Seedling Vigour Related Traits, Yield and Yield Components in Rice (Oryza sativa L.)

The present study was carried out in the Autumn 2020-21 using a Randomized Complete Block Design (RCBD) with three replications. Forty-two different genotypes of rice were evaluated in this investigation. These genotypes were assessed based on 21 quantitative traits, which includes yield and yield related traits and early seedling vigour related traits. The Mahalanobis D2 statistic was used for characterizing the genotypes. Based on the D2 analysis, the 42 rice genotypes were grouped into seven clusters. Among these clusters, cluster I was the largest, consisting of 22 genotypes. Cluster III exhibited the highest intracluster distance (22.04), while the maximum inter-cluster distance was observed between clusters II and III (49.06), followed by clusters III and VII (45.84). These results highlight the significance of the genotypes present in these clusters for harnessing heterosis and exploiting the desirable traits associated with them.

Assessment of genetic diversity for seed vigor traits in rice (Oryza sativa L.) through principal component and cluster analysis

Seed vigor, an important characteristic of seed quality attributes, determines the rate of early, rapid, uniform germination, emergenceand growth of strong seedling in any environmental condition. In the present set of experiment, 44 rice (Oryza sativa L.) varieties wereassessed for different seed vigor component traits. For evaluation of these traits, basic statistics, correlation, principal component (PC) andcluster analysis were carried out to obtain genetic diversity for seed vigor traits and early seedling vigor among rice varieties specifically to select the best varieties and important seed vigor traits for its possible use in future rice breeding programme. The estimation of descriptive statistics of 20 quantitative seed vigor-related traits indicated existence of variability among the varieties. The 44 varieties were grouped into five clusters on the basis of average linkage and dendogram. Varieties in Cluster I are considered to possess very high vigor traits and cluster IV with least seed vigor traits. Principal component (PC) analysis showed first 5 PCs having Eigen value >1 explaining 77.01% of the total variation with different seed vigor traits. In the biplot analysis between PCs 1 and 2, the varieties remained scattered in all four quadrants, showing large genetic variation in quantitative traits. Seed vigor index-I, seed vigor index-II, seed dry weight, shoot length, reserve mobilization, germination percentage, dehydrogenase, mean germination rate, germination speed, and mean germination time contributed to high variability among the varieties. The seed vigor traits were positively correlated with germination percentage, shoot length, seedling dry weight, speed of germination, mean germination rate, reserve mobilization, superoxide dismutase, dehydrogenase and alpha-amylase. The positive correlation among these seed vigor-contributing traits suggested that these characteristics are important for direct selection of high seed vigor varieties and early emergence.

Characterization of Rice (Oryza sativa L.) Germplasm for Early Seedling Vigour-related Traits under Direct Seeded Condition

In pursuit of boosting rice production while maintaining economic feasibility within resource constraints, the shift from the traditional puddled-transplanted rice system to direct-seeded rice is gaining significance. Early seedling vigour (ESV) is an important character crucial for direct-seeded rice to outcompete and suppress weed growth. This study evaluated hundred rice germplasm accessions for their early seedling vigour-related traits. Mesocotyl and coleoptile lengths, chlorophyll content, alpha-amylase, speed of emergence, shoot and root characteristics, and vigour indices exhibited notable variability as indicated by their high PCV and GCV. Moreover, they were predominantly under the influence of additive gene effects, as illustrated by their high heritability and genetic advance as per cent of mean. This suggests that these traits are heritable and could be effectively exploited through selective breeding efforts. Positive correlations were found between seedling vigour and traits like emergence (%), speed of emergence, chlorophyll content, and alpha-amylase activity. Based on PCA, Vigour index-I, II, total seedling length, and chlorophyll contents were regarded as major discriminators in rice germplasm for direct seeded traits. The superior genotypes for seedling vigour such as Honduras and Gharib, could be used as donors in the rice breeding programs to develop direct seeded rice cultivars.

Haplotype analysis of QTLs governing early seedling vigor-related traits under dry-direct-seeded rice (Oryza sativa L.) conditions.

The eventual shifting of cultivation method from puddle transplanted rice to direct-seeded rice (DSR) to save water prompted researchers to develop DSR-suitable varieties. To achieve this, identification of molecular markers associated with must-have traits for DSR, especially early seedling vigour related traits is crucial. In the present investigation, the haplotype analysis using flanking markers of three important quantitative trait loci (QTLs) for early seedling vigour-related traits viz., qSV-6a (RM204 and RM402) for root length; qVI (RM20429 and RM3) for seedling vigour index; qGP-6 (RM528 and RM400) for germination percentage revealed that the marker alleles were found to show significant associations with qVI and qGP-6 QTLs. The majority of genotypes with high early seedling vigour are with qVIHap-1 (220 and 160 bp) and qGPHap-1 (290 and 290 bp). The rice genotypes with superior haplotypes for early seedling vigour are BMF536, BMF540, BMF525, MM129 and MDP2. In conclusion, here we demonstrated that the markers RM20429 and RM3 are associated with seedling vigour index whereas RM528 and RM400 are associated with germination percentage. Therefore, these markers can be utilized to develop varieties suitable for DSR conditions through haplotype-based breeding. In addition, the rice genotypes with superior haplotypes can be of immense value to use as donors or can be released as varieties also under DSR conditions.

Genetic analysis of early seedling vigour in Oryza glaberrima accessions under laboratory and direct-seeded rice conditions

Genetic analysis of early seedling vigour in Oryza glaberrima accessions under laboratory and direct-seeded rice conditions

Identification of molecular markers and putative candidate genes associated with early seedling vigour traits in rice (Oryza sativa L.)

Identification of molecular markers and putative candidate genes associated with early seedling vigour traits in rice (Oryza sativa L.)

Assessment of allelic and genetic diversity, and population structure among farmers' rice varieties using microsatellite markers and morphological traits

Traditional rice varieties grown by the farmers serve as valuable genetic resources for future rice improvement. These varieties are highly adapted to varied agro-ecological conditions. However, they are rapidly lost because of the adoption of high-yielding varieties. The extent of allelic and genetic diversity present in the germplasm is a prerequisite for the improvement of any crop and conservation strategies under adverse impacts of climate. Farmers' rice varieties are usually poor yielders but are allelic treasurer for different traits, especially biotic and abiotic stresses, grain qualities, early seedling vigor, input use efficiency, etc. Therefore, the present study was aimed for a detailed understanding of allelic and genetic diversity, and population structure of 607 farmers' rice varieties using 36 fluorescently labeled microsatellite markers and 53 morphological traits. A total of 363 alleles was detected with an average of 10.33 alleles per locus and moderately high Nei's allelic/gene diversity (0.502) was detected. Polymorphic information content ranged from 0.685 to 0.987 with an average of 0.901. 34 unique, 236 rare, 84 low-frequency and 44 high-frequency alleles were detected. 53 morphological traits harbored a total of 195 variables with an average of 4.217 variables per trait. 50 out of 53 morphological traits showed polymorphism and highly significant differences among varieties. High genetic diversity was observed among 607 farmers' rice varieties both at molecular (0.653) and phenotypic (0.656) levels. The dendrogram based on both microsatellite markers and morphological traits grouped the 607 farmers' rice varieties into three major groups. A moderate population structure was observed with two independent subpopulations SP1 and SP2, which have membership percentages of 82.6 % and 17.4 %, fixation index values of 0.19 and 0.194, respectively. The AMOVA could explain 63 % of the total variation among varieties and 34 % within varieties. Our results showed that the farmers' rice varieties of Odisha harbored higher levels of both allelic and genetic diversity. Hence, these varieties would be useful for the identification of novel and elite alleles, and serve as a source of donors for the development of climate-smart varieties with improved grain yield and qualities, and input use efficiency, which would be sustainable in changing climate scenario conditions and improve farmers' income.

The ecology and quantitative genetics of seed and seedling traits in upland and lowland ecotypes of a perennial grass.

Plants have evolved diverse reproductive allocation strategies and seed traits to aid in dispersal, persistence in the seed bank, and establishment. In particular, seed size, dormancy, and early seedling vigor are thought to be key functional traits with important recruitment and fitness consequences across abiotic stress gradients. Selection for favored seed-trait combinations, or against maladaptive combinations, is likely an important driver shaping recruitment strategies. Here, we test for seed-trait plasticity and patterns of recruitment using two genotypes representative of contrasting upland and lowland ecotypes of Panicum hallii with field experiments in native versus foreign habitats. Furthermore, we test whether seed traits have been under directional selection in P. hallii using the v-test based on trait variance in a genetic cross. Finally, we evaluate the genetic architecture of ecotypic divergence for these traits with quantitative trait locus (QTL) mapping. Field experiments reveal little plasticity but support a hypothesis of adaptation divergence among ecotypes based on recruitment. Patterns of segregation within recombinant hybrids provides strong support for directional selection driving ecotypic divergence in seed traits. Genetic mapping revealed a polygenic architecture with evidence of genetic correlation between seed mass, dormancy, and seedling vigor. Our results suggest that the evolution of these traits may involve constraints that affect the direction of adaptive divergence. For example, seed size and germination percentage shared two colocalized QTL with antagonistic additive effects. This supports the hypothesis of a functional genetic relationship between these traits, resulting in either large seed/strong dormancy or small seed/weak dormancy trait combinations. Overall, our study provides insights into the factors facilitating and potentially constraining ecotypic differentiation in seed traits.

Influence of differential root and shoot growth rate on seedling vigour index in rice

Early seedling vigour is an important trait in direct seeded rice which determines the growth and yield. It is a complex trait and is found to be associated with germination and seedling growth. The rice genotypes, BPT 5204 and PB 1850-27 were screened for early seedling vigour traits and the data was recorded on germination percentage, root length, shoot length, seedling length, seedling fresh weight and seedling dry weight. The seedling vigour index I and seedling vigour index II were calculated for both the genotypes. It was observed that seedling vigour index I and II was found higher in PB 1850-27 as compared to BPT 5204. The principal component analysis was done to study differential root and shoot growth rate in F1 plants with parents. It was observed that growth rate in F1 seedlings was found higher than both the parents. The root growth in F1 plants resemble BPT 5204 during initial days of germination, while shoot growth pattern exhibited similarity only with PB 1850-27. The F2 population exhibited segregation for mean root and shoot length.

The impact of different seed priming techniques on growth and early seedling vigour of sunflower (Helianthus annuus L. cv. PAC334)

The impact of different seed priming techniques on growth and early seedling vigour of sunflower (Helianthus annuus L. cv. PAC334)

Mitochondria-Targeted SmsHSP24.1 Overexpression Stimulates Early Seedling Vigor and Stress Tolerance by Multi-Pathway Transcriptome-Reprogramming.

Among the diverse array of heat shock proteins across the three domains of life, mitochondria-targeted small heat shock proteins (sHSPs) are evolved in the plant lineage. However, they remained mysterious and understudied. In this study, we reported a systematic study of a novel mitochondria-targeted nuclear sHSP from eggplant (Solanum melongena L.; SmsHSP24.1). Differential expression of SmsHSP24.1 indicated its positive role exerted during stress conditions. Escherichia coli-BL21 cell line overexpressing the SmsHSP24.1 showed excellent thermo-tolerance ability, tolerating up to 52°C. Spectrometry and electron microscopy revealed a multimeric structure of the protein which acted as a molecular chaperone at high temperatures. Overexpression of SmsHSP24.1 significantly enhanced resistance against heat, drought, and salt stresses and showed rapid germination in constitutively overexpressed eggplant lines. RNA-seq analysis reveals an apparent upregulation of a set of reactive oxygen species (ROS) scavenging enzymes of the glutathione (GHS) pathway and mitochondrial electron transport chain (ETC). Significant upregulation was also observed in auxin biosynthesis and cell-wall remodeling transcripts in overexpressed lines. qPCR, biochemical and physiological analysis further aligned with the finding of transcriptome analysis and suggested an essential role of SmsHSP24.1 under various stress responses and positive physiological influence on the growth of eggplants. Therefore, this gene has immense potential in engineering stress-resilient crop plants.

Laboratory phenomics predicts field performance and identifies superior indica haplotypes for early seedling vigour in dry direct-seeded rice

Seedling vigour is an important agronomic trait and is gaining attention in Asian rice (Oryza sativa) as cultivation practices shift from transplanting to forms of direct seeding. To understand the genetic control of rice seedling vigour in dry direct seeded (aerobic) conditions we measured multiple seedling traits in 684 accessions from the 3000 Rice Genomes (3K-RG) population in both the laboratory and field at three planting depths. Our data show that phenotyping of mesocotyl length in laboratory conditions is a good predictor of field performance. By performing a genome wide association study, we found that the main QTL for mesocotyl length, percentage seedling emergence and shoot biomass are co-located on the short arm of chromosome 7. We show that haplotypes in the indica subgroup from this region can be used to predict the seedling vigour of 3K-RG accessions. The selected accessions may serve as potential donors in genomics-assisted breeding programs.

Multiple‐generation seed maturity effects on seedling vigour in a production environment

AbstractMaturity is not only critical for vigour and other seed quality characteristics but also impacts the subsequent plant performance. If these impacts on the subsequent plant are long lasting, the potential to produce vigorous, mature seed may also be affected. This scenario lends itself to the concept of seed maturity memory (SMM) – an understanding of how seed maturity may impact subsequent generations of plants and the vigour of the seeds with different maturity they produce. This study aimed to assess the existence and perpetuation of SMM in peanut, with an emphasis on early seedling vigour. Field physiological measurements and bioassay assessments were carried out on the second generation (G2) and third generation (G3) of peanut seeds with distinct parental maturity backgrounds. Our results suggested maintaining mature seed in both prior and offspring generations helped maintain high seed vigour in subsequent generations. The SMM effects varied between cultivars, with TUFRunner™ ‘727’ exhibiting SMM, whereas FloRun™ ‘107’ did not show SMM in the effects from first generation (G1) to G2 maturities. Overall, a seed resulting from parental plants established from immature seed somewhere in their pedigree was less vigorous than that maintained mature seeds in their pedigree. However, patterns of possible SMM were not always consistent, which could be partially attributed to differing environmental conditions each generation of seed experienced during development. These results highlight the importance of maintaining mature seeds in agricultural production and bring up the issue of ensuring seed maturity consistency during stress memory research assessing vigour characteristics.

Primary Root and Mesocotyl Elongation in Maize Seedlings: Two Organs with Antagonistic Growth below the Soil Surface.

Maize illustrates one of the most complex cases of embryogenesis in higher plants that results in the development of early embryo with distinctive organs such as the mesocotyl, seminal and primary roots, coleoptile, and plumule. After seed germination, the elongation of root and mesocotyl follows opposite directions in response to specific tropisms (positive and negative gravitropism and hydrotropism). Tropisms represent the differential growth of an organ directed toward several stimuli. Although the life cycle of roots and mesocotyl takes place in darkness, their growth and functions are controlled by different mechanisms. Roots ramify through the soil following the direction of the gravity vector, spreading their tips into new territories looking for water; when water availability is low, the root hydrotropic response is triggered toward the zone with higher moisture. Nonetheless, there is a high range of hydrotropic curvatures (angles) in maize. The processes that control root hydrotropism and mesocotyl elongation remain unclear; however, they are influenced by genetic and environmental cues to guide their growth for optimizing early seedling vigor. Roots and mesocotyls are crucial for the establishment, growth, and development of the plant since both help to forage water in the soil. Mesocotyl elongation is associated with an ancient agriculture practice known as deep planting. This tradition takes advantage of residual soil humidity and continues to be used in semiarid regions of Mexico and USA. Due to the genetic diversity of maize, some lines have developed long mesocotyls capable of deep planting while others are unable to do it. Hence, the genetic and phenetic interaction of maize lines with a robust hydrotropic response and higher mesocotyl elongation in response to water scarcity in time of global heating might be used for developing more resilient maize plants.

QTL Mapping and Phenotypic Variation for Seedling Vigour Traits in Barley (Hordeum vulgare L.).

Seed vigour is considered a critical stage for barley production, and cultivars with early seedling vigour (ESV) facilitate rapid canopy formation. In this study, QTLs for 12 ESV-related traits were mapped using 185 RILs derived from a Xena x H94061120 evaluated across six independent environments. DArT markers were used to develop a genetic map (1075.1 cM; centimorgans) with an average adjacent-marker distance of 3.28 cM. In total, 46 significant QTLs for ESV-related traits were detected. Fourteen QTLs for biomass yield were found on all chromosomes, two of them co-localized with QTLs on 1H for grain yield. The related traits: length of the first and second leaves and dry weight of the second leaf, biomass yield and grain yield, had high heritability (>30%). Meanwhile, a significant correlation was observed between grain yield and biomass yield, which provided a clear image of these traits in the selection process. Our results demonstrate that a pleiotropic QTL related to the specific leaf area of the second leaf, biomass yield, and grain yield was linked to the DArT markers bPb-9280 and bPb-9108 on 1H, which could be used to significantly improve seed vigour by marker-assisted selection and facilitate future map-based cloning efforts.