Genetic Aspects and Molecular Causes of Seed Longevity in Plants-A Review

Unraveling the Mechanistic Basis for Control of Seed Longevity

Seed longevity, which holds paramount importance for agriculture and biodiversity conservation, continues to represent a formidable frontier in plant biology research. While advances have been made in identifying regulatory elements, the precise mechanisms behind seed lifespan determination remain intricate and context-specific. This comprehensive review compiles extensive findings on seed longevity across plant species, focusing on the genetic and environmental underpinnings. Inter-species differences in seed lifespan are tied to genetic traits, with numerous Seed Longevity-Associated Genes (SLAGs) uncovered. These SLAGs encompass transcription factors and enzymes involved in stress responses, repair pathways, and hormone signaling. Environmental factors, particularly seed developmental conditions, significantly modulate seed longevity. Moreover, this review deliberates on the prospects of genetically engineering seed varieties with augmented longevity by precise manipulation of crucial genetic components, exemplifying the promising trajectory of seed science and its practical applications within agriculture and biodiversity preservation contexts. Collectively, our manuscript offers insights for improving seed performance and resilience in agriculture's evolving landscape.

Role of functional genes for seed vigor related traits through genome-wide association mapping in finger millet (Eleusine coracana L. Gaertn.)

Finger millet (Eleusine coracana (L.) Gaertn.) is a calcium-rich, nutritious and resilient crop that thrives even in harsh environmental conditions. In such ecologies, seed longevity and seedling vigor are crucial for sustainable crop production amid climate change. The current study explores the genetics of accelerated aging on seed longevity traits across 221 diverse accessions of finger millet through genome-wide association approach (GWAS). A significant variation was identified in germination percentage, germination rate indices, mean germination time, seedling vigor indices and dry weight upon aging treatment. GWAS model from 11,832 high-quality SNPs identified through Genotyping-by-Sequencing (GBS) approach produced 491 marker-trait associations (MTAs) for 27 traits, of which 54 were FDR-corrected. A pleiotropic SNP, FM_SNP_9478 identified on chromosome 7B was associated with the traits viz., germination after aging, germination index after aging and their relative measures. Functional annotation revealed DET1 and expansin-A2 influenced seed coat integrity, critical for germination and aging resilience. Probable protein phosphatase 2C3 and piezo-type ion channels contributed to mechanical sensing and stress adaptation in seeds. Beta-amylase and acetyl-CoA carboxylase 2 were identified for seed metabolism and stress response. These insights lay the framework for targeted breeding efforts to improve seed quality and resilience under diverse production conditions.

A comparative study on germination of wheat grains with different anthocyanin pigmentation of the pericarp in natural or induced aging

One of promising areas of wheat breeding is the creation of varieties with a high concentration of anthocyanins in the grain for the production of functional food products. Nonetheless, the question of how these compounds affect seed viability after long-term storage has remained unexplored. A comparative study on seed viability was conducted using a set of near-isogenic lines on the background of spring wheat variety Saratovskaya 29. These sister lines carry different combinations of recombinant DNA regions (on chromosomes 2A and 7D) containing dominant and recessive alleles at loci Pp3 and Pp-D1 (Pp: Purple pericarp), which determine the anthocyanin color of coleoptiles and of the pericarp. Seeds were germinated on two layers of water-moistened filter paper in a climatic chamber at a constant temperature of 20 °C on a 12-hour daylight cycle. During long-term natural storage of the seeds for up to 9 years in a dry ventilated room in Kraft bags at 20 ± 2 °C, the tested wheat samples experienced a loss of seed germination capacity of ~50 %; anthocyanins were found to not participate in the preservation of germination capacity. Nonetheless, anthocyanins contributed to the preservation of seed viability under unfavorable short-term conditions of a temperature rise to 48 °C at 100 % humidity. The accelerated aging test did not predict poor germination capacity after long-term seed storage. The results showed a neutral role of anthocyanins in the maintenance of seed germination capacity for 6-9 years under natural storage conditions at 20 ± 2 °C. A small statistically significant increase in grain germination capacity during natural aging was associated with the presence of a recombinant region containing the Pp-D1 gene on wheat chromosome 7D.

Seed longevity and genome damage

Seeds are the mode of propagation for most plant species and form the basis of both agriculture and ecosystems. Desiccation tolerant seeds, representative of most crop species, can survive maturation drying to become metabolically quiescent. The desiccated state prolongs embryo viability and provides protection from adverse environmental conditions, including seasonal periods of drought and freezing often encountered in temperate regions. However, the capacity of the seed to germinate declines over time and culminates in the loss of seed viability. The relationship between environmental conditions (temperature and humidity) and the rate of seed deterioration (ageing) is well defined, but less is known about the biochemical and genetic factors that determine seed longevity. This review will highlight recent advances in our knowledge that provide insight into the cellular stresses and protective mechanisms that promote seed survival, with a focus on the roles of DNA repair and response mechanisms. Collectively, these pathways function to maintain the germination potential of seeds. Understanding the molecular basis of seed longevity provides important new genetic targets for the production of crops with enhanced resilience to changing climates and knowledge important for the preservation of plant germplasm in seedbanks.

Seed Longevity and Ageing: A Review on Physiological and Genetic Factors with an Emphasis on Hormonal Regulation

Upon storage, seeds inevitably age and lose their viability over time, which determines their longevity. Longevity correlates with successful seed germination and enhancing this trait is of fundamental importance for long-term seed storage (germplasm conservation) and crop improvement. Seed longevity is governed by a complex interplay between genetic factors and environmental conditions experienced during seed development and after-ripening that will shape seed physiology. Several factors have been associated with seed ageing such as oxidative stress responses, DNA repair enzymes, and composition of seed layers. Phytohormones, mainly abscisic acid, auxins, and gibberellins, have also emerged as prominent endogenous regulators of seed longevity, and their study has provided new regulators of longevity. Gaining a thorough understanding of how hormonal signalling genes and pathways are integrated with downstream mechanisms related to seed longevity is essential for formulating strategies aimed at preserving seed quality and viability. A relevant aspect related to research in seed longevity is the existence of significant differences between results depending on the seed equilibrium relative humidity conditions used to study seed ageing. Hence, this review delves into the genetic, environmental and experimental factors affecting seed ageing and longevity, with a particular focus on their hormonal regulation. We also provide gene network models underlying hormone signalling aimed to help visualize their integration into seed longevity and ageing. We believe that the format used to present the information bolsters its value as a resource to support seed longevity research for seed conservation and crop improvement.

Genetic Variability in Seed Longevity and Germination Traits in a Tomato MAGIC Population in Contrasting Environments

The stable production of high vigorous seeds is pivotal to crop yield. Also, a high longevity is essential to avoid progressive loss of seed vigour during storage. Both seed traits are strongly influenced by the environment during seed development. Here, we investigated the impact of heat stress (HS) during fruit ripening on tomato seed lifespan during storage at moderate relative humidity, speed (t50) and homogeneity of germination, using a MAGIC population that was produced under optimal and HS conditions. A plasticity index was used to assess the extent of the impact of HS for each trait. HS reduced the average longevity and germination homogeneity by 50% within the parents and MAGIC population. However, there was a high genetic variability in the seed response to heat stress. A total of 39 QTLs were identified, including six longevity QTLs for seeds from control (3) and HS (3) conditions, and six plasticity QTLs for longevity, with only one overlapping with a longevity QTL under HS. Four out of the six longevity QTL co-located with t50 QTL, revealing hotspots for seed quality traits. Twenty-one QTLs with intervals below 3 cM were analyzed using previous transcriptome and gene network data to propose candidate genes for seed vigour and longevity traits.

Maize heat shock proteins-prospection, validation, categorization and in silico analysis of the different ZmHSP families

Among the plant molecular mechanisms capable of effectively mitigating the effects of adverse weather conditions, the heat shock proteins (HSPs), a group of chaperones with multiple functions, stand out. At a time of full progress on the omic sciences, they look very promising in the genetic engineering field, especially in order to conceive superior genotypes, potentially tolerant to abiotic stresses (AbSts). Recently, some works concerning certain families of maize HSPs (ZmHSPs) were published. However, there was still a lack of a study that, with a high degree of criteria, would fully conglomerate them. Using distinct but complementary strategies, we have prospected as many ZmHSPs candidates as possible, gathering more than a thousand accessions. After detailed data mining, we accounted for 182 validated ones, belonging to seven families, which were subcategorized into classes with potential for functional parity. In them, we identified dozens of motifs with some degree of similarity with proteins from different kingdoms, which may help explain some of their still poorly understood means of action. Through in silico and in vitro approaches, we compared their expression levels after controlled exposure to several AbSts' sources, applied at diverse tissues, on varied phenological stages. Based on gene ontology concepts, we still analyzed them from different perspectives of term enrichment. We have also searched, in model plants and close species, for potentially orthologous genes. With all these new insights, which culminated in a plentiful supplementary material, rich in tables, we aim to constitute a fertile consultation source for those maize researchers attracted by these interesting stress proteins.

Insights into mechanisms of seed longevity in soybean: a review

Soybean, a crop of international importance, is challenged with the problem of seed longevity mainly due to its genetic composition and associated environmental cues. Soybean's fragile seed coat coupled with poor DNA integrity, ribosomal dysfunction, lipid peroxidation and poor antioxidant system constitute the rationale for fast deterioration. Variability among the genotypes for sensitivity to field weathering contributed to their differential seed longevity. Proportion and density of seed coat, glassy state of cells, calcium and lignin content, pore number, space between seed coat and cotyledon are some seed related traits that are strongly correlated to longevity. Further, efficient antioxidant system, surplus protective proteins, effective nucleotide and protein repair systems and free radical scavenging mechanisms also contributed to the storage potential of soybean seeds. Identification of molecular markers and QTLs associated with these mechanisms will pave way for enhanced selection efficiency for seed longevity in soybean breeding programs. This review reflects on the morphological, biochemical and molecular bases of seed longevity along with pointers on harvest, processing and storage strategies for extending vigour and viability in soybean.

Genetic Analyses of Seed Longevity in Capsicum annuum L. in Cold Storage Conditions

Seed longevity is the most important trait in the genebank management system. No seed can remain infinitely viable. There are 1241 accessions of Capsicum annuum L. available at the German Federal ex situ genebank at IPK Gatersleben. C. annuum (Capsicum) is the most economically important species of the genus Capsicum. So far, there is no report that has addressed the genetic basis of seed longevity in Capsicum. Here, we convened a total of 1152 Capsicum accessions that were deposited in Gatersleben over forty years (from 1976 to 2017) and assessed their longevity by analyzing the standard germination percentage after 5-40 years of storage at -15/-18 °C. These data were used to determine the genetic causes of seed longevity, along with 23,462 single nucleotide polymorphism (SNP) markers covering all of the 12 Capsicum chromosomes. Using the association-mapping approach, we identified a total of 224 marker trait associations (MTAs) (34, 25, 31, 35, 39, 7, 21 and 32 MTAs after 5-, 10-, 15-, 20-, 25-, 30-, 35- and 40-year storage intervals) on all the Capsicum chromosomes. Several candidate genes were identified using the blast analysis of SNPs, and these candidate genes are discussed.

Choosing the Right Path for the Successful Storage of Seeds

Seeds are the most commonly used source of storage material to preserve the genetic diversity of plants. However, prior to the deposition of seeds in gene banks, several questions need to be addressed. Here, we illustrate the scheme that can be used to ensure that the most optimal conditions are identified to enable the long-term storage of seeds. The main questions that need to be answered pertain to the production of viable seeds by plants, the availability of proper protocols for dormancy alleviation and germination, seed tolerance to desiccation and cold storage at -20 °C. Finally, it is very important to fully understand the capability or lack thereof for seeds or their explants to tolerate cryogenic conditions. The proper storage regimes for orthodox, intermediate and recalcitrant seeds are discussed.

A GBS-Based GWAS Analysis of Leaf and Stripe Rust Resistance in Diverse Pre-Breeding Germplasm of Bread Wheat (Triticum aestivum L.)

Yellow (YR) and leaf (LR) rusts caused by Puccinia striiformis f. sp. tritici (Pst) and Puccinia triticina, respectively, are of utmost importance to wheat producers because of their qualitative and quantitative effect on yield. The search for new loci resistant to both rusts is an ongoing challenge faced by plant breeders and pathologists. Our investigation was conducted on a subset of 168 pre-breeding lines (PBLs) to identify the resistant germplasm against the prevalent local races of LR and YR under field conditions followed by its genetic mapping. Our analysis revealed a range of phenotypic responses towards both rusts. We identified 28 wheat lines with immune response and 85 resistant wheat genotypes against LR, whereas there were only eight immune and 52 resistant genotypes against YR. A GWAS (genome-wide association study) identified 190 marker-trait associations (MTAs), where 120 were specific to LR and 70 were specific to YR. These MTAs were confined to 86 quantitative trait loci (QTLs), where 50 QTLs carried MTAs associated with only LR, 29 QTLs carried MTAs associated with YR, and seven QTLs carried MTAs associated with both LR and YR. Possible candidate genes at the site of these QTLs are discussed. Overall, 70 PBLs carried all seven LR/YR QTLs. Furthermore, there were five PBLs with less than five scores for both LR and YR carrying positive alleles of all seven YR/LR QTLs, which are fit to be included in a breeding program for rust resistance induction.

QTL Analysis for Bread Wheat Seed Size, Shape and Color Characteristics Estimated by Digital Image Processing

The size, shape, and color of wheat seeds are important traits that are associated with yield and flour quality (size, shape), nutritional value, and pre-harvest sprouting (coat color). These traits are under multigenic control, and to dissect their molecular and genetic basis, quantitative trait loci (QTL) analysis is used. We evaluated 114 recombinant inbred lines (RILs) in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative, ITMI/MP) grown in 2014 season. We used digital image analysis for seed phenotyping and obtained data for seven traits describing seed size and shape and 48 traits of seed coat color. We identified 212 additive and 34 pairs of epistatic QTLs on all the chromosomes of wheat genome except chromosomes 1A and 5D. Many QTLs were overlapping. We demonstrated that the overlap between QTL regions was low for seed size/shape traits and high for coat color traits. Using the literature and KEGG data, we identified sets of genes in Arabidopsis and rice from the networks controlling seed size and color. Further, we identified 29 and 14 candidate genes for seed size-related loci and for loci associated with seed coat color, respectively.

Seed-to-Seedling Transition: Novel Aspects

Transition from seed to seedling represents a critical stage in plants’ life cycles. This process includes three significant events in the seeds: (i) tissue hydration, (ii) the mobilization of reserve nutrients, and (iii) the activation of metabolic activity. Global metabolic rearrangements lead to the initiation of radicle growth and the resumption of vegetative development. It requires massive reprogramming of the transcriptome, proteome, metabolome, and attendant signaling pathways, resulting in the silencing of seed-maturation genes and the activation of vegetative growth genes. This Special Issue discusses the mechanisms of genetic, epigenetic, and hormonal switches during seed-to-seedling transitions. Detailed information has also been covered regarding the influence of germination features on seedling establishment.