Identification of Genes and MicroRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses

Genetic variation for tolerance to pre-harvest sprouting in mungbean (Vigna radiata) genotypes

Pre-harvest sprouting (PHS) is one of the important abiotic stresses in mungbean which significantly reduces yield and quality of the produce. This study was conducted to evaluate the genetic variability for tolerance to pre-harvest sprouting in diverse mungbean genotypes while simultaneously deciphering the association of yield contributing traits with PHS. Eighty-three diverse mungbean genotypes (23 released varieties, 23 advanced breeding lines and 37 exotic germplasm lines) were investigated for tolerance to PHS, water imbibition capacities by pods, pod and seed physical traits. Wide variation in PHS was recorded which ranged between 17.8% to 81% (mean value 54.34%). Germplasm lines exhibited higher tolerance to PHS than the high-yielding released varieties. Correlation analysis revealed PHS to be positively associated with water imbibition capacity by pods (r = 0.21) and germinated pod % (r = 0.78). Pod length (r = -0.13) and seeds per pod (r = -0.13) were negatively influencing PHS. Positive associations between PHS and water imbibition capacity by pods, germinated pod % and 100-seed weight was further confirmed by multivariate analysis. Small-seeded genotypes having 100-seed weight <3 g exhibited higher tolerance to PHS compared to bold-seeded genotypes having 100-seed weight more than 3.5 g. Fresh seed germination among the selected PHS tolerant and susceptible genotypes ranged from 42% (M 204) to 98% (Pusa 1131). A positive association (r = 0.79) was recorded between fresh seed germination and PHS. Genotypes M 1255, M 145, M 422, M 1421 identified as potential genetic donors against PHS could be utilized in mungbean breeding programs.

Analysis of the global transcriptome and miRNAome associated with seed dormancy during seed maturation in rice (Oryza sativa L. cv. Nipponbare)

BACKGROUND

Seed dormancy is a biological mechanism that prevents germination until favorable conditions for the subsequent generation of plants are encountered. Therefore, this mechanism must be effectively established during seed maturation. Studies investigating the transcriptome and miRNAome of rice embryos and endosperms at various maturation stages to evaluate seed dormancy are limited. This study aimed to compare the transcriptome and miRNAome of rice seeds during seed maturation.

RESULTS

Oryza sativa L. cv. Nipponbare seeds were sampled for embryos and endosperms at three maturation stages: 30, 45, and 60 days after heading (DAH). The pre-harvest sprouting (PHS) assay was conducted to assess the level of dormancy in the seeds at each maturation stage. At 60 DAH, the PHS rate was significantly increased compared to those at 30 and 45 DAH, indicating that the dormancy is broken during the later maturation stage (45 DAH to 60 DAH). However, the largest number of differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) were identified between 30 and 60 DAH in the embryo and endosperm, implying that the gradual changes in genes and miRNAs from 30 to 60 DAH may play a significant role in breaking seed dormancy. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses confirmed that DEGs related to plant hormones were most abundant in the embryo during 45 DAH to 60 DAH and 30 DAH to 60 DAH transitions. Alternatively, most of the DEGs in the endosperm were related to energy and abiotic stress. MapMan analysis and quantitative real-time polymerase chain reaction identified four newly profiled auxin-related genes (OsSAUR6/12/23/25) and one ethylene-related gene (OsERF087), which may be involved in seed dormancy during maturation. Additionally, miRNA target prediction (psRNATarget) and degradome dataset (TarDB) indicated a potential association between osa-miR531b and ethylene biosynthesis gene (OsACO4), along with osa-miR390-5p and the abscisic acid (ABA) exporter-related gene (OsMATE19) as factors involved in seed dormancy.

CONCLUSIONS

Analysis of the transcriptome and miRNAome of rice embryos and endosperms during seed maturation provided new insights into seed dormancy, particularly its relationship with plant hormones such as ABA, auxin, and ethylene.

QTL mapping and improvement of pre-harvest sprouting resistance using japonica weedy rice

The stability of cultivation and production in terms of crop yield has been threatened by climate change due to global warming. Pre-harvest sprouting (PHS) is a threat to crops, especially staple foods, including rice, because of reductions in yield and quality. To address the problem of precocious germination before harvest, we performed quantitative trait loci (QTL) analysis for PHS using F₈ RILs populations derived from japonica weedy rice in Korea. QTL analysis revealed that two stable QTLs, qPH7 and qPH2, associated with PHS resistance were identified on chromosomes 7 and 2, respectively, explaining approximately 38% of the phenotypic variation. The QTL effect in the tested lines significantly decreased the degree of PHS, based on the number of QTLs included. Through fine mapping for main QTL qPH7, the region for the PHS was found to be anchored within 23.575-23.785 Mbp on chromosome 7 using 13 cleaved amplified sequence (CAPS) markers. Among 15 open reading frames (ORFs) within the detected region, one ORF, Os07g0584366, exhibited upregulated expression in the resistant donor, which was approximately nine times higher than that of susceptible japonica cultivars under PHS-inducing conditions. Japonica lines with QTLs related to PHS resistance were developed to improve the characteristics of PHS and design practical PCR-based DNA markers for marker-assisted backcrosses of many other PHS-susceptible japonica cultivars.

Dual-function DEFENSIN 8 mediates phloem cadmium unloading and accumulation in rice grains

Grain cadmium (Cd) is translocated from source to sink tissues exclusively via phloem, though the phloem Cd unloading transporter has not been identified yet. Here, we isolated and functionally characterized a defensin-like gene DEFENSIN 8 (DEF8) highly expressed in rice (Oryza sativa) grains and induced by Cd exposure in seedling roots. Histochemical analysis and subcellular localization detected DEF8 expression preferentially in pericycle cells and phloem of seedling roots, as well as in phloem of grain vasculatures. Further analysis demonstrated that DEF8 is secreted into extracellular spaces possibly by vesicle trafficking. DEF8 bound to Cd in vitro, and Cd efflux from protoplasts as well as loading into xylem vessels decreased in the def8 mutant seedlings compared with the wild type. At maturity, significantly less Cd accumulation was observed in the mutant grains. These results suggest that DEF8 is a dual function protein that facilitates Cd loading into xylem and unloading from phloem, thus mediating Cd translocation from roots to shoots and further allocation to grains, representing a phloem Cd unloading regulator. Moreover, essential mineral nutrient accumulation as well as important agronomic traits were not affected in the def8 mutants, suggesting DEF8 is an ideal target for breeding low grain Cd rice.

Seed Dormancy and Pre-Harvest Sprouting in Rice-An Updated Overview

Pre-harvest sprouting is a critical phenomenon involving the germination of seeds in the mother plant before harvest under relative humid conditions and reduced dormancy. As it results in reduced grain yield and quality, it is a common problem for the farmers who have cultivated the rice and wheat across the globe. Crop yields need to be steadily increased to improve the people’s ability to adapt to risks as the world’s population grows and natural disasters become more frequent. To improve the quality of grain and to avoid pre-harvest sprouting, a clear understanding of the crops should be known with the use of molecular omics approaches. Meanwhile, pre-harvest sprouting is a complicated phenomenon, especially in rice, and physiological, hormonal, and genetic changes should be monitored, which can be modified by high-throughput metabolic engineering techniques. The integration of these data allows the creation of tailored breeding lines suitable for various demands and regions, and it is crucial for increasing the crop yields and economic benefits. In this review, we have provided an overview of seed dormancy and its regulation, the major causes of pre-harvest sprouting, and also unraveled the novel avenues to battle pre-harvest sprouting in cereals with special reference to rice using genomics and transcriptomic approaches.