Genotyping of endosperms to determine seed dormancy genes regulating germination through embryonic, endospermic, or maternal tissues in rice

ABA biosynthesis gene OsNCED3 contributes to preharvest sprouting resistance and grain development in rice

Preharvest sprouting (PHS) is an unfavorable trait in cereal crops and causes serious yield loss. However, the molecular mechanism underlying PHS remains largely elusive. Here, we identified a member of 9-cis-epoxycarotenoid dioxygenase family, OsNCED3, which regulates PHS and grain development in rice (Oryza sativa L.). OsNCED3 encodes a chloroplast-localized abscisic acid (ABA) biosynthetic enzyme highly expressed in the embryo of developing seeds. Disruption of OsNCED3 by CRISPR/Cas9-mediated mutagenesis led to a lower ABA and higher gibberellic acid (GA) levels (thus a skewed ABA/GA ratio) in the embryo, promoting embryos growth and breaking seed dormancy before seed maturity and harvest, thus decreased seed dormancy and enhanced PHS in rice. However, the overexpression of OsNCED3 enhanced PHS resistance by regulating proper ABA/GA ratio in the embryo. Intriguingly, the overexpression of OsNCED3 resulted in increased grain size and weight, whereas the disruption of OsNCED3 function decreased grain size and weight. Nucleotide diversity analyses suggested that OsNCED3 may be selected during japonica populations adaptation of seed dormancy and germination. Taken together, we have identified a new OsNCED regulator involved rice PHS and grain development, and provide a potential target gene for improving PHS resistance and grain development in rice.

Rice GERMIN-LIKE PROTEIN 2-1 Functions in Seed Dormancy under the Control of Abscisic Acid and Gibberellic Acid Signaling Pathways

Seed dormancy is a natural phenomenon in plants. It ensures that seeds complete the grain-filling stage before germination and prevents germination in unsuitable ecological conditions. In this study, we determined the previously unknown function of the rice (Oryza sativa) gene GERMIN-LIKE PROTEIN 2-1 (OsGLP2-1) in seed dormancy. Using artificial microRNA and CRISPR/CAS9 approaches, suppression of OsGLP2-1 expression in rice resulted in the release of dormancy in immature seeds. Conversely, overexpression of OsGLP2-1 driven by the OsGLP2-1 native promoter led to greater seed dormancy. Seed scutellum-specific expression of OsGLP2-1 was increased by exogenous abscisic acid, but decreased with gibberellic acid treatment. We provide evidence that OsGLP2-1 is antagonistically controlled at the transcriptional level by ABA INSENSITIVE5 and GAMYB transcription factors. We conclude that OsGLP2-1 acts as a buffer, maintaining appropriate equilibrium for the regulation of primary dormancy during seed development in rice.

QTL mapping for pre-harvest sprouting resistance in japonica rice varieties utilizing genome re-sequencing

Pre-harvest sprouting (PHS) leads to serious economic losses because of reductions in yield and quality. To analyze the quantitative trait loci (QTLs) for PHS resistance in japonica rice, PHS rates on panicles were measured in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae (PHS resistant) and Unbong40 (PHS susceptible) under two different environmental conditions—field (summer) and greenhouse (winter) environments. Genome re-sequencing of the parental varieties detected 266,773 DNA polymorphisms including 248,255 single nucleotide polymorphisms and 18,518 insertions/deletions. We constructed a genetic map comprising 239 kompetitive allele-specific PCR and 49 cleaved amplified polymorphic sequence markers. In the field environment, two major QTLs, qPHS-3^FD and qPHS-11^FD, were identified on chromosomes 3 and 11, respectively, whereas three major QTLs, qPHS-3^GH, qPHS-4^GH, and qPHS-11^GH, were identified on chromosomes 3, 4, and 11, respectively, in the greenhouse environment. qPHS-11^GH and qPHS-11^FD had similar locations on chromosome 11, suggesting the existence of a gene conferring stable PHS resistance effects under different environmental conditions. The QTLs identified in this study can be used to improve the PHS resistance of japonica varieties, and they may improve our understanding of the genetic basis of PHS resistance.

Assembling seed dormancy genes into a system identified their effects on seedbank longevity in weedy rice

Seed dormancy (SD) and longevity (SL) may share developmental and genetic mechanisms, as both traits are developed in the same maternal environment and evolved to coordinate the timing of germination and the life span of seedbanks. To test the hypothesis, allelic variants at the SD1-2, 7-1, 7-2, and 12 loci from weedy and cultivated rice (Oryza sativa) were assembled into the same genetic background, and 16 homozygous lines selected as a tetragenic system. These lines were evaluated for SD measured by germination at 7, 21, 35, and 150 days of after-ripening (DAR), and for SL measured by the seed decay rate and survivability in the soil of a rice field for 7 months. Pyramiding the alleles from weedy rice lengthened the dormancy duration, and seeds survived in the soil remained dormant at the excavation. Germination levels at 7 to 150 DAR were correlated positively with the seed decay rate (r = 0.41-0.53) and negatively with the survivability (r = -0.45 to -0.28) in the tetragenic system. All four loci contributed to genotypic variation for each of the SD and SL measurements through main and/or epistatic (two- to four-order interactions) effects. SD7-1 (identical to the pericarp color gene Rc) played a major role in regulating seedbank longevity when interacted with the other SD gene(s). This research provided evidence that natural genes controlling SD are involved in regulation of soil seedbank longevity. Thus, accumulation of SD genes in a population could result in persistence of wild plants and weeds in conventional tillage systems.

JAZ proteins modulate seed germination through interaction with ABI5 in bread wheat and Arabidopsis

Appropriate regulation of crop seed germination is of significance for agriculture production. In this study, we show that TaJAZ1, most closely related to Arabidopsis JAZ3, negatively modulates abscisic acid (ABA)-inhibited seed germination and ABA-responsive gene expression in bread wheat. Biochemical interaction assays demonstrate that the C-terminal part containing the Jas domain of TaJAZ1 physically interacts with TaABI5. Similarly, Arabidopsis jasmonate-ZIM domain (JAZ) proteins also negatively modulate ABA responses. Further we find that a subset of JAZ proteins could interact with ABI5 using the luciferase complementation imaging assays. Choosing JAZ3 as a representative, we demonstrate that JAZ3 interacts with ABI5 in vivo and represses the transcriptional activation activity of ABI5. ABA application could abolish the enrichment of JAZ proteins in the ABA-responsive gene promoter. Furthermore, we find that ABA application could induce the expression of jasmonate (JA) biosynthetic genes and then increase the JA concentrations partially dependent on the function of ABI5, consequently leading to the degradation of JAZ proteins. This study sheds new light on the crosstalk between JA and ABA in modulating seed germination in bread wheat and Arabidopsis.

Germination characteristics among different sheepgrass (Leymus chinensis) germplasm during the seed development and after-ripening stages

Sheepgrass (Leymus chinensis (Trin.) Tzvel) is an important forage grass in the Eurasian steppe. However, little information is available concerning its seed morphological features and germination characteristics during seed development and after-ripening among different germplasm. To clarify the appropriate seed harvest time and the effects of germplasm, seed development and after-ripening on seed germination, 20 germplasm of sheepgrass were selected. Moreover, the seed morphological and physical changes as well as the seed germination and dormancy characteristics of sheepgrass during seed development stages were analyzed using a seven—d gradient of day after pollination (DAP). The results indicated that the seed water content decreased significantly during 35–42 DAP and that the highest seed germination rate of most germplasm was observed at 35–42 DAP. Thus, 35–42 DAP may be the best time to harvest sheepgrass to obtain the maximum seed germination rate and avoid seed shattering. Furthermore, our results indicated that there were six types of germination patterns, including germplasm with increasing germination rates in the developing seed, such as S19 and S13, and germplasm that maintained a consistently low germination rate, such as S10. Moreover, we compared the seed germination rate of eight germplasm during seed development in both 2016 and 2017, and the results indicated that the seed germination patterns of the eight germplasm were highly consistent between the two consecutive years, suggesting that germplasm rather than year is the major factor in determining germination during seed development. The effect of after-ripening on seed germination was different among the germplasm where four types of germination patterns were revealed for 10 germplasm and resulted in various dormancy features. A two-factor ANOVA analysis suggested that the germplasm of the sheepgrass has a large influence on seed germination, whether during seed development or after-ripening. Thus, these findings lay the foundation for future studies on seed dormancy and germination and may guide the breeding of new cultivars of sheepgrass with better germination performance.

Comparative Mapping of Seed Dormancy Loci Between Tropical and Temperate Ecotypes of Weedy Rice (Oryza sativa L.)

Genotypic variation at multiple loci for seed dormancy (SD) contributes to plant adaptation to diverse ecosystems. Weedy rice (Oryza sativa) was used as a model to address the similarity of SD genes between distinct ecotypes. A total of 12 quantitative trait loci (QTL) for SD were identified in one primary and two advanced backcross (BC) populations derived from a temperate ecotype of weedy rice (34.3°N Lat.). Nine (75%) of the 12 loci were mapped to the same positions as those identified from a tropical ecotype of weedy rice (7.1°N Lat.). The high similarity suggested that the majority of SD genes were conserved during the ecotype differentiation. These common loci are largely those collocated/linked with the awn, hull color, pericarp color, or plant height loci. Phenotypic correlations observed in the populations support the notion that indirect selections for the wild-type morphological characteristics, together with direct selections for germination time, were major factors influencing allelic distributions of SD genes across ecotypes. Indirect selections for crop-mimic traits (e.g., plant height and flowering time) could also alter allelic frequencies for some SD genes in agroecosystems. In addition, 3 of the 12 loci were collocated with segregation distortion loci, indicating that some gametophyte development genes could also influence the genetic equilibria of SD loci in hybrid populations. The SD genes with a major effect on germination across ecotypes could be used as silencing targets to develop transgene mitigation (TM) strategies to reduce the risk of gene flow from genetically modified crops into weed/wild relatives.

Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.)

Seed dormancy is an important agronomic trait affecting grain yield and quality because of pre-harvest germination and is influenced by both environmental and genetic factors. However, our knowledge of the factors controlling seed dormancy remains limited. To better reveal the molecular mechanism underlying this trait, a genome-wide association study was conducted in an indica-only population consisting of 453 accessions genotyped using 5,291 SNPs. Nine known and new significant SNPs were identified on eight chromosomes. These lead SNPs explained 34.9% of the phenotypic variation, and four of them were designed as dCAPS markers in the hope of accelerating molecular breeding. Moreover, a total of 212 candidate genes was predicted and eight candidate genes showed plant tissue-specific expression in expression profile data from different public bioinformatics databases. In particular, LOC_Os03g10110, which had a maize homolog involved in embryo development, was identified as a candidate regulator for further biological function investigations. Additionally, a polymorphism information content ratio method was used to screen improvement footprints and 27 selective sweeps were identified, most of which harbored domestication-related genes. Further studies suggested that three significant SNPs were adjacent to the candidate selection signals, supporting the accuracy of our genome-wide association study (GWAS) results. These findings show that genome-wide screening for selective sweeps can be used to identify new improvement-related DNA regions, although the phenotypes are unknown. This study enhances our knowledge of the genetic variation in seed dormancy, and the new dormancy-associated SNPs will provide real benefits in molecular breeding.

Map-Based Cloning of Seed Dormancy1-2 Identified a Gibberellin Synthesis Gene Regulating the Development of Endosperm-Imposed Dormancy in Rice

Natural variation in seed dormancy is controlled by multiple genes mapped as quantitative trait loci in major crop or model plants. This research aimed to clone and characterize the Seed Dormancy1-2 (qSD1-2) locus associated with endosperm-imposed dormancy and plant height in rice (Oryza sativa). qSD1-2 was delimited to a 20-kb region, which contains OsGA20ox2 and had an additive effect on germination. Naturally occurring or induced loss-of-function mutations of the gibberellin (GA) synthesis gene enhanced seed dormancy and also reduced plant height. Expression of this gene in seeds (including endospermic cells) during early development increased GA accumulation to promote tissue morphogenesis and maturation programs. The mutant allele prevalent in semidwarf cultivars reduced the seed GA content by up to 2-fold at the early stage, which decelerated tissue morphogenesis including endosperm cell differentiation, delayed abscisic acid accumulation by a shift in the temporal distribution pattern, and postponed dehydration, physiological maturity, and germinability development. As the endosperm of developing seeds dominates the moisture equilibrium and desiccation status of the embryo in cereal crops, qSD1-2 is proposed to control primary dormancy by a GA-regulated dehydration mechanism. Allelic distribution of OsGA20ox2, the rice Green Revolution gene, was associated with the indica and japonica subspeciation. However, this research provided no evidence that the primitive indica- and common japonica-specific alleles at the presumably domestication-related locus functionally differentiate in plant height and seed dormancy. Thus, the evolutionary mechanism of this agriculturally important gene remains open for discussion.