Overexpression of OsSAP16 Regulates Photosynthesis and the Expression of a Broad Range of Stress Response Genes in Rice (Oryza sativa L.)

Aeluropus littoralis stress-associated protein promotes water deficit resilience in engineered durum wheat

Global climate change-related water deficit negatively affect the growth, development and yield performance of multiple cereal crops, including durum wheat. Therefore, the improvement of water-deficit stress tolerance in durum wheat varieties in arid and semiarid areas has become imperative for food security. Herein, we evaluated the water deficiency resilience potential of two marker-free transgenic durum wheat lines (AlSAP-lines: K9.3 and K21.3) under well-watered and water-deficit stress conditions at both physiological and agronomic levels. These two lines overexpressed the AlSAP gene, isolated from the halophyte grass Aeluropus littoralis, encoding a stress-associated zinc finger protein containing the A20/AN1 domains. Under well-watered conditions, the wild-type (WT) and both AlSAP-lines displayed comparable performance concerning all the evaluated parameters. Ectopic transgene expression exerted no adverse effects on growth and yield performance of the durum wheat plants. Under water-deficit conditions, no significant differences in the plant height, leaf number, spike length, and spikelet number were observed between AlSAP-lines and WT plants. However, compared to WT, the AlSAP-lines exhibited greater dry matter production, greater flag leaf area, improved net photosynthetic rate, stomatal conductance, and water use efficiency. Notably, the AlSAP-lines displayed 25 % higher grain yield (GY) than the WT plants under water-deficit conditions. The RT-qPCR-based selected stress-related gene (TdDREB1, TdLEA, TdAPX1, and TdBlt101-2) expression analyses indicated stress-related genes enhancement in AlSAP-durum wheat plants under both well-watered and water-deficit conditions, potentially related to the water-deficit resilience. Collectively, our findings support that the ectopic AlSAP expression in durum wheat lines enhances water-deficit resilience ability, thereby potentially compensate for the GY loss in arid and semi-arid regions.

Combined QTL-sequencing, linkage mapping, and RNA-sequencing identify candidate genes and KASP markers for low-temperature germination in Oryza sativa L. ssp. Japonica

MAIN CONCLUSION

Through QTL-seq, QTL mapping and RNA-seq, six candidate genes of qLTG9 can be used as targets for cold tolerance functional characterization, and six KASP markers can be used for marker-assisted breeding to improve the germination ability of japonica rice at low temperature. The development of direct-seeded rice at high latitudes and altitudes depends on the seed germination ability of rice under a low-temperature environment. However, the lack of regulatory genes for low-temperature germination has severely limited the application of genetics in improving the breeds. Here, we used cultivars DN430 and DF104 with significantly different low-temperature germination (LTG) and 460 F_2:3 progeny derived from them to identify LTG regulators by combining QTL-sequencing, linkage mapping, and RNA-sequencing. The QTL-sequencing mapped qLTG9 within a physical interval of 3.4 Mb. In addition, we used 10 Kompetitive allele-specific PCR (KASP) markers provided by the two parents, and qLTG9 was optimized from 3.4 Mb to a physical interval of 397.9 kb and accounted for 20.4% of the phenotypic variation. RNA-sequencing identified qLTG9 as eight candidate genes with significantly different expression within the 397.9 kb interval, six of which possessed SNPs on the promoter and coding regions. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) completely validated the results of these six genes in RNA-sequencing. Subsequently, six non-synonymous SNPs were designed using variants in the coding region of these six candidates. Genotypic analysis of these SNPs in 60 individuals with extreme phenotypes indicated these SNPs determined the differences in cold tolerance between parents. The six candidate genes of qLTG9 and the six KASP markers could be used together for marker-assisted breeding to improve LTG.

Pepper stress-associated protein 14 is a substrate of CaSnRK2.6 that positively modulates abscisic acid-dependent osmotic stress responses

The phytohormone abscisic acid (ABA) plays a prominent role in various abiotic stress responses of plants. In the ABA-dependent osmotic stress response, SnRK2.6, one of the subclass III SnRK2 kinases, has been identified as playing a key role by phosphorylating and activating downstream genes. Although several modulatory proteins have been reported to be phosphorylated by SnRK2.6, the identities of the full spectrum of downstream targets have yet to be sufficiently established. In this study, we identified CaSAP14, a stress-associated protein in pepper (Capsicum annuum), as a downstream target of CaSnRK2.6. We elucidated the physical interaction between SnRK2.6 and CaSAP14, both in vitro and in vivo, and accordingly identified a C-terminal C2H2-type zinc finger domain of CaSAP14 as being important for their interaction. CaSAP14-silenced pepper plants showed dehydration- and high salt-sensitive phenotypes, whereas overexpression of CaSAP14 in Arabidopsis conferred tolerance to dehydration, high salinity, and mannitol treatment, with plants showing ABA-hypersensitive phenotypes. Furthermore, an in-gel kinase assay revealed that CaSnRK2.6 phosphorylates CaSAP14 in response to exogenous ABA, dehydration, and high-salinity stress. Collectively, these findings suggest that CaSAP14 is a direct substrate of CaSnRK2.6 and positively modulates dehydration- and high salinity-induced osmotic stress responses.

OsSAP6 Positively Regulates Soda Saline-Alkaline Stress Tolerance in Rice

BACKGROUND

Soil salinization is a worldwide environmental problem, especially in the arid and semiarid regions of northeastern China, which are heavily affected by soda saline-alkaline stress. At present, there is an urgent need to improve the soda saline-alkaline stress tolerance of rice.

RESULTS

Stress-associated proteins are involved in regulating the abiotic stresses in plants. There are 18 members of the rice stress-associated protein (OsSAP) gene family. In this study, the expression levels of OsSAP6 in leaves and roots were upregulated with increasing NaHCO₃ stress duration. OsSAP6 was located in nucleus and cytoplasm. The bud length and total root length of OsSAP6 overexpression rice were significantly longer than those of Lj11 (Oryza sativa longjing11) during germination stage, and the survival rates, plant height and malondialdehyde content at the seedling stage showed tolerance growth of saline-alkaline stress. The expression of OsCu/Zn-SOD, OsAPX2, and OsCAT1 in transgenic lines was increased significantly under SAE (soda saline-alkali soil eluent) stress. OsSAP6 interacts with OsPK5 according to yeast two-hybrid screening and luciferase complementation experiments. The expression of OsPK5 increased under NaHCO₃ and H₂O₂ stress, and the overexpression of OsPK5 in rice improved soda saline-alkaline tolerance.

CONCLUSION

Overexpression of OsSAP6 in rice significantly enhanced saline-alkaline tolerance compared with the wild type. It is speculated that OsSAP6 responds to soda salinity stress and interacts with OsPK5 to positively regulate soda saline-alkaline tolerance through ROS homeostasis. This study revealed the features of OsSAP6 involved in response to soda saline-alkaline stress and the interaction with OsPK5, which provided resources for breeding aimed at improving the soda saline-alkaline stress tolerance of rice.

Identification and Analysis of Stress-Associated Proteins (SAPs) Protein Family and Drought Tolerance of ZmSAP8 in Transgenic Arabidopsis

Stress-associated proteins (SAPs), a class of A20/AN1 zinc finger proteins, play vital roles in plant stress response. However, investigation of SAPs in maize has been very limited. Herein, to better trace the evolutionary history of SAPs in maize and plants, 415 SAPs were identified in 33 plant species and four species of other kingdoms. Moreover, gene duplication mode exploration showed whole genome duplication contributed largely to SAP gene expansion in angiosperms. Phylogeny reconstruction was performed with all identified SAPs by the maximum likelihood (ML) method and the SAPs were divided into five clades. SAPs within the same clades showed conserved domain composition. Focusing on maize, nine ZmSAPs were identified. Further promoter cis-elements and stress-induced expression pattern analysis of ZmSAPs indicated that ZmSAP8 was a promising candidate in response to drought stress, which was the only AN1-AN1-C2H2-C2H2 type SAP in maize and belonged to clade I. Additionally, ZmSAP8 was located in the nucleus and had no transactivation activity in yeast. Overexpressing ZmSAP8 enhanced the tolerance to drought stress in Arabidopsis thaliana, with higher seed germination and longer root length. Our results should benefit the further functional characterization of ZmSAPs.

Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems

Rice (Oryza sativa) was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.

Cloning and Characterization of TaSAP7-A, a Member of the Stress-Associated Protein Family in Common Wheat

Stress association proteins (SAPs) are A20/AN1 zinc-finger domain proteins, which play important roles in plant adaptation to abiotic stress and plant development. The functions of SAPs in some plants were reported, but little is known about it in wheat (Triticum aestivum L.). In this study, we characterized a novel 2AN1-type stress association protein gene TaSAP7-A, which was mapped to chromosome 5A in wheat. Subcellular localization indicated that TaSAP7-A was distributed in the nucleus and cytoplasm. Unlike previously known A20/AN1-type SAP genes, TaSAP7-A was negatively regulated to abiotic stress tolerance. Overexpressing TaSAP7-A Arabidopsis lines were hypersensitive to ABA, osmotic and salt stress at germination stage and post-germination stage. Overexpression of TaSAP7-A Arabidopsis plants accelerated the detached leaves' chlorophyll degradation. Association analysis of TaSAP7-A haplotypes and agronomic traits showed that Hap-5A-2 was significantly associated with higher chlorophyll content at jointing stage and grain-filling stage. These results jointly revealed that TaSAP7-A is related to the chlorophyll content in the leaves of Arabidopsis and wheat. Both in vivo and in vitro experiments demonstrated that TaSAP7-A interacted with TaS10B, which was the component of regulatory subunit in 26S proteasome. In general, TaSAP7-A was a regulator of chlorophyll content, and favorable haplotypes should be helpful for improving plant chlorophyll content and grain yield of wheat.

Identification of a Major QTL and Candidate Gene Analysis of Salt Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.) Using QTL-Seq and RNA-Seq

BACKGROUND

Salt stress is one of the main abiotic stresses that limits rice production worldwide. Rice salt tolerance at the bud burst stage directly affects the seedling survival rate and the final yield in the direct seeding cultivation model. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for salt tolerance at the bud burst stage are limited.

RESULTS

Here, an F_2:3 population derived from a cross between IR36 (salt-sensitive) and Weiguo (salt-tolerant) was used to identify salt-tolerant QTL interval at the bud burst stage using a whole-genome sequencing-based QTL-seq containing 40 extreme salt-tolerant and 40 extreme salt-sensitive individuals. A major QTL, qRSL7, related to relative shoot length (RSL) was detected on chromosome 7 using ΔSNP index algorithms and Euclidean Distance (ED) algorithms. According to single nucleotide polymorphisms (SNPs) between the parents, 25 Kompetitive allele-specific PCR (KASP) markers were developed near qRSL7, and regional QTL mapping was performed using 199 individuals from the F_2:3 population. We then confirmed and narrowed down qRSL7 to a 222 kb genome interval. Additionally, RNA sequencing (RNA-seq) was performed for IR36 and Weiguo at 36 h after salt stress and control condition at the bud burst stage, and 5 differentially expressed genes (DEGs) were detected in the candidate region. The qRT-PCR results showed the same expression patterns as the RNA-seq data. Furthermore, sequence analysis revealed a 1 bp Indel difference in Os07g0569700 (OsSAP16) between IR36 and Weiguo. OsSAP16 encodes a stress-associated protein whose expression is increased under drought stress.

CONCLUSION

These results indicate that OsSAP16 was the candidate gene of qRSL7. The results is useful for gene cloning of qRSL7 and for improving the salt tolerance of rice varieties by marker assisted selection (MAS).

Natural variation reveals that OsSAP16 controls low-temperature germination in rice

Low temperature affects seed germination in plants, and low-temperature germination (LTG) is an important agronomic trait. Natural variation of LTG has been reported in rice, but the molecular basis for this variation is largely unknown. Here we report the phenotypic analysis of LTG in 187 rice natural accessions and a genome-wide association study (GWAS) of LTG in this collection. A total of 53 quantitative trait loci (QTLs) were found to be associated with LTG, of which 20 were located in previously reported QTLs. We further identified Stress-Associated Protein 16 (OsSAP16), coding for a zinc-finger domain protein, as a causal gene for one of the major LTG QTLs. Loss of OsSAP16 function reduces germination while greater expression of OsSAP16 enhances germination at low temperature. In addition, accessions with extremely high and low LTG values have correspondingly high and low OsSAP16 expression at low temperatures, suggesting that variation in expression of the OsSAP16 gene contributes to LTG variation. As the first case of identification of an LTG gene through GWAS, this study indicates that GWAS of natural accessions is an effective strategy in genetically dissecting LTG processes and gaining molecular understanding of low-temperature response and germination.