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).
Background
Salinity-alkalinity stress is one of the major factors limiting rice production. Damage caused by alkaline salt stress is more severe than that caused by neutral salt stress. Alkali ...tolerance at the bud stage in rice directly affects seedling survival and final yield when using the direct seeding cultivation model. However, genetic resources (QTLs and genes) for rice breeders to improve alkali tolerance are limited. In this study, we combined linkage mapping and a genome-wide association study (GWAS) to analyze the genetic structure of this trait in
japonica
rice at the bud stage.
Results
A population of 184 recombinant inbred lines (RILs) was utilized to map quantitative trait loci (QTLs) for the root length under control condition (RL), alkaline stress (ARL) and relative root length (RRL) at the bud stage. A major QTL related to alkali tolerance at the rice bud stage,
qAT11
, was detected on chromosome 11. Interestingly, a GWAS identified a lead SNP (Chr_21,999,659) in
qAT11
that was significantly associated with alkaline tolerance. After filtering by linkage disequilibrium (LD), haplotype analysis, quantitative real-time PCR, we obtained three candidate genes (
LOC_Os11g37300
,
LOC_Os11g37320
and
LOC_Os11g37390
). In addition, we performed phenotype verification on the CRISPR/Cas9 mutant of
LOC_Os11g37390
.
Conclusion
Based on these results,
LOC_Os11g37300
,
LOC_Os11g37320
and
LOC_Os11g37390
were the candidate genes contributing to alkaline tolerance in
japonica
rice. This study provides resources for breeding aimed at improving rice responses to alkalinity stress.
The widespread use but low recovery rate of agricultural films has led to microplastic accumulation in farmlands, which poses a serious threat to the health of the soil ecosystem. There is an urgent ...need for early warning and monitoring of soil microplastics pollution, as well as the performance of bioremediation research. In this study, earthworms were used as test organisms to carry out toxicological tests under low-density polyethylene (LDPE) stress. A canonical correlation analysis model (CCA) was established to analyze the relationship between oxidative stress and microbial community. A path analysis model (PA) was also constructed to examine the detoxification mechanism of earthworms under LDPE stress. The results showed that low concentrations (100 and 500 mg/kg) of LDPE did not cause oxidative damage to earthworms but stimulated their physiological metabolism. Meanwhile, 1000 mg/kg LDPE concentrations caused oxidative damage to earthworms and altered their internal microbial community structure. Furthermore, at 1500 mg/kg LDPE concentrations, the oxidative stress to the earthworms is aggravated, and their physiological responses work in conjunction with the microbial community to cope with the adverse condition. Lastly, treatment with 2000 mg/kg LDPE induced the appearance of LDPE tolerant populations in the microbial community in vivo. Taken together, our results provide a theoretical basis for revealing the physiological response of earthworms when challenged in a polluted environment and provide a model for pollution remediation and ecological security monitoring of soil ecosystems.
Display omitted
•Eisenia fetida is used for soil ecological security monitoring of microplastics pollution.•CCA and PA are combined to study the life maintenance mechanism of earthworm.•Extracting the utilization intensity of single carbon source as original date.•Microbes and the oxidative stress are independent at low concentration (< 500 mg/kg).•Under 1500 mg/kg LDPE stress, microbes are working in conjunction with the oxidative stress.
Caffeic acid O-methyltransferase (COMT) is one of the core enzymes involved in lignin synthesis. However, there is no systematic study on the rice COMT gene family. We identified 33 COMT genes ...containing the methyltransferase-2 domain in the rice genome using bioinformatic methods and divided them into Group I (a and b) and Group II. Motifs, conserved domains, gene structure and SNPs density are related to the classification of OsCOMTs. The tandem phenomenon plays a key role in the expansion of OsCOMTs. The expression levels of fourteen and thirteen OsCOMTs increased or decreased under salt stress and drought stress, respectively. OsCOMTs showed higher expression levels in the stem. The lignin content of rice was measured in five stages; combined with the expression analysis of OsCOMTs and multiple sequence alignment, we found that OsCOMT8, OsCOMT9 and OsCOMT15 play a key role in the synthesis of lignin. Targeted miRNAs and gene ontology annotation revealed that OsCOMTs were involved in abiotic stress responses. Our study contributes to the analysis of the biological function of OsCOMTs, which may provide information for future rice breeding and editing of the rice genome.
Cold stress is one of the major abiotic stress factors influencing photosynthesis in rice. In the present study, a linkage analysis and genome-wide association study (GWAS) of photosynthesis-related ...traits (PRT) at the grain filling stage of rice, including net photosynthetic rate (Pn), stomatal conductance (Sc), transpiration rate (Tr), and intercellular CO
2
concentration (Ci), were performed under cold stress using a recombinant inbred line population and single-nucleotide polymorphism (SNP) re-sequencing data of 295 japonica varieties. Twenty-nine additive QTLs (A-QTLs) were detected, and 17 out of the 29 QTLs were cold stress-related.
qPn7
-
1
,
qTr1
,
qTr7
-
1
,
qTr7
-
2
,
qCi7
-
1
and
qSc7
-
1
were specifically expressed under the cold stress and control conditions in different years, with one major pleiotropic QTL interval (RM1306–RM70) detected. In addition, additive × environment interaction QTLs revealed that
qPn7
-
1
,
qTr1
,
qTr7
-
1
,
qCi7
-
1
,
qSc7
-
1
, and
qSc8
-
1
were influenced mainly by genetic factors, suggesting they could be exploited in cold tolerance breeding activities. Ten SNPs were associated significantly with PRT under cold-water stress based on GWAS, and three out the ten were included in the major QTL interval of RM1306–RM70, verifying the QTLs detected in multiple environments by linkage analysis. According to the major QTL genotypes linked to PRT, phenotypically superior RIL47 could be considered for genetic improvement of PRT under cold water stress. The results could facilitate the fine mapping of QTLs related to Pn, Tr, Ci, and Sc under the cold stress condition through the marker-assisted selection approaches.
Rice (
Oryza sativa L.
) is a saline-alkali-sensitive crop. Saline-alkali environments can seriously affect the growth, development, and yield of rice. The mechanisms of salt tolerance and alkali ...tolerance in rice are different; thus, it is very important to study and explore the alkali-tolerant gene loci to improve the saline-alkali tolerance of rice varieties. In this study, the
japonica
rice varieties Dongnong 425 (DN425) and Changbai 10 (CB10) and a hybridized recombinant inbred line (RIL) population were used as materials to be irrigated with Na
2
CO
3
solution under field test conditions. A resistant pool (R-pool) and a sensitive pool (S-pool) were constructed by selecting the lines with extremely high and extremely low 1000-grain weight (TGW), respectively, from the RIL population under alkali treatment. Four candidate TGW regions on chromosomes (Chr.) 2 and 3 were associated using the bulked segregant analysis (BSA) strategy assisted by next-generation sequencing (NGS) technology (NGS-assisted BSA). Using the linkage analysis, QTL-
qATGW2-2
in the candidate region was mapped within a range of 116 Kb between the SSR marker RM13592 and the Indel marker Indel3 of Chr. 2, which contained 18 predictive genes. The BSA sequencing results showed that
Os02g39884
contained a nonsynonymous substitution mutation SNP (nsSNP), leading to the transformation of a residue from arginine (cGg) to glutamine (cAg); thus,
Os02g39884
was inferred to be the candidate gene of
qATGW2-2
. The results of the qRT-PCR analysis also confirmed this. This paper provides important information for the rapid and accurate identification of the alkali-tolerant gene loci in rice.
Rice (Oryza sativa L.) is one of the most widely grown food crops, and its yield and quality are particularly important for a warm-saturated diet. Cold stress restricts rice growth, development, and ...yield; however, the specific mechanism of cold tolerance in rice remains unknown.
The analysis of leaf physiological and photosynthetic characteristics showed that the two rice varieties were significantly affected by cold stress, but the cold-tolerant variety KY131 had more stable physiological characteristics, maintaining relatively good photosynthetic capacity. To better explore the transcriptional regulation mechanism and biological basis of rice response to cold stress, a comprehensive analysis of the rice transcriptome and lipidome under low temperature and control temperature conditions was carried out. The transcriptomic analysis revealed that lipid metabolism, including membrane lipid and fatty acid metabolism, may be an important factor in rice cold tolerance, and 397 lipid metabolism related genes have been identified. Lipidomics data confirmed the importance of membrane lipid remodeling and fatty acid unsaturation for rice adaptation to cold stress. This indicates that the changes in the fluidity and integrity of the photosynthetic membrane under cold stress lead to the reduction of photosynthetic capacity, which could be relieved by increased levels of monogalactosyldiacylglycerol that mainly caused by markedly increased expression of levels of 1,2-diacylglycerol 3-beta-galactosyltransferase (MGD). The upregulation of phosphatidate phosphatase (PAP2) inhibited the excessive accumulation of phosphatidate (PA) to produce more phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG), thereby preventing of membrane phase transition under cold stress. In addition, fatty acid β-oxidation is worth further study in rice cold tolerance. Finally, we constructed a metabolic model for the regulatory mechanism of cold tolerance in rice, in which the advanced lipid metabolism system plays a central role.
Lipidome analysis showed that membrane lipid composition and unsaturation were significantly affected, especially phospholipids and galactolipids. Our study provides new information to further understand the response of rice to cold stress.
Main conclusion
We projected meta-QTL (MQTL) for drought, salinity, cold state, and high metal ion tolerance in rice using a meta-analysis based on high-density consensus maps. In addition, a ...genome-wide association analysis was used to validate the results of the meta-analysis, and four new chromosome intervals for mining abiotic stress candidate genes were obtained.
Drought, severe cold, high salinity, and high metallic ion concentrations severely restrict rice production. Consequently, the breeding of abiotic stress-tolerant variety is being paid increasingly more attention. This study aimed to identify meta-quantitative trait loci (MQTL) for abiotic stress tolerance in rice, as well as the molecular markers and potential candidate genes of the MQTL regions. We summarized 2785 rice QTL and conducted a meta-analysis of 159 studies. We found 82 drought tolerance (DT), 70 cold tolerance (CT), 70 salt tolerance (ST), and 51 heavy metal ion tolerance (IT) meta-QTL, as well as 20 DT, 11 CT, 22 ST, and 5 IT candidate genes in the MQTL interval. Thirty-one multiple-tolerance related MQTL regions, which were highly enriched, were also detected, and 13 candidate genes related to multiple-tolerance were obtained. In addition, the correlation between DT, CT, and ST was significant in the rice genome. Four candidate genes and four MM-QTL regions were detected simultaneously by GWAS and meta-analysis. The four candidate genes showed distinct genetic differentiation and substantial genetic distance between
indica
and
japonica
rice, and the four MM-QTL are potential intervals for mining abiotic stress-related candidate genes. The candidate genes identified in this study will not only be useful for marker-assisted selection and pyramiding but will also accelerate the fine mapping and cloning of the candidate genes associated with abiotic stress-tolerance mechanisms in rice.
Cold stress caused by low temperatures is an important factor restricting rice production. Identification of cold-tolerance genes that can stably express in cold environments is crucial for molecular ...rice breeding. In this study, we employed high-throughput quantitative trait locus sequencing (QTL-seq) analyses in a 460-individual F.sub.2:3 mapping population to identify major QTL genomic regions governing cold tolerance at the seedling stage in rice. A novel major QTL (qCTS6) controlling the survival rate (SR) under low-temperature conditions of 9degreesC/10 days was mapped on the 2.60-Mb interval on chromosome 6. Twenty-seven single-nucleotide polymorphism (SNP) markers were designed for the qCST6 region based on re-sequencing data, and local QTL mapping was conducted using traditional linkage analysis. Eventually, we mapped qCTS6 to a 96.6-kb region containing 13 annotated genes, of which seven predicted genes contained 13 non-synonymous SNP loci. Quantitative reverse transcription PCR analysis revealed that only Os06g0719500, an OsbZIP54 transcription factor, was strongly induced by cold stress. Haplotype analysis confirmed that +376 bp (T>A) in the OsbZIP54 coding region played a key role in regulating cold tolerance in rice. We identified OsbZIP54 as a novel regulatory gene associated with rice cold-responsive traits, with its Dongfu-104 allele showing specific cold-induction expression serving as an important molecular variation for rice improvement. This result is expected to further exploration of the genetic mechanism of rice cold tolerance at the seedling stage and improve cold tolerance in rice varieties by marker-assisted selection.
Background
Salinity-alkalinity stress is one of the major factors limiting rice production. The damage caused by alkaline salt stress to rice growth is more severe than that caused by neutral salt ...stress. At present, the genetic resources (quantitative trait loci (QTLs) and genes) that can be used by rice breeders to improve alkalinity tolerance are limited. Here, we assessed the alkalinity tolerance of rice at the seedling stage and performed a genome-wide association study (GWAS) based on genotypic data including 788,396 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 295
japonica
rice varieties.
Results
We used the score of alkalinity tolerance (SAT), the concentrations of Na
+
and K
+
in the shoots (SNC and SKC, respectively) and the Na
+
/K
+
ratio of shoots (SNK) as indices to assess alkalinity tolerance at the seedling stage in rice. Based on population structure analysis, the
japonica
rice panel was divided into three subgroups. Linkage disequilibrium (LD) analysis showed that LD decay occurred at 109.77 kb for the whole genome and varied between 13.79 kb and 415.77 kb across the 12 chromosomes, at which point the pairwise squared correlation coefficient (
r
2
) decreased to half of its maximum value. A total of eight QTLs significantly associated with the SAT, SNC and SNK were identified by genome-wide association mapping. A common QTL associated with the SAT, SNC and SNK on chromosome 3 at the position of 15.0 Mb, which explaining 13.36~13.64% of phenotypic variation, was selected for further analysis. The candidate genes were filtered based on LD decay, Gene Ontology (GO) enrichment, RNA sequencing data, and quantitative real-time PCR (qRT-PCR) analysis. Moreover, sequence analysis revealed one 7-bp insertion/deletion (indel) difference in
LOC_Os03g26210
(
OsIRO3
) between the alkalinity-tolerant and alkalinity-sensitive rice varieties.
OsIRO3
encodes a bHLH-type transcription factor and has been shown to be a negative regulator of the Fe-deficiency response in rice.
Conclusion
Based on these results,
OsIRO3
maybe a novel functional gene associated with alkalinity tolerance in
japonica
rice. This study provides resources for improving alkalinity tolerance in rice, and the functional molecular marker could be verified to breed new rice varieties with alkalinity tolerance via marker-assisted selection (MAS).
PDF
