Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage

Cold tolerance at the bud burst stage (CTB) is a key trait for direct-seeded rice. Although quantitative trait loci (QTL) affecting CTB in rice have been mapped using traditional linkage mapping and genome-wide association study (GWAS) methods, the underlying genes remain unknown. In this study, we evaluated the CTB phenotype of 339 cultivars in the Rice Diversity Panel II (RDP II) collection. GWAS identified four QTLs associated with CTB (qCTBs), distributed on chromosomes 1–3. Among them, qCTB-1-1 overlaps with Osa-miR319b, a known cold tolerance micro RNA gene. The other three qCTBs have not been reported. In addition, we characterised the candidate gene OsRab11C1 for qCTB-1-2 that encodes a Rab protein belonging to the small GTP-binding protein family. Overexpression of OsRab11C1 significantly reduced CTB, while gene knockout elevated CTB as well as cold tolerance at the seedling stage, suggesting that OsRab11C1 negatively regulates rice cold tolerance. Molecular analysis revealed that OsRab11C1 modulates cold tolerance by suppressing the abscisic acid signalling pathway and proline biosynthesis. Using RDP II and GWAS, we identified four qCTBs that are involved in CTB and determined the function of the candidate gene OsRab11C1 in cold tolerance. Our results demonstrate that OsRab11C1 is a negative regulator of cold tolerance and knocking out of the gene by genome-editing may provide enhanced cold tolerance in rice. Supplementary Information The online version contains supplementary material available at 10.1186/s12284-021-00538-0.


Background
Rice (Oryza sativa L.), a major food resource for humans, grows in tropical to temperate regions worldwide. Cold stress is one of the environmental restrictions that most strongly influences rice growth and development, especially at the early seedling and reproductive stages (Liu et al. 2018). At the early seedling stage, low temperature leads to reduced germination, weak seedling establishment, and subsequent yield loss (Yang et al. 2020a). Direct-seeded rice (DSR), a labour-saving and efficient method, has been adopted in many rice growing areas. However, cold stress at the germination and bud burst stages is a major limitation for DSR due to high sensitivity to cold at these stages (Yang et al. 2020b). Improving low-temperature germinability (LTG) and cold tolerance at the bud burst stage (CTB) in rice is the most economical and effective solution to this problem.
Both LTG and CTB are complex genetic traits controlled by multi-genes or quantitative trait loci (QTL). Traditional linkage mapping and genome-wide association study (GWAS) approaches have identified more than 60 LTG-related QTLs and 40 CTB-associated QTLs (Liu et al. 2018;Yang et al. 2020a). To date, only qLTG3-1 and Wang et al. Rice (2021) 14:98 OsSAP16 have been cloned and functionally characterised from two identified QTLs for LTG in rice (Fujino et al. 2008;Wang et al. 2018). The QTL gene qLTG3-1, encoding a protein of unknown function, is conserved in many plants and is highly expressed in the embryo, which may accelerate vacuolation to weaken tissues covering the embryo, and promote seed germination (Fujino et al. 2008). The rice zinc finger domain protein OsSAP16 (Stress-Associated Protein 16) is the causal gene of the QTL qLVG7-2 ; loss of OsSAP16 function reduces germination, while overexpression enhances germination under low temperature.
Previous studies suggest that small GTP-binding proteins (G-proteins) may be involved in the pathway regulating cold tolerance in rice (Nahm et al. 2003;Chen et al. 2011;Xu and Cai 2014). The Rab-type small G-protein OsRAB7 functions in response to cold stress by altering expression in rice (Nahm et al. 2003). Ran-type small G-proteins OsRNA1 and OsRNA2 promote the assembly of the nuclear envelope to avoid damage from cold stress (Chen et al. 2011;Liu et al. 2018). The cloned COLD1 gene confers chilling tolerance in japonica rice at the seedling stage and encodes a plasma membrane-localised regulator of G-protein signalling (Ma et al. 2015).
Due to the availability of high-density single-nucleotide polymorphism (SNP) maps and diverse rice germplasm resources, GWAS has become an established strategy for efficient and high-throughput gene identification in rice . Based on Rice Diversity Panel I (RDP I, consisting of 413 cultivars collected from 82 countries), GWAS has been performed on various rice traits (Zhao et al. 2011;Kang et al. 2016;Wang et al. 2018). Our previous GWAS results based on RDP I revealed 67 cold tolerance QTLs at the young seedling stage, and a novel candidate cold resistant gene, Osryh1, was identified ). More recently, RDP II has been developed, providing a higher-density dataset of 700K SNPs, and this has been applied to investigate disease resistance (rice blast and rice black-streaked dwarf virus disease) and agronomic characters (tillering) using GWAS Feng et al. 2019;Jiang et al. 2019;Liu et al. 2020). Therefore, GWAS using high-density SNPs within the RDP II population holds promise for dissecting the genetic architecture of a variety of complex traits in rice.
As yet, no causal genes for QTLs of CTB (qCTBs) have been identified, hence the genetic basis and underlying molecular mechanism remain poorly understood. In the present study, we performed GWAS using the 339 RDP II cultivars  to investigate CTB in rice. We identified four qCTBs strongly associated with CTB variation, distributed on chromosomes 1-3. Among them, qCTB-1-1 overlaps with the microRNA gene Osa-miR319b that has a known function in cold tolerance. The other three qCTBs have not been reported.
In addition, we characterised the candidate gene OsRab11C1 for qCTB-1-2 (Pitakrattananukool et al. 2012), a Rab-type G-protein that is highly conserved in partially tolerant rice cultivars. Overexpression of OsRab11C1 significantly reduced CTB, while gene knockout elevated CTB as well as cold tolerance at the seedling stage. These results provide new insight into G-protein function in the CTB pathway, and a candiate gene for engineering cold tolerant rice cultivars via genome editing.

GWAS of qCTBs
To map the QTLs corresponding to qCTBs, we performed GWAS using the CTB phenotypes and the highdensity SNP datasets of the 339 rice cultivars. Seventeen significantly associated SNPs [− Log 10 (p-value) ≥ 4.3] were detected ( Fig. 1C; Additional file 3: Table S3). Any locus bracketed by two significantly associated SNPs within a 200 kb interval region was considered a qCTB.
The analysis identified four qCTBs in the rice genome (Additional file 4: Table S4). To identify candidate genes, we analysed a 200 kb genomic region of the Nipponbare (NPB) reference genome for each qCTB and selected genes such as those known to be related to cold responses as candidates. A total of 138 candidate genes were predicted for the four qCTBs (Additional file 4: Table S4). Among them, qCTB-1-1 overlapped with Osa-miR319b ). The remaining three qCTBs were identified for the first time in this study.
To confirm the association between OsRab11C1 and qCTB-1-2, we constructed a linkage disequilibrium (LD) map for 200 kb region of OsRab11C1, which showed the SNP-1.27301128 (LOD = 0.08) locating in OsRab11C1 was not associated with qCTB-1-2 ( Fig. 2A). Next we sequenced OsRab11C1 in the genomic DNA of 10 highly cold-tolerant and 10 cold-sensitive cultivars. The results revealed seven mutations (deletions and insertions) in the promoter and coding regions of OsRab11C1 between cold-tolerant and cold-sensitive cultivars (Fig. 2B). The only SNP, at position 1241 bp in the second exon of OsRab11C1, changes the amino acid from alanine (A) in cold-tolerant cultivars to valine (V) in cold-sensitive cultivars, which may affect gene/protein function. These results implicated OsRab11C1 as a strong candidate gene for qCTB-1-2. . The x-axis shows survival rate and the y-axis represents the number of cultivars. B Rice cultivars numbers (left y-axis) of each subgroup (x-axis) used in the study, and the average survival rate (right y-axis) with error bars for each subgroup. C Manhattan plots of the association between SNPs and CTB phenotypes based on GWAS. The x-axis shows the genomic coordinates and the y-axis represents the LOD score for each SNP

OsRab11C1 Expression Pattern and Sub-cellular Localization
Next, we investigated the OsRab11C1 expression pattern under cold treatment. We performed a quantitative real-time PCR (qRT-PCR) assay using total RNA isolated from seedlings of cold-tolerant cultivar NPB and coldsensitive cultivar 896 ("JUMA" in the aus subgroup from Bangladesh) sampling at 0, 6, 12, 24, 48 and 72 h after 4 °C cold treatment. As shown in Fig. 3A, expression of OsRab11C1 was not altered significantly in NPB, but was strongly induced in 896. This result is consistent with that from genetic analysis showing that OsRab11C1 is a negative regulator of rice cold tolerance described below.
To investigate the tissue specificity of OsRab11C1 gene expression, we also probed the expression of OsRab11C1 in nine different tissues and found that OsRab11C1 was highly expressed in roots (Fig. 3B). According to the Gen-Script website (https:// www. gensc ript. com/ wolf-psort. html), OsRab11C1 was predicted to be mainly localized in the cytoplasm. To confirm this, we cloned the OsRab11C1 coding region from NPB into the pYBA1132-GFP (green fluorescent protein) vector and transfected the OsRab11C1-pYBA1132-GFP construct into rice protoplasts of NPB. The results show that OsRab11C1-GFP was co-localized with red fluorescent protein (RFP) in the entire rice cell (Fig. 3C).

OsRab11C1 Negatively Regulates Rice Cold Tolerance
To validate whether OsRab11C1 does indeed control rice cold tolerance, we knocked out OsRab11C1 (OsRab11C1-KO) in the NPB background using the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) gene editing system. The guide RNA (gRNA) is located at position 102-123 bp in the coding region of OsRab11C1. We sequenced the gRNA targeted region and selected two T 0 plants (CR-6 and CR-15) containing insertions and deletions in the target region for subsequent phenotype analysis (Fig. 4A). We also generated overexpression lines of OsRab11C1 (OsRab11C1-OE) under the control of the maize ubiquitin promoter in the NPB background. The relative expression level of OsRab11C1 in the two overexpression lines (OX-23 and OX-44) were 177-and 400-fold higher than that in NPB, respectively (Fig. 4B).
We used homozygous T 1 plants of CR-6, CR-15, OX-23 and OX-44 for cold tolerance evaluation. At the bud burst stage under cold stress, the growth of the knockout mutants CR-6 and CR-15 was better than that of wild-type (WT) NPB plants, but not statistically different ( Fig. 4C and 4D). By contrast, OX-23 and OX-44 overexpression plants grew quite slowly after cold treatment ( Fig. 4C and 4D). Interestingly, both CR-6 and CR-15 seedlings showed stronger cold tolerance than NPB and overexpression seedlings after cold treatment (Fig. 4E), and the seedling mortality of CR-6 and CR-15 was only ~ 30% compared with 60-70% for NPB, OX-23 and OX-44 (Fig. 4F). These results indicate that OsRab11C1 negatively regulates cold tolerance in rice.

Suppression of Abscisic Acid (ABA) Signalling and Proline Biosynthesis Pathways by OsRab11C1
To further explore the mechanism of OsRab11C1-mediated cold responses, we measured the expression levels of three marker genes (OsPYL3, OsABF2 and OsPPC09) in OsRab11C1-OE and knockout mutants, and WT plants, using qRT-PCR. These genes are critical for ABA signal transduction under cold stress (Hossain et al. 2010;Chen et al. 2014;Tian et al. 2015). The results showed that the relative expression levels of OsPYL3, OsABF2 and OsPPC09 in OsRab11C1-OE plants were significantly down-regulated, while they were up-regulated in OsRab11C1 mutant plants, compared with those in WT plants ( Fig. 5A-C), suggesting that OsRab11C1 negatively regulates cold responses by suppressing the ABA signalling pathway in rice.
We also measured the levels of proline, a molecule that protects plants against cellar damage. As shown in Fig. 5D, the average proline content in 2-week-old seedlings of WT, mutant CR-6 and OX-23 plants under normal growth conditions (25 °C) were 63.20, 51.87 and 51.53 μg/ml, respectively. After 4 °C cold treatment, the average proline content in CR-6 plants was increased to 101.34 μg/ml, significantly higher than in WT plants (84.80 μg/ml). By contrast, the average proline content in OX-23 plants was decreased to 40.43 μg/ml, much lower than in WT plants. These results suggest that OsRab11C1 also negatively regulates proline biosynthesis in rice.

Discussion
As climate change advances, cold stress at the seedling stage is becoming a major challenge for both indica and japonica rice production in many countries. To save labour and reduce cost, direct seeding is replacing traditional puddle transplanting in small farms. However, the low germination rate and slow seedling growth of most modern rice cultivars severely hinders the wide application of this technique in Asia and Africa. One of the reasons is the lack of availability of rice varieties for direct seedling with strong cold tolerance. In this study, we identified 40 highly tolerant varieties from all subgroups in RDP II exhibiting at least 90% survival rate under cold treatment at the bud burst stage. Among the 16 varieties with 100% survival rate, most (10) are from Asian countries such as Bangladesh and the Philippines, and four are from South American countries including Brazil and Columbia. These varieties can be directly used as parental lines in genetic crosses in local breeding programs. Therefore, our study has provided valuable cold tolerance materials for both indica and japonica rice breeding programs.
Among the four qCTBs identified in this study, qCTB-1-1 is co-localised with known cold tolerance gene Osa-miR319b . The other three qCTBs are newly discovered cold tolerance QTLs. These loci are candidates for further genetic analysis to determine their roles in rice cold tolerance. In addition, DNA markers could be developed from these loci for molecular breeding programs.
We genetically characterised the Rab small G-protein gene OsRab11C1, which is the causal gene of qCTB-1-2 for rice cold tolerance. Previous research demonstrated that other small G-protein genes including OsRAN1, OsRAN2 and OsRYH1 regulated cold tolerance in rice (Chen et al. 2011;Xu and Cai 2014;Wang et al. 2016). Interestingly, unlike these genes that act as positive regulators for rice cold tolerance, OsRab11C1 plays a negative role for CTB, expanding the functions of GTPase-mediated cold tolerance in rice. Whether the function of OsRab11C1 in other plants is conserved remains to be investigated. In addition, it will be interesting to identify the regulator(s) of OsRab11C1 in cold signalling transduction. COLD1 interacts with the G-protein α subunit to activate the Ca 2+ channel to sense low temperature and accelerate G-protein GTPase activity (Ma et al. 2015;Zhu 2016). It remains to be determined if COLD1 can interact with OsRab11C1 in rice cells.

Relative expression
ABA is a key phytohormone and signalling molecule in response to cold stress in plants (Cutler et al. 2010;Zhu 2016;Liu et al. 2018). Several genes involved in ABA signal transduction, such as OsPYL3, OsABF2 and OsPP2C09, are important for plant cold tolerance (Hossain et al. 2010;Chen et al. 2014;Tian et al. 2015). Relationships between Rab proteins and ABA signalling have not been clearly demonstated. Herein, we found that the

Conclusions
Cold tolerance is one of the major challenges in rice production in many rice growing regions. From the RDP II population, we identified 40 highly tolerant rice cultivars with survival rate over 90% after cold treatment at the bud burst stage. Using the cold phenotypes of RPD II and GWAS, we identifyed four qCTBs. Among them, qCTB-1-1 ais co-localized with known cold-associated gene and the other three have not been reported..We further characterised the candidate gene OsRab11C1 for qCTB-1-2, which encodes a Rab-type small GTP-binding protein.
Overexpression of the gene significantly reduces CTB, while gene knockout elevates CTB as well as cold tolerance at the seedling stage. Molecular analysis indicates that OsRab11C1 modulates cold tolerance by suppressing the ABA signalling pathway. Our results demonstrate that OsRab11C1 negatively regulates rice cold tolerance and can be used for enhancing rice cold tolerance at the early stages via genome-editing or marker-aided selection.

Plant Materials
The 339  56 ARO, 64 AUS, and 7 ADM). The 700K SNP dataset of the 339 RDP II cultivars was generated from a previous study ).

Evaluation of CTB
The cold tolerance score was defined by the survival rate which is the percentage of rice seedlings survived from the bud stage to the seedling stage after cold treatment following the formula: cold tolerance (%) = number of seedlings/number of buds × 100) (Han et al. 2004). About 25 seeds of each cultivar were germinated in Petri dishes in an incubator at 37 °C for three days. The germinated seeds were then transferred into a growth chamber for one day at 25 °C with a relative humidity (RH) of 75% and a 14 h light and 10 h dark photoperiod. Germinated rice seeds were subjected to cold treatment at 4 °C with the same relative humidity and photoperiod for seven days.
After seven days of exposure to cold stress, the cold tolerance scores of the 339 rice cultivars were calculated. The experiment was repeated three times under the same environment, and the average cold tolerance scores from three replicates were used for GWAS.

GWAS of Rice Cold Tolerance at the Bud Burst Stage
Like our previous GWAS on rice blast, the 416,065 SNPs of 339 RDP II accessions were generated from the 700K SNP RDP II genotypes using P-link with the criterion of minor allele frequency ≥ 5%. GWAS was performed and Manhattan and Q-Q plots were generated. SNPs with − Log 10 (P-value) ≥ 4.3 − log 10 (1/M) = 4.3, (M = 416,065) were considered to be significant association ).

Identification of QTLs and Selection of Cold Tolerance Candidate Genes
QTLs were identified in the 200 kb interval regions using the Nipponbare genome as a reference. Candidate genes around the peak SNPs were selected, and all of the reported temperature-related genes in plants were assumed to be candidate genes .

Sequence Analysis of Genomic DNA from OsRab11C1
The full-length sequence, from − 2000 bp upstream of the 5'-untranslated region (UTR) to + 1000 bp downstream of the 3'-UTR of OsRab11C1, was downloaded from the Rice Genome Annotation Project website (http:// rice. plant biolo gy. msu. edu/ analy ses_ search_ blast. shtml). Gene-specific primers were designed for cloning OsRab11C1 from cultivars that were highly cold tolerant and highly cold sensitive. DNA sequencing of the cloned genes was performed by Sangon Biotech Company (Wuhan, China). Sequence alignment was performed with SeqMan (http:// seqman. softw are. infor mer. com/).
All primers used in the study are shown in Additional file 6: Table S6.

Gene Expression Analysis
For analysis of the expression pattern and tissue specificity of OsRab11C1, total RNA was extracted from root, coleoptile and leaf tissues collected from three seeds of each cultivars using an RNA extraction kit (Promega Biotech, http:// www. prome ga. com. cn). First-strand cDNA synthesis was performed using HiScript II QRT Super-Mix (Vazyme, http:// www. vazyme. com). Gene expression levels were calculated based on analysis of variance (ANOVA) of three technical replicates. The OsUbq gene (LOC_Os03g61970) was included as an internal control. Three independent replicates were performed. Genespecific primers for OsRab11C1 are shown in Additional file 6: Table S6.

Construction of Vectors and Genetic Transformation
The CRISPR/Cas9 vector system was provided by Dr. YG Liu's laboratory (South China Agriculture University, Guangzhou, China) (Li et al. 2017). The gene-specific targets were designed online (http:// skl. scau. edu. cn/ prime rdesi gn/) and the target mutation types were analysed on the website (http:// skl. scau. edu. cn/ dsdec ode/). CRISPR constructs were transformed into NPB using an agrobacterium-mediated transformation method (Liu et al. 2020). All transgenic plants and their progeny were examined by PCR amplification using specific primers targeting the gRNA region. All primer sequences for the constructs are listed in Additional file 6: Table S6.
To overexpress OsRab11C1, we used the overexpression vector pCAMBIA1300 described previously (He et al. 2018). The 1599 bp full-length coding sequence region was cloned using gene-specific primers from cDNA obtained by reverse transcription using mRNA from NPB seedlings. The resulting gene was cloned into the pCAMBIA1300 vector to generate the overexpression construct, which was transformed into Agrobacterium tumefaciens strain EHA105 and subsequently transformed into NPB. All transgenic plants and their progeny were examined by PCR amplification using specific primers.

Sub-cellular Localization of OsRab11C1
The overexpression construct OsRab11C1-pYBA1132-GFP was transfected into rice protoplasts of NPB following the method reported previously (He et al. 2018).

Determination of Cellular Proline Levels
Two-week-old seedlings (0.1 g) of NPB and OsRab11C1 transgenic rice lines (CR-6 and OX-23) with or without 4 °C cold treatment were homogenised in 2 ml of