Genetic analysis of cold tolerance at the germination and booting stages in rice by association mapping

Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding

Direct seeding is employed to circumvent the labor-intensive process of rice (Oryza sativa) transplantation, but this approach requires varieties with vigorous low-temperature germination (LTG) when sown in cold climates. To investigate the genetic basis of LTG, we identified the quantitative trait locus (QTL) qLTG11 from rice variety Arroz da Terra, which shows rapid seed germination at lower temperatures, using QTL-seq. We delineated the candidate region to a 52-kb interval containing GENERAL REGULATORY FACTOR14h (GF14h) gene, which is expressed during seed germination. The Arroz da Terra GF14h allele encodes functional GF14h, whereas Japanese rice variety Hitomebore harbors a 4-bp deletion in the coding region. Knocking out functional GF14h in a near-isogenic line (NIL) carrying the Arroz da Terra allele decreased LTG, whereas overexpressing functional GF14h in Hitomebore increased LTG, indicating that GF14h is the causal gene behind qLTG11. Analysis of numerous Japanese rice accessions revealed that the functional GF14h allele was lost from popular varieties during modern breeding. We generated a NIL in the Hitomebore background carrying a 172-kb genomic fragment from Arroz da Terra including GF14h. The NIL showed superior LTG compared to Hitomebore, with otherwise comparable agronomic traits. The functional GF14h allele from Arroz da Terra represents a valuable resource for direct seeding in cold regions.

Advances and opportunities in unraveling cold-tolerance mechanisms in the world's primary staple food crops

Temperatures below or above optimal growth conditions are among the major stressors affecting productivity, end-use quality, and distribution of key staple crops including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays L.). Among temperature stresses, cold stress induces cellular changes that cause oxidative stress and slowdown metabolism, limit growth, and ultimately reduce crop productivity. Perception of cold stress by plant cells leads to the activation of cold-responsive transcription factors and downstream genes, which ultimately impart cold tolerance. The response triggered in crops to cold stress includes gene expression/suppression, the accumulation of sugars upon chilling, and signaling molecules, among others. Much of the information on the effects of cold stress on perception, signal transduction, gene expression, and plant metabolism are available in the model plant Arabidopsis but somewhat lacking in major crops. Hence, a complete understanding of the molecular mechanisms by which staple crops respond to cold stress remain largely unknown. Here, we make an effort to elaborate on the molecular mechanisms employed in response to low-temperature stress. We summarize the effects of cold stress on the growth and development of these crops, the mechanism of cold perception, and the role of various sensors and transducers in cold signaling. We discuss the progress in cold tolerance research at the genome, transcriptome, proteome, and metabolome levels and highlight how these findings provide opportunities for designing cold-tolerant crops for the future.

Uncovering Novel QTLs and Candidate Genes for Salt Tolerance at the Bud Burst Stage in Rice through Genome-Wide Association Study

Salt stress is one of the most important factors limiting rice growth and yield increase. Salt tolerance of rice at the bud burst (STB) stage determines whether germinated seeds can grow normally under salt stress, which is very important for direct seeding. However, reports on quantitative trait loci (QTLs) and candidate genes for STB in rice are very limited. In this study, a natural population of 130 indica and 81 japonica rice accessions was used to identify STB-related QTLs and candidate genes using a genome-wide association study (GWAS). Nine QTLs, including five for relative shoot length (RSL), two for relative root length (RRL), and two for relative root number (RRN), were identified. Five of these STB-related QTLs are located at the same site as the characterized salt tolerance genes, such as OsMDH1, OsSRFP1, and OsCDPK7. However, an important QTL related to RSL, qRSL1-2, has not been previously identified and was detected on chromosome 1. The candidate region for qRSL1-2 was identified by linkage disequilibrium analysis, 18 genes were found to have altered expression levels under salt stress through the RNA-seq database, and 10 of them were found to be highly expressed in the shoot. It was also found that, eight candidate genes (LOC_Os01g62980, LOC_Os01g63190, LOC_Os01g63230, LOC_Os01g63280, LOC_Os01g63400, LOC_Os01g63460, and LOC_Os01g63580) for qRSL1-2 carry different haplotypes between indica and japonica rice, which exactly corresponds to the significant difference in RSL values between indica and japonica rice in this study. Most of the accessions with elite haplotypes were indica rice, which had higher RSL values. These genes with indica-japonica specific haplotypes were identified as candidate genes. Rice accessions with elite haplotypes could be used as important resources for direct seeding. This study also provides new insights into the genetic mechanism of STB.

Meta-QTL and ortho analysis unravels the genetic architecture and key candidate genes for cold tolerance at seedling stage in rice

Rice, a critical cereal crop, grapples with productivity challenges due to its inherent sensitivity to low temperatures, primarily during the seedling and booting stages. Recognizing the polygenic complexity of cold stress signaling in rice, a meta-analysis was undertaken, focusing on 20 physiological traits integral to cold tolerance. This initiative allowed the consolidation of genetic data from 242 QTLs into 58 meta-QTLs, thereby significantly constricting the genetic and physical intervals, with 84% of meta-QTLs (MQTLs) being reduced to less than 2 Mb. The list of 10,505 genes within these MQTLs, was further refined utilizing expression datasets to pinpoint 46 pivotal genes exhibiting noteworthy differential regulation during cold stress. The study underscored the presence of several TFs such as WRKY, NAC, CBF/DREB, MYB, and bHLH, known for their roles in cold stress response. Further, ortho-analysis involving maize, barley, and Arabidopsis identified OsWRKY71, among others, as a prospective candidate for enhancing cold tolerance in diverse crop plants. In conclusion, our study delineates the intricate genetic architecture underpinning cold tolerance in rice and propounds significant candidate genes, offering crucial insights for further research and breeding strategies focused on fortifying crops against cold stress, thereby bolstering global food resilience.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01412-1.

Genetic dissection of cold tolerance at the budding stage of rice in an indica-japonica recombination inbred line population

Rice is highly cold-sensitive, and thus, the promotion of cold resistance in buds is essential. In this study, we conducted a mapping analysis to identify quantitative trait loci (QTLs) associated with cold tolerance in buds. The analysis was performed using a recombinant inbred line (RIL) population consisting of 192 lines derived from the cold-tolerant strain 02428 and the cold-sensitive strain YZX. Seven additive loci on chromosomes 1, 4, 5, and 6 were identified, of which loci 3 and 7 were found in two crop seasons, indicating stability. Three epistatic interactions, one present over two seasons, were found. Loci 3 and 7 pyramided with two main-effect QTLs observed to control the rate of low-temperature germination in our previous study. Two materials with good cold resistance at the germination and bud stages were obtained, namely, G93 and G146. Transcriptome sequencing analysis of the two parent buds after cold treatment found that genes expressed differentially between the two parents were related to photosynthesis, energy metabolism, and reactive oxygen scavenging. Five candidate genes, namely, Os01g0385400, Os01g0388000, Os06g0287700, Os06g0289200, and Os06g0291100, were selected in the two stable intervals based on gene expression profiles and annotations. These genetic loci exhibit strong potential as targets for breeding cold tolerance in buds and require additional investigation. In conclusion, this work provides valuable genetic resources that can be utilized to improve the cold tolerance of rice.

QTL mapping and identification of candidate genes for cold tolerance at the germination stage in wild rice

BACKGROUND

Cold damage stress significantly affects rice growth (germination and seedling) and causes serious losses in yield in temperate and high-altitude areas around the globe.

OBJECTIVE

This study aimed to explore the cold tolerance (CT) locus of rice and create new cold-tolerant germplasm. We constructed a chromosome segment substitution line (CSSL) with strong CT and fine mapped quantitative trait loci (QTLs) associated with CT by performing the whole-genome resequencing of CSSL with phenotypes under cold treatment.

METHODS

A chromosome CSSL, including 271 lines from a cross between the cold-tolerant wild rice Y11 (Oryza rufipogon Griff.) and the cold-sensitive rice variety GH998, was developed to map QTLs conferring CT at the germination stage. The whole-genome resequencing was performed on CSSL for mapping QTLs of associated with CT at the germination stage.

RESULTS

A high-density linkage map of the CSSLs was developed using the whole-genome resequencing of 1484 bins. The QTL analysis using 615,466 single-nucleotide polymorphisms (SNPs) led to the identification of 2 QTLs related to germination rate at low-temperature on chromosome 8 (qCTG-8) and chromosome 11 (qCTG-11). The qCTG-8 and qCTG-11 explained 14.55% and 14.31% of the total phenotypic variation, respectively. We narrowed down qCTG-8 and qCTG-11 to 195.5 and 78.83-kb regions, respectively. The expression patterns of important candidate genes in different tissues, and of RNA-sequencing (RNA-seq) in CSSLs, were identified based on gene sequences in qCTG-8 and qCTG-11 cold-induced expression analysis. LOC_Os08g01120 and LOC_Os08g01390 were identified as candidate genes in qCTG-8, and LOC_Os11g32880 was identified as a candidate gene in qCTG-11.

CONCLUSIONS

This study demonstrated a general method that could be used to identify useful loci and genes in wild rice and aid in the future cloning of candidate genes of qCTG-8 and qCTG-11. The CSSLs with strong CT were supported for breeding cold-tolerant rice varieties.

Identification of a key locus, qNL3.1, associated with seed germination under salt stress via a genome-wide association study in rice

Two causal OsTTL and OsSAPK1 genes of the key locus qNL3.1 significantly associated with seed germination under salt stress were identified via a genome-wide association study, which could improve rice seed germination under salt stress. Rice is a salt-sensitive crop, and its seed germination determines subsequent seedling establishment and yields. In this study, 168 accessions were investigated for the genetic control of seed germination under salt stress based on the germination rate (GR), germination index (GI), time at which 50% germination was achieved (T₅₀) and mean level (ML). Extensive natural variation in seed germination was observed among accessions under salt stress. Correlation analysis showed significantly positive correlations among GR, GI and ML and a negative correlation with T₅₀ during seed germination under salt stress. Forty-nine loci significantly associated with seed germination under salt stress were identified, and seven of these were identified in both years. By comparison, 16 loci were colocated with the previous QTLs, and the remaining 33 loci might be novel. qNL3.1, colocated with qLTG-3, was simultaneously identified with the four indices in two years and might be a key locus for seed germination under salt stress. Analysis of candidate genes showed that two genes, the similar to transthyretin-like protein OsTTL and the serine/threonine protein kinase OsSAPK1, were the causal genes of qNL3.1. Germination tests indicated that both Osttl and Ossapk1 mutants significantly reduced seed germination under salt stress compared to the wild type. Haplotype analysis showed that Hap.1 of OsTTL and Hap.1 of OsSAPK1 genes were excellent alleles, and their combination resulted in high seed germination under salt stress. Eight accessions with elite performance of seed germination under salt stress were identified, which could improve rice seed germination under salt stress.

Identification of Rice Accessions Having Cold Tolerance at the Seedling Stage and Development of Novel Genotypic Assays for Predicting Cold Tolerance

Rice is susceptible to cold stress at the seedling stage, which can delay growth and decrease yield. We evaluated 187 rice accessions for cold tolerance at the seedling stage and developed genotypic assays for three markers. All japonica (20/20) and 20/140 indica accessions were highly cold tolerant. Two SNP markers specific for COLD1 and LOC_Os10g34840 were practical to use by normal agarose gel. The SNP marker specific for COLD1 was highly specific for predicting cold tolerance. However, the sensitivity of this marker was low as several cold-tolerant indica accessions lacked the cold-tolerant allele. The LOC_Os10g34840 marker was slightly more sensitive than the COLD1 marker for predicting highly cold-tolerant accessions. An insertion/deletion variant in the NAC6 gene was identified as a novel cold tolerance marker. The NAC6 marker predicted more highly cold-tolerant accessions compared with the other two markers. The SNP marker specific for LOC_Os10g34840 and the NAC6 marker were present in several tested subgroups, suggesting their wide effects and distribution. The three markers combined predicted the most highly cold-tolerant accessions, indicating that the marker combination is superior for applications such as marker-assisted breeding. The cold-tolerant accessions and the genotypic marker assays will be useful for future rice breeding.

Genome-Wide Association Mapping Identifies New Candidate Genes for Cold Stress and Chilling Acclimation at Seedling Stage in Rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a chilling-sensitive staple food crop, and thus, low temperature significantly affects rice growth and yield. Many studies have focused on the cold shock of rice although chilling acclimation is more likely to happen in the field. In this paper, a genome-wide association study (GWAS) was used to identify the genes that participated in cold stress and chilling accumulation. A total of 235 significantly associated single-nucleotide polymorphisms (SNPs) were identified. Among them, we detected 120 and 88 SNPs for the relative shoot fresh weight under cold stress and chilling acclimation, respectively. Furthermore, 11 and 12 quantitative trait loci (QTLs) were identified for cold stress and chilling acclimation, respectively, by integrating the co-localized SNPs. Interestingly, we identified 10 and 15 candidate genes in 11 and 12 QTLs involved in cold stress and chilling acclimation, respectively, and two new candidate genes (LOC_Os01g62410, LOC_Os12g24490) were obviously up-regulated under chilling acclimation. Furthermore, OsMYB3R-2 (LOC_Os01g62410) that encodes a R1R2R3 MYB gene was associated with cold tolerance, while a new C3HC4-type zinc finger protein-encoding gene LOC_Os12g24490 was found to function as a putative E3 ubiquitin-protein ligase in rice. Moreover, haplotype, distribution, and Wright’s fixation index (FST) of both genes showed that haplotype 3 of LOC_Os12g24490 is more stable in chilling acclimation, and the SNP (A > T) showed a difference in latitudinal distribution. FST analysis of SNPs in OsMYB3R-2 (LOC_Os01g62410) and LOC_Os12g24490 indicated that several SNPs were under selection in rice indica and japonica subspecies. This study provided new candidate genes in genetic improvement of chilling acclimation response in rice.

Global identification of quantitative trait loci and candidate genes for cold stress and chilling acclimation in rice through GWAS and RNA-seq

Associated analysis of GWAS with RNA-seq had detected candidate genes responsible for cold stress and chilling acclimation in rice. Haplotypes of two candidate genes and geographic distribution were analyzed. To explore new candidate genes and genetic resources for cold tolerance improvement in rice, genome-wide association study (GWAS) mapping experiments with 351 rice core germplasms was performed for three traits (survival rate, shoot length and chlorophyll content) under three temperature conditions (normal temperature, cold stress and chilling acclimation), yielding a total of 134 QTLs, of which 54, 59 and 21 QTLs were responsible for normal temperature, cold stress and chilling acclimation conditions, respectively. Integrated analysis of significant SNPs in 134 QTLs further identified 116 QTLs for three temperature treatments, 53, 43 and 18 QTLs responsible for normal temperature, cold stress and chilling acclimation, respectively, and 2 QTLs were responsible for both cold stress and chilling acclimation. Matching differentially expressed genes from RNA-seq to 43 and 18 QTLs for cold stress and chilling acclimation, we identified 69 and 44 trait-associated candidate genes, respectively, to be classified into six and five groups, particularly involved in metabolisms, reactive oxygen species scavenging and hormone signaling. Interestingly, two candidate genes LOC_Os01g04814, encoding a vacuolar protein sorting-associating protein 4B, and LOC_Os01g48440, encoding glycosyltransferase family 43 protein, showed the highest expression levels under chilling acclimation. Haplotype analysis revealed that both genes had a distinctive differentiation with subpopulation. Haplotypes of both genes with more japonica accessions have higher latitude distribution and higher chilling tolerance than the chilling sensitive indica accessions. These findings reveal the new insight into the molecular mechanism and candidate genes for cold stress and chilling acclimation in rice.

Cold-adaptive evolution at the reproductive stage in Geng/japonica subspecies reveals the role of OsMAPK3 and OsLEA9

Cold stress at the reproductive stage severely affects the production and geographic distribution of rice. The Geng/japonica subpopulation gradually developed stronger cold adaptation than the Xian/indica subpopulation during the long-term domestication of cultivated rice. However, the evolutionary path and natural alleles underlying the cold adaptability of intra-Geng subspecies remain largely unknown. Here, we identified MITOGEN-ACTIVATED PROTEIN KINASE 3 (OsMAPK3) and LATE EMBRYOGENESIS ABUNDANT PROTEIN 9 (OsLEA9) as two important regulators for the cold adaptation of Geng subspecies from a combination of transcriptome analysis and genome-wide association study. Transgenic validation showed that OsMAPK3 and OsLEA9 confer cold tolerance at the reproductive stage. Selection and evolution analysis suggested that the Geng version of OsMAPK3 (OsMAPK3^Geng ) directly evolved from Chinese Oryza rufipogon III and was largely retained in high-latitude and high-altitude regions with low temperatures during domestication. Later, the functional nucleotide polymorphism (FNP-776) in the Kunmingxiaobaigu and Lijiangxiaoheigu version of the OsLEA9 (OsLEA9^KL ) promoter originated from novel variation of intra-Geng was selected and predominantly retained in temperate Geng to improve the adaptation of Geng together with OsMAPK3^Geng to colder climatic conditions in high-latitude areas. Breeding potential analysis suggested that pyramiding of OsMAPK3^Geng and OsLEA9^KL enhanced the cold tolerance of Geng and promotes the expansion of cultivated rice to colder regions. This study not only highlights the evolutionary path taken by the cold-adaptive differentiation of intra-Geng, but also provides new genetic resources for rice molecular breeding in low-temperature areas.

Phenotypic and Molecular Characterization of Rice Genotypes’ Tolerance to Cold Stress at the Seedling Stage

Rice plants are affected by low-temperature stress during germination, vegetative growth, and reproductive stages. Thirty-nine rice genotypes including 36 near-isogenic lines (NILs) of BRRI dhan29 were evaluated to investigate the level of cold tolerance under artificially induced low temperature at the seedling stage. Three cold-related traits, leaf discolouration (LD), survivability, and recovery rate, were measured to determine the level of cold tolerance. Highly significant variation among the genotypes was observed for LD, survivability, and recovery rate. Three NILs, IR90688-74-1-1-1-1-1, IR90688-81-1-1-1-1-1, and IR90688-103-1-1-1-1-1, showed tolerance in all three traits, while IR90688-118-1-1-1-1-1 showed cold tolerance with LD and recovery rate. IR90688-92-1-1-1-1-1, IR90688-125-1-1-1-1-1, IR90688-104-1-1-1-1-1, IR90688-124-1-1-1-1-P2, IR90688-15-1-1-1-1-1, and IR90688-27-1-1-1-1-1 showed significantly higher yield coupled with short growth duration and good grain quality. Genetic analysis with SSRs markers revealed that the high-yielding NILs were genetically 67% similar to BRRI dhan28 and possessed cold tolerance at the seedling stage. These cold-tolerant NILs could be used as potential resources to broaden the genetic base of the breeding germplasm to develop high-yielding cold-tolerant rice varieties.

Long-Term Dynamic of Cold Stress during Heading and Flowering Stage and Its Effects on Rice Growth in China

Short episodes of low-temperature stress during reproductive stages can cause significant crop yield losses, but our understanding of the dynamics of extreme cold events and their impact on rice growth and yield in the past and present climate remains limited. In this study, by analyzing historical climate, phenology and yield component data, the spatial and temporal variability of cold stress during the rice heading and flowering stages and its impact on rice growth and yield in China was characterized. The results showed that cold stress was unevenly distributed throughout the study region, with the most severe events observed in the Yunnan Plateau with altitudes higher than 1800 m. With the increasing temperature, a significant decreasing trend in cold stress was observed across most of the three ecoregions after the 1970s. However, the phenological-shift effects with the prolonged growing period during the heading and flowering stages have slowed down the cold stress decreasing trend and led to an underestimation of the magnitude of cold stress events. Meanwhile, cold stress during heading and flowering will still be a potential threat to rice production. The cold stress-induced yield loss is related to both the intensification of extreme cold stress and the contribution of related components to yield in the three regions.

Chilling tolerance in rice: Past and present

Rice is generally sensitive to chilling stress, which seriously affects growth and yield. Since early in the last century, considerable efforts have been made to understand the physiological and molecular mechanisms underlying the response to chilling stress and improve rice chilling tolerance. Here, we review the research trends and advances in this field. The phenotypic and biochemical changes caused by cold stress and the physiological explanations are briefly summarized. Using published data from the past 20 years, we reviewed the past progress and important techniques in the identification of quantitative trait loci (QTL), novel genes, and cellular pathways involved in rice chilling tolerance. The advent of novel technologies has significantly advanced studies of cold tolerance, and the characterization of QTLs, key genes, and molecular modules have sped up molecular design breeding for cold tolerance in rice varieties. In addition to gene function studies based on overexpression or artificially generated mutants, elucidating natural allelic variation in specific backgrounds is emerging as a novel approach for the study of cold tolerance in rice, and the superior alleles identified using this approach can directly facilitate breeding.

NILs of Cold Tolerant Japonica Cultivar Exhibited New QTLs for Mineral Elements in Rice

Chilling stress at booting stage can cause floret deterioration and sterility by limiting the supply of food chain and the accumulation of essential mineral elements resulting in reduction of yield and grain quality attributes in rice. Genomic selection of chilling tolerant rice with reference to the accumulation of mineral elements will have great potential to cope with malnutrition and food security in times of climate change. Therefore, a study was conducted to explore the genomic determinants of cold tolerance and mineral elements content in near-isogenic lines (NILs) of japonica rice subjected to chilling stress at flowering stage. Detailed morphological analysis followed by quantitative analysis of 17 mineral elements revealed that the content of phosphorus (P, 3,253 mg/kg) and potassium (K, 2,485 mg/kg) were highest while strontium (Sr, 0.26 mg/kg) and boron (B, 0.34 mg/kg) were lowest among the mineral elements. The correlation analysis revealed extremely positive correlation of phosphorus (P) and copper (Cu) with most of the cold tolerance traits. Among all the effective ear and the second leaf length correlation was significant with half of the mineral elements. As a result of comparative analysis, some QTLs (qBRCC-1, qBRCIC-2, qBRZC-6, qBRCHC-6, qBRMC-6, qBRCIC-6a, qBRCIC-6b, qBRCHC-6, and qBRMC-6) identified for calcium (Ca), zinc (Zn), chromium (Cr) and magnesium (Mg) on chromosome number 1, 2, and 6 while, a novel QTL (qBCPC-1) was identified on chromosome number 1 for P element only. These findings provided bases for the identification of candidate genes involved in mineral accumulation and cold tolerance in rice at booting stage.

Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS

BACKGROUND

Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there have been limited studies focusing on cold tolerance at the bud burst stage; therefore, considerable attention should be given to the genetic basis of cold tolerance at this stage.

RESULTS

In this study, a natural population consisting of 211 rice landraces collected from 15 provinces in China and other countries was used for the first time to evaluate cold tolerance at the bud burst stage. Population structure analysis showed that this population was divided into two groups and was rich in genetic diversity. Our evaluation results confirmed that japonica rice was more tolerant to cold at the bud burst stage than indica rice. A genome-wide association study (GWAS) was performed with the phenotypic data of 211 rice landraces and a 36,727 SNP dataset under a mixed linear model. Twelve QTLs (P < 0.0001) were identified for the seedling survival rate (SR) after treatment at 4 °C, in which there were five QTLs (qSR2-2, qSR3-1, qSR3-2, qSR3-3 and qSR9) that were colocalized with those from previous studies and seven QTLs (qSR2-1, qSR3-4, qSR3-5, qSR3-6, qSR3-7, qSR4 and qSR7) that were reported for the first time. Among these QTLs, qSR9, harboring the most significant SNP, explained the most phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were identified as candidates for qSR9.

CONCLUSION

This natural population consisting of 211 rice landraces combined with high-density SNPs will serve as a better choice for identifying rice QTLs/genes in the future, and the detected QTLs associated with cold tolerance at the bud burst stage in rice will be conducive to further mining favorable genes and breeding rice varieties under cold stress.

Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.)

Background

Rice (Oryza sativa L.) is a food crop for humans worldwide. However, temperature has an effect during the vegetative and reproductive stages. In high-latitude regions where rice is cultivated, cold stress is a major cause of yield loss and plant death. Research has identified a group of plant-specific transcription factors, DNA binding with one zinc fingers (DOFs), with a diverse range of functions, including stress signaling and stress response during plant growth. The aim of this study was to identify Dof genes in two rice subspecies, indica and japonica, and screen for Dof genes that may be involved in cold tolerance during plant growth.

Results

A total of 30 rice Dofs (OsDofs) were identified using bioinformatics and genome-wide analyses and phylogenetically analyzed. The 30 OsDOFs were classified into six subfamilies, and 24 motifs were identified based on protein sequence alignment. The chromosome locations of OsDofs were determined and nine gene duplication events were identified. A joint phylogenetic analysis was performed on DOF protein sequences obtained from four monocotyledon species to examine the evolutionary relationship of DOF proteins. Expression profiling of OsDofs from two japonica cultivars (Longdao5, which is cold-tolerant, and Longjing11, which is cold-sensitive) revealed that OsDof1 and OsDof19 are cold-inducible genes. We examined the seed setting rates in OsDof1- and OsDof19-overexpression and RNAi lines and found that OsDof1 showed a response to cold stress.

Conclusions

Our investigation identified OsDof1 as a potential target for genetic breeding of rice with enhanced cold tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08104-0.

Stepwise selection of natural variations at CTB2 and CTB4a improves cold adaptation during domestication of japonica rice

The improvement of cold adaptation has contributed to the increased growing area of rice. Standing variation and de novo mutation are distinct natural sources of beneficial alleles in plant adaptation. However, the genetic mechanisms and evolutionary patterns underlying these sources in a single population during crop domestication remain elusive. Here we cloned the CTB2 gene, encoding a UDP-glucose sterol glucosyltransferase, for cold tolerance in rice at the booting stage. A single standing variation (I408V) in the conserved UDPGT domain of CTB2 originated from Chinese Oryza rufipogon and contributed to the cold adaptation of Oryza sativa ssp. japonica. CTB2 is located in a 56.8 kb region, including the previously reported gene CTB4a in which de novo mutation arose c. 3200 yr BP in Yunnan province, China, conferring cold tolerance. Standing variation of CTB2 and de novo mutation of CTB4a underwent stepwise selection to facilitate cold adaptation to expand rice cultivation from high-altitude to high-latitude regions. These results provide an example of stepwise selection on two kinds of variation and describe a new molecular mechanism of cold adaptation in japonica rice.

Population genetic structure and association mapping for iron toxicity tolerance in rice

Iron (Fe) toxicity is a major abiotic stress which severely reduces rice yield in many countries of the world. Genetic variation for this stress tolerance exists in rice germplasms. Mapping of gene(s)/QTL controlling the stress tolerance and transfer of the traits into high yielding rice varieties are essential for improvement against the stress. A panel population of 119 genotypes from 352 germplasm lines was constituted for detecting the candidate gene(s)/QTL through association mapping. STRUCTURE, GenAlEx and Darwin softwares were used to classify the population. The marker-trait association was detected by considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) analyses. Wide genetic variation was observed among the genotypes present in the panel population for the stress tolerance. Linkage disequilibrium was detected in the population for iron toxicity tolerance. The population was categorized into three genetic structure groups. Marker-trait association study considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) showed significant association of leaf browning index (LBI) with markers RM471, RM3, RM590 and RM243. Three novel QTL controlling Fe-toxicity tolerance were detected and designated as qFeTox4.3, qFeTox6.1 and qFeTox10.1. A QTL reported earlier in the marker interval of C955-C885 on chromosome 1 is validated using this panel population. The present study showed that QTL controlling Fe-toxicity tolerance to be co-localized with the QTL for Fe-biofortification of rice grain indicating involvement of common pathway for Fe toxicity tolerance and Fe content in rice grain. Fe-toxicity tolerance QTL qFeTox6.1 was co-localized with grain Fe-biofortification QTLs qFe6.1 and qFe6.2 on chromosome 6, whereas qFeTox10.1 was co-localized with qFe10.1 on chromosome 10. The Fe-toxicity tolerance QTL detected from this mapping study will be useful in marker-assisted breeding programs.

Advances in the Identification of Quantitative Trait Loci and Genes Involved in Seed Vigor in Rice

Seed vigor is a complex trait, including the seed germination, seedling emergence, and growth, as well as seed storability and stress tolerance, which is important for direct seeding in rice. Seed vigor is established during seed development, and its level is decreased during seed storage. Seed vigor is influenced by genetic and environmental factors during seed development, storage, and germination stages. A lot of factors, such as nutrient reserves, seed dying, seed dormancy, seed deterioration, stress conditions, and seed treatments, will influence seed vigor during seed development to germination stages. This review highlights the current advances on the identification of quantitative trait loci (QTLs) and regulatory genes involved in seed vigor at seed development, storage, and germination stages in rice. These identified QTLs and regulatory genes will contribute to the improvement of seed vigor by breeding, biotechnological, and treatment approaches.

Genetic architecture to cause dynamic change in tiller and panicle numbers revealed by genome-wide association study and transcriptome profile in rice

Panicle number (PN) is one of the three yield components in rice. As one of the most unstable traits, the dynamic change in tiller number (DCTN) may determine the final PN. However, the genetic basis of DCTN and its relationship with PN remain unclear. Here, 377 deeply re-sequenced rice accessions were used to perform genome-wide association studies (GWAS) for tiller/PN. It was found that the DCTN pattern rather than maximum tiller number or effective tiller ratio is the determinant factor of high PN. The DCTN pattern that affords more panicles exhibits a period of stable tillering peak between 30 and 45 days after transplant (called DT30 and DT45, respectively), which was believed as an ideal pattern contributing to the steady transition from tiller development to panicle development (ST-TtP). Consistently, quantitative trait loci (QTL) expressed near DT30-DT45 were especially critical to the rice DCTN and in supporting the ST-TtP. The spatio-temporal expression analysis showed that the expression pattern of keeping relatively high expression in root at 24:00 (R24-P2) from about DT30 to DT45 is a typical expression pattern of cloned tiller genes, and the candidate genes with R24-P2 can facilitate the prediction of PN. Moreover, gene OsSAUR27 was identified by an integrated approach combining GWAS, bi-parental QTL mapping and transcription. These findings related to the genetic basis underlying the DCTN will provide the genetic theory in making appropriate decisions on field management, and in developing new varieties with high PN and ideal dynamic plant architecture.

The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice (Oryza sativa L.)

BACKGROUND

Direct seeding is an efficient cultivation technique in rice. However, poor low temperature germinability (LTG) of modern rice cultivars limits its application. Identifying the genes associated with LTG and performing molecular breeding is the fundamental way to address this issue. However, few LTG QTLs have been fine mapped and cloned so far.

RESULTS

In the present study, the LTG evaluation of 375 rice accessions selected from the Rice Diversity Panel 2 showed that there were large LTG variations within the population, and the LTG of Indica group was significantly higher than that of Japonica and Aus groups (p < 0.01). In total, eleven QTLs for LTG were identified through genome-wide association study (GWAS). Among them, qLTG_sRDP2-3/qLTG_JAP-3, qLTG_AUS-3 and qLTG_sRDP2-12 are first reported in the present study. The QTL on chromosome 10, qLTG_sRDP2-10a had the largest contribution to LTG variations in 375 rice accessions, and was further validated using single segment substitution line (SSSL). The presence of qLTG_sRDP2-10a could result in 59.8% increase in LTG under 15 °C low temperature. The expression analysis of the genes within qLTG_sRDP2-10a region indicated that LOC_Os10g22520 and LOC_Os10g22484 exhibited differential expression between the high and low LTG lines. Further sequence comparisons revealed that there were insertion and deletion sequence differences in the promoter and intron region of LOC_Os10g22520, and an about 6 kb variation at the 3' end of LOC_Os10g22484 between the high and low LTG lines, suggesting that the sequence variations of the two genes could be the cause for their differential expression in high and low LTG lines.

CONCLUSION

Among the 11 QTLs identified in this study, qLTG_sRDP2-10a could also be detected in other three studies using different germplasm under different cold environments. Its large effect and stable expression make qLTG_sRDP2-10a particularly valuable in rice breeding. The two genes, LOC_Os10g22484 and LOC_Os10g22520, were considered as the candidate genes underlying qLTG_sRDP2-10a. Our results suggest that integrating GWAS and SSSL can facilitate identification of QTL for complex traits in rice. The identification of qLTG_sRDP2-10a and its candidate genes provide a promising source for gene cloning of LTG and molecular breeding for LTG in rice.

Association of molecular markers with physio-biochemical traits related to seed vigour in rice

Eighteen physio-biochemical traits influencing seed vigour were studied for their association with molecular markers using a mini core set constituted from 120 germplasm lines. High genetic variation was detected in the parameters namely chlrophyll a, Chlrophyll b, total chlorophyll, carotenoids, total anthocyanin content, gamma-oryzanols, total phenolics content, superoxide dismutase, catalase, guaicol peroxidase, total soluble sugar, total protein, seed vigour index -I and seed vigour index -II. Strong positive correlation of seed vigour index II was observed with amylose content, total anthocyanin content, catalase, total phenolic content and total flavonoid content while a negative association was observed for gamma-oryzanol content. High gene diversity (0.7169) and informative markers value (0.6789) were estimated from the investigation. Three genetic structure groups were observed in the panel population and genotypes were grouped in the subpopulations based on the seed vigour trait. Differences in the fixation indices of the three sub populations indicated existence of linkage disequilibrium in the studied panel population. Association of the traits namely total flavonoids, superoxide dismutase, catalase, chlorophyll a, Chlorophyll b, total chlorophyll, carotenoids, starch, amylose, total anthocyanin, gamma-oryzanol, total phenolics with the molecular markers were detected by Generalized Linear Model and Mixed Linear Model showing > 0.10 R² value. Association of the trait, total flavonoids with marker RM7364 located on chromosome 8 reported in earlier study was validated in this investigation. The validated markers and the novel markers detected showing higher R² value will be useful for improvement of seed vigour in rice.

Identification of QTLs involved in cold tolerance during the germination and bud stages of rice (Oryza sativa L.) via a high-density genetic map

Low-temperature tolerance during the germination and bud stages is an important characteristic of direct-seeded rice (DSR). Recombinant inbred lines (RILs) derived from indica rice H335, which is highly tolerant to low temperature, and indica rice CHA-1, which is sensitive to low temperature, were used to identify quantitative trait loci (QTLs) associated with low-temperature tolerance during the germination and bud stages. a total of 11 QTLs were detected based on a high-density genetic map; among these, six QTLs explained 5.13-9.42% of the total phenotypic variation explained (PVE) during the germination stage, and five QTLs explained 4.17-6.42% of the total PVE during the bud stage. All QTLs were distributed on chromosome 9, and all favourable alleles originated from H335. The physical position of each QTL was determined, and 11 QTLs were combined into five genetic loci; three of these loci are involved during the germination stage (loci 1, 2, and 3), and three are involved during the bud stage (loci 3, 4, and 5). Loci 2, 4 and 5 were repeatedly detected in the wet season (WS) and dry season (DS). Notably, loci 3 was detected during both the germination and bud stages. These loci are good candidates for future studies of gene function and could serve as highly valuable genetic factors for improving cold tolerance during the germination and bud stages of rice.

Coordination of light, circadian clock with temperature: The potential mechanisms regulating chilling tolerance in rice

Rice (Oryza sativa L.) is a major staple food crop for over half of the world's population. As a crop species originated from the subtropics, rice production is hampered by chilling stress. The genetic mechanisms of rice responses to chilling stress have attracted much attention, focusing on chilling-related gene mining and functional analyses. Plants have evolved sophisticated regulatory systems to respond to chilling stress in coordination with light signaling pathway and internal circadian clock. However, in rice, information about light-signaling pathways and circadian clock regulation and their roles in chilling tolerance remains elusive. Further investigation into the regulatory network of chilling tolerance in rice is needed, as knowledge of the interaction between temperature, light, and circadian clock dynamics is limited. Here, based on phenotypic analysis of transgenic and mutant rice lines, we delineate the relevant genes with important regulatory roles in chilling tolerance. In addition, we discuss the potential coordination mechanism among temperature, light, and circadian clock in regulating chilling response and tolerance of rice, and provide perspectives for the ongoing chilling signaling network research in rice.

Glycosyltransferase OsUGT90A1 helps protect the plasma membrane during chilling stress in rice

Due to its subtropical origins, rice (Oryza sativa) is sensitive to low-temperature stress. In this study, we identify LOC_Os04g24110, annotated to encode the UDP-glycosyltransferase enzyme UGT90A1, as a gene associated with the low-temperature seedling survivability (LTSS) quantitative trait locus qLTSS4-1. Differences between haplotypes in the control region of OsUGT90A1 correlate with chilling tolerance phenotypes, and reflect differential expression between tolerant and sensitive accessions rather than differences in protein sequences. Expression of OsUGT90A1 is initially enhanced by low temperature, and its overexpression helps to maintain membrane integrity during cold stress and promotes leaf growth during stress recovery, which are correlated with reduced levels of reactive oxygen species due to increased activities of antioxidant enzymes. In addition, overexpression of OsUGT90A1 in Arabidopsis improves freezing survival and tolerance to salt stress, again correlated with enhanced activities of antioxidant enzymes. Overexpression of OsUGT90A1 in rice decreases root lengths in 3-week-old seedlings while gene-knockout increases the length, indicating that its differential expression may affect phytohormone activities. We conclude that higher OsUGT90A1 expression in chilling-tolerant accessions helps to maintain cell membrane integrity as an abiotic stress-tolerance mechanism that prepares plants for the resumption of growth and development during subsequent stress recovery.

Genome-Wide Association Mapping to Identify Genetic Loci for Cold Tolerance and Cold Recovery During Germination in Rice

Low temperature significantly affects rice growth and yield. Temperatures lower than 15°C are generally detrimental for germination and uniform seedling stand. To investigate the genetic architecture underlying cold tolerance during germination in rice, we conducted a genome-wide association study using a novel diversity panel of 257 rice accessions from around the world and the 7K SNP marker array. Phenotyping was conducted in controlled growth chambers under dark conditions at 13°C. The rice accessions were measured for low-temperature germinability, germination index, coleoptile length under cold stress, plumule length at 4-day recovery, and plumule length recovery rate. A total of 51 QTLs were identified at p < 0.001 and 17 QTLs were identified using an FDR < 0.05 across the different chilling indices with the whole panel of accessions. At the threshold of p < 0.001, a total of 20 QTLs were identified in the subset of japonica accessions, while 9 QTLs were identified in the subset of indica accessions. Considering the recurring SNPs and linked SNPs across different chilling indices, we identified 31 distinct QTL regions in the whole panel, 13 QTL regions in the japonica subset, and 7 distinct QTL regions in the indica subset. Among these QTL regions, three regions were common between the whole panel and japonica, three regions were common between the whole panel and indica, and one region was common between indica and japonica. A subset of QTL regions was potentially colocalized with previously identified genes and QTLs, including 10 from the japonica subset, 4 from the indica subset, and 6 from the whole panel. On the other hand, a total of 21 potentially novel QTL regions from the whole panel, 10 from the japonica subset, and 1 from the indica subset were identified. The results of our study provide useful information on the genetic architecture underlying cold tolerance during germination in rice, which in turn can be used for further molecular study and crop improvement for low-temperature stressed environments.

Linkage disequilibrium mapping for grain Fe and Zn enhancing QTLs useful for nutrient dense rice breeding

BACKGROUND

High yielding rice varieties are usually low in grain iron (Fe) and zinc (Zn) content. These two micronutrients are involved in many enzymatic activities, lack of which cause many disorders in human body. Bio-fortification is a cheaper and easier way to improve the content of these nutrients in rice grain.

RESULTS

A population panel was prepared representing all the phenotypic classes for grain Fe-Zn content from 485 germplasm lines. The panel was studied for genetic diversity, population structure and association mapping of grain Fe-Zn content in the milled rice. The population showed linkage disequilibrium showing deviation of Hardy-Weinberg's expectation for Fe-Zn content in rice. Population structure at K = 3 categorized the panel population into distinct sub-populations corroborating with their grain Fe-Zn content. STRUCTURE analysis revealed a common primary ancestor for each sub-population. Novel quantitative trait loci (QTLs) namely qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected using association mapping. Four QTLs, namely qFe3.3, qFe7.3, qFe8.1 and qFe12.2 for grain Fe content were detected to be co-localized with qZn3.1, qZn7, qZn8.3 and qZn12.3 QTLs controlling grain Zn content, respectively. Additionally, some Fe-Zn controlling QTLs were co-localized with the yield component QTLs, qTBGW, OsSPL14 and qPN. The QTLs qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qZn6, qZn7 and gRMm9-1 for grain Fe-Zn content reported in earlier studies were validated in this study.

CONCLUSION

Novel QTLs, qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected for these two traits. Four Fe-Zn controlling QTLs and few yield component QTLs were detected to be co-localized. The QTLs, qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qFe3.3, qFe7.3, qZn6, qZn7, qZn2.2, qZn8.3 and qZn12.3 will be useful for biofortification of the micronutrients. Simultaneous enhancement of Fe-Zn content may be possible with yield component traits in rice.

Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

An attempt was made in the current study to identify the main-effect and co-localized quantitative trait loci (QTLs) for germination and early seedling growth traits under low-temperature stress (LTS) conditions in rice. The plant material used in this study was an early backcross population of 230 introgression lines (ILs) in BCIF7 generation derived from the Weed Tolerant Rice-1 (WTR-1) (as the recipient) and Haoannong (HNG) (as the donor). Genetic analyses of LTS tolerance revealed a total of 27 main-effect quantitative trait loci (M-QTLs) mapped on 12 chromosomes. These QTLs explained more than 10% of phenotypic variance (PV), and average PV of 12.71% while employing 704 high-quality SNP markers. Of these 27 QTLs distributed on 12 chromosomes, 11 were associated with low-temperature germination (LTG), nine with low-temperature germination stress index (LTGS), five with root length stress index (RLSI), and two with biomass stress index (BMSI) QTLs, shoot length stress index (SLSI) and root length stress index (RLSI), seven with seed vigor index (SVI), and single QTL with root length (RL). Among them, five significant major QTLs (qLTG(I) 1 , qLTGS(I) 1-2 , qLTG(I) 5 , qLTGS(I) 5 , and qLTG(I) 7 ) mapped on chromosomes 1, 5, and 7 were associated with LTG and LTGS traits and the PV explained ranged from 16 to 23.3%. The genomic regions of these QTLs were co-localized with two to six QTLs. Most of the QTLs were growth stage-specific and found to harbor QTLs governing multiple traits. Eight chromosomes had more than four QTLs and were clustered together and designated as promising LTS tolerance QTLs (qLTTs), as qLTT 1 , qLTT 2 , qLTT 3 , qLTT 5 , qLTT 6 , qLTT 8 , qLTT 9 , and qLTT 11 . A total of 16 putative candidate genes were identified in the major M-QTLs and co-localized QTL regions distributed on different chromosomes. Overall, these significant genomic regions of M-QTLs are responsible for multiple traits and this suggested that these could serve as the best predictors of LTS tolerance at germination and early seedling growth stages. Furthermore, it is necessary to fine-map these regions and to find functional markers for marker-assisted selection in rice breeding programs for cold tolerance.

Overexpression of ABA Receptor PYL10 Gene Confers Drought and Cold Tolerance to Indica Rice

Abscisic acid (ABA) plays versatile functions in regulating plant development and tolerance to various biotic and abiotic stresses. Towards elucidating the functions of one of the ABA receptors (ABARs) in rice, OsPYL10 was cloned from drought tolerant rice cv. Nagina 22 and was overexpressed under stress inducible RD29A promoter in a mega rice variety MTU1010 by using Agrobacterium mediated genetic transformation. Four single copy transgenic lines selected based on Southern blot analysis were used for physiological and molecular analysis. PYL10 receptor appears to regulate its ligand ABA accumulation as PYL10 overexpressing transgenics accumulated 2-3.3-fold higher levels of ABA than that of WT in flag leaf at anthesis under non-stress conditions. The enhanced accumulation of ABA was associated with enhanced expression of genes for ABA biosynthesis viz., ZEP1, NCED1, NCED2, NCED3, and NCED4 in transgenics than in WT plants. At seedling stage, PYL10 transgenics showed significantly higher survival rate under cold stress as compared with WT plants. qRT-PCR analysis showed that expression levels of cold responsive genes viz., DREB1F, MYB3R2, TPP1, COR410, DEHYDRIN, and LEA3 were significantly higher in PYL10 overexpressing transgenic lines as compared to WT plants under cold stress. PYL10 transgenic and WT plants grown in the same pot were subjected to -80 kPa drought stress and recovery treatments at vegetative and reproductive stages. At vegetative stage drought stress, three overexpressing lines showed significantly higher grain yield (40-58%) and at reproductive stage drought stress one of these overexpression lines showed two-fold higher grain yield than that of WT plants. Excised leaf water loss analysis showed that PYL10 transgenic lost about 20% less water than WT plants. At reproductive stage, OsPYL10 transgenic maintained higher RWC, membrane stability index, chlorophyll content, and accumulated lower amount of MDA and H2O2 as compared with WT plants. qRT-PCR analysis showed that expression levels of RAB16, Dehydrin, LEA3, and ABA45 were higher in PYL10 transgenics as compared with WT plants under drought stress. Thus, overall results showed that OsPYL10 overexpression has potential to improve both drought and cold stress tolerance of indica rice.

The bZIP73 transcription factor controls rice cold tolerance at the reproductive stage

Cold temperature during the reproductive stage often causes great yield loss of grain crops in subtropical and temperate regions. Previously we showed that the rice transcription factor bZIP73^Jap plays an important role in cold adaptation at the seedling stage. Here we further demonstrate that bZIP73^Jap also confers cold stress tolerance at the reproductive stage. bZIP73^Jap was up-regulated under cold treatment and predominately expressed in panicles at the early binucleate and flowering stages. bZIP73^Jap forms heterodimers with bZIP71, and co-expression of bZIP73^Jap and bZIP71 transgenic lines significantly increased seed-setting rate and grain yield under natural cold stress conditions. bZIP73^Jap :bZIP71 not only repressed ABA level in anthers, but also enhanced soluble sugar transport from anthers to pollens and improved pollen grain fertility, seed-setting rate, and grain yield. Interestingly, bZIP73^Jap :bZIP71 also regulated the expression of qLTG3-1^Nip , and qLTG3-1^Nip overexpression lines greatly improved rice tolerance to cold stress during the reproductive stage. Therefore, our work establishes a framework for rice cold stress tolerance through the bZIP71-bZIP73^Jap -qLTG3-1^Nip -sugar transport pathway. Together with our previous work, our results provide a powerful tool for improving rice cold stress tolerance at both the seedling and the reproductive stages.

Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage

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 (r²) 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).

Association mapping reveals multiple QTLs for grain protein content in rice useful for biofortification

Rice is the staple food for majority of the global population. But, rice grain has low protein content (PC). Mapping of QTLs controlling grain PC is essential for enhancement of the trait through breeding programs. A shortlisted panel population for grain protein content was studied for genetic diversity, population structure and association mapping for grain PC. Phenotyping results showed a wide variation for grain PC. The panel population showed a moderate level of genetic diversity estimated through 98 molecular markers. AMOVA and structure analysis indicated linkage disequilibrium for grain PC and deviation of Hardy-Weinberg's expectation. The analysis showed 15% of the variation among populations and 73% among individuals in the panel population. STRUCTURE analysis categorized the panel population into three subpopulations. The analysis also revealed a common primary ancestor for each subpopulation with few admix individuals. Marker-trait association using 98 molecular markers detected 7 strongly associated QTLs for grain PC by both MLM and GLM analysis. Three novel QTLs qPC3.1, qPC5.1 and qPC9.1 were detected for controlling the grain PC. Four reported QTLs viz., qPC3, QPC8, qPC6.1 and qPC12.1 were validated for use in breeding programs. Reported QTLs, qPC6, qPC6.1 and qPC6.2 may be same QTL controlling PC in rice. A very close marker RM407 near to protein controlling QTL, qProt8 and qPC8, was detected. The study provided clue for simultaneous improvement of PC with high grain yield in rice. The strongly associated markers with grain PC, namely qPC3, qPC3.1, qPC5.1, qPC6.1, qPC8, qPC9.1 and qPC12.1, will be useful for their pyramiding for developing protein rich high yielding rice.

Identifying natural genotypes of grain number per panicle in rice (Oryza sativa L.) by association mapping

INTRODUCTION

As one of the main yield components, grain number per panicle (GNP) played critical role in the rice yield improvement. The identification of natural advantageous variations under different situations will promote the sustainable genetic improvement in rice yield.

OBJECTIVES

This study was designed to identify natural genotypes in a rice mini-core collection, to examine the genotypic effects across the indica and japonica genetic background in different environments, and excavating the superior genotypes that had drove the modern genetic improvement.

METHODS

The association mapping of GNP was carried out using a mini-core collection including 154 indica and 119 japonica accessions in seven different environments. Genotypic effects of each genotype for each QTL were calculated and genotype frequency distortion between the commercial rice cultivars and landraces was screened by χ²-test.

RESULTS

In total, 74 QTLs containing stable and sensitive QTLs in various environments were detected. Within them, 20 positive and 24 negative genotypes in indica, and 24 positive and 16 negative genotypes in japonica were identified. When checking the accumulation of positive genotypes identified in indica across cultivars in each of the two subspecies, it indicated that increased number of positive genotypes identified in indica results in the substantially increased GNP in both indica and japonica across all of the environments, while this trend was not obvious for the positive genotypes identified in japonica especially in short day environments. Moreover, the positive and negative genotype frequency distortion between the landraces and commercial rice cultivars indicated that both positive selection of positive genotypes and negative selection of negative genotypes had driven the genetic improvement on GNP.

CONCLUSION

Our findings suggested that the accumulation of positive genotypes and purifying negative genotypes played equivalently important roles in the improvement of rice yield, but the efficient use for some QTLs or genotypes depends on the comprehensive evaluation of their effect under diverse genetic backgrounds and environments.

Genetic analysis of roots and shoots in rice seedling by association mapping

The vigorous shoots and roots help to improve drought resistance and post-transplanting recovery in rice seedlings (Oryza sativa L.). Hundreds of loci related to root system have been identified recently, but little research has been done on shoot traits, and the relationship between roots and shoots development is also still unclear. The objective of this study was to identify associated loci for roots and shoots in rice seedlings as well as to screen pleiotropic QTLs involved in coordinated development of roots and shoots. Using mini core collection of 273 cultivated rice accessions and 280 simple-sequence repeat markers, we investigated six traits [root length (RL), root thickness (RT), root weight (RW), shoot length (SL), shoot weight (SW) and ratio of root-to-shoot mass] in seedlings. Study was performed in hydroponic medium and genetic analysis was performed by association mapping using general linear model (GLM) with population structure (Q) and mixed linear model (MLM) involving Q and familial relatedness (K). Two subgroups indica and japonica showed significant differences in RT, RW and SW. Maximum correlation was observed between RW and SW. Using GLM 65 QTLs for root and 43 QTLs associated with shoot traits were detected. Among them, seven QTLs were present between RL and RW and five common QTLs were detected between SL and SW with high phenotypic variation effects (PVEs). Two key pleiotropic QTLs were also identified involved in collaborative development of roots and shoots in rice seedlings. Importantly, 17 and 10 QTLs were identified for root and shoot traits respectively in both studies of GLM and MLM. More common QTLs with high PVEs between root and shoot traits suggested that longitudinal growth (RL and SL) played an important role in accumulation of biomass (RW and SW). Considering the obvious phenotypic differences and fewer common QTLs between indica and japonica, we suggested that there could be different mechanisms of seedling development between both subpopulations. Key pleiotropic QTLs and QTLs identified for root and shoot traits in both studies of GLM and MLM could be preferentially used in marker-assisted breeding for strong rice seedling.

QTL and QTL networks for cold tolerance at the reproductive stage detected using selective introgression in rice

Low temperature stress is one of the major abiotic stresses limiting the productivity of Geng (japonica) rice grown the temperate regions as well as in tropical high lands worldwide. To develop rice varieties with improved cold tolerance (CT) at the reproductive stage, 84 BC2 CT introgression lines (ILs) were developed from five populations through backcross breeding. These CT ILs plus 310 random ILs from the same BC populations were used for dissecting genetic networks underlying CT in rice by detecting QTLs and functional genetic units (FGUs) contributing to CT. Seventeen major QTLs for CT were identified using five selective introgression populations and the method of segregation distortion. Of them, three QTLs were confirmed using the random populations and seven others locate in the regions with previously reported CT QTLs/genes. Using multi-locus probability tests and linkage disequilibrium (LD) analyses, 46 functional genetic units (FGUs) (37 single loci and 9 association groups or AGs) distributed in 37 bins (~20%) across the rice genome for CT were detected. Together, each of the CT loci (bins) was detected in 1.7 populations, including 18 loci detected in two or more populations. Putative genetic networks (multi-locus structures) underlying CT were constructed based on strong non-random associations between or among donor alleles at the unlinked CT loci/FGUs identified in the CT ILs, suggesting the presence of strong epistasis among the detected CT loci. Our results demonstrated the power and usefulness of using selective introgression for simultaneous improvement and genetic dissection of complex traits such as CT in rice.

Identification of Genes Related to Cold Tolerance and a Functional Allele That Confers Cold Tolerance

Cold stress is a major factor limiting rice (Oryza sativa) production worldwide, especially at the seedling and booting stages. The identification of genes associated with cold tolerance (CT) in rice is important for sustainable food production. Here, we report the results of a genome-wide association study to identify the genetic loci associated with CT by using a 1,033-accession diversity panel. We identified five CT-related genetic loci at the booting stage. Accessions carrying multiple cold-tolerant alleles displayed a higher seed-setting rate than did accessions that had no cold-tolerant alleles or carried a single allele. At the seedling stage, eight genetic loci related to CT have been identified. Among these, LOC_Os10g34840 was identified as the candidate gene for the qPSR10 genetic locus that is associated with CT in rice seedlings. A single-nucleotide polymorphism (SNP), SNP2^G, at position 343 in LOC_Os10g34840 is responsible for conferring CT at the seedling stage in rice. Further analysis of the haplotype network revealed that SNP2^G was present in 80.08% of the temperate japonica accessions but only 3.8% of the indica ones. We used marker-assisted selection to construct a series of BC₄F₃ near-isogenic lines possessing the cold-tolerant allele SNP2^G When subjected to cold stress, plants carrying SNP2^G survived better as seedlings and showed higher grain weight than plants carrying the SNP2^A allele. The CT-related loci identified here and the functional verification of LOC_Os10g34840 will provide genetic resources for breeding cold-tolerant varieties and for studying the molecular basis of CT in rice.

Overexpression of a New Zinc Finger Protein Transcription Factor OsCTZFP8 Improves Cold Tolerance in Rice

Cold stress is one of the most important abiotic stresses in rice. C₂H₂ zinc finger proteins play important roles in response to abiotic stresses in plants. In the present study, we isolated and functionally characterized a new C₂H₂ zinc finger protein transcription factor OsCTZFP8 in rice. OsCTZFP8 encodes a C₂H₂ zinc finger protein, which contains a typical zinc finger motif, as well as a potential nuclear localization signal (NLS) and a leucine-rich region (L-box). Expression of OsCTZFP8 was differentially induced by several abiotic stresses and was strongly induced by cold stress. Subcellular localization assay and yeast one-hybrid analysis revealed that OsCTZFP8 was a nuclear protein and has transactivation activity. To characterize the function of OsCTZFP8 in rice, the full-length cDNA of OsCTZFP8 was isolated and transgenic rice with overexpression of OsCTZFP8 driven by the maize ubiquitin promoter was generated using Agrobacterium-mediated transformation. Among 46 independent transgenic lines, 6 single-copy homozygous overexpressing lines were selected by Southern blot analysis and Basta resistance segregation assay in both T₁ and T₂ generations. Transgenic rice overexpressing OsCTZFP8 exhibited cold tolerant phenotypes with significantly higher pollen fertilities and seed setting rates than nontransgenic control plants. In addition, yield per plant of OsCTZFP8-expressing lines was significantly (p < 0.01) higher than that of nontransgenic control plants under cold treatments. These results demonstrate that OsCTZFP8 was a C₂H₂ zinc finger transcription factor that plays an important role in cold tolerance in rice.

Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

A region containing three genes on chromosome 1 of indica rice was associated with cold tolerance at the bud burst stage; these results may be useful for breeding cold-tolerant lines. Low temperature at the bud burst stage is one of the major abiotic stresses limiting rice growth, especially in regions where rice seeds are sown directly. In this study, we investigated cold tolerance of rice at the bud burst stage and conducted a genome-wide association study (GWAS) based on the 5K rice array of 249 indica rice varieties widely distributed in China. We improved the method to assess cold tolerance at the bud burst stage in indica rice, and used severity of damage (SD) and seed survival rate (SR) as the cold-tolerant indices. Population structure analysis demonstrated that the Chinese indica panel was divided into three subgroups. In total, 47 significant single-nucleotide polymorphism (SNP) loci associated with SD and SR, were detected by association mapping based on mixed linear model. Because some loci overlapped between SD and SR, the loci contained 13 genome intervals and most of them have been reported previously. A major QTL for cold tolerance on chromosome 1 at the position of 31.6 Mb, explaining 13.2% of phenotypic variation, was selected for further analysis. Through LD decay, GO enrichment, RNA-seq data, and gene expression pattern analyses, we identified three genes (LOC_Os01g55510, LOC_Os01g55350 and LOC_Os01g55560) that were differentially expressed between cold-tolerant and cold-sensitive varieties, suggesting they may be candidate genes for cold tolerance. Together, our results provide a new method to assess cold tolerance in indica rice, and establish the foundation for isolating genes related to cold tolerance that could be used in rice breeding.

Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage

Cold-tolerance in rice may be related to increased cellulose deposition in the cell wall, membrane fatty acids unsaturation and differential expression of several newly identified genes. Low temperature exposure during early vegetative stages limits rice plant's growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated (10 °C) leaves from two genotypes, cold-tolerant (CT) and cold-sensitive (CS), was performed. Differentially expressed genes were identified: 831 and 357 sequences more expressed in the tolerant and in the sensitive genotype, respectively. The genes with higher expression in the CT genotype were used in systems biology analyses to identify protein-protein interaction (PPI) networks and nodes (proteins) that are hubs and bottlenecks in the PPI. From the genes more expressed in the tolerant plants, 60% were reported as affected by cold in previous transcriptome experiments and 27% are located within QTLs related to cold tolerance during the vegetative stage. Novel cold-responsive genes were identified. Quantitative RT-PCR confirmed the high-quality of RNAseq libraries. Several genes related to cell wall assembly or reinforcement are cold-induced or constitutively highly expressed in the tolerant genotype. Cold-tolerant plants have increased cellulose deposition under cold. Genes related to lipid metabolism are more expressed in the tolerant genotype, which has higher membrane fatty acids unsaturation, with increasing levels of linoleic acid under cold. The CT genotype seems to have higher photosynthetic efficiency and antioxidant capacity, as well as more effective ethylene, Ca²⁺ and hormone signaling than the CS. These genes could be useful in future biotechnological approaches aiming to increase cold tolerance in rice.

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.

Genetic Architecture and Candidate Genes for Deep-Sowing Tolerance in Rice Revealed by Non-syn GWAS

Dry direct-seeding of rice is rapidly increasing in China, but variable planting depth associated with machine sowing can lead to low seedling emergence rates. Phenotype analysis of 621 rice accessions showed that mesocotyl length (ML) was induced by deep soil covering and was important in deep-sowing tolerance in the field. Here, we performed and compared GWAS using three types of SNPs (non-synonymous SNP, non-synonymous SNPs and SNPs within promoters and 3 million randomly selected SNPs from the entire set of SNPs) and found that Non-Syn GWAS (GWAS using non-synonyomous SNP) decreased computation time and eliminated confounding by other loci relative to GWAS using randomly selected SNPs. Thirteen QTLs were finally detected, and two new major-effect genes, named OsML1 and OsML2, were identified by an integrated analysis. There were 2 and 7 non-synonymous SNPs in OsML1 and OsML2, respectively, from which 3 and 4 haplotypes were detected in cultivated rice. Combinations of superior haplotypes of OsML1 and OsML2 increased ML by up to 4 cm, representing high emergence rate (85%) in the field with 10 cm of soil cover. The studies provide key loci and naturally occurring alleles of ML that can be used in improving tolerance to dry direct-seeding.

Fine mapping of QTL qCTB10-2 that confers cold tolerance at the booting stage in rice

The QTL qCTB10 - 2 controlling cold tolerance at the booting stage in rice was delimited to a 132.5 kb region containing 17 candidate genes and 4 genes were cold-inducible. Low temperature at the booting stage is a major abiotic stress-limiting rice production. Although some QTL for cold tolerance in rice have been reported, fine mapping of those QTL effective at the booting stage is few. Here, the near-isogenic line ZL31-2, selected from a BC₇F₂ population derived from a cross between cold-tolerant variety Kunmingxiaobaigu (KMXBG) and the cold-sensitive variety Towada, was used to map a QTL on chromosome 10 for cold tolerance at the booting stage. Using BC₇F₃ and BC₇F₄ populations, we firstly confirmed qCTB10-2 and gained confidence that it could be fine mapped. QTL qCTB10-2 explained 13.9 and 15.9% of the phenotypic variances in those two generations, respectively. Using homozygous recombinants screened from larger BC₇F₄ and BC₇F₅ populations, qCTB10-2 was delimited to a 132.5 kb region between markers RM25121 and MM0568. 17 putative predicted genes were located in the region and only 5 were predicted to encode expressed proteins. Expression patterns of these five genes demonstrated that, except for constant expression of LOC_Os10g11820, LOC_Os10g11730, LOC_Os10g11770, and LOC_Os10g11810 were highly induced by cold stress in ZL31-2 compared to Towada, while LOC_Os10g11750 showed little difference. Our results provide a basis for identifying the genes underlying qCTB10-2 and indicate that markers linked to the qCTB10-2 locus can be used to improve the cold tolerance of rice at the booting stage by marker-assisted selection.

Genome wide association analysis of cold tolerance at germination in temperate japonica rice (Oryza sativa L.) varieties

A pool of 200 traditional, landraces and modern elite and old cultivars of rice, mainly japonica varieties adapted to temperate regions, have been used to perform a genome wide association study to detect chromosome regions associated to low temperature germination (LTG) regulation using a panel of 1672 SNP markers. Phenotyping was performed by determining growth rates when seeds were germinated at 25° and 15°C in order to separate the germination vigorousness from cold tolerance effects. As expected, the ability to produce viable seedlings varied widely among rice cultivars and also depended greatly on temperature. Furthermore, we observed a differential response during seed germination and in coleoptile elongation. Faster development at 15°C was observed in seeds from varieties traditionally used as cold tolerant parents by breeders, along with other potentially useful cultivars, mainly of Italian origin. When phenotypic data were combined with the panel of SNPs for japonica rice cultivars, significant associations were detected for 31 markers: 7 were related to growth rate at 25°C and 24 to growth rates at 15°. Among the latter, some chromosome regions were associated to LTG while others were related to coleoptile elongation. Individual effects of the associated markers were low, but by combining favourable alleles in a linear regression model we estimated that 27 loci significantly explained the observed phenotypic variation. From these, a core panel of 13 markers was selected and, furthermore, two wide regions of chromosomes 3 and 6 were consistently associated to rice LTG. Varieties with higher numbers of favourable alleles for the panels of associated markers significantly correlated with increased phenotypic values at both temperatures, thus corroborating the utility of the tagged markers for marker assisted selection (MAS) when breeding japonica rice for LTG.

Natural variation in CTB4a enhances rice adaptation to cold habitats

Low temperature is a major factor limiting rice productivity and geographical distribution. Improved cold tolerance and expanded cultivation to high-altitude or high-latitude regions would help meet growing rice demand. Here we explored a QTL for cold tolerance and cloned the gene, CTB4a (cold tolerance at booting stage), encoding a conserved leucine-rich repeat receptor-like kinase. We show that different CTB4a alleles confer distinct levels of cold tolerance and selection for variation in the CTB4a promoter region has occurred on the basis of environmental temperature. The newly generated cold-tolerant haplotype Tej-Hap-KMXBG was retained by artificial selection during temperate japonica evolution in cold habitats for low-temperature acclimation. Moreover, CTB4a interacts with AtpB, a beta subunit of ATP synthase. Upregulation of CTB4a correlates with increased ATP synthase activity, ATP content, enhanced seed setting and improved yield under cold stress conditions. These findings suggest strategies to improve cold tolerance in crop plants.

Low temperature is a major factor limiting productivity in rice. Here the authors show that the CTB4a gene confers cold tolerance to japonica varieties adapted to cold habitats at the booting stage of development, and propose that CTB4a acts via an interaction with the beta subunit of ATP synthase.

Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis

Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA accessions.

Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice

Rice crop is sensitive to cold stress at seedling stage. A panel of population representing 304 shortlisted germplasm lines was studied for seedling stage chilling tolerance in indica rice. Six phenotypic classes were exposed to six low temperature stress regimes under control phenotyping facility to investigate response pattern. A panel of 66 genotypes representing all phenotypic classes was used for ensuring genetic diversity, population structure and association mapping for the trait using 58 simple sequence repeat (SSR) and 2 direct trait linked markers. A moderate level of genetic diversity was detected in the panel population for the trait. Deviation of Hardy-Weinberg's expectation was detected in the studied population using Wright's F statistic. The panel showed 30% variation among population and 70% among individuals. The entire population was categorized into three sub-populations through STRUCTURE analysis. This revealed tolerance for the trait had a common primary ancestor for each sub-population with few admix individuals. The panel population showed the presence of many QTLs for cold stress tolerance in the individuals representing like genome-wide expression of the trait. Nineteen SSR markers were significantly associated at chilling stress of 8°C to 4°C for 7-21 days duration. Thus, the primers linked to the seedling stage cold tolerance QTLs namely qCTS9, qCTS-2, qCTS6.1, qSCT2, qSCT11, qSCT1a, qCTS-3.1, qCTS11.1, qCTS12.1, qCTS-1b, and CTB2 need to be pyramided for development of strongly chilling tolerant variety.

Assessment of Five Chilling Tolerance Traits and GWAS Mapping in Rice Using the USDA Mini-Core Collection

Rice (Oryza sativa L.) is often exposed to cool temperatures during spring planting in temperate climates. A better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. To dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. Based on these assays, five chilling tolerance indices were calculated and assessed using 202 O. sativa accessions from the Rice Mini-Core (RMC) collection. Significant differences between RMC accessions made the five indices suitable for genome-wide association study (GWAS) based quantitative trait loci (QTL) mapping. For young seedling stage indices, japonica and indica subspecies clustered into chilling tolerant and chilling sensitive accessions, respectively, while both subspecies had similar low temperature germinability distributions. Indica subspecies were shown to have chilling acclimation potential. GWAS mapping uncovered 48 QTL at 39 chromosome regions distributed across all 12 rice chromosomes. Interestingly, there was no overlap between the germination and seedling stage QTL. Also, 18 QTL and 32 QTL were in regions discovered in previously reported bi-parental and GWAS based QTL mapping studies, respectively. Two novel low temperature seedling survivability (LTSS)-QTL, qLTSS3-4 and qLTSS4-1, were not in a previously reported QTL region. QTL with strong effect alleles identified in this study will be useful for marker assisted breeding efforts to improve chilling tolerance in rice cultivars and enhance gene discovery for chilling tolerance.

Breeding approaches and genomics technologies to increase crop yield under low-temperature stress

Improved knowledge about plant cold stress tolerance offered by modern omics technologies will greatly inform future crop improvement strategies that aim to breed cultivars yielding substantially high under low-temperature conditions. Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front. Here, we review the crucial cellular and metabolic alterations in plants that follow LT stress along with the signal transduction and the regulatory network describing the plant cold tolerance. The significance of plant genetic resources to expand the genetic base of breeding programmes with regard to cold tolerance is highlighted. Also, the genetic architecture of cold tolerance trait as elucidated by conventional QTL mapping and genome-wide association mapping is described. Further, global expression profiling techniques including RNA-Seq along with diverse omics platforms are briefly discussed to better understand the underlying mechanism and prioritize the candidate gene (s) for downstream applications. These latest additions to breeders' toolbox hold immense potential to support plant breeding schemes that seek development of LT-tolerant cultivars. High-yielding cultivars endowed with greater cold tolerance are urgently required to sustain the crop yield under conditions severely challenged by low-temperature.

Genome-wide Association Mapping of Cold Tolerance Genes at the Seedling Stage in Rice

BACKGROUND

Rice is a temperature-sensitive crop and its production is severely affected by low temperature in temperate and sub-tropical regions. To understand the genetic basis of cold tolerance in rice, we evaluated the cold tolerance at the seedling stage (CTS) of 295 rice cultivars in the rice diversity panel 1 (RDP1), these cultivars were collected from 82 countries.

RESULTS

The evaluations revealed that both temperate and tropical japonica rice cultivars are more tolerant to cold stress than indica and AUS cultivars. Using the cold tolerance phenotypes and 44 K SNP chip dataset of RDP1, we performed genome-wide association mapping of quantitative trait loci (QTLs) for CTS. The analysis identified 67 QTLs for CTS that are located on 11 chromosomes. Fifty-six of these QTLs are located in regions without known cold tolerance-related QTLs.

CONCLUSION

Our study has provided new information on the genetic architecture of rice cold tolerance and has also identified highly cold tolerant cultivars and CTS-associated SNP markers that will be useful rice improvement.