Delimitation of a QTL region controlling cold tolerance at booting stage of a cultivar, 'Lijiangxintuanheigu', in rice, Oryza sativa L

Analysis of genome-wide association studies of low-temperature germination in Xian and Geng rice

Rice is the leading global staple crop. Low temperatures pose negative impacts on rice's optimal growth and development. Rice cultivars acclimating to low temperatures exhibited improved seedling emergence under direct-seeded sowing conditions, yet little is known about the genes that regulate germination at low temperatures (LTG). In this research investigation, we've performed whole genome sequencing for the 273 rice plant materials. Using the best linear unbiased prediction (BLUP) values for each rice material, we identified 7 LTG-related traits and performed the efficient genetic analysis and genome-wide association study (GWAS). As a result of this, 95 quantitative trait loci (QTLs) and 1001 candidate genes associated with LTG in rice were identified. Haplotype analysis and functional annotation of the candidate genes resulted in the identification of three promising candidate genes (LOC_Os08g30520 for regulating LTG4 and LTG5, LOC_Os10g02625 for regulating LTG6, LTg7 and LTG8, and LOC_Os12g31460 for regulating LTG7, LTg8 and LTG9) involving in the regulation of LTG in rice. This research provides a solid foundation for addressing the LTG issue in rice and will be valuable in future direct-seeded rice breeding programs.

QTL detection and candidate gene identification of qCTB1 for cold tolerance in the Yunnan plateau landrace rice

Cold stress is one of the main abiotic stresses that affects rice growth and production worldwide. Dissection of the genetic basis is important for genetic improvement of cold tolerance in rice. In this study, a new source of cold-tolerant accession from the Yunnan plateau, Lijiangxiaoheigu, was used as the donor parent and crossed with a cold-sensitive cultivar, Deyou17, to develop recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis for cold tolerance at the early seedling and booting stages in rice. In total, three QTLs for cold tolerance at the early seedling stage on chromosomes 2 and 7, and four QTLs at the booting stage on chromosomes 1, 3, 5, and 7, were identified. Haplotype and linear regression analyses showed that QTL pyramiding based on the additive effect of these favorable loci has good potential for cold tolerance breeding. Effect assessment in the RIL and BC3F3 populations demonstrated that qCTB1 had a stable effect on cold tolerance at the booting stage in the genetic segregation populations. Under different cold stress conditions, qCTB1 was fine-mapped to a 341-kb interval between markers M3 and M4. Through the combination of parental sequence comparison, candidate gene-based association analysis, and tissue and cold-induced expression analyses, eight important candidate genes for qCTB1 were identified. This study will provide genetic resources for molecular breeding and gene cloning to improve cold tolerance in rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01488-3.

Progress in the study of functional genes related to direct seeding of rice

Rice is a major food crop in the world. Owing to the shortage of rural labor and the development of agricultural mechanization, direct seeding has become the main method of rice cultivation. At present, the main problems faced by direct seeding of rice are low whole seedling rate, serious weeds, and easy lodging of rice in the middle and late stages of growth. Along with the rapid development of functional genomics, the functions of a large number of genes have been confirmed, including seed vigor, low-temperature tolerance germination, low oxygen tolerance growth, early seedling vigor, early root vigor, resistance to lodging, and other functional genes related to the direct seeding of rice. A review of the related functional genes has not yet been reported. In this study, the genes related to direct seeding of rice are summarized to comprehensively understand the genetic basis and mechanism of action in direct seeding of rice and to lay the foundation for further basic theoretical research and breeding application research in direct seeding of rice.

qCTB7 positively regulates cold tolerance at booting stage in rice

KEY MESSAGE

LOC_Os07g07690 on qCTB7 is associated with cold tolerance at the booting stage in rice, and analysis of transgenic plants demonstrated that qCTB7 influenced cold tolerance by altering the morphology and cytoarchitecture of anthers and pollen. Cold tolerance at the booting stage (CTB) in rice can significantly affect yield in high-latitude regions. Although several CTB genes have been isolated, their ability to induce cold tolerance is insufficient to ensure adequate rice yields in cold regions at high latitudes. Here, we identified the PHD-finger domain-containing protein gene qCTB7 using QTL-seq and linkage analysis through systematic measurement of CTB differences and the spike fertility of the Longjing31 and Longdao3 cultivars, resulting in the derivation of 1570 F2 progeny under cold stress. We then characterized the function of qCTB7 in rice. It was found that overexpression of qCTB7 promoted CTB and the same yield as Longdao3 under normal growing conditions while the phenotype of qctb7 knockout showed anther and pollen failure under cold stress. When subjected to cold stress, the germination of qctb7 pollen on the stigma was reduced, resulting in lower spike fertility. These findings indicate that qCTB7 regulates the appearance, morphology, and cytoarchitecture of the anthers and pollen. Three SNPs in the promoter region and coding region of qCTB7 were identified as recognition signals for CTB in rice and could assist breeding efforts to improve cold tolerance for rice production in high latitudes.

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

MAIN CONCLUSION

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

QTL and Candidate Genes: Techniques and Advancement in Abiotic Stress Resistance Breeding of Major Cereals

At least 75% of the world's grain production comes from the three most important cereal crops: rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). However, abiotic stressors such as heavy metal toxicity, salinity, low temperatures, and drought are all significant hazards to the growth and development of these grains. Quantitative trait locus (QTL) discovery and mapping have enhanced agricultural production and output by enabling plant breeders to better comprehend abiotic stress tolerance processes in cereals. Molecular markers and stable QTL are important for molecular breeding and candidate gene discovery, which may be utilized in transgenic or molecular introgression. Researchers can now study synteny between rice, maize, and wheat to gain a better understanding of the relationships between the QTL or genes that are important for a particular stress adaptation and phenotypic improvement in these cereals from analyzing reports on QTL and candidate genes. An overview of constitutive QTL, adaptive QTL, and significant stable multi-environment and multi-trait QTL is provided in this article as a solid framework for use and knowledge in genetic enhancement. Several QTL, such as DRO1 and Saltol, and other significant success cases are discussed in this review. We have highlighted techniques and advancements for abiotic stress tolerance breeding programs in cereals, the challenges encountered in introgressing beneficial QTL using traditional breeding techniques such as mutation breeding and marker-assisted selection (MAS), and the in roads made by new breeding methods such as genome-wide association studies (GWASs), the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and meta-QTL (MQTL) analysis. A combination of these conventional and modern breeding approaches can be used to apply the QTL and candidate gene information in genetic improvement of cereals against abiotic stresses.

Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice

Rice, a cold-sensitive crop, is a staple food for more than 50% of the world’s population. Low temperature severely compromises the growth of rice and challenges China’s food safety. Dongxiang wild rice (DXWR) is the most northerly common wild rice in China and has strong cold tolerance, but the genetic basis of its cold tolerance is still unclear. Here, we report quantitative trait loci (QTLs) analysis for seedling cold tolerance (SCT) using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that were derived from a cross of DXWR, and an indica cultivar, GZX49. A total of 10 putative QTLs were identified for SCT under 4 °C cold treatment, each explaining 2.0–6.8% of the phenotypic variation in this population. Furthermore, transcriptome sequencing of DXWR seedlings before and after cold treatment was performed, and 898 and 3413 differentially expressed genes (DEGs) relative to 0 h in cold-tolerant for 4 h and 12 h were identified, respectively. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) analysis were performed on these DEGs. Using transcriptome data and genetic linkage analysis, combined with qRT-PCR, sequence comparison, and bioinformatics, LOC_Os08g04840 was putatively identified as a candidate gene for the major effect locus qSCT8. These findings provided insights into the genetic basis of SCT for the improvement of cold stress potential in rice breeding programs.

QTL mapping for cold tolerance and higher overwintering survival rate in winter rapeseed (Brassica napus)

The cold tolerance of winter rapeseed (Brassica napus) cultivars is critically important for winter survival and yield formation in northern China. Few studies have examined the genetic mechanism underlying the overwintering survival of B. napus. Here, an F₂ population including 174 lines and an F_2:3 population including 174 lines were generated to identify the quantitative trait loci (QTLs) related to the cold tolerance of B. napus. A genetic linkage map including 1,017 markers merged into 268 bins covering 793.53 cM was constructed. A total of 16 QTLs for two cold-tolerance indicators related to overwintering success were detected among the two populations. These QTLs were responsible for explaining 0.97%-12.74% of the phenotypic variation. Two major QTLs, qOWRTA07 and qOWRLA07, explaining more than 10% of the phenotypic variation were identified in overlapping regions, and we suspected that these two QTLs might represent the same QTL mapped between the two bins, c07b004 and c07b005, corresponding to the physical interval from 21.4 M to 23.4 M on chromosome A07. One gene, BnaA07G0198300ZS, contained the candidate region for overwintering rate (OWR). RT-qPCR analysis showed that the expression of this gene significantly differed between the two parents (NST57 and CY12), and its expression was higher in NST57 than in CY12. This gene may be involved in the cold-response during overwintering period of B. napus. These results are important for the molecular breeding to improve the cold tolerance and overwintering success of winter oilseed rape.

OsWRKY115 on qCT7 links to cold tolerance in rice

qCT7, a novel QTL for increasing seedling cold tolerance in rice, was fine-mapped to a 70.9-kb region on chromosome 7, and key OsWRKY115 was identified in transgenic plants. Cold stress caused by underground cold-water irrigation seriously limits rice productivity. We systemically measured the cold-responsive traits of 2,570 F2 individuals derived from two widely cultivated rice cultivars, Kong-Yu-131 and Dong-Nong-422, to identify the major genomic regions associated with cold tolerance. A novel major QTL, qCT7, was mapped on chromosome 7 associated with the cold tolerance and survival, using whole-genome re-sequencing with bulked segregant analysis. Local QTL linkage analysis with F₂ and fine mapping with recombinant plant revealed a 70.9-kb core region on qCT7 encoding 13 protein-coding genes. Only the LOC_Os07g27670 expression level encoding the OsWRKY115 transcription factor on the locus was specifically induced by cold stress in the cold-tolerant cultivar. Moreover, haplotype analysis and the KASP8 marker indicated that OsWRKY115 was significantly associated with cold tolerance. Overexpression and knockout of OsWRKY115 significantly affected cold tolerance in seedlings. Our experiments identified OsWRKY115 as a novel regulatory gene associated with cold response in rice, and the Kong-Yu-131 allele with specific cold-induced expression may be an important molecular variant.

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.

Revision of the relationship between anther morphology and pollen sterility by cold stress at the booting stage in rice

BACKGROUND AND AIMS

Cold stress in rice (Oryza sativa) plants at the reproductive stage prevents normal anther development and causes pollen sterility. Tapetum hypertrophy in anthers has been associated with pollen sterility in response to cold at the booting stage. Here, we re-examined whether the relationships between anther abnormality and pollen sterility caused by cold stress at the booting stage in rice can be explained by a monovalent factor such as tapetum hypertrophy.

METHODS

After exposing plants to a 4-d cold treatment at the booting stage, we collected and processed anthers for transverse sectioning immediately and at the flowering stage. We anatomically evaluated the effect of cold treatment on anther internal morphologies, pollen fertilities and pollen numbers in the 13 cultivars with various cold sensitivities.

KEY RESULTS

We observed four types of morphological anther abnormalities at each stage. Pollen sterility was positively correlated with the frequency of undeveloped locules, but not with tapetum hypertrophy as commonly believed. In cold-sensitive cultivars grown at low temperatures, pollen sterility was more frequent than anther morphological abnormalities, and some lines showed remarkably high pollen sterility without any anther morphological alterations. Most morphological anomalies occurred only in specific areas within large and small locules. Anther length tended to shorten in response to cold treatment and was positively correlated with pollen number. One cultivar showed a considerably reduced pollen number, but fertile pollen grains under cold stress. We propose three possible relationships to explain anther structure and pollen sterility and reduction due to cold stress.

CONCLUSIONS

The pollen sterility caused by cold stress at the booting stage was correlated with the frequency of entire locule-related abnormalities, which might represent a phenotypic consequence, but not a direct cause of pollen abortion. Multivalent factors might underlie the complicated relationships between anther abnormality and pollen sterility in rice.

Genome-Wide Association Study Reveals the Genetic Basis of Chilling Tolerance in Rice at the Reproductive Stage

A genome-wide association study (GWAS) was used to investigate the genetic basis of chilling tolerance in a collection of 117 rice accessions, including 26 Korean landraces and 29 weedy rices, at the reproductive stage. To assess chilling tolerance at the early young microspore stage, plants were treated at 12 °C for 5 days, and tolerance was evaluated using seed set fertility. GWAS, together with principal component analysis and kinship matrix analysis, revealed five quantitative trait loci (QTLs) associated with chilling tolerance on chromosomes 3, 6, and 7. The percentage of phenotypic variation explained by the QTLs was 11-19%. The genomic region underlying the QTL on chromosome 3 overlapped with a previously reported QTL associated with spikelet fertility. Subsequent bioinformatic and haplotype analyses suggested three candidate chilling-tolerance genes within the QTL linkage disequilibrium block: Os03g0305700, encoding a protein similar to peptide chain release factor 2; Os06g0495700, encoding a beta tubulin, autoregulation binding-site-domain-containing protein; and Os07g0137800, encoding a protein kinase, core-domain-containing protein. Further analysis of the detected QTLs and the candidate chilling-tolerance genes will facilitate strategies for developing chilling-tolerant rice cultivars in breeding programs.

Combining QTL-seq and linkage mapping to fine map a candidate gene in qCTS6 for cold tolerance at the seedling stage in rice

BACKGROUND

Cold stress caused by low temperatures is an important factor restricting rice production. Identification of cold-tolerance genes that can stably express in cold environments is crucial for molecular rice breeding.

RESULTS

In this study, we employed high-throughput quantitative trait locus sequencing (QTL-seq) analyses in a 460-individual F2:3 mapping population to identify major QTL genomic regions governing cold tolerance at the seedling stage in rice. A novel major QTL (qCTS6) controlling the survival rate (SR) under low-temperature conditions of 9°C/10 days was mapped on the 2.60-Mb interval on chromosome 6. Twenty-seven single-nucleotide polymorphism (SNP) markers were designed for the qCST6 region based on re-sequencing data, and local QTL mapping was conducted using traditional linkage analysis. Eventually, we mapped qCTS6 to a 96.6-kb region containing 13 annotated genes, of which seven predicted genes contained 13 non-synonymous SNP loci. Quantitative reverse transcription PCR analysis revealed that only Os06g0719500, an OsbZIP54 transcription factor, was strongly induced by cold stress. Haplotype analysis confirmed that +376 bp (T>A) in the OsbZIP54 coding region played a key role in regulating cold tolerance in rice.

CONCLUSION

We identified OsbZIP54 as a novel regulatory gene associated with rice cold-responsive traits, with its Dongfu-104 allele showing specific cold-induction expression serving as an important molecular variation for rice improvement. This result is expected to further exploration of the genetic mechanism of rice cold tolerance at the seedling stage and improve cold tolerance in rice varieties by marker-assisted selection.

Identification of Candidate Genes Conferring Cold Tolerance to Rice (Oryza sativa L.) at the Bud-Bursting Stage Using Bulk Segregant Analysis Sequencing and Linkage Mapping

Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice. The identification of cold-tolerance quantitative trait loci (QTL) in species that can stably tolerate cold environments is crucial for the molecular breeding of rice with such traits. In our study, high-throughput QTL-sequencing analyses were performed in a 460-individual F_{2 : 3} mapping population to identify the major QTL genomic regions governing cold tolerance at the bud-bursting (CTBB) stage in rice. A novel major QTL, qCTBB9, which controls seed survival rate (SR) under low-temperature conditions of 5°C/9 days, was mapped on the 5.40-Mb interval on chromosome 9. Twenty-six non-synonymous single-nucleotide polymorphism (nSNP) markers were designed for the qCTBB9 region based on re-sequencing data and local QTL mapping conducted using traditional linkage analysis. We mapped qCTBB9 to a 483.87-kb region containing 58 annotated genes, among which six predicted genes contained nine nSNP loci. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed that only Os09g0444200 was strongly induced by cold stress. Haplotype analysis further confirmed that the SNP 1,654,225 bp in the Os09g0444200 coding region plays a key role in regulating the cold tolerance of rice. These results suggest that Os09g0444200 is a potential candidate for qCTBB9. Our results are of great significance to explore the genetic mechanism of rice CTBB and to improve the cold tolerance of rice varieties by marker-assisted selection.

Differentiation, evolution and utilization of natural alleles for cold adaptability at the reproductive stage in rice

Genetic studies on cold tolerance at the reproductive stage in rice could lead to significant reductions in yield losses. However, knowledge about the genetic basis and adaptive differentiation, as well as the evolution and utilization of the underlying natural alleles, remains limited. Here, 580 rice accessions in two association panels were used to perform genome-wide association study, and 156 loci associated with cold tolerance at the reproductive stage were identified. Os01g0923600 and Os01g0923800 were identified as promising candidate genes in qCTB1t, a major associated locus. Through population genetic analyses, 22 and 29 divergent regions controlling cold adaptive differentiation inter-subspecies (Xian/Indica and Geng/Japonica) and intra-Geng, respectively, were identified. Joint analyses of four cloned cold-tolerance genes showed that they had different origins and utilizations under various climatic conditions. bZIP73 and OsAPX1 differentiating inter-subspecies evolved directly from wild rice, whereas the novel mutations CTB4a and Ctb1 arose in Geng during adaptation to colder climates. The cold-tolerant Geng accessions have undergone stronger selection under colder climate conditions than other accessions during the domestication and breeding processes. Additive effects of dominant allelic variants of four identified genes have been important in adaptation to cold in modern rice varieties. Therefore, this study provides valuable information for further gene discovery and pyramiding breeding to improve cold tolerance at the reproductive stage in rice.

Identification of candidate genes controlling chilling tolerance of rice in the cold region at the booting stage by BSA-Seq and RNA-Seq

Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.

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.

Quantitative Trait Loci for Freezing Tolerance in a Lowland x Upland Switchgrass Population

Low-temperature related abiotic stress is an important factor affecting winter survival in lowland switchgrass when grown in northern latitudes in the United States. A better understanding of the genetic architecture of freezing tolerance in switchgrass will aid the development of lowland switchgrass cultivars with improved winter survival. The objectives of this study were to conduct a freezing tolerance assessment, generate a genetic map using single nucleotide polymorphism (SNP) markers, and identify QTL (quantitative trait loci) associated with freezing tolerance in a lowland × upland switchgrass population. A pseudo-F2 mapping population was generated from an initial cross between the lowland population Ellsworth and the upland cultivar Summer. The segregating progenies were screened for freezing tolerance in a controlled-environment facility. Two clonal replicates of each genotype were tested at six different treatment temperatures ranging from -15 to -5°C at an interval of 2°C for two time periods. Tiller emergence (days) and tiller number were recorded following the recovery of each genotype with the hypothesis that upland genotype is the source for higher tiller number and early tiller emergence. Survivorship of the pseudo-F2 population ranged from 89% at -5°C to 5% at -15°C with an average LT50 of -9.7°C. Genotype had a significant effect on all traits except tiller number at -15°C. A linkage map was constructed from bi-allelic single nucleotide polymorphism markers generated using exome capture sequencing. The final map consisted of 1618 markers and 2626 cM, with an average inter-marker distance of 1.8 cM. Six significant QTL were identified, one each on chromosomes 1K, 5K, 5N, 6K, 6N, and 9K, for the following traits: tiller number, tiller emergence days and LT50. A comparative genomics study revealed important freezing tolerance genes/proteins, such as COR47, DREB2B, zinc finger-CCCH, WRKY, GIGANTEA, HSP70, and NRT2, among others that reside within the 1.5 LOD confidence interval of the identified QTL.

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 a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy

BACKGROUND

Cold stress can cause serious abiotic damage that limits the growth, development and yield of rice. Cold tolerance during the booting stage of rice is a key factor that can guarantee a high and stable yield under cold stress. The cold tolerance of rice is controlled by quantitative trait loci (QTLs). Based on the complex genetic basis of cold tolerance in rice, additional efforts are needed to detect reliable QTLs and identify candidate genes. In this study, recombinant inbred lines (RILs) derived from a cross between a cold sensitive variety, Dongnong422, and strongly cold-tolerant variety, Kongyu131, were used to screen for cold-tolerant loci at the booting stage of rice.

RESULTS

A novel major QTL, qPSST6, controlling the percent seed set under cold water treatment (PSST) under the field conditions of 17 °C cold water irrigation was located on the 28.4 cM interval on chromosome 6. Using the combination of bulked-segregant analysis (BSA) and next-generation sequencing (NGS) technology (Seq-BSA), a 1.81 Mb region that contains 269 predicted genes on chromosome 6 was identified as the candidate region of qPSST6. Two genes, LOC_Os06g39740 and LOC_Os06g39750, were annotated as "response to cold" by gene ontology (GO) analysis. qRT-PCR analysis revealed that LOC_Os06g39750 was strongly induced by cold stress. Haplotype analysis also demonstrate a key role of LOC_Os06g39750 in regulating the PSST of rice, suggesting that it was the candidate gene of qPSST6.

CONCLUSIONS

The information obtained in this study is useful for gene cloning of qPSST6 and for breeding cold-tolerant varieties of rice using marker assisted selection (MAS).

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.

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.

Thermal stress impacts reproductive development and grain yield in rice

Rice is highly sensitive to temperature stress (cold and heat), particularly during the reproductive and grain-filling stages. In this review, we discuss the effects of low- and high-temperature sensitivity in rice at various reproductive stages (from meiosis to grain development) and propose strategies for improving the tolerance of rice to terminal thermal stress. Cold stress impacts reproductive development through (i) delayed heading, due to its effect on anther respiration, which increases sucrose accumulation, protein denaturation and asparagine levels, and decreases proline accumulation, (ii) pollen sterility owing to tapetal hypertrophy and related nutrient imbalances, (iii) reduced activity of cell wall bound invertase in the tapetum of rice anthers, (iv) impaired fertilization due to inhibited anther dehiscence, stigma receptivity and ability of the pollen tube to germinate through the style towards the ovary, and (v) floret sterility, which increases grain abortion, restricts grain size, and thus reduces grain yield. Heat stress affects grain formation and development through (i) poor anther dehiscence due to restricted closure of the locules, leading to reduced pollen dispersal and fewer pollen on the stigma, (ii) changes in pollen proteins resulting in significant reductions in pollen viability and pollen tube growth, leading to spikelet sterility, (iii) delay in heading, (iv) reduced starch biosynthesis in developing grain, which reduces starch accumulation, (v) increased chalkiness of grain with irregular and round-shaped starch granules, and (vi) a shortened grain-filling period resulting in low grain weight. However, physiological and biotechnological tools, along with integrated management and adaptation options, as well as conventional breeding, can help to develop new rice genotypes possessing better grain yield under thermal stress during reproductive and grain-filling phases.

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.

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.

Combining mapping of physiological quantitative trait loci and transcriptome for cold tolerance for counteracting male sterility induced by low temperatures during reproductive stage in rice

Male sterility induced by low temperatures (LTs) during the reproductive stage is a major constraint for temperate zone rice. To detect physiological quantitative trait loci (QTLs), we modeled genotypic variation in the physiological processes involved in low temperature spikelet sterility on the basis of anther length (AL), a proxy for microspore and pollen grain number per anther. The model accounted for 83% of the genotypic variation in potential AL at normal temperature and the ability to maintain AL at LT. We tested the model on 208 recombinant inbred lines of cold-tolerant 'Tohoku-PL3' (PL3) × cold-sensitive 'Akihikari' (AH) for 2 years. QTLs for spikelet fertility (FRT) at LT were detected on chromosomes 5 (QTL for Cold Tolerance at Reproductive stage, qCTR5) and 12 (qCTR12). qCTR12 was annotated with the ability to maintain AL under LTs. qCTR5 was in a region shared with QTLs for culm length and heading date. Genome-wide expression analysis showed 798 genes differentially expressed in the spikelets between the parents at LTs. Of these, 12 were near qCTR5 and 23 were near qCTR12. Gene expression analysis confirmed two candidate genes for qCTR5 (O-methyltransferase ZRP4, Os05g0515600; beta-1,3-glucanase-like protein, Os05g0535100) and one for qCTR12 (conserved hypothetical protein, Os12g0550600). Nucleotide polymorphisms (21 deletions, 2 insertions and 10 single nucleotide polymorphisms) in PL3 were found near the candidate conserved hypothetical protein (Os12g0550600) and upstream in PL3, but not in AH. Haplotype analysis revealed that this gene came from 'Kuchum'. The combination of mapping physiological QTLs with gene expression analysis can be extended to identify other genes for abiotic stress response in cereals.

New insights into the genetic basis of natural chilling and cold shock tolerance in rice by genome-wide association analysis

In order to understand cold adaptability and explore additional genetic resources for the cold tolerance improvement of rice, we investigated the genetic variation of 529 rice accessions under natural chilling and cold shock stress conditions at the seedling stage using genome-wide association studies; a total of 132 loci were identified. Among them, 12 loci were common for both chilling and cold shock tolerance, suggesting that rice has a distinct and overlapping genetic response and adaptation to the two stresses. Haplotype analysis of a known gene OsMYB2, which is involved in cold tolerance, revealed indica-japonica differentiation and latitude tendency for the haplotypes of this gene. By checking the subpopulation and geographical distribution of accessions with tolerance or sensitivity under these two stress conditions, we found that the chilling tolerance group, which mainly consisted of japonica accessions, has a wider latitudinal distribution than the chilling sensitivity group. We conclude that the genetic basis of natural chilling stress tolerance in rice is distinct from that of cold shock stress frequently used for low-temperature treatment in the laboratory and the cold adaptability of rice is associated with the subpopulation and latitudinal distribution.

Detection of QTLs for cold tolerance of rice cultivar 'Kuchum' and effect of QTL pyramiding

A QTL for cold tolerance at the booting stage of rice cultivar 'Kuchum' was detected and delimited into a 1.36 Mb region, and a cold-tolerant line was developed by QTL pyramiding. Low temperature in summer causes pollen sterility in rice, resulting in a serious loss of yield. The second most widely grown rice cultivar in Japan, 'Hitomebore', has been developed as a cultivar highly tolerant to low temperature at the booting stage. However, even 'Hitomebore' exhibits sterility at a temperature lower than 18.5 °C. Further improvement of cold tolerance of rice is required. In the present study, QTLs for cold tolerance in a Bhutanese rice variety, 'Kuchum', were analyzed using backcrossed progenies and a major QTL, named qCT-4, was detected on chromosome 4. Evaluating cold tolerance of seven types of near isogenic lines having 'Kuchum' alleles around qCT-4 with a 'Hitomebore' genetic background, qCT-4 was delimited to a region of ca. 1.36 Mb between DNA markers 9_1 and 10_13. Homozygous 'Kuchum' alleles at qCT-4 showed an effect of increasing seed fertility by ca. 10 % under cold-water treatment. Near isogenic lines of 'Hitomebore' having 'Silewah' alleles of Ctb1 and Ctb2 and a 'Hokkai PL9' allele of qCTB8 did not exhibit higher cold tolerance than that of 'Hitomebore'. On the other hand, a qLTB3 allele derived from a Chinese cultivar 'Lijiangxintuanheigu' increased cold tolerance of 'Hitomebore', and pyramiding of the qCT-4 allele and the qLTB3 allele further increased seed fertility under cold-water treatment. Since NILs of 'Hitomebore' with the 'Kuchum' allele of qCT-4 were highly similar to 'Hitomebore' in other agronomic traits, the qCT-4 allele is considered to be useful for developing a cold-tolerant cultivar.

Identification and Fine Mapping of a Stably Expressed QTL for Cold Tolerance at the Booting Stage Using an Interconnected Breeding Population in Rice

Cold stress is one of the major abiotic stresses that impede rice production. A interconnected breeding (IB) population consisted of 497 advanced lines developed using HHZ as the recurrent parent and eight diverse elite indica lines as the donors were used to identify stably expressed QTLs for CT at the booting stage. A total of 41,754 high-quality SNPs were obtained through re-sequencing of the IB population. Phenotyping was conducted under field conditions in two years and three locations. Association analysis identified six QTLs for CT on the chromosomes 3, 4 and 12. QTL qCT-3-2 that showed stable CT across years and locations was fine-mapped to an approximately 192.9 kb region. Our results suggested that GWAS applied to an IB population allows better integration of gene discovery and breeding. QTLs can be mapped in high resolution and quickly utilized in breeding.

Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping

Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs.

Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress

Rice is highly sensitive to cold stress during reproductive developmental stages, and little is known about the mechanisms of cold responses in rice anther. Using the HiSeq™ 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Pei'ai64S) were analyzed at the fertility sensitive stage under cold stress. Approximately 243 million clean reads were obtained from four libraries and aligned against the oryza indica genome and 1497 and 5652 differentially expressed genes (DEGs) were identified in P64S and Y58S, respectively. Both gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for these DEGs. Functional classification of DEGs was also carried out. The DEGs common to both genotypes were mainly involved in signal transduction, metabolism, transport, and transcriptional regulation. Most of the DEGs were unique for each comparison group. We observed that there were more differentially expressed MYB (Myeloblastosis) and zinc finger family transcription factors and signal transduction components such as calmodulin/calcium dependent protein kinases in the Y58S comparison group. It was also found that ribosome-related DEGs may play key roles in cold stress signal transduction. These results presented here would be particularly useful for further studies on investigating the molecular mechanisms of rice responses to cold stress.

Mapping of quantitative trait loci (QTL) associated with plant freezing tolerance and cold acclimation

Most agronomic traits are determined by quantitative trait loci (QTL) and exhibit continuous distribution in segregating populations. The genetic architecture and the hereditary characteristics of these traits are much more complicated than those of oligogenic traits and need adapted strategies for deciphering. The model plant Arabidopsis thaliana is widely studied for quantitative traits, especially via the utilization of natural genetic diversity. Here we describe a QTL-mapping protocol for analyzing freezing tolerance after cold acclimation in this species based on its specific genetic tools. Nevertheless, this approach can also be applied for the elucidation of complex traits in other plant species.

Fine mapping of qRC10-2, a quantitative trait locus for cold tolerance of rice roots at seedling and mature stages

Cold stress causes various injuries to rice seedlings in low-temperature and high-altitude areas and is therefore an important factor affecting rice production in such areas. In this study, root conductivity (RC) was used as an indicator to map quantitative trait loci (QTLs) of cold tolerance in Oryza rufipogon Griff., Dongxiang wild rice (DX), at its two-leaf stage. The correlation coefficients between RC and the plant survival rate (PSR) at the seedling and maturity stages were –0.85 and –0.9 (P = 0.01), respectively, indicating that RC is a reliable index for evaluating cold tolerance of rice. A preliminary mapping group was constructed from 151 BC₂F₁ plants using DX as a cold-tolerant donor and the indica variety Nanjing 11 (NJ) as a recurrent parent. A total of 113 codominant simple-sequence repeat (SSR) markers were developed, with a parental polymorphism of 17.3%. Two cold-tolerant QTLs, named qRC10-1 and qRC10-2 were detected on chromosome 10 by composite interval mapping. qRC10-1 (LOD = 3.1, RM171-RM1108) was mapped at 148.3 cM, and qRC10-2 (LOD = 6.1, RM25570-RM304) was mapped at 163.3 cM, which accounted for 9.4% and 32.1% of phenotypic variances, respectively. To fine map the major locus qRC10-2, NJ was crossed with a BC₄F₂ plant (L188-3), which only carried the QTL qRC10-2, to construct a large BC₅F₂ fine-mapping population with 13,324 progenies. Forty-five molecular markers were designed to evenly cover qRC10-2, and 10 markers showed polymorphisms between DX and NJ. As a result, qRC10-2 was delimited to a 48.5-kb region between markers qc45 and qc48. In this region, Os10g0489500 and Os10g0490100 exhibited different expression patterns between DX and NJ. Our results provide a basis for identifying the gene(s) underlying qRC10-2, and the markers developed here may be used to improve low-temperature tolerance of rice seedling and maturity stages via marker-assisted selection (MAS).

Key Message

With root electrical conductivity used as a cold-tolerance index, the quantitative trait locus qRC10-2 was fine mapped to a 48.5-kb candidate region, and Os10g0489500 and Os10g0490100 were identified as differently expressed genes for qRC10-2.

Low temperature-responsive changes in the anther transcriptome's repeat sequences are indicative of stress sensitivity and pollen sterility in rice strains

Genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine responses to low temperatures in rice (Oryza sativa). We focused particularly on the rice anther at the booting stage, because a low temperature at this stage can result in pollen abortion. The five rice strains examined in this study showed different pollen fertilities due to a low-temperature treatment during the booting stage. The microarray analyses demonstrated that the low-temperature stress caused genome-wide changes in the transcriptional activities not only of genes but also of repeat sequences in the rice anther. The degree of the temperature-responsive changes varied among the five rice strains. Interestingly, the low-temperature-sensitive strains revealed more changes in the transcriptome when compared with the tolerant strains. The expression patterns of the repeat sequences, including miniature inverted-repeat transposable elements, transposons, and retrotransposons, were correlated with the pollen fertilities of the five strains, with the highest correlation coefficient being 0.979. Even in the low-temperature-sensitive strains, the transcriptomes displayed distinct expression patterns. The elements responding to the low temperatures were evenly distributed throughout the genome, and the major cis-motifs involved in temperature-responsive changes were undetectable from the upstream sequences in the corresponding repeats. The genome-wide responses of transcription to the temperature shift may be associated with chromatin dynamics, which facilitates environmental plasticity. A genome-wide analysis using repeat sequences suggested that stress tolerance could be conferred by insensitivity to the stimuli.

Rice and cold stress: methods for its evaluation and summary of cold tolerance-related quantitative trait loci

Cold stress adversely affects rice (Oryza sativa L.) growth and productivity, and has so far determined its geographical distribution. Dissecting cold stress-mediated physiological changes and understanding their genetic causes will facilitate the breeding of rice for cold tolerance. Here, we review recent progress in research on cold stress-mediated physiological traits and metabolites, and indicate their roles in the cold-response network and cold-tolerance evaluation. We also discuss criteria for evaluating cold tolerance and evaluate the scope and shortcomings of each application. Moreover, we summarize research on quantitative trait loci (QTL) related to cold stress at the germination, seedling, and reproductive stages that should provide useful information to accelerate progress in breeding cold-tolerant rice.

Comparative transcriptome profiling of chilling stress responsiveness in two contrasting rice genotypes

Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed a differential constitutive gene expression prior to stress and distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. A set of genes with higher basal expression were identified in chilling-tolerant LTH compared with chilling-sensitive IR29, indicating their possible role in intrinsic tolerance to chilling stress. Under chilling stress, the major effect on gene expression was up-regulation in the chilling- tolerant genotype and strong repression in chilling-sensitive genotype. Early responses to chilling stress in both genotypes featured commonly up-regulated genes related to transcription regulation and signal transduction, while functional categories for late phase chilling regulated genes were diverse with a wide range of functional adaptations to continuous stress. Following the cessation of chilling treatments, there was quick and efficient reversion of gene expression in the chilling-tolerant genotype, while the chilling-sensitive genotype displayed considerably slower recovering capacity at the transcriptional level. In addition, the detection of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, were involved in chilling stress tolerance. A number of the chilling-regulated genes identified in this study were co-localized onto previously fine-mapped cold-tolerance-related QTLs, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for chilling tolerance in rice.