Quantitative Trait Loci For Cold Tolerance Research Articles

Identification of QTLs for cold tolerance at the booting and flowering stages in rice (Oryza sativa L.)

Rice growth and productivity are greatly affected by cold stress, which is likely to become more of a hindrance for high and stable rice yields. To identify cold tolerance at the booting and flowering stages in rice, a recombinant inbred line was developed by crossing a cold-tolerant japonica cultivated variety, Jileng1, with a cold-sensitive indica cultivated variety, Milyang23. The seed setting rate (SST) of the parents and RIL population were investigated under different temperature environments, and the SST and cold stress tolerance index under natural low temperature were used to evaluate cold tolerance and quantitative trait locus (QTL) mapping. Fifteen QTLs were detected on chromosomes 1, 2, 3, 5, 7, 11 and 12, with log-likelihood values ranging from 2.64 to 4.76. These QTLs account for 3.34% to 12.02% of the phenotypic variance explained. Three QTLs, qCtb1, qCtb5 and qCtb12, were repeatedly detected in different conditions, and they were considered stably expressed QTLs. qCtb5 was localized to chromosome 5 marker between CMB0526.3 and ID5014265. In this interval or nearby, many cold-resistance QTLs have been identified in previous studies, so qCtb5 is considered a major cold-tolerance QTL. Thirteen QTLs with environmental interactions were also detected, and QTLs detected in single environment were all found to be involved in environmental interactions. These results show that environmental interactions have a significant effect on cold tolerance in rice. Stable expression of major QTLs will help to fine mapping cold-tolerance genes and provide gene resources to cultivate cold-tolerance rice varieties.

Mapping quantitative trait loci for cold tolerance in rice at seedling stage

Rice plants are sensitive to cold stress at various growth stages starting from germination to maturity. Exploitation of cold tolerance for the development of cold tolerant varieties may help in saving crop loss or cost of production in the cold prone environment. Introgression of quantitative trait loci (QTLs) conferring cold tolerance in the elite variety may be the most effective and sustainable approach to address this issue. A F2:3 mapping population of a cross between a cold susceptible variety (BR1) and a cold tolerant variety (BR18) was used to map QTLs for cold tolerance at seedling stage. Three significant QTLs on chromosomes 1, 3 and 12 associated with cold tolerance were mapped between the markers intervals of RM220-RM10829, RM546-RM7 and RM27877-RM463, respectively at a threshold LOD of 4.3 through composite interval mapping. Phenotypic contributions of these QTLs were 50.7, 39 and 52.7%, respectively. Marker information of such a large effect QTL could be used in the breeding program after necessary validation to develop cold tolerant high yielding rice varieties.

Dissecting the genetics of cold tolerance in a multiparental maize population.

We identify the largest amount of QTLs for cold tolerance in maize; mainly associated with photosynthetic efficiency, which opens new possibilities for genomic selection for cold tolerance in maize. Breeding for cold tolerance in maize is an important objective in temperate areas. The objective was to carry out a highly efficient study of quantitative trait loci (QTLs) for cold tolerance in maize. We evaluated 406 recombinant inbred lines from a multi-parent advanced generation intercross (MAGIC) population in a growth chamber under cold and control conditions, and in the field at early and normal sowing. We recorded cold tolerance-related traits, including the number of days from sowing to emergence, chlorophyll content and maximum quantum efficiency of photosystem II (Fv/Fm). Association mapping was based on genotyping with near one million single nucleotide polymorphism (SNP) markers. We found 858 SNPs significantly associated with all traits, most of them under cold conditions and early sowing. Most QTLs were associated with chlorophyll and Fv/Fm. Many candidate genes coincided between the current research and previous reports. These results suggest that (1) the MAGIC population is an efficient tool for identifying QTLs for cold tolerance; (2) most QTLs for cold tolerance were associated with Fv/Fm; (3) most of these QTLs were located in specific genomic regions, particularly bin 10.04; (4) the current study allows genetically improving cold tolerance with genome-wide selection.

Detection of QTLs for cold tolerance at the booting stage in near-isogenic lines derived from rice landrace Lijiangxintuanheigu

Chilling damage significantly reduces grain yield in rice, while exploring major quantitative trait loci (QTLs) has the potential to improve rice production. Mapping of QTLs for 5 cold tolerance-related traits at the booting stage was conducted with SSR markers and inclusive composite interval mapping (ICIM) approach, based on 105 near-isogenic lines derived from a backcross between Lijiangxintuanheigu (LTH, cold-tolerant landrace) and Towada (cold-sensitive cultivar). Phenotype values were investigated under five cold-stress environments and analysed by the best linear unbiased prediction (BLUP). Twenty-one QTLs were identified on chromosomes 1, 2, 3, 4, 6, 7, 10 and 11, and the amount of variation (R<sup>2</sup>) explained by each QTL ranged from 7.71 to 29.66%, with five co-located QTL regions. Eight novel major loci (qSF-2, qSF-6a, qSF-7, qGW-6, qDGWP-4, qDSWPP-4, qDWPP-1 and qDWPP-4b) were detected in several environments and BLUP, and their alleles were contributed by LTH with R<sup>2 </sup>variance from 12.24 to 29.66%. These favourable QTLs would facilitate elucidation of the genetic mechanism of cold tolerance and provide strategies for breeding high-productive rice.

Genome-Wide Association Mapping for Cold Tolerance in a Core Collection of Rice (Oryza sativa L.) Landraces by Using High-Density Single Nucleotide Polymorphism Markers From Specific-Locus Amplified Fragment Sequencing.

Understanding the genetic mechanism of cold tolerance in rice is important to mine elite genes from rice landraces and breed excellent cultivars for this trait. In this study, a genome-wide association study (GWAS) was performed using high-density single nucleotide polymorphisms (SNPs) obtained using specific-locus amplified fragment sequencing (SLAF-seq) technology from a core collection of landraces of rice. A total of 67,511 SNPs obtained from 116,643 SLAF tags were used for genotyping the 150 accessions of rice landraces in the Ting’s rice core collection. A compressed mixed liner model was used to perform GWAS by using the high-density SNPs for cold tolerance in rice landraces at the seedling stage. A total of 26 SNPs were found to be significantly (P < 1.48 × 10-7) associated with cold tolerance, which could explained phenotypic variations ranging from 26 to 33%. Among them, two quantitative trait loci (QTLs) were mapped closely to the previously cloned/mapped genes or QTLs for cold tolerance. A newly identified QTL for cold tolerance in rice was further characterized by sequencing, real time-polymerase chain reaction, and bioinformatics analyses. One candidate gene, i.e., Os01g0620100, showed different gene expression levels between the cold tolerant and sensitive landraces under cold stress. We found the difference of coding amino acid in Os01g0620100 between cold tolerant and sensitive landraces caused by polymorphism within the coding domain sequence. In addition, the prediction of Os01g0620100 protein revealed a WD40 domain that was frequently found in cold tolerant landraces. Therefore, we speculated that Os01g0620100 was highly important for the response to cold stress in rice. These results indicated that rice landraces are important sources for investigating rice cold tolerance, and the mapping results might provide important information to breed cold-tolerant rice cultivars by using marker-assisted selection.

Mapping QTLs for cold tolerance at seedling stage using an Oryza sativa × O. rufipogon backcross inbred line population

Tolerance to low temperature is an important factor affecting the growth and development of rice (Oryza sativa L.) at an early growing season in the temperate region, and at high altitudes of tropical regions. In this study, a backcross inbred line (BIL) population derived from an interspecific cross between Xieqingzao B (O. sativa L.) and an accession of Dongxiang wild rice (O. rufipogon Griff.) was used to identify quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage. Seedlings were treated with a temperature of 6°C for 2 days and seedling mortality was measured for QTL mapping. QTL analysis was performed on the whole BIL population and on one subpopulation that showed Xieqingzao B homozygous at QTL detected in the whole population. One major QTL, qSCT8, and one QTL, qSCT4.3, with smaller effect was found in the whole population. The QTLs qSCT8 and qSCT4.3 were mapped on chromosome 8 and 4, explaining 60.96% and 8.83% of the phenotypic variance, respectively. In the subpopulation, three QTLs, qSCT4.1, qSCT4.2 and qSCT12, accounting for 56.22%, 57.62% and 53.09% of the phenotypic variance, respectively, were detected on chromosome 4 and 12. At all five loci, the alleles introduced from the Dongxiang wild rice were effective in decreasing seedling mortality. Our results provide a basis for fine mapping and cloning of QTLs associated with cold tolerance, and the markers linked with QTLs could be used to improve the cold tolerance of rice varieties by marker-assisted selection.

Identification and validation of QTLs for cold tolerance at the booting stage and other agronomic traits in a rice cross of a Japanese tolerant variety, Hananomai, and a NERICA parent, WAB56-104

In Africa, cold temperatures occur in the highlands of East and Southern Africa and in some areas of the Sahel region of West Africa leading to substantial rice yield losses. Cold tolerance (CT) at booting stage on basis of spikelet fertility after cold water irrigation was evaluated using F2 population derived from a cross between temperate japonica, Hananomai, and tropical japonica, WAB56-104. Two Quantitative trait loci (QTLs) for CT were detected on chromosome 8 and 10 with enhanced effects on the trait coming from Hananomai and WAB56-104 allele, respectively. The QTLs explained 30% and 33% of phenotypic variation in spikelet fertility, respectively. CT was negatively correlated with panicle number (r = −0.35, p < 0.01) and positively correlated with panicle weight (r = 0.61, p < 0.001). Selected BC1F4 and BC1F5 genotypes having homozygous alleles for both CT QTLs exhibited higher spikelet fertility under cold stress. The identified QTLs will be useful in the development of cold-tolerant varieties for production in high altitude areas through marker-assisted selection.

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.

Effects of the number of pollen grains on cold tolerance at the booting stage in rice lines with QTLs for cold tolerance

This study was conducted to clarify the relationship between the number of pollen grains per anther and spikelet fertility under low temperature conditions in the rice cultivars and lines including lines with quantitative trait loci (QTL) for cold tolerance, adapted to the Tohoku region of northern Japan. Cold-water treatment decreased anther length, the number of pollen grains per anther, and spikelet fertility in all cultivars and lines. The number of pollen grains was proportional to anther length in all cultivars and lines and under all temperatures. Spikelet fertility decreased with decreasing the number of pollen grains in cold-water treatments at 18.5 and 19.3 °C. ‘Ouu 415’, with the qLTB3 QTL for cold tolerance, had 28% more pollen grains and 9% higher spikelet fertility than the recurrent parent, ‘Hitomebore’, in the 18.5 °C cold-water treatment, suggesting that qLTB3 increased both parameters. Lines with the qCTB8 QTL for cold tolerance had significantly more pollen grains in two of the three years and significantly higher spikelet fertility in all three years in the 19.3 °C cold-water treatment, suggesting that qCTB8 reinforced cold tolerance. Ctb1, a proposed cold-tolerance QTL, had no effect on the number of pollen grains or spikelet fertility. In conclusion, the cultivars and lines with more pollen grains had a higher cold tolerance. Some of QTLs were inferred to increase the number of pollen grains and reinforce cold tolerance.

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.

Mapping QTLs for cold tolerance at germination and the early seedling stage in rice (Oryza sativa L.)

Cold tolerance is an important breeding target in rice production. We studied quantitative trait loci (QTLs) controlling cold tolerance at germination (CTG) and early seedling (CTS) stages, using recombinant inbred lines derived from a japonica × indica cross. CTG was evaluated based on the percentage rate of germination at 15 °C for 12 days after pre-incubation of imbibed seeds at 20 °C for 2 days. For CTS, seven-day-old seedlings grown at 25 °C were subjected to two consecutive periods of three-day cold stress at 4 °C with an intervening eight-day recovery at 25 °C. CTS evaluation was according to an arbitrary five-point rating system at the fifth day of recovery after each stress period. No correlations were found between CTG and CTS, while a weak correlation was detected between CTS after the first and second stress. By the composite interval mapping, five QTLs for CTG explaining 5.7%–9.3% of the total phenotypic variance (PVE) and nine for CTS with PVE of 5.8%–35.6% were detected. Only one of these QTLs was common, indicating growth-stage specificity of cold tolerance. Four of the five QTLs after the second cold stress were different from the ones after the first cold stress. Analysis of variance test showed significant interactions between alleles at the QTL sites and the two stress conditions with respect to the mean CTS scores. A possible involvement of cold acclimation and usefulness of japonica germplasms in breeding for cold tolerance in indica rice was discussed.

Identification of QTLs for cold tolerance at seedling stage in rice (Oryza sativa L.) using two distinct methods of cold treatment

Cold water irrigation and growth in low temperature phytotron are two commonly used methods to evaluate cold tolerance of rice at the seedling stage and the cold sensitive seedlings exhibit different injury symptoms, respectively. However, so far no one has systematically dissected the differences of cold tolerance at seedling stage in rice under the two cold environments. We used a recombinant inbred line (RIL) population derived from a cross of a cold-tolerant japonica cultivar, Lijiangxintuanheigu and a cold sensitive indica cultivar, Sanhuangzhan-2 for this study. The cold sensitive seedlings exhibited leaf yellowing after cold water irrigation and leaf rolling during growth in the low temperature phytotron. Leaf yellowing and leaf rolling in RILs was significantly correlated, but the correlation coefficient was low. A total of four quantitative trait locus (QTLs) on chromosomes 1, 6, 9 and 12 were detected using leaf yellowing and percent seedling survival as indicators of cold tolerance after cold water irrigation, while five QTLs on chromosomes 7, 8, 9, 11 and 12 were detected using leaf rolling and percent seedling survival as indicators of cold tolerance during growth in the low temperature phytotron. The two QTLs, qCTS-9 and qCTS-12 were detected using different evaluation indicators under the two cold environments. Our results suggest that rice cold tolerance mechanisms at the seedling stage differ between the two environments, but the detection of common QTL implies the existence of overlap in the metabolic pathways for cold tolerance. The two common QTLs have potential value in rice breeding.

Microarray-Assisted Fine-Mapping of Quantitative Trait Loci for Cold Tolerance in Rice

Many important agronomic traits, including cold stress resistance, are complex and controlled by quantitative trait loci (QTLs). Isolation of these QTLs will greatly benefit the agricultural industry but it is a challenging task. This study explored an integrated strategy by combining microarray with QTL-mapping in order to identify cold-tolerant QTLs from a cold-tolerant variety IL112 at early-seedling stage. All the early seedlings of IL112 survived normally for 9 d at 4-5°C, while Guichao2 (GC2), an indica cultivar, died after 4 d under the same conditions. Using the F2:3 population derived from the progeny of GC2 and IL112, we identified seven QTLs for cold tolerance. Furthermore, we performed Affymetrix rice whole-genome array hybridization and obtained the expression profiles of IL112 and GC2 under both low-temperature and normal conditions. Four genes were selected as cold QTL-related candidates, based on microarray data mining and QTL-mapping. One candidate gene, LOC_Os07g22494, was shown to be highly associated with cold tolerance in a number of rice varieties and in the F2:3 population, and its overexpression transgenic rice plants displayed strong tolerance to low temperature at early-seedling stage. The results indicated that overexpression of this gene (LOC_Os07g22494) could increase cold tolerance in rice seedlings. Therefore, this study provides a promising strategy for identifying candidate genes in defined QTL regions.

Identification of Cold‐Tolerant Breeding Lines by Quantitative Trait Loci Associated with Cold Tolerance in Rice

ABSTRACTLow temperature or cold stress is one of the major abiotic stresses limiting rice (Oryza sativa L.) production and productivity in the temperate rice growing regions as well as in tropical high lands worldwide. Low temperature at the reproductive stage causes high sterility and decreases production. In this study, we assessed recombinant inbred lines (RILs) that possessed cold‐tolerance genes and/or quantitative trait loci (QTL) from the donor line IR66160‐121‐4‐4‐2 in the genetic background of a cold‐sensitive japonica cultivar, Geumobyeo. The selected 15 RILs with QTL for cold tolerance were phenotyped for three main agronomic traits—culm length (CL), days to heading (DTH), and spikelet fertility (SF)—which were most affected during cold stress. The RILs with cold‐tolerant and cold‐sensitive parents were evaluated under cold‐water (18–19°C) irrigation in the field and cold‐air temperature (17–18°C) in the temperature‐controlled greenhouse. The RILs showed significant differences in these traits compared to the cold‐sensitive parent. Traits CL and DTH exhibited positive correlation with SF in the selected breeding lines. The SF of the selected breeding lines was higher (51–81%) than that of the cold‐sensitive parent, Geumobyeo (7%). Our results confirmed that cold tolerance was associated with SF but the traits CL and DTH were differently associated with cold tolerance. The cold‐tolerant breeding lines selected in this study had at least one of the three QTL associated with cold tolerance. The breeding lines confirmed to have cold tolerance are useful to breed cold‐tolerant cultivars and increase our understanding of the mechanism of cold tolerance in rice.

Identification and fine mapping of a major quantitative trait locus originating from wild rice, controlling cold tolerance at the seedling stage

Cold tolerance at the seedling stage (CTSS) is an important trait affecting stable rice production in temperate climates and areas of high elevation. In this study, 331 single nucleotide polymorphism (SNP) markers were developed and used along with phenotypic evaluation to identify quantitative trait loci (QTLs) associated with CTSS from a mapping population of 184 F(2) plants derived from a cold tolerant wild rice, W1943 (Oryza rufipogon), and a sensitive indica cultivar, Guang-lu-ai 4 (GLA4). Three QTLs were detected on chromosomes 3, 10 and 11. A major locus, qCtss11 (QTL for cold tolerance at seedling stage), was located on the long arm of chromosome 11 explaining about 40% of the phenotypic variation. Introduction of the W1943 allele of qCtss11 to the GLA4 genetic background increased CTSS. Based on the phenotypic and genotypic assessment of advanced backcross progenies, qCtss11 was dissected as a single Mendelian factor. A high-resolution genetic map was constructed using 23 markers across the qCtss11 locus. As a result, qCtss11 was fine mapped to a 60-kb candidate region defined by marker AK24 and GP0030 on chromosome 11, in which six genes were annotated. Expression and resequence analyses of the six candidates supported the hypothesis that Os11g0615600 and/or Os11g0615900 are causal gene(s) of the CTSS.

Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line

Low temperature at the booting stage is a serious abiotic stress in rice, and cold tolerance is a complex trait controlled by many quantitative trait loci (QTL). A QTL for cold tolerance at the booting stage in cold-tolerant near-isogenic rice line ZL1929-4 was analyzed. A total of 647 simple sequence repeat (SSR) markers distributed across 12 chromosomes were used to survey for polymorphisms between ZL1929-4 and the cold-sensitive japonica cultivar Towada, and nine were polymorphic. Single marker analysis revealed that markers on chromosome 7 were associated with cold tolerance. By interval mapping using an F(2) population from ZL1929-4 x Towada, a QTL for cold tolerance was detected on the long arm of chromosome 7. The QTL explained 9 and 21% of the phenotypic variances in the F(2) and F(3) generations, respectively. Recombinant plants were screened for two flanking markers, RM182 and RM1132, in an F(2) population with 2,810 plants. Two-step substitution mapping suggested that the QTL was located in a 92-kb interval between markers RI02905 and RM21862. This interval was present in BAC clone AP003804. We designated the QTL as qCTB7 (quantitative trait locus for cold tolerance at the booting stage on chromosome 7), and identified 12 putative candidate genes.

Identification and analysis of QTLs controlling cold tolerance at the reproductive stage and validation of effective QTLs in cold-tolerant genotypes of rice (Oryza sativa L.)

Low temperature or cold stress is one of the major constraints of rice production and productivity in temperate rice-growing countries and high-altitude areas in the tropics. Even though low temperature affects the rice plant in all stages of growth, the percent seed set is damaged severely by cold and this reduces the yield potential of cultivars significantly. In this study, a new source of cold-tolerant line, IR66160-121-4-4-2, was used as a donor parent with a cold-sensitive cultivar, Geumobyeo, to produce 153 F(8) recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis. QTL analysis with 175 polymorphic simple sequence repeat (SSR) markers and composite interval mapping identified three main-effect QTLs (qPSST-3, qPSST-7, and qPSST-9) on chromosomes 3, 7, and 9. The SSR markers RM569, RM1377, and RM24545 were linked to the identified QTLs for cold tolerance with respect to percent seed set using cold-water (18-19 degrees C) irrigation in the field and controlled air temperature (17 degrees C) in the greenhouse. The total phenotypic variation for cold tolerance contributed by the three QTLs was 27.4%. RILs with high percent seed set under cold stress were validated with linked DNA markers and by haplotype analysis that revealed the contribution of progenitor genomes from the tropical japonica cultivar Jimbrug (Javanica) and temperate japonica cultivar Shen-Nung89-366. Three QTLs contributed by the cold-tolerant parent were identified which showed additive effect on percent seed set under cold treatment. This study demonstrated the utility of a new phenotyping method as well as the identification of SSR markers associated with QTLs for selection of cold-tolerant genotypes to improve temperate rice production.

Quantitative Trait Locus Analysis for Cold Tolerance at the Booting Stage in a Rice Cultivar, Hatsushizuku

We evaluated cold tolerance at the booting stage on the basis of seed fertility after cool-water treatment for three years (2005-2007) in 114 recombinant inbred lines (RILs) between temperate japonicas, Kirara397 (cold-sensitive) and Hatsushizuku (cold-tolerant). Composite interval mapping (CIM) was performed to identify quantitative trait locus (QTL) for cold tolerance. A QTL for cold tolerance at the booting stage was reproducibly detected in three trials on chromosome 1. Contribution of the QTL to the phenotypic variation ranged from 16.2 to 47.3%, and their additive effects were all towards Hatsushizuku. We also analyzed QTL for heading time and culm length, which are thought to affect cold tolerance. A QTL for heading time and that for culm length was detected every three years on the neighboring regions of chromosome 10, while no QTL for the two traits was detected on chromosome 1. These results suggest that the QTL on chromosome 1 has a major effect on the variation of cold tolerance between Kirara397 and Hatsushizuku without affecting heading time and culm length.

A quantitative trait locus for cold tolerance at the booting stage on rice chromosome 8

A quantitative trait locus (QTL) for cold tolerance at the booting stage of a cold-tolerant rice breeding line, Hokkai-PL9, was analyzed. A total of 487 simple sequence repeat (SSR) markers distributed throughout the genome were used to survey for polymorphism between Hokkai-PL9 and a cold-sensitive breeding line, Hokkai287, and 54 markers were polymorphic. Single marker analysis revealed that markers on chromosome 8 are associated with cold tolerance. By interval mapping using an F(2) population between Hokkai-PL9 and Hokkai287, a QTL for cold tolerance was detected on the short arm of chromosome 8. The QTL explains 26.6% of the phenotypic variance, and its additive effect is 11.4%. Substitution mapping suggested that the QTL is located in a 193-kb interval between SSR markers RM5647 and PLA61. We tentatively designated the QTL as qCTB8 (quantitative trait locus for cold tolerance at the booting stage on chromosome 8).

A genome scan of a four-way tilapia cross supports the existence of a quantitative trait locus for cold tolerance on linkage group 23

A genome scan, searching for quantitative trait loci (QTL) for the traits cold tolerance and body weight in tilapia, was performed on a cross between a (Oreo- chromis niloticusSarotherodon galilaeus )m ale and a( O. mossambicusO. aureus) female. Fifty-four microsatellites and 23 ampli¢ed fragment length polymorphism (AFLP) primer combinations were genotyped and tested for marker^trait associations. Sex-speci¢c linkage maps were constructed from this data. Twenty-three point-wise signi¢cant marker^ trait associations were found in the genome scan, and putative QTL were subsequently tested in another (OnSg) � (OmOa) family. None of the putative QTL from the ¢rst experiment were signi¢- cant in the second experiment. However, one micro- satellite, UNH130, found to be associated to weight in the ¢rst experiment, was found to be strongly asso- ciated to cold tolerance in the second experiment. Since QTL for cold tolerance and body weight were recently found on the linkage group containing UNH130 (linkage group 23) in another study, this linkage group was investigated more closely using in- terval mapping. The results provide indications, but not conclusive evidence, of a QTL for cold tolerance on linkage group 23.