Trait Loci For Cold Tolerance Research Articles

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.

Mapping of quantitative trait loci for cold tolerance at the early seedling stage in landrace rice Xiang 743

Cold tolerance at the early seedling stage of rice is one of the major determinants for uniform seedling growth. The trait is complex and controlled by quantitative trait loci (QTLs). In this study, a linkage map consisting of 129 SSR markers was constructed, spanning 2,051.1 cM with ranging from 4.3 to 36.5 cM between adjacent markers. QTLs analysis at the early seedling stage was performed using two F2:3 populations derived from the cross of the highly cold tolerant Hunan landrace Xiang 743, as a donor, with two cold-sensitive varieties Katy and Dular, respectively. A total of seven QTLs were identified in the population of Xiang 743/Katy and distributed on six chromosomes, accounting for 47.26 % of phenotypic contribution. No epistatic interaction was detected between the putative QTLs. In addition, a total of five QTLs were detected in the population of Xiang 743/Dular, and all the alleles increasing the tolerance were from Xiang 743 and located in similar intervals as identified in the population of Xiang 743/Katy. A major locus on chromosome eight was detected with LOD value of 6.11 and 15.83 and phenotypic contribution of 14.45 and 38.94 %, in Xiang 743/Katy and Xiang 743/Dular populations, respectively. The identification of QTLs will be useful for incorporating them into cold-sensitive elite cultivars to improve seedling cold tolerance in future rice breeding programs.

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 MessageWith 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.

Quantitative trait loci for cold tolerance of rice recombinant inbred lines in low temperature environments.

Low temperature is one of the major environmental stresses in rice cultivation in high-altitude and high-latitude regions. In this study, we cultivated a set of recombinant inbred lines (RIL) derived from Dasanbyeo (indica) / TR22183 (japonica) crosses in Yanji (high-latitude area), Kunming (high-altitude area), Chuncheon (cold water irrigation) and Suwon (normal) to evaluate the main effects of quantitative trait loci (QTL) and epistatic QTL (E-QTL) with regard to their interactions with environments for cold-related traits. Six QTLs for spikelet fertility (SF) were identified in three cold treatment locations. Among them, four QTLs on chromosomes 2, 7, 8, and 10 were validated by several near isogenic lines (NILs) under cold treatment in Chuncheon. A total of 57 QTLs and 76 E-QTLs for nine cold-related traits were identified as distributing on all 12 chromosomes; among them, 19 QTLs and E-QTLs showed significant interactions of QTLs and environments (QEIs). The total phenotypic variation explained by each trait ranged from 13.2 to 29.1% in QTLs, 10.6 to 29.0% in EQTLs, 2.2 to 8.8% in QEIs and 1.0% to 7.7% in E-QTL × environment interactions (E-QEIs). These results demonstrate that epistatic effects and QEIs are important properties of QTL parameters for cold tolerance at the reproductive stage. In order to develop cold tolerant varieties adaptable to wide-ranges of cold stress, a strategy facilitating marker-assisted selection (MAS) is being adopted to accumulate QTLs identified from different environments.

Identification of quantitative trait loci for cold tolerance during the germination and seedling stages in rice (Oryza sativa L.)

Low temperature is a serious abiotic stress affecting rice production in subtropical and temperate areas. In this study, cold tolerance of rice at the germination and seedling stages were evaluated using one recombinant inbred line (RIL) population derived from a cross between Daguandao (japonica), with highly cold-tolerant at the seedling stage, and IR28 (indica), with more cold-tolerant at the germination stage, and the quantitative trait loci (QTL) mapping was conducted using the multiple interval mapping (MIM) approach. Continuous segregation in low temperature germinability (LTG) and cold tolerance at the seedling stage (CTS) were observed among the RIL populations. Most RILs were moderately susceptible or tolerant at the germination stage, but were susceptible at the seedling stage. No significant relationship was found in cold tolerance between the germination and seedling stages. A total of seven QTLs were identified with limit of detection (LOD) >3.0 on chromosomes 3, 8, 11 and 12, and the amount of variation (R2) explained by each QTL ranged from 5.5 to 22.4%. The rice LTG might be regulated by two minor QTLs, with the CTS controlled by one major QTL [qCTS8.1 (LOD = 16.1, R2 = 22.4%)] and several minor loci. Among these loci, one simultaneously controls LTG (qLTG11.1) and CTS (qCTS11.1). Several cold-tolerance-related QTLs identified in previous studies were found to be near the QTLs detected here, and three QTLs are novel alleles. The alleles from Daguandao at six QTLs increased cold tolerance and could be good sources of genes for cold tolerance. In addition, only one digenic interaction was detected for CTS, with a R2 value of 6.4%. Those major or minor QTLs could be used to significantly improve cold tolerance by marker-assisted selection (MAS) in rice.

Detection of a novel quantitative trait locus for cold tolerance at the booting stage derived from a tropical japonica rice variety Silewah

Cold stress at the booting stage in rice induces spikelet sterility because of aberrant microspore development, which often seriously damages seed production. Some breeding lines with high cold tolerance were developed by using tropical japonica variety Silewah as a donor of cold tolerance; however, the genetic factors that confer cold tolerance of this variety have not been comprehensively analyzed. In this study, phenotypic and molecular characterization of novel cold-tolerant strains derived from crosses with Silewah was performed to identify quantitative trait loci (QTLs) responsible for cold tolerance. Molecular marker analysis revealed that 2 cold-tolerant strains carried chromosomal segments of Silewah at the same genomic regions on chromosomes 3, 4 and 11. Single marker analysis in segregating population confirmed that the allele of Silewah on chromosome 3 (qCTB3-Silewah) conferred cold tolerance. The effect of qCTB3-Silewah was supported by the fact that this allele had been a target of selection during developing a breeding line by phenotypic selection from backcrossed progenies with an elite variety as a recurrent parent. qCTB3 is a different QTL from those reported for Silewah previously, suggesting that different QTLs might be exploited in different breeding programs depending on the genetic backgrounds and environmental conditions.

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.

Map-based cloning of the rice cold tolerance gene Ctb1

Low temperatures during the booting stage reduce rice yields by causing cold-induced male sterility. We previously mapped a quantitative trait locus for cold tolerance, Ctb1, to a 56-kb region containing 7 putative genes. In this study we further mapped Ctb1 to a 17-kb region containing two genes that encode an F-box protein and a ser/thr protein kinase. The F-box protein gene was preferentially expressed in young panicles, while the ser/thr protein kinase gene was expressed in leaves and young panicles. Both genes were cloned from a cold-tolerant variety, Norin-PL8, and introduced into a cold-sensitive variety, Hokkai241, and a cold-sensitive line, BT4-74-8. The cold tolerance of T 2 and T 3 progenies was assessed by measuring the degree of spikelet fertility in plants treated with cool water irrigation (19 °C, 25 cm) or cool air (12 °C, 4 days). The results indicated that the F-box protein gene confers cold tolerance. Cold tolerance is associated with greater anther length, and the transgenic plants had longer anthers than non-transformed controls. The F-box protein interacts with a subunit of the E3 ubiquitin ligase, Skp1, suggesting that an ubiquitin–proteasome pathway is involved in cold tolerance at the booting stage.

Identification and mapping of quantitative trait loci for cold tolerance at the booting stage in a japonica rice near-isogenic line

Near-isogenic lines (NILs) are preferred materials for mapping quantitative trait loci (QTLs) and for evaluating gene action or interaction. We developed a set of NILs with cold tolerance at the booting stage by backcrossing the strongly cold-tolerant japonica landrace, Kunmingxiaobaigu (KMXBG) to cold-sensitive japonica cultivar, Towada, as the recipient parent. A BC 4F 5 line was selected as a parent to construct a BC 5F 2 segregating population from which BC 5F 3 lines were developed. Cold tolerance at the booting stage was evaluated on the basis of spikelet fertility of main panicles over 2 years and two locations. Using a LOD significance threshold of 3.0, compositive interval mapping based on a mixed linear model revealed eight QTLs on chromosomes 1, 4, 5, 10 and 11. They were tentatively designated qCTB-1-1, qCTB-4-1, qCTB-4-2, qCTB-5-1, qCTB-5-2, qCTB-10-1, qCTB-10-2 and qCTB-11-1. All alleles for cold tolerance were contributed by KMXBG, and the marker intervals containing them were narrowed to 0.6–5.6 cM. Genetic distances between the peaks of the QTL and nearest markers varied from 0 to 1.3 cM. The variance explained by a single QTL ranged from 0.90 to 14.86%. Four QTLs, qCTB-1-1, qCTB-4-1, qCTB-5-1, qCTB-5-2 and qCTB-10-1, were detected in two or more trials. Comparisons with previous studies indicated that these QTLs were reliable. Our study sets a foundation for cloning cold-tolerance genes and provides opportunities to understand the mechanism of cold tolerance at the booting stage.

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.

Mapping of Quantitative Trait Loci for Cold Tolerance in Weedy Rice

A quantitative trait locus (QTL) analysis was carried out with a recombinant inbred line (RIL) population to identify the chromosomal regions responsible for cold tolerance of rice (Oryza sativa L.). The RIL population, consisting of 80 lines, was developed from a cross between the indica cultivar, Milyang 23 and the japonica weedy rice, Hapcheonaengmi 3. The population was genotyped with 2 morphological and 132 DNA markers, providing an average interval size of 11.3 cM, and was also evaluated for traits related to agricultural performance in cold water and in control plots. The RILs showed delayed heading and reduced culm length in the cold water plot and the differences in heading date and culm length between two plots were statistically significant. Cold tolerance was measured as days to heading, culm length, spikelet fertility, leaf discoloration, and panicle exsertion in the cold water plot, and difference in days to heading and the reduction ratio of culm length between two plots. A total of 14 QTLs for 7 traits were identified using single point and composite interval analysis. The number of QTLs per trait ranged from one to three. Phenotypic variation associated with each QTL ranged from 5.8 to 32.8%. No digenic interaction was detected. Several QTLs associated with cold tolerance were clustered in a few chromosomal blocks. For 11 (78.6%) of the QTLs identified in this study, the Hapcheonaengmi 3-derived alleles contributed desirable effects and favorable alleles were detected for difference in days to heading, spikelet fertility, panicle exsertion and leaf discoloration. From this study, it can be concluded that weedy rice is useful as a source of valuable alleles for breeding cold tolerance in rice.

Analysis of Quantitative Trait Loci for Cold Tolerance at the Booting Stage of Rice

We analyzed the quantitative trait loci (QTLs) for cold tolerance at the booting stage of a cold-tolerant rice variety, Norin-PL8, which harbors cold tolerance genes derived from a cold-tolerant variety, Silewah. We foundthat 5 segments on chromosomes 1 (2 segments), 3, 4 and 8 were incorporated from Silewah into Norin-PL8. The association between the incorporated segments and cold tolerance was examined using BC 1 F 5 lines between Norin-PL8 and Kirara397, which is a cold-sensitive commercial variety. The segment on the short arm of chromosome 3 and that on the long arm of chromosome 4 were associated with cold tolerance, indicating the presence of QTLs for cold tolerance on chromosomes 3 and 4. Interval mapping on the long arm of chromosome 4 suggested that 2 QTLs were located in the centromeric half of the incorporated segment. In order to confirm the results of interval mapping, we developed a set of near-isogenic lines (NILs). Comparison of the levels of cold tolerance of the NILs indicated that either the proximal end or the center of the segment is necessary for cold tolerance. Based on these results, it was concluded that there are at least 3 QTLs for cold tolerance on chromosomes 3 and 4.

Identification of two closely linked quantitative trait loci for cold tolerance on chromosome 4 of rice and their association with anther length

Norin-PL8 is a cold-tolerant variety of rice (Oryza sativa L.) that was developed by introgressing chromosomal segments from a cold-tolerant javanica variety, Silewah. We previously detected quantitative trait loci (QTLs) for cold tolerance of Norin-PL8 in the introgressions on chromosomes 3 and 4. We provide fine mapping of the QTLs on chromosome 4 and the association between the QTLs and anther length, which has been reported to be a major component of cold tolerance. Interval mapping using a segregating population derived from an advanced backcross progeny indicated that a QTL for cold tolerance is probably located from the center to the proximal end of the introgression. For fine mapping, we developed a set of near-isogenic lines (NILs) from recombinants in the segregating population. Comparison of cold tolerance between the NILs indicated that either the proximal end or the center of the introgression is necessary for cold tolerance. From these results, we concluded that there are at least two QTLs for cold tolerance, tentatively designated as Ctb-1 and Ctb-2, in the introgression on chromosome 4. The map distance between Ctb-1 and Ctb-2 is estimated to be 4.7–17.2 cM. In order to investigate the mechanism underlying cold tolerance by the QTLs, we compared anther lengths of the NILs. The results indicate that both Ctb-1 and Ctb-2 are associated with anther length.

GENETIC MAPPING OF RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS IN CITRUS

Genetic mapping with RAPD markers has been initiated in Citrus. Reproducible polymorphism of amplified DNA fragments has been revealed with approximately half of the 80 random primers thus far tested. Apparent segregating loci revealed with these primers are being analyzed for reproducibility, inheritance, and linkage using 60 BC, progeny from an intergeneric cross of Citrus grandis (L.) Osb. × [C. grandis × Poncirus trifoliata (L.) Raf.]. This progeny population has been previously used to map 57 isozyme and RFLP markers [Durham et al., Theor. Appl. Genet. (1992) 84:39]. Thus far 70 RAPD markers have been placed on the map; a current map will be presented. We hope to use a highly populated linkage map to map quantitative trait loci for cold tolerance in this cross between very cold-sensitive C. grandis and extremely cold-hardy P. trifoliata. As a part of this project, we have thus far isolated 6 unique cold acclimation responsive cDNA clones through differential screening of a library constructed from cold acclimated tissue of P. trifoliata. Work is also in progress to place these clones on the linkage map.