Mapping of QTLs associated with cold tolerance during the vegetative stage in rice

Low-temperature stress is an important factor affecting the growth and development of rice (Oryza sativa L.) in temperate and high-elevation areas. Cold stress may cause various seedling injuries, delayed heading and yield reduction due to spikelet sterility. In this study, 181 microsatellite marker loci were used to identify quantitative trait loci (QTLs) associated with cold tolerance at the vegetative stage in 191 recombinant inbred lines (RILs) derived from a cross of a cold-tolerant temperate japonica cultivar (M-202) with a cold-sensitive indica cultivar (IR50). Different temperature regimes were applied in growth chambers on 191 RILs. The temperature regimes imposed in the growth chamber simulated cold-stress injuries at the seedling and late vegetative stages. In this study a major QTL was identified on chromosome 12, designated as qCTS12a, that was closely associated with cold-induced necrosis and wilting tolerance, and accounted for 41% of the phenotypic variation. A number of QTLs with smaller effects were also detected on eight rice chromosomes.     

水稻萌发耐淹性的遗传分析

水稻(Oryza sativa)萌发耐淹性受到复杂的网络调控, 其分子机制不同于苗期耐淹性的相关机制, 萌发耐淹性的强弱影响着直播稻的成苗率。通过对256份水稻核心种质的萌发耐淹性评估, 发现粳稻和籼稻之间的萌发耐淹性差异并不显著, 都存在广泛的遗传变异。利用以粳稻R0380为供体亲本, 籼稻RP2334为轮回亲本的170个高代回交自交系构建含146个分子标记的连锁图谱, 以低氧胚芽鞘长度为性状指标, 通过复合区间作图法检测到影响萌发耐淹性的4个QTLs(quantitative trait loci), 分别定位于第2(2个)、3(1个)和8号(1个)染色体。贡献率最大的QTL为qGS2.2, 其值为17.34%, 增效等位基因来自轮回亲本籼稻RP2334; 其余3个QTLs的增效等位基因均来自供体亲本粳稻R0380, 贡献率分别为12.86%、9.37%和14.60%。     

Identification of QTLs with main, epistatic and QTL?×?environment interaction effects for salt tolerance in rice seedlings under different salinity conditions

Salt tolerance of rice (Oryza sativa L.) at the seedling stage is one of the major determinants of its stable establishment in saline soil. One population of recombinant inbred lines (RILs, F (2:9)) derived from a cross between the salt-tolerant variety Jiucaiqing and the salt-sensitive variety IR26 was used to determine the genetic mechanism of four salt tolerance indices, seedling height (SH), dry shoot weight (DSW), dry root weight (DRW) and Na/K ratios (Na/K) in roots after 10 days in three salt concentrations (0.0, 0.5 and 0.7 % NaCl). The main effect QTLs (M-QTLs) and epistatic QTLs (E-QTLs) were detected by QTL IciMapping program using single environment phenotypic values. Eleven M-QTLs and 11 E-QTLs were identified for the salt tolerance indices. There were six M-QTLs and two E-QTLs identified for SH, three M-QTLs and five E-QTLs identified for DSW, two M-QTLs and one E-QTL identified for DRW, and three E-QTLs identified for Na/K. The phenotypic variation explained by each M-QTL and E-QTL ranged from 7.8 to 23.9 % and 13.3 to 73.7 %, respectively. The QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values. Six M-QTLs and five E-QTLs were identified. The phenotypic variation explained by each QTL and QTL × environment interaction ranged from 0.95 to 6.90 % and 0.02 to 0.50 %, respectively. By comparing chromosomal positions of these M-QTLs with those previously identified, five M-QTLs qSH1.3, qSH12.1, qSH12.2, qDSW12.1 and qDRW11 might represent novel salt tolerance genes. Five selected RILs with high salt tolerance had six to eight positive alleles of the M-QTLs, indicating that pyramiding by marker-assisted selection (MAS) of M-QTLs can be applied in rice salt tolerance breeding programs.     

基于染色体置换系的普通野生稻耐盐性QTL定位

本研究分别利用SSR标记、InDel标记以及简化基因组测序技术对一套以普通野生稻为供体亲本,9311为受体亲本的染色体置换系进行基因型鉴定,并通过对其不同生育期的耐盐性鉴定,共发掘2个与发芽期耐盐相关的QTL,13个与苗期耐盐性相关的QTL。其中与苗期存活率相关的QTL qSSR5.1、苗期耐盐等级相关的QTL qSSG5.1均被定位于同一位点,该位点对苗期存活率、苗期耐盐等级均具有增效作用,贡献率分别为6.36%、8.13%。在此QTL内包含与非生物胁迫相关基因OsDi19-1。经序列比对发现,OsDi19-1启动子区域在两亲本间存在较大差异,且受到盐胁迫时该基因表达量上升。同时,鉴定出水稻芽期耐盐的优异种质资源CSSL72、苗期耐盐的优异种质资源CSSL23、CSSL153,为水稻育种中耐盐性的改良提供了新的种质资源。     

Quantitative trait loci mapping of resistance to Laodelphax striatellus (Homoptera: Delphacidae) in rice using recombinant inbred lines

Laodelphax striatellus Fallén (Homoptera: Delphacidae), is a serious pest in rice, Oryza sativa L., production. A mapping population consisting of 81 recombinant inbred lines (RILs), derived from a cross between japonica' Kinmaze' and indica' DV85' rice, was used to detect quantitative trait loci (QTLs) for the resistance to L. striatellus. Seedbox screening test (SST), antixenosis test, and antibiosis test were used to evaluate the resistance response of the two parents and 81 RILs to L. striatellus at the seedling stage, and composite interval mapping was used for QTL analysis. When the resistance was measured by SST method, two QTLs conferring resistance to L. striatellus were mapped on chromosome 11, namely, Qsbph11a and Qsbph11b, with log of odds scores 2.51 and 4.38, respectively. The two QTLs explained 16.62 and 27.78% of the phenotypic variance in this population, respectively. In total, three QTLs controlling antixenosis against L. striatellus were detected on chromosomes 3, 4, and 11, respectively, accounting for 37.5% of the total phenotypic variance. Two QTLs expressing antibiosis to L. striatellus were mapped on chromosomes 3 and 11, respectively, explaining 25.9% of the total phenotypic variance. The identified QTL located between markers XNpb202 and C1172 on chromosome 11 was detected repeatedly by three different screening methods; therefore, it may be important to confer the resistance to L. striatellus. Once confirmed in other mapping populations, these QTLs should be useful in breeding for resistance to L. striatellus by marker-assisted selection of different resistance genes in rice varieties.     

QTLs mapping of physiological traits related to salt tolerance in young rice seedlings

Oryza sativa L. F₂ population and F_2:3 derived from a cross between salt tolerance cv. Tarommahali and salt sensitive cv. Khazar were used in this study. A linkage map based on F₂ population was constructed (74 SSR markers on 192 individuals), which covered a total of 1231.50 cM with an average two locus interval of 19.83 cM. Two QTLs related to Na⁺/K⁺ ratio were found on chromosome 3 and 6. qDM-3 and qDM-8 (for dry mass of shoot) are major QTLs with very large effects explained 20.90 and 17.72 % of the total phenotypic variance, respectively. Major locus for DM (qDM-3) was bracketed by RM1022 — RM6283 spread over 13.6 cM on chromosome 3. Major part of the variability for standard tolerance ranking (STR) was explained by the qSTR-6 flanked by RM3727 — RM340 on chromosome 6, which exhibited phenotypic variance of 17.25 % and peak likelihood ratio (LR) of 17.51. The length of this QTL is 8.8 cM and identification of any tightly linked markers in this region will serve as a candidate gene for fine-mapping. qSTR-3 overlapped with qNA-3 and qNAK-3. The qSTR-3 may contain a new major gene for salt stress tolerance at seedling stage in rice. Major QTLs identified in this paper, after fine-mapping, could be used for marker assisted selection.     

Heavy genetic load associated with the subspecific differentiation of japonica rice (Oryza sativa ssp. japonica L.)

Genetic load in the genome of the model species, rice, was genetically dissected by mapping quantitative trait loci (QTLs) affecting the radiosensitivity of 226 recombinant inbred lines (RILs) to gamma-ray- and spaceflight-induced radiation. The parents and RILs varied considerably in their radiosensitivity to gamma-ray irradiation. A total of 28 QTLs affecting the two index traits, seedling height (SH) and seed fertility (SF), of radiosensitivity were identified. The japonica parent, Lemont, was much more sensitive to gamma-ray irradiation than the indica parent, Teqing, and its alleles at almost all QTLs were associated with increased radiosensitivity, suggesting a much higher genetic load in the japonica genome of rice. Six QTLs (QSh2a, QSh2b, QSh5a, QSh7, QSf3b, and QSf10b) were located in the genomic regions particularly sensitive to radiation and thus might represent possible 'mutation hot spots' in the japonica genome. Detailed characterization of these genomic regions may shed light on the evolution and subspecific differentiation of rice.     

QTL Analysis of Na+ and K+ Concentrations in Roots and Shoots under Different Levels of NaCl Stress in Rice (Oryza sativa L.)

The key to plant survival under NaCl salt stress is maintaining a low Na⁺ level or Na⁺/K⁺ ratio in the cells. A population of recombinant inbred lines (RILs, F_2∶9) derived from a cross between the salt-tolerant japonica rice variety Jiucaiqing and the salt-sensitive indica variety IR26, was used to determine Na⁺ and K⁺ concentrations in the roots and shoots under three different NaCl stress conditions (0, 100 and 120 mM NaCl). A total of nine additive QTLs were identified by QTL Cartographer program using single-environment phenotypic values, whereas eight additive QTLs were identified by QTL IciMapping program. Among these additive QTLs, five were identified by both programs. Epistatic QTLs and QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values, and one additive QTL and nine epistatic QTLs were identified. There were three epistatic QTLs identified for Na⁺ in roots (RNC), three additive QTLs and two epistatic QTLs identified for Na⁺ in shoots (SNC), four additive QTLs identified for K⁺ in roots (RKC), four additive QTLs and three epistatic QTLs identified for K⁺ in shoots (SKC) and one additive QTL and one epistatic QTL for salt tolerance rating (STR). The phenotypic variation explained by each additive, epistatic QTL and QTL×environment interaction ranged from 8.5 to 18.9%, 0.5 to 5.3% and 0.7 to 7.5%, respectively. By comparing the chromosomal positions of these additive QTLs with those previously identified, five additive QTLs, qSNC9, qSKC1, qSKC9, qRKC4 and qSTR7, might represent novel salt tolerance loci. The identification of salt tolerance in selected RILs showed that a major QTL qSNC11 played a significant role in rice salt tolerance, and could be used to improve salt tolerance of commercial rice varieties with marker-assisted selection (MAS) approach.     

Locating QTLs controlling several adult root traits in an elite Chinese hybrid rice

This study aimed to elucidate the genetics of the adult root system in elite Chinese hybrid rice. Several adult root traits in a recombinant inbred line (RIL) population of Xieyou 9308 and two backcross F₁ (BCF₁) populations derived from the RILs were phenotyped under hydroponic culture at heading stage for quantitative trait locus (QTL) mapping and other statistical analysis. There a total of eight QTLs detected for the root traits. Among of them, a pleiotropic QTL was repeatedly flanked by RM180 and RM5436 on the short arm of chromosome 7 for multiple traits across RILs and its BCF₁ populations, accounting for 6.88% to 25.26% of the phenotypic variances. Only additive/dominant QTLs were detected for the root traits. These results can serve as a foundation for facilitating future cloning and molecular breeding.     

以色列野生二粒小麦(Triticum dicoccoides)耐盐性鉴定

采用水培法对从以色列引进的分属8个自然群体的93份野生二粒小麦进行了耐盐性初步鉴定.结果表明:①供试材料中仅有高耐盐材料3份,耐盐材料7份 ,耐盐性较好的材料仅占参试材料总数的10.7%;②8个自然群体的野生二粒小麦的耐盐性存在较大差异,其中3号群体耐盐性明显高于其他群体,说明来自Tabigha地区的野生二粒小麦具有丰富的耐盐基因源;③将经过鉴定的耐盐性较好的野生二粒小麦与普通小麦中的耐盐品种进行比较研究发现,以色列耐盐性较好的野生二粒小麦的耐盐性不如普通小麦中的茶淀红和SW10两个耐盐品种.     

水稻新种质资源的耐盐性鉴定评价

用0.5%的NaCl溶液作灌溉水,对2000-2002年江苏省水稻区域试验参试品系和近年引进的部分水稻种质资源进行苗期耐盐性鉴定.结果表明:株高矮化是苗期盐胁迫的一种形态特征;耐盐性鉴定易受环境影响;就整体而言,籼稻种质资源的苗期耐盐性好于粳稻;综合2年结果,籼156和64608两种质资源的苗期耐盐性较强.     

OsGA20ox1, a candidate gene for a major QTL controlling seedling vigor in rice

Seedling vigor is among the major determinants of stable stand establishment in direct-seeded rice (Oryza sativa L.) in temperate regions. Quantitative trait loci (QTL) for seedling vigor were identified using 250 recombinant inbred lines (RILs) derived from a cross between two japonica rice cultivars Kakehashi and Dunghan Shali. Seedling heights measured at 14 days after sowing were 20.3 and 29.4 cm for Kakehashi and Dunghan Shali, respectively. For the RILs, the height ranged from 14.1 to 31.7 cm. Four putative QTLs associated with seedling height were detected. qPHS3-2, the major QTL that was located on the long arm of chromosome 3, accounted for 26.2 % of the phenotypic variance. Using progeny of the near isogenic lines (NILs) produced by the backcross introduction of a chromosome segment carrying this major QTL into an elite cultivar Iwatekko, we fine-mapped qPHS3-2 to a 81-kb interval between two markers, ID_CAPS_01 and RM16227. Within this mapped region, we identified the gene OsGA20ox1, which is related to gibberellin (GA) biosynthesis. The relative expression levels of GA20ox1 in seedlings of Dunghan Shali and NILs were higher than that of Iwatekko. Concomitantly, the amount of endogenous active GA was higher in Dunghan Shali and the NILs compared to the level detected in Iwatekko. These results indicate that OsGA20ox1 is a strong candidate gene for major QTL controlling seedling vigor in rice.     

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 F₈ 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°C) irrigation in the field and controlled air temperature (17°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.     

Comparison of QTLs for rice seedling morphology under different water supply conditions

The variation of seedling characteristics under different water supply conditions is strongly associated with drought resistance in rice (Oryza sativa L.) and a better elucidation of its genetics is helpful for improving rice drought resistance. Ninety-six doubled-haploid (DH)rice lines of an indica and japonica cross were grown in both flooding and upland conditions and QTLs for morphological traits at seedling stage were examined using 208 restriction fragment length polymorphism (RFLP) and 76 microsatellite (SSR) markers. A total of 32 putative QTLs were associated with the four seedling traits: average of three adventitious root lengths (ARL), shoot height (SH), shoot biomass (SW), and root to shoot dry weight ratio (RSR). Five QTLs detected were the same under control and upland conditions. The ratio between the mean value of the seedling trait under upland and flooding conditions was used for assessing drought tolerance. A total of six QTLs for drought tolerance were detected. Comparative analysis was performed for the QTLs detected in this case and those reported from two other populations with the same upland rice variety Azucena as parent. Several identical QTLs for seedling elongation across the three populations with the positive alleles from the upland rice Azucena were detected, which suggests that the alleles of Azucena might be involved in water stress-accelerated elongation of rice under different genetic backgrounds. Five cell wall-related candidate genes for OsEXP1, OsEXP2, OsEXP4, EXT, and EGase were mapped on the intervals carrying the QTLs for seedling traits.     

Identification of quantitative trait loci associated with salt tolerance at seedling stage from Oryza rufipogon

Soil salinity is one of the major abiotic stresses affecting plant growth and crop production.In the present study,salt tolerance at rice seedling stage was evaluated using 87 introgression lines (ILs),which were derived from a cross between an elite indica cultivar Teqing and an accession of common wild rice (Oryza rufipogon Griff.).Substantial variation was observed for four traits including salt tolerance score (STS),relative root dry weight (RRW),relative shoot dry weight (RSW) and relative total dry weight (RTW).STS was significantly positively correlated with all other three traits.A total of 15 putative quantitative trait loci (QTLs) associated with these four traits were detected using single-point analysis,which were located on chromosomes 1,2,3,6,7,9 and 10 with 8％-26％ explaining the phenotypic variance.The O.rufipogon-derived alleles at 13 QTLs (86.7％) could improve the salt tolerance in the Teqing background.Four QTL clusters affecting RRW,RSW and RTW were found on chromosomes 6,7,9 and 10,respectively.Among these four QTL clusters,a major cluster including three QTLs (qRRW10,qRSW10 and qRTW10) was found near the maker RM271 on the long arm of chromosome 10,and the O.rufipogon-derived alleles at these three loci increased RRW,RSW and RTW with additive effects of 22.7％,17.3％ and 18.5％,respectively,while the phenotypic variance explained by these three individual QTLs for the three traits varied from 19％ to 26％.In addition,several salt tolerant ILs were selected and could be used for identifying and utilizing favorable salt tolerant genes from common wild rice and used in the salt tolerant rice breeding program.     

QTLs conferring cold tolerance at the booting stage of rice using recombinant inbred lines from a <Emphasis Type="Italic">japonica</Emphasis> × <Emphasis Type="Italic">indica</Emphasis> cross

Low temperature stress is common for rice grown in temperate regions and at high elevations in the tropics. The most senstive stage to this stress is booting, about 11 days before heading. Japonica cultivars are known to be more tolerant than indicas. We constructed a genetic map using 191 recombinant inbred lines derived from a cross between a temperate japonica, M-202, and a tropical indica, IR50, in order to locate quantitative trait loci (QTLs) conferring cold tolerance. The map with a total length of 1,276.8 cM and an average density of one marker every 7.1 cM was developed from 181 loci produced by 175 microsatellite markers. Cold tolerance was measured as the degree of spikelet sterility of treated plants at a 12 degrees C temperature for 5 days in the growth chamber. QTLs on chromosomes 1, 2, 3, 5, 6, 7, 9 and 12 were identified to confer cold tolerance at the booting stage. The QTL contribution to the phenotypic variation ranged from 11 to 17%. The two QTLs with the highest contribution to variation, designated qCTB2a and qCTB3, were derived from the tolerant parent, M-202, each explaining approximately 17% of the phenotypic variance. Two of the eight QTLs for cold tolerance were contributed by IR50.     

Mapping QTLs of root morphological traits at different growth stages in rice

Roots are a vital organ for absorbing soil moisture and nutrients and influence drought resistance. The identification of quantitative trait loci (QTLs) with molecular markers may allow the estimation of parameters of genetic architecture and improve root traits by molecular marker-assisted selection (MAS). A mapping population of 120 recombinant inbred lines (RILs) derived from a cross between japonica upland rice 'IRAT109' and paddy rice 'Yuefu' was used for mapping QTLs of developmental root traits. All plant material was grown in PVC-pipe. Basal root thickness (BRT), root number (RN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW) and root volume (RV) were phenotyped at the seedling (I), tillering (II), heading (III), grain filling (IV) and mature (V) stages, respectively. Phenotypic correlations showed that BRT was positively correlated to MRL at the majority of stages, but not correlated with RN. MRL was not correlated to RN except at the seedling stage. BRT, MRL and RN were positively correlated to RFW, RDW and RV at all growth stages. QTL analysis was performed using QTLMapper 1.6 to partition the genetic components into additive-effect QTLs, epistatic QTLs and QTL-by-year interactions (Q x E) effect. The results indicated that the additive effects played a major role for BRT, RN and MRL, while for RFW, RDW and RV the epistatic effects showed an important action and Q x E effect also played important roles in controlling root traits. A total of 84 additive-effect QTLs and 86 pairs of epistatic QTLs were detected for the six root traits at five stages. Only 12 additive QTLs were expressed in at least two stages. This indicated that the majority of QTLs were developmental stage specific. Two main effect QTLs, brt9a and brt9b, were detected at the heading stage and explained 19% and 10% of the total phenotypic variation in BRT without any influence from the environment. These QTLs can be used in breeding programs for improving root traits.     

Dynamic Quantitative Trait Loci Analysis of Seed Reserve Utilization during Three Germination Stages in Rice

In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of seed reserve utilization during the early (day 6), middle (day 10) and late (day 14) germination stages. The seedling dry weight (SDW) and weight of the mobilized seed reserve (WMSR) were increased, while the seed reserve utilization efficiency (SRUE) decreased, during the process of seed germination. The SDW and WMSR were affected by the seed weight, while the SRUE was not affected by the seed weight. A total of twenty unconditional and twenty-one conditional additive QTLs and eight epistatic QTLs were identified at three germination stages, and the more QTLs were expressed at the late germination stage. Among them, twelve additive and three epistatic QTLs for SDW, eight additive and three epistatic QTLs for WMSR and thirteen additive and two epistatic QTLs for SRUE were identified, respectively. The phenotypic variation explained by each additive QTL, epistatic QTL and QTL × development interaction ranged from 6.10 to 23.91%, 1.79 to 6.88% and 0.22 to 2.86%, respectively. Two major additive QTLs qWMSR7.1 and qSRUE4.3 were identified, and each QTL could explain more than 20% of the total phenotypic variance. By comparing the chromosomal positions of these additive QTLs with those previously identified, eleven QTLs might represent novel genes. The best four cross combinations of each trait for the development of RIL populations were selected. The selected RILs and the identified QTLs might be applicable to improve rice seed reserve utilization by the marker-assisted selection approach.     

Identification and mapping of the QTL for aluminum tolerance introgressed from the new source, <Emphasis Type="SmallCaps">ORYZA RUFIPOGON</Emphasis> Griff., into indica rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

This study was conducted to identify and map the quantitative trait locus (QTL) controlling Al tolerance in rice using molecular markers. A population of 171 F(6) recombinant inbred lines (RILs) derived from the cross of Oryza sativa (IR64), the Al susceptible parent, and Oryza rufipogon, the Al tolerant parent, was evaluated for Al tolerance using a nutrient solution with and without 40 ppm of active Al(+3). A genetic map, consisting of 151 molecular markers covering 1,755 cM with an average distance of 11.6 cM between loci, was constructed. Nine QTLs were dentified including one for root length under non-stress conditions (CRL), three for root length under Al stress (SRL) and five for relative root length (RRL). O. rufipogon contributed favorable alleles for each of the five QTLs for RRL, which is a primary parameter for Al tolerance, and individually they explained 9.0-24.9% of the phenotypic variation. Epistatic analysis revealed that CRL was conditioned by an epistatic effect, whereas SRL and RRL were controlled by additive effects. Comparative genetic analysis showed that QTLs for RRL, which mapped on chromosomes 1 and 9, appear to be consistent among different rice populations. Interestingly, a major QTL for RRL, which explained 24.9% of the phenotypic variation, was found on chromosome 3 of rice, which is conserved across cereal species. These results indicate the possibilities to use marker-assisted selection and pyramiding QTLs for enhancing Al tolerance in rice. Positional cloning of such QTLs introgressed from O. rufipogon will provide a better understanding of the Al tolerance mechanism in rice and the evolutionary genetics of plant adaptation to acid-soil conditions across cereal species.