Magnitude of inbreeding depression and genetic variation analysis of agro‐morphological traits in orchardgrass

Inbreeding depression is the reduction in the fitness of inbred offspring relative to progeny from unrelated parents. In orchardgrass (Dactylis glomerata L.), limited efforts have been made to evaluate the effects of deliberate selfing on agro‐morphological traits and to estimate the genetic variation of traits. Twenty‐five genotypes of orchardgrass, along with 25 S₁ (full‐sibs) and 25 families of half‐sibs, were created in 2012 and used to assess the consequences of the first generation of inbreeding and outcrossing for offspring fitness and to estimate heritabilities, genetic parameters and correlations of agro‐morphological traits during the period of 2013–2014 in the field. Different levels of inbreeding depression were observed for the traits, with higher values for plant height, days to inflorescence emergence and dry matter yield. The degree of inbreeding or outbreeding effects varied among the studied genotypes. This facilitates the development of inbred lines for further studies. The results showed that some of the studied genotypes were self‐fertile, thereby indicating the possibility of developing inbred lines from these genotypes. Heritabilities ranged from 0.10 for the number of stems per plant to 0.64 for spread among the studied populations. Spread had high heritability as well as high correlation with forage yield, thereby indicating that this trait could be used to improve forage yield indirectly.     

Effect of generation of inbreeding, cutting treatment and year on agronomic traits in berseem populations

The selfing effect in berseem clover (Trifolium alexandrinum L.) was analysed by comparing generation means for nine agronomic traits (dry matter yield, plant height, leaf-stem ratio, harvest index, seed yield and its components). Parents, S₁, S₂, S₃, and S₄ generations of six populations of different geographical origin (3 from Egypt and 3 from southern Italy) were investigated to estimate the relative changes with increasing homozygosity and to prove the effectiveness of selfing in a breeding program. The experiment was carried out at Foggia (Italy) under field conditions for two years (1995 and 1996) adopting two cutting treatments: at fifth internode elongation (A) and flowering (B). The mean values decreased with the advancement in selfing generations in both years and cutting treatments for the most of the traits. Treatment B yielded more biomass and seed yield than treatment A in both years. Cutting treatments did not affect the adaptability of the selfed progenies of populations with different geographical origin, in fact, the Italian populations were more productive for dry matter under both cutting treatments (856.6 g m^-2 on average), whereas Egyptian populations proved superior for seed yield particularly under treatment B (62.5 g m^-2 on average). Inbreeding depression was greater for forage dry matter and seed yield (−62and −79% on average, respectively), whereas the plant height and 1000-seed weight were the least susceptible traits (−26 and −19% on average, respectively). Estimates of the parameters of the stability analysis showed that not all populations responded to inbreeding level and environment variations to the same degree. Differences were evident under treatment A, only. Development of self-fertile, relatively vigorous inbred lines of berseem clover with different degrees of homozygosity appears possible. Genotypes tolerant to selfing from Egyptian and Italian groups have been obtained by inbreeding and selection for self-fertility; they could be utilised as basis for producing new breeding activities. This revised version was published online in July 2006 with corrections to the Cover Date.     

Effects of inbreeding on nodal root system morphology and architecture of white clover (<Emphasis Type="Italic">Trifolium repens</Emphasis> L.)

Plants of white clover (Trifolium repens L.) cultivar Crau, a self-fertile Crau genotype, and nine generations of inbred progeny were raised in sand culture in a glasshouse experiment. Digital images of the root systems were made and root morphological characteristics were determined on all the plants. Root architectural parameters were measured on the Crau parent and the S₁, S₄, S₆, and S₉ inbred lines. The clover roots became shorter and thicker with inbreeding but the number of root tips per plant was unchanged. Root architecture (branching pattern) was largely unaffected by inbreeding. It is concluded that inbreeding white clover will lead to shorter, thicker roots, and reduced nutrient uptake efficiency compared with the parent clover. The degree to which these deleterious traits are overcome during the development of F₁ hybrids needs to be determined.     

Efficiency of early generation testing in pickling cucumber

Summary Early testing was evaluated for efficiency as a procedure for selecting among lines for yield (total and marketable fruit number), earliness and fruit quality (shape, color and seedcell size) in 24 sets of lines developed at random from a pickling cucumber (Cucumis sativus L.) population. The advantage of early testing was calculated using the regression of S₆ on S₁ performance. The amount of effort required in worker-hours and the theoretical gain from selection were also considered in estimating the advantage of early testing. Early testing for specific combining ability and for general combining ability was up to 2.05 times as efficient as late testing for total yield, and up to 2.29 times as efficient as late testing for earliness. Early testing was not efficient for selection for the fruit quality traits measured, nor for inbred performance per se.     

A comparison of traditional and haploid-derived breeding populations of oilseed rape (Brassica napus L.) for fatty acid composition of the seed oil

Summary Microspore embryogenesis technology allows plant breeders to efficiently generate homozygous micros-pore-derived breeding populations of oilseed rape (Brassica napus L.) without traditional generations of inbreeding. This study was conducted to compare the frequency distribution of microspore-derived population and single seed descent populations with respect to fatty acids of seed oil. Both microspore-derived populations and single seed descent populations were produced from each of three crosses made between selected parents containing contrasting amount of erucic, oleic, linoleic and linolenic acids. The fatty acid content of F₃ plants derived lines (F₅ seed) developed by single seed descent was compared to that of microspore-derived populations. The means, ranges and distribution pattern of seed fatty acid contents were similar in both populations for each fatty acid studied, although a few heterozygous lines were observed in the single seed descent populations. The results indicated that microspore-derived population form random, homozygous F₁ plant derived gametic arrays for all fatty acids evaluated. Selection for altered fatty acid composition in microspore-derived and single seed descent homozygous populations should be equally efficient, in the absence of linkage of traits investigated.     

Validating a segment on the short arm of chromosome 6 responsible for genetic variation in the hull silicon content and yield traits of rice

Rice is a typical silicon-accumulating plant and the beneficial effect of silicon on rice has long been recognized. In a previous study using 244 recombinant inbred lines (RILs) of an indica rice cross, Zhenshan 97B/Milyang 46 grown in 2003, four QTLs were detected for hull silicon content. QTL qHUS-6 had the largest effect among these, and the same interval also had significant effects on yield traits in the same population. The primary objective of this study was to validate the QTL effect in this region on HUS and yield traits. The same RIL population and another RIL population of lower heterogeneity were grown in 2004. QTL qHUS-6 was found to have significant additive effects on hull silicon content with a consistent direction in the two populations. From a residual heterozygous line selected from RILs of the same cross, 15 F_2:3 lines that differed only in a 2.15-Mb segment extending from RM587 to RM6119 on the short arm of chromosome 6 were derived. In these lines, qHUS-6 displayed a major effect, so did QTLs for yield traits previously detected in the same region. Two more QTLs for HUS detected in 2003, qHUS-1-1 and qHUS-1-2, also had consistent effects in the Zhenshan 97B/Milyang 46 RIL population in 2004. Thus this study verified three candidate regions for fine mapping HUS QTLs and determining the genetic relationship between silicon content and yield traits in rice.     

Variation and covariation for quantitative resistance to head blight (Fusarium culmorum) in two testcross series of S2 lines in winter rye

The amount of genetic variation among inbred lines and testcrosses, and covariation between both genetic materials, are of crucial importance for selection efficiency in hybrid breeding. To estimate these quantitative genetic parameters for resistance of winter rye (Secale cereale) to head blight caused by Fusarium culmorum, 88 three-way cross hybrids, produced by crossing each of 44 S₂ Carsten inbred lines with two unrelated Petkus single-cross testers, were evaluated along with the parental lines over 2 years. Resistance traits were head-blight rating and grain weight per spike relative to the non-inoculated control. Significant genotypic variation occurred among lines and in both testcross series. S₂ lines displayed considerably more variation than testcross series. Genotype × environment interaction was more marked among the inbred lines, while estimates of heritability were similar for both genetic materials. Testcrosses showed heterosis for head-blight resistance. No relationship existed between S₂ lines and the two testcross series for any resistance trait. This might be caused by an association between inbreeding and Fusarium-head-blight susceptibility and different inbreeding depression among the S₂ population. The phenotypic correlations between the testcross series were moderate for both traits (r = 0.58, P < 0.01). In conclusion, Fusarium-head-blight resistance has to be selected at the respective heterozygosity levels.     

Assessing inbreeding in perennial ryegrass (Lolium perenne) as a step towards F1 hybrid breeding

Perennial ryegrass is an important turf and forage grass in temperate regions worldwide. Limited genetic gains have been made with current breeding strategies compared with other grass crops, such as rice and maize, which benefit from Filial 1 (F1) hybrid breeding. One of the largest constraints on hybrid breeding in ryegrass is self-incompatibility preventing inbreeding, as homozygous parental lines are required to develop hybrids with maximal hybrid vigour. Obligate outcrossing in ryegrass has resulted in cultivars with high levels of heterozygosity, lacking trait uniformity across the population. A naturally occurring self-fertile (SF) locus that overcomes the self-incompatibility system has been identified in a European perennial ryegrass population. This study crossed the SF locus into an elite cultivar, producing a self-compatible population that was inbred for several generations. Genotyping-by-sequencing (GBS) was used to assess the population structure and degree of inbreeding in the self-compatible population. Phenotypic analysis indicated that increased homozygosity did not necessarily affect growth and performance. This study concludes that self-compatible ryegrass is a promising tool for hybrid breeding and agronomic improvement of perennial ryegrass.     

Inbreeding Depression and Other Genetic Effects in Populations of Maize Containing Highland Tropical Germplasm

A variety cross diallel of five populations of maize (Zea mays L.) was evaluated in a cool, temperate environment. Two of the parental populations were Corn Belt Dent synthetics (AS3 and BS22), one was developed from selected lines from a CIMMYT population developed for highland regions of the tropics and four Corn Belt Dent inbred lines (NZS3), and the other two had the pedigrees ‘Criollo de Toluca’× AS3² (NZS1) and ‘San Gerónimo’× BS222 (NZS2). ‘Criollo de Toluca’ is from the highlands of Mexico and ‘San Gerönimo’ is from the highlands of Peru. The objective was to study the influence of introgressing highland tropical germplasm into elite Corn Belt Dent synthetics on genetic effects, especially inbreeding depression, and to develop recommendations for the utilization of the introgressed populations. Inbreeding depression explained the greatest proportion of the variation among entries for grain yield, days to silking and plant height, but not for grain moisture at harvest and root lodging. For grain yield, NZS1, NZS2, and NZS3 had high levels of inbreeding depression and the difference between NZS1 and AS3 was statistically significant. High levels of root lodging were associated with NZS1 and high grain moisture at harvest with NZS2. These results indicate that a recurrent selection method, such as S₁ selection, which effectively reduces inbreeding depression, should be used in early cycles of selection with introgressed populations containing highland tropical germplasm.     

Effects of inbreeding on cut-flower yield in gerbera

Summary Inbreeding depression for cut-flower yield was found in gerbera (Gerbera hybrida, Compositae). A selection experiment for cut-flower yield in the Davis population was conducted over sixteen generations and the mean cut-flower yield increased from 10.3 flowers to 28.3 flowers. Cut-flower yield was recorded on individual plants grown in the greenhouse and inbreeding coefficients were calculated for each plant based on its pedigree. The effects of inbreeding on yield were estimated by covariance analysis models. The results of this study indicate that first, inbreeding increased 1% per generation in this population and secondly, inbreeding had the negative effect of reducing cut-flower yield by one-quarter flower per generation for every one percent increase in inbreeding.     

Association of isozyme genotypes with agronomic and seed composition traits in soybean

Summary Two crosses between Glycine max (L.) Merr. and G. soja Sieb. & Zucc. parents were used to study the association between isozyme marker loci and agronomic and seed composition traits in soybean. The parents possessed different alleles at six isozyme loci for Cross 1 (A80-244036 × PI 326581) and at eight isozyme loci for Cross 2 (A81-157007 × PI 342618A). A total of 480 BC₂F_4:6 lines from the two crosses was evaluated for 13 traits in two environments. Lines were grouped in locus classes from 0 to 5 according to the number of loci homozygous for the G. soja alleles that they possessed. Within each locus class, each isozyme genotype was represented by five random lines.Selection for G. max alleles at the isozyme loci was not effective in recovering the recurrent parent phenotype in either cross. In cross 1, however, BC₂F₄-derived lines in the 0- or 1- locus class more closely resembled the G. max parent than lines in the 4- or 5- locus classes for most of the agronomic and seed composition traits evaluated. Significant associations were found between particular isozyme genotypes and every trait analyzed. The estimated effect of genes linked to the Pgm1 locus was a delay in maturity of 6.0±3.4 days. In cross 1, the Idh2 locus was associated with a significant effect on linolenic acid content. The percentage of variation accounted for by the models of estimation varied according to the heritability of the trait. The R² was high (up to 78%) for maturity, lodging, and vining, and low (up to 21%) for seed yield. Most of the variation was associated with the BC₂F₁ family from which the lines were derived. There was little evidence that digenic epistasis was an important source of variation.Journal Paper No. J-13505 of the Iowa Agric. Home Econ. Exp. Stn., Ames, IA, Project 2475.     

Comparative efficiency of honeycomb and conventional pedigree methods of selection for yield and fiber quality in cotton (Gossypium spp.)

The effectiveness of honeycomb pedigree selection (HPS) as compared to conventional pedigree selection (CPS) was studied in one intraspecific (G. hirsutum L. × G. hirsutum L.) cross population (population I) and one interspecific (G. hirsutum L. × G. barbadense L.) cross population (population II). Combined selection for yield and lint quality traits was applied for four cycles at two locations for population I and atone location for population II. Finally, the best F₆ lines derived by each method, together with the unselected population derived by single seed descent (SSD) and three check cultivars, were tested in comparative experiments, separately for each cross, at the same locations. In both populations the analysis of variance indicated significant differences among the groups of the material tested for seed cotton yield, mean boll weight, micronaire reading, staple length, and uniformity ratio. No significant differences were found with respect to plant height, lint percentage, and fiber strength in population I and with respect to lint percentage and fiber strength in population II. In population I, on the basis of mean seed cottonyield and number of superior lines derived by each method as compared to the check varieties and the unselected SSD population, HPS-lines were superior to CPS-lines for seedcotton yield, fiber length and boll weight. HPS-lines, however, did not differ significantly in seedcotton yield from the best check cultivar Eva. Finally, the material derived by CPS was earlier in maturity than the material derived by HPS and SSD. Also in population II, on the basis of mean seedcotton yield and number of superior lines derived by each method as compared to the unselected SSD population, HPS-lines were superior to CPS-lines. No significant differences, however, were identified between the material of the two methods for lint quality traits. It was concluded that in both populations HPS was more effective than CPS in identifying lines with high yielding ability and good lint quality. This superiority of HPS is attributed, at least partially, to its effectiveness in early generation selection. This revised version was published online in August 2006 with corrections to the Cover Date.     

Inbreeding depression in garden and glasshouse chrysanthemums: germination and survivorship

Summary Sixty-six chrysanthemum (Dendranthema grandiflora) inbred selections, noninbred cultivars and hybrids, and D. makinoi were the base populations from which up to three generations of inbreds were obtained using multiple plant descent. Each parent possessed pseudo-self compatibility (PSC), which allowed seed set following self pollination. Rapid-generation cycling (laboratory seed ripening to heart stage and subsequent embryo rescue) reduced generation time and minimized confounding maternal with zygotic inbreeding depression during post heart-stage seed development. Selection criteria were male/female fertility and PSC. Two stages of the life cycle were chosen to evaluate inbreeding depression: germination (seed development to germination) and survivorship (fertile individuals at anthesis). PSC was environmentally interactive and genotype dependent, causing variable levels of self seed set between and within populations and generations. By the end of the second generation, families from all noninbred cultivars, D. makinoi, and one F₁ hybrid were eliminated from the experiment due to self incompatibility and/or inbreeding depression. Post-germination inbreeding depression was severe in several advanced inbreds. Inbred progeny of most F₁ or F₂ hybrids expressed less or equal amounts of inbreeding depression compared to advanced inbreds. Linear regression coefficients for either germination or survivorship on percent homozygosity were negative. Correlation coefficients between percent germination and survivorship (as a percent of seed set) were highly significant for Minnesota inbreds (r=0.67, P0.002) and hybrids (r=0.67, P0.006). The correlation coefficient was higher when percent germination and survivorship (as a percent of germinated seedlings) were compared (r=0.95, P0.001).Abbreviations F Fisher's Coefficient of Inbreeding - IBD Inbreeding Depression - PSC Pseudo-self Compatibility - RGC Rapid Generation Cycle - SI Self Incompatibility     

Identification of QTLs for BYDV tolerance in bread wheat

We searched for QTLs involved in tolerance to barley yellow dwarf (BYD), a serious viral disease of small grain cereals in two wheat populations, Opata × Synthetic (ITMI)and Frontana × INIA66 (F × I), for which marker data had previously been generated. The populations were evaluated in replicated field trials under artificial inoculation with a BYDV-PAV-Mex isolate and under disease-free conditions. Disease symptoms (yellowing, dwarfism and biomass reduction) were visually recorded and agronomic traits (number of tillers,height, biomass, yield and thousand-kernel weight) were measured on five plants per plot. Phenotypic data on all evaluated traits showed normal distribution with high correlation between visual estimates and measured values. Heritabilities were mostly moderate to high in the 114 lines of the ITMI population, and from low to moderate in the 117 lines of the F × I population. QTL analyses were based on genetic maps containing 443 loci for the ITMI population and 317 loci for the F × I population. Using composite interval mapping, 22 QTLs in the ITMI population and seven in the F × I population were detected, explaining9.8–43.3% of total phenotypic variation (σ² _P)per agronomic trait in the first population, and 4.1–13.7% in the second. Individual QTLs explained less than 15.8%of σ² _P. In the F × I population a minor QTL explaining 7% of σ² _P for yellowing was detected on the short arm of 7D, linked to leaf tip necrosis, a morphological marker for linked genes Bdv1, Yr18 andLr34. A QTL consistently detected for several traits on 2D in the ITMI population and on the short arm of group 6 chromosome(6S) in F × I explained 10–15% of σ² _P. The large number of QTLs having mostly small effects and the continuous distribution of all evaluated traits confirmed the polygenic nature and complexity of BYD tolerance in wheat. This revised version was published online in August 2006 with corrections to the Cover Date.     

Heritability of β-glucan, groat percentage, and crown rust resistance in two oat crosses

Summary Parent-offspring regression was used to estimate heritability for three traits (-glucan content, groat percentage, and resistance to crown rust (Puccinia coronata Cda. f. sp. avenae Eriks.) in oat (Avena sativa L.). The populations used were derived from two crosses, Nova x Marion QC and Sylva x Marion QC. Marion QC was used as a parent because other research had shown that it is relatively high in -glucan, a trait for which heritability had not previously been estimated. Nova and Sylva are similar in adaptation to Marion QC, and Sylva may be a source of general resistance to crown rust. Random F₅ plants were grown in a greenhouse, and their F₆ and F₇ progeny were grown in replicated field trials. Heritability estimates for the two grain quality traits were based on regression of F₆ values on F₅ values, F₇ values on F₆ values, and F₇ values on F₅ values. Heritability estimates for -glucan content were between 0.27 and 0.45. The highest estimate was the one based on the F₆ and F₇ generations of Sylva x Marion QC: 0.45, compared to estimates of 0.32 or less for earlier generations of the same cross, and to estimates of 0.35 or less for all generations of Nova x Marion QC. Heritability estimates for groat percentage were all between 0.23 and 0.32. The F₆ and F₇ generations were evaluated for resistance to crown rust resistance. The Sylva x Marion QC cross seemed to segregate for heritable resistance (h ²=0.31) but the Nova x Marion QC cross did not (h ²=0.07). Several lines from the Sylva x Marion QC cross had low symptoms in both the F₆ and F₇ generations. There were no strong genetic correlations among the traits.     

Effect of inbreeding and growth regulators on the in vitro androgenesis of wheatgrass, Agropyron glaucum

The capacity of haploid production by anther culture has been analysed in 42 crossbred genotypes (wild type) and in 32 genotypes from inbreeding generations (I₂-I₃) of wheatgrass, Agropyron glaucum. On potato-2 medium, about 50% of the genotypes investigated were capable of embryoid and callus induction. For the regeneration of haploid plants, five media containing various growth regulators were used. The crossbred genotypes were superior to the inbred lines in all the androgenesis parameters examined.     

Genetic Structure of Three Open-Pollinated Faba Bean Varieties (Vicia faba L.)*

To study the genetic structure of open-pollinated faba bean varieties, three sets of genotypes were generated from each of the varieties ‘Minica’, ‘Kristall’, and ‘Deiniol’: (1) inbred lines developed by single-seed descent in bee-proof isolation cages, (2) intravanetal and (3) intervarietal F₁-hybrids produced by controlled hand crossing. In 1989 and 1990, a total of 144 entries, including the three open-pollinated source varieties, were grown in single-row plots with two replications at two locations in Western Germany. Performance data of the inbred lines revealed relatively large genotypic variability within each variety, for all the characters studied, which was greater in ‘Deiniol’ and ‘Kristall’ than in ‘Minica’. An average yield heterosis of 20 %, 39 % and 57 %, respectively, was found for the intravarietal hybrids, whereas that of the intervarietal hybrids varied between 70 and 73 %. Compared to the mean yield of the inbred lines the superiority of the open-pollinated source variety was small and not significant in ‘Minica’ (6 %), but it was large and highly significant in ‘Kristall’ (22 %) and ‘Deiniol’ (37 %). The present investigation revealed in faba bean that similar performance levels of open-pollinated varieties may result from either high per se performance under inbreeding with low heterosis values or from lower per se performance but with high heterosis values.     

Prediction of heterosis using QTLs for yield traits in rapeseed (Brassica napus L.)

Three double low (erucic acid and glucosinolates) self-incompatible lines and 22 varieties from different origins were selected to produce 66 hybrids according to a NC II mating design. Field experiments for identification of hybrid performance and heterosis were conducted in two successive rapeseed growing seasons in Wuhan, China. After heterosis identifications, SI-1300 and Eagle were chosen to construct an F₂ segregating population. One hundred and eighty four F_2:3 lines were planted at Wuhan and Jingmen to test yield traits. F₂ plants and the 25 parents were analyzed using simultaneously AFLP (amplified fragment length polymorphism) and SSR (simple sequence repeat) markers. A total of 270 and 718 polymorphic loci were detected in the F₂ population and among the 25 parental lines, respectively. Of the 718 polymorphic loci, 178 were significantly correlated to yield traits. With the use of one-way ANOVA, 84 common QTLs were detected for 12 traits at two trial locations. Although the genetic distances based on general/specific heterozygosities and single-locus QTLs showed significant correlations with hybrid performance and heterosis for some yield traits, the determination coefficients were low. The results suggested that neither heterozygosities nor QTLs for yield traits were suitable to predict hybrid performance and heterosis in Brassica napus.     

Breeding maize lines for complete and partial resistance to maize streak virus (MSV)

Summary S₁ to S₅ inbred lines, derived from a maize population bred for its overall resistance to three tropical viruses, were screened for resistance to maize streak virus (MSV) by artificial plant infection using viruliferous leafhoppers. Symptoms were rated and intra-line frequency distributions studied for all pedigree inbred lines. Mortality due to MSV was very low among these inbreds. Symptoms appeared later, developed slower and were less severe than in the susceptible control hybrid. Results of a study of 500 S₁ and 93 S₂ lines suggested that resistance is under genetic control via a system involving loci with major genes (with dominance for resistance) controlling high to complete resistance, associated with a genetic system involving loci with minor genes controlling partial resistance. Lines expressing complete resistance to MSV were developed from 5 cycles of inbreeding and selection. The relevance of such complete and partial resistance is discussed.Abbreviations MRPS Mean Rating for Plants exhibiting Symptoms     

Identification of Quantitative Trait Loci Associated with Aluminum Tolerance in Rice (Oryza Sativa L.)

Summary Quantitative trait loci (QTL) analysis for Al tolerance was performed in rice using a mapping population of 98 BC₁F₁₀ lines (backcross inbred lines: BILs), derived from a cross of Al-tolerant cultivar of rice (Oryza sativa L. cv. Nipponbare) and Al-sensitive cultivar (cv. Kasalath). Three characters related to Al tolerance, including root elongation under non-stress conditions (CRE), root elongation under Al stress (SRE) and the relative root elongation (RRE) under Al stress versus non-stress conditions, were evaluated for the BILs and the parents at seedling stage. A total of seven QTLs for the three traits were identified. Among them, three putative QTLs for CRE (qCRE-6, qCRE-8 and qCRE-9) were mapped on chromosomes 6, 8 and 9, respectively. One QTL for SRE (qSRE-4) was identified on chromosome 4. Three QTLs (qRRE-5, qRRE-9 and qRRE-10) for RRE were detected on chromosomes 5, 9, 10 and accounted for 9.7–11.8% of total phenotypic variation. Interestingly, the QTL qRRE-5 appears to be syntenic with the genomic region carrying a major Al tolerance gene on chromosome 6 of maize. Another QTL, qRRE-9, appears to be similar among different rice populations, while qRRE-10 is unique in the BIL population. The common QTLs for CRE and RRE indicate that candidate genes conferring Al tolerance in the rice chromosome 9 may be associated with root growth rates. The existence of QTLs for Al tolerance was confirmed in substitution lines for corresponding chromosomal segments. These results also provide the possibilities of enhancing Al tolerance in rice through using marker-assisted selection (MAS) and pyramiding QTLs.