Genetic structure of three Oryza AA genome species (O. rufipogon, O. nivara and O. sativa) as assessed by SSR analysis on the Vientiane Plain of Laos

Microsatellite (SSR) markers can reveal a high level of polymorphic loci, and are increasingly being used in population genetic structure studies. On the Vientiane plain of Laos all components of the rice crop complex exist, wild annual (O. nivara), wild perennial (O. rufipogon) and weedy relatives of rice as well as rice itself. To understand gene flow in the rice complex, the genetic structures of O. rufipogon (10 populations), O. nivara (10 populations) and O. sativa (24 samples) from across the Vientiane Plain, Laos, were compared. Higher genetic differentiation was detected among O. nivara populations (G _ST = 0.77, R _ST = 0.71) than O. rufipogon populations (G _ST = 0.29, R _ST = 0.28), whereas genetic diversity for all populations of these two wild species showed similar values (H _T = 0.77 and 0.64 in O. rufipogon and O. nivara, respectively). Based on neighbor-joining tree constructed on the basis of genetic distance (D _A), three genetic clusters were detected, corresponding to (1) O. sativa samples, (2) O. nivara populations and (3) O. rufipogon populations. Pairwise tests confirmed the genetic differentiation of the three species. Although none of the wild rice individuals used in this study had any cultivated-specific phenotypic traits, genetic admixture analysis detected more than 10% O. sativa membership in three O. rufipogon and one O. nivara populations, indicating that O. sativa alleles may cryptically persist in natural populations of O. rufipogon and O. nivara on the Vientiane Plain.     

Transgene flow to hybrid rice and its male-sterile lines

Gene flow from genetically modified (GM) crops to the same species or wild relatives is a major concern in risk assessment. Transgenic rice with insect and/or disease resistance, herbicide, salt and/or drought tolerance and improved quality has been successfully developed. However, data on rice gene flow from environmental risk assessment studies are currently insufficient for the large-scale commercialization of GM rice. We have provided data on the gene flow frequency at 17 distances between a GM japonica line containing the bar gene as a pollen donor and two indica hybrid rice varieties and four male-sterile (ms) lines. The GM line was planted in a 640m² in an isolated experimental plot (2.4 ha), which simulates actual conditions of rice production with pollen competition. Results showed that: (1) under parallel plantation at the 0-m zone, the transgene flow frequency to the ms lines ranged from 3.145 to 36.116% and was significantly higher than that to hybrid rice cultivars (0.037–0.045%). (2) Gene flow frequency decreased as the distance increased, with a sharp cutoff point at about 1–2 m; (3) The maximum distance of transgene flow was 30–40 m to rice cultivars and 40–150 m to ms lines. We believe that these data will be useful for the risk assessment and management of transgenic rice lines, especially in Asia where 90% of world's rice is produced and hybrid rice varieties are extensively used. Shirong Jia, Feng Wang and Lei Shi contributed equally to this investigation.     

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon‐like population, referred to as Taxon A, and O. meridionalis‐like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short‐ and long‐read next‐generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.     

Assessment of gene flow from a herbicide-resistant indica rice (Oryza sativa L.) to the Costa Rican weedy rice (Oryza sativa) in Tropical America: factors affecting hybridization rates and characterization of F1 hybrids

Herbicide-resistant rice cultivars allow selective weed control. A glufosinate indica rice has been developed locally. However, there is concern about weedy rice becoming herbicide resistant through gene flow. Therefore, assessment of gene flow from indica rice cultivars to weedy rice is crucial in Tropical America. A field trial mimicking crop–weed growing patterns was established to assess the rate of hybridization between a Costa Rican glufosinate-resistant rice line (PPT-R) and 58 weedy rice accessions belonging to six weedy rice morphotypes. The effects of overlapping anthesis, morphotype, weedy accession/PPT-R percentage, and the particular weedy accession on hybridization rates were evaluated. Weedy rice accessions with short overlapping anthesis (4–9 days) had lower average hybridization rates (0.1%) than long anthesis overlapping (10–14 days) accessions (0.3%). Hybridization also varied according to weedy rice morphotype and accession. Sativa-like morphotypes (WM-020, WM-120) hybridized more readily than intermediate (WM-023, WM-073, WM-121) and rufipogon-like (WM-329) morphotypes. No hybrids were identified in 11 of the 58 accessions analyzed, 21 accessions had hybridization rates from 0.01% to 0.09%, 21 had rates from 0.1% to 0.9%, and 5 had frequencies from 1% to 2.3%. Another field trial was established to compare the weedy rice-PPT-R F₁ hybrids with their parental lines under noncompetitive conditions. F₁ hybrids had a greater phenotypic variation. They had positive heterosis for vegetative trait and reproductive potential (number of spikelets and panicle length) traits, but negative heterosis for seed set. This study demonstrated the complexity of factors affecting hybridization rates in Tropical America and suggested that the phenotype of F₁ hybrids facilitate their identification in the rice fields.     

Diversity and evolution of rice progenitors in Australia

In the thousands of years of rice domestication in Asia, many useful genes have been lost from the gene pool. Wild rice is a key source of diversity for domesticated rice. Genome sequencing has suggested that the wild rice populations in northern Australia may include novel taxa, within the AA genome group of close (interfertile) wild relatives of domesticated rice that have evolved independently due to geographic separation and been isolated from the loss of diversity associated with gene flow from the large populations of domesticated rice in Asia. Australian wild rice was collected from 27 sites from Townsville to the northern tip of Cape York. Whole chloroplast genome sequences and 4,555 nuclear gene sequences (more than 8 Mbp) were used to explore genetic relationships between these populations and other wild and domesticated rices. Analysis of the chloroplast and nuclear data showed very clear evidence of distinctness from other AA genome Oryza species with significant divergence between Australian populations. Phylogenetic analysis suggested the Australian populations represent the earliest‐branching AA genome lineages and may be critical resources for global rice food security. Nuclear genome analysis demonstrated that the diverse O. meridionalis populations were sister to all other AA genome taxa while the Australian O. rufipogon‐like populations were associated with the clade that included domesticated rice. Populations of apparent hybrids between the taxa were also identified suggesting ongoing dynamic evolution of wild rice in Australia. These introgressions model events similar to those likely to have been involved in the domestication of rice.     

Are habitat fragmentation,local adaptation and isolation‐by‐distance driving population divergence in wild rice Oryza rufipogon?

Habitat fragmentation weakens the connection between populations and is accompanied with isolation by distance (IBD) and local adaptation (isolation by adaptation, IBA), both leading to genetic divergence between populations. To understand the evolutionary potential of a population and to formulate proper conservation strategies, information on the roles of IBD and IBA in driving population divergence is critical. The putative ancestor of Asian cultivated rice (Oryza sativa) is endangered in China due to habitat loss and fragmentation. We investigated the genetic variation in 11 Chinese Oryza rufipogon populations using 79 microsatellite loci to infer the effects of habitat fragmentation, IBD and IBA on genetic structure. Historical and current gene flows were found to be rare (m_h = 0.0002–0.0013, m_c = 0.007–0.029), indicating IBD and resulting in a high level of population divergence (F_ST = 0.343). High within‐population genetic variation (H_E = 0.377–0.515), relatively large effective population sizes (N_e = 96–158), absence of bottlenecks and limited gene flow were found, demonstrating little impact of recent habitat fragmentation on these populations. Eleven gene‐linked microsatellite loci were identified as outliers, indicating local adaptation. Hierarchical AMOVA and partial Mantel tests indicated that population divergence of Chinese O. rufipogon was significantly correlated with environmental factors, especially habitat temperature. Common garden trials detected a significant adaptive population divergence associated with latitude. Collectively, these findings imply that IBD due to historical rather than recent fragmentation, followed by local adaptation, has driven population divergence in O. rufipogon.     

Phylogenetic relationships of annual and perennial wild rice: probing by direct DNA sequencing

Summary The phylogenetic relationships between Asian wild rice strains were analyzed by direct sequencing of PCR-amplified DNA fragments. The sequence of three introns located in the phytochrome gene was determined for eight strains of the Asian wild rice, Oryza rufipogon, and one strain of the related African species, Oryza longistaminata. The number of nucleotide substitutions per site between various strains within a single species, O. rufipogon, ranged between 0.0017 and 0.0050, while those between two related species, O. rufipogon and O. longistaminate, were 0.043–0.049 (23–26 within 532 bp). Taken together with the sequence differences of the 10-kDa prolamin gene, a model is proposed for the phylogenetic relationships and evolutionary history of annuals and perennials within O. rufipogon.     

Contrasting population genetic structure and gene flow between <Emphasis Type="Italic">Oryza rufipogon</Emphasis> and <Emphasis Type="Italic">Oryza nivara</Emphasis>

The cross compatible wild relatives of crops have furnished valuable genes for crop improvement. Understanding the genetics of these wild species may enhance their further use in breeding. In this study, sequence variation of the nuclear Lhs1 gene was used to investigate the population genetic structure and gene flow of Oryza rufipogon and O. nivara, two wild species most closely related to O. sativa. The two species diverge markedly in life history and mating system, with O. rufipogon being perennial and outcrossing and O. nivara being annual and predominantly inbreeding. Based on sequence data from 105 plants representing 11 wild populations covering the entire geographic range of these wild species, we detected significantly higher nucleotide variation in O. rufipogon than in O. nivara at both the population and species levels. At the population level the diversity in O. rufipogon (Hd = 0.712; θ _sil = 0.0017) is 2–3 folds higher than that in O. nivara (Hd = 0.306; θ _sil = 0.0005). AMOVA partitioning indicated that genetic differentiation among O. nivara populations (78.2%) was much higher than that among O. rufipogon populations (52.3%). The different level of genetic diversity and contrasting population genetic structure between O. rufipogon and O. nivara might be explained by their distinct life histories and mating systems. Our simulation using IM models demonstrated significant gene flow from O. nivara to O. rufipogon, indicating a directional introgression from the annual and selfing species into the perennial and outcrossing species. The ongoing introgression has played an important role in shaping current patterns of genetic diversity of these two wild species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Ecological divergence in the presence of gene flow in two closely related Oryza species (Oryza rufipogon and O. nivara)

Ecological divergence plays a prominent role in the process of speciation, but how divergence occurs in the face of gene flow is still less clear, and remains controversial among evolutionists. Here we investigated the nucleotide diversity, divergence and gene flow between Oryza nivara and O. rufipogon using sequences of seven chloroplast and nuclear loci. By analysing samples from 26 wild populations across the geographic ranges of the two species, we showed that both species were highly structured and O. rufipogon maintained a higher level of species‐wide diversity than O. nivara. Notably, phylogenetic, amova and F_ST analyses were unable to detect significant nucleotide differentiation between the two species. We estimated that the two species began to diverge at c. 0.16 million years ago. Our coalescent‐based simulations strongly rejected the simple isolation model of zero migration between species, but rather provided unambiguous evidence of bidirectional gene flow between species, particularly from O. rufipogon to O. nivara. Our simulations also indicated that gene flow was recurrent during the divergence process rather than arising from secondary contact after allopatric divergence. In conjunction with different morphological and life‐history traits and habitat preference in the two species, this study supports the hypothesis that these Oryza species are better treated as ecotypes that diverged quite recently and are still under the process of divergence. Importantly, we demonstrate the ecological divergence between O. rufipogon and O. nivara in the presence of significant gene flow, implying that natural selection plays a primary role in driving the divergence of the two Oryza species.     

A loss‐of‐function allele of OsHMA3 associated with high cadmium accumulation in shoots and grain of Japonica rice cultivars

Excessive cadmium (Cd) accumulation in rice poses a risk to food safety. OsHMA3 plays an important role in restricting Cd translocation from roots to shoots. A non‐functional allele of OsHMA3 has been reported in some Indica rice cultivars with high Cd accumulation, but it is not known if OsHMA3 allelic variation is associated with Cd accumulation in Japonica cultivars. In this study, we identified a Japonica cultivar with consistently high Cd accumulation in shoots and grain in both field and greenhouse experiments. The cultivar possesses an OsHMA3 allele with a predicted amino acid mutation at the 380^th position from Ser to Arg. The haplotype had no Cd transport activity when the gene was expressed in yeast, and the allele did not complement a known nonfunctional allele of OsHMA3 in F₁ test. The allele is present only in temperate Japonica cultivars among diversity panels of 1483 rice cultivars. Different cultivars possessing this allele showed greatly increased root‐to‐shoot Cd translocation and a shift in root Cd speciation from Cd―S to Cd―O bonding determined by synchrotron X‐ray absorption spectroscopy. Our study has identified a new loss‐of‐function allele of OsHMA3 in Japonica rice cultivars leading to high Cd accumulation in shoots and grain.     

Utilization of the bar gene to develop an efficient method for detection of the pollen-mediated gene flow in Chinese cabbage (Brassica rapa spp. pekinensis)

To develop an efficient screening method for detection of the transgene in Chinese cabbage (Brassica rapa spp. pekinensis) utilizing Basta spray, optimal conditions for Basta application were examined in this study. Two transgenic Chinese cabbage lines were obtained through Agrobacterium-mediated transformation and used as transgenic positive controls in the Basta screening experiment. Differential concentrations of glufosinate-ammonium were sprayed into three different growth stages of 12 commercial Chinese cabbage cultivars. The results showed that no plants could survive higher than 0.05% glufosinate-ammonium, and plants at the 2–3 leaf stage were most vulnerable to glufosinate-ammonium. On the other hand, no damage was observed in the transgenic control plants. Reliability of the Basta spray method was proven by showing perfect co-segregation of the tolerance to glufosinate-ammonium and the presence of the bar gene in T₁ segregating populations of the transgenic lines, as revealed by both PCR and Southern blot analyses. Using the developed Basta screening method, we tried to investigate the transgene flow through pollen dispersal, but failed to detect any transgene-containing non-transgenic Chinese cabbages whose parents had been planted adjacent to transgenic Chinese cabbages in field conditions. However, the transgene was successfully detected using Basta spray from the non-transgenic plants bearing the transgene introduced by hand-pollination. Since the Basta spray method developed in this study is easy to apply and economical, it will be a valuable tool for understanding the mechanism of gene flow through pollen transfer and for establishing a biosafety test protocol for genetically modified (GM) Chinese cabbage cultivars.     

Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild‐to‐weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed‐shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.     

Evidences of introgression from cultivated rice to Oryza rufipogon (Poaceae) populations based on SSR fingerprinting: implications for wild rice differentiation and conservation

Crop-to-wild introgression may play an important role in evolution of wild species. Asian cultivated rice (Oryza sativa L.) is of a particular concern because of its cross-compatibility with the wild ancestor, O. rufipogon Griff. The distribution of cultivated rice and O. rufipogon populations is extensively sympatric, particularly in Asia where many wild populations are surrounded by rice fields. Consequently, gene flow from cultivated rice may have a potential to alter genetic composition of wild rice populations in close proximity. In this study, we estimated introgression of cultivated rice with O. rufipogon based on analyses of 139 rice varieties (86 indica and 53 japonica ecotypes) and 336 wild individuals from 11 O. rufipogon populations in China. DNA fingerprinting based on 17 selected rice simple sequence repeat (SSR) primer pairs was adopted to measure allelic frequencies in rice varieties and O. rufipogon samples, and to estimate genetic associations between wild and cultivated rice through cluster analysis. We detected consanguinity of cultivated rice in O. rufipogon populations according to the admixture model of the STRUCTURE program. The analyses showedz that four wild rice populations, DX-P1, DX-P2, GZ-P2, and HL-P, contained some rare alleles that were commonly found in the rice varieties examined. In addition, the four wild rice populations that scattered among the rice varieties in the cluster analysis showed a closer affinity to the cultivars than the other wild populations. This finding supports the contention of substantial gene flow from crop to wild species when these species occur close to each other. The introgressive populations had slightly higher genetic diversity than those that were isolated from rice. Crop-to-wild introgression may have accumulative impacts on genetic variations in wild populations, leading to significant differentiation in wild species. Therefore, effective measure should be taken to avoid considerable introgression from cultivated rice, which may influence the effective in-situ conservation of wild rice species.     

Heat-tolerant basmati rice engineered by over-expression of hsp101

Rice is sensitive to high-temperature stress at almost all the stages of its growth and development. Considering the crucial role of heat shock protein 101 (Hsp101) in imparting thermotolerance to cells, we introduced Arabidopsis thaliana hsp101 (Athsp101) cDNA into the Pusa basmati 1 cultivar of rice (Oryza sativa L.) by Agrobacterium-mediated transformation. Stable integration and expression of the transgene into the rice genome was demonstrated by Southern, northern and western blot analyses. There appeared no adverse effect of over-expression of the transgene on overall growth and development of transformants. The genetic analysis of tested T₁ lines showed that the transgene segregated in a Mendelian fashion. We compared the survival of T₂ transgenic lines after exposure to different levels of high-temperature stress with the untransformed control plants. The transgenic rice lines showed significantly better growth performance in the recovery phase following the stress. This thermotolerance advantage appeared to be solely due to over-expression of Hsp101 as neither the expression of low-molecular-weight heat shock proteins (HSPs) nor of other members of Clp family proteins was altered in the transgenic rice. The production of high temperature tolerant transgenic rice cultivars would provide a stability advantage under supra-optimal temperature regime thereby improving its overall performance.     

A large-scale field study of transgene flow from cultivated rice (Oryza sativa) to common wild rice (O. rufipogon) and barnyard grass (Echinochloa crusgalli)

The introgression of transgenes into wild relatives or weeds through pollen-mediated gene flow is a major concern in environmental risk assessment of transgenic crops. A large-scale (1.3–1.8 ha) rice gene flow study was conducted using transgenic rice containing the bar gene as a pollen donor and Oryza rufipogon as a recipient. There was a high frequency of transgene flow (11%−18%) at 0–1 m, with a steep decline with increasing distance to a detection limit of 0.01% by 250 m. To our knowledge, this is the highest frequency and longest distance of gene flow from transgenic rice to O. rufipogon reported so far. On the basis of these data, an adequate isolation distance from both conventional and transgenic rice should be taken for in situ conservation of common wild rice. Meanwhile, there is no evidence of transgene introgression into barnyard grass, even when it has coexisted with transgenic rice containing the bar gene for five successive years. Thus, the environmental risk of gene flow to this weedy species is of little concern.     

Identification and characterization of OsEBS,a gene involved in enhanced plant biomass and spikelet number in rice

Common wild rice (Oryza rufipogon Griff.) is an important genetic reservoir for rice improvement. We investigated a quantitative trait locus (QTL), qGP5‐1, which is related to plant height, leaf size and panicle architecture, using a set of introgression lines of O. rufipogon in the background of the Indica cultivar Guichao2 (Oryza sativa L.). We cloned and characterized qGP5‐1 and confirmed that the newly identified gene OsEBS (enhancing biomass and spikelet number) increased plant height, leaf size and spikelet number per panicle, leading to an increase in total grain yield per plant. Our results showed that the increased size of vegetative organs in OsEBS‐expressed plants was enormously caused by increasing cell number. Sequence alignment showed that OsEBS protein contains a region with high similarity to the N‐terminal conserved ATPase domain of Hsp70, but it lacks the C‐terminal regions of the peptide‐binding domain and the C‐terminal lid. More results indicated that OsEBS gene did not have typical characteristics of Hsp70 in this study. Furthermore, Arabidopsis (Arabidopsis thaliana) transformed with OsEBS showed a similar phenotype to OsEBS‐transgenic rice, indicating a conserved function of OsEBS among plant species. Together, we report the cloning and characterization of OsEBS, a new QTL that controls rice biomass and spikelet number, through map‐based cloning, and it may have utility in improving grain yield in rice.     

Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon

Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local‐level species separation is recognized by Bayesian clustering and neighbor‐joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by F_ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (H_E = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (H_E = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.     

Quantitative trait loci for yield and yield components in an Oryza sativa×Oryza rufipogon BC2F2 population evaluated in an upland environment

An advanced backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with eight agronomic traits in a BC₂F₂ population derived from an interspecific cross between Caiapo, an upland Oryza sativa subsp. japonica rice variety from Brazil, and an accession of Oryza rufipogon from Malaysia. Caiapo is one of the most-widely grown dryland cultivars in Latin America and may be planted as a monoculture or in a multicropping system with pastures. The objectives of this study were: (1) to determine whether trait-enhancing QTLs from O. rufipogon would be detected in 274 BC₂F₂ families grown under the drought-prone, acid soil conditions to which Caiapo was adapted, (2) to compare the performance with and without pasture competition, and (3) to compare putative QTL-containing regions identified in this study with those previously reported for populations adapted to irrigated, low-land conditions. Based on analyses of 125 SSLP and RFLP markers distributed throughout the genome and using single-point, interval, and composite interval mapping, two putative O. rufipogon derived QTLs were detected for yield, 13 for yield components, four for maturity and six for plant height.We conclude that advanced backcross QTL analysis offers a useful germplasm enhancement strategy for the genetic improvement of cultivars adapted to stress-prone environments. Although the phenotypic performance of the wild germplasm would not suggest its value as a breeding parent, it is noteworthy that 56% of the trait-enhancing QTLs identified in this study were derived from O. rufipogon. This figure is similar to the 51% of favorable QTLs derived from the same parent in crosses with a high-yielding hybrid rice cultivar evaluated under irrigated conditions in a previous study. In conclusion, parallel studies in rice using AB-QTL analysis provide increasing evidence that certain regions of the rice genome are likely to harbor genes of interest for plant improvement in multiple environments. Received: 3 September 1999 / Accepted: 16 May 2000