Recombinant Inbred Research Articles

Identifications of two different mechanisms for sorghum midge resistance through QTL mapping.

Sorghum midge is the one of the most damaging insect pests of grain sorghum production worldwide. At least three different mechanisms are involved in midge resistance. The genetic bases of these mechanisms, however, are poorly understood. In this study, for the first time, quantitative trait loci associated with two of the mechanisms of midge resistance, antixenosis and antibiosis, were identified in an RI (recombinant inbred) population from the cross of sorghum lines ICSV745 x 90562. Two genetic regions located on separate linkage groups were found to be associated with antixenosis and explained 12% and 15%, respectively, of the total variation in egg numbers/spikelet laid in a cage experiment. One region was significantly associated with antibiosis and explained 34.5% of the variation of the difference of egg and pupal counts in the RI population. The identification of genes for different mechanisms of midge resistance will be particularly useful for exploring new sources of midge resistance and for gene pyramiding of different mechanisms for increased security in sorghum breeding through marker-assisted selection.

Genetics of Seed Abortion and Reproductive Traits in Soybean

In soybean [Glycine max (L.) Merr.], yield or seed number is determined by the number of seeds per pod, the number of pods per plant, and the number of plants per row. Seeds per pod is a function of the number of ovules per pod and the success of seed set (lack of seed abortion). The objective of this study was to define the genetic basis for seed set. In this study, recombinant inbred (RI) segregants of soybean have been used to identify genetic components, quantitative trait loci (QTLs) that regulate different parameters of seed set. The numbers of ovules per pod and abortions were measured in RI segregants of soybean, as were positions and developmental stages of abortions within pods. Quantitative trait loci were identified from segregants of the Minsoy-Noir 1 RI population grown in Utah and Minnesota. These were confirmed in Minsoy-Archer or Noir 1-Archer RI populations grown in Minnesota. The average abortion frequency in the three RI populations ranged from 10 to 29%. Abortions occurred most frequently in the basal position of the pod and embryo development ceased most often at one of two developmental stages: embryos failed to develop (or ovules were not fertilized), or embryos were partially developed and ceased growth just after cotyledon differentiation. Quantitative trait loci were found on several linkage groups, including U11, U13, and U22. The QTLs in U11 were linked to QTLs for flowering date, reproductive period (RP), and maturity. Two separate QTLs on U13 were linked to genes for male and female sterility (Msl, Ms6, or St5) and to genes for disease resistance, respectively. One of two distinct QTLs on U22 was associated with a previously identified QTL for water use efficiency. Also of interest was a QTL on U3 linked to Lfl that determined the number of ovules per pod, suggesting a common regulation of leaf and flower primordia.

The Genetics of Innate Immunity in the Lung

Lipopolysaccharide elicits a vigorous inflammatory response and has been linked to the progression of asthma and other forms of airway disease. An improved understanding of the innate immune response to lipopolysaccharide should lead to novel therapies to treat these diseases. Towards this end, we challenged 32 recombinant inbred (RI) strains of (C57BL/6J X DBA/2J) [BXD] mice with aerosolized lipopolysaccharide and compared their biological responses by assaying concentrations of tumor necrosis factor-α and polymorphonuclear cells in the lavage fluid.

A molecular marker map in 'Kanota' x 'Ogle' hexaploid oat (Avena spp.) enhanced by additional markers and a robust framework.

Molecular mapping of cultivated oats was conducted to update the previous reference map constructed using a recombinant inbred (RI) population derived from Avena byzantina C. Koch cv. Kanota x Avena sativa L. cv. Ogle. In the current work, 607 new markers were scored, many on a larger set of RI lines (133 vs. 71) than previously reported. A robust, updated framework map was developed to resolve linkage associations among 286 markers. The remaining 880 markers were placed individually within the most likely framework interval using chi2 tests. This molecular framework incorporates and builds on previous studies, including physical mapping and linkage mapping in additional oat populations. The resulting map provides a common tool for use by oat researchers concerned with structural genomics, functional genomics, and molecular breeding.

Identification of quantitative trait loci associated with pre-harvest sprouting resistance in rice ( Oryza sativa L.)

One of the most important agronomic problems in rice production ( Oryza sativa L.) in high humidity climates is pre-harvest sprouting (PHS). This study was conducted to identify quantitative trait loci (QTLs) for PHS resistance using a recombinant inbred (RI) population derived from a cross between a japonica variety Asominori (relatively susceptible to PHS) and an indica variety IR24 (highly resistant to PHS). Knowledge of the genomic positions of QTLs for PHS resistance in rice could greatly simplify selection of the trait. A total of six QTLs for PHS resistance in rice were detected with 289 restriction fragment length polymorphism (RFLP) markers by both one marker analysis ( P<0.005) and composite interval mapping (CIM) (LOD>2.0). The two QTLs, located on chromosome 1, accounted for 10.7–20.0% of total phenotypic variations, and the other four QTLs, located on chromosome 4, 5, 7 and 8, respectively, explained 12.3–25.3% of total phenotypic variation. As a result, four alleles from IR24 on chromosomes 1 (two QTLs), 5, 7 and two alleles from Asominori on chromosomes 4, 8 contributed to PHS resistance in rice, respectively. The RFLP markers tightly linked to PHS resistance in rice may be useful for breeding varieties with greater resistance to PHS and adaptable to high humidity climates during the maturation period through the use of marker-assisted selection.

Dopamine D2 Receptor Binding, Drd2 Expression and the Number of Dopamine Neurons in the BXD Recombinant Inbred Series: Genetic Relationships to Alcohol and Other Drug Associated Phenotypes

Background: It has not been established to what extent the natural variation in dopamine systems contribute to the variation in ethanol response. The current study addresses this issue by measuring D2 dopamine (DA) receptor binding, the expression of Drd2, the number of midbrain DA neurons in the BXD recombinant inbred (RI) series and then compares these strain means with those previously reported for a variety of ethanol and other drug‐related phenotypes.Methods: Data were collected for 21 to 23 of the BXD RI strains and the parental strains. D2 DA receptor autoradiography was performed using 125I‐epidepride as the ligand [Kanes S, Dains K, Cipp L, Gatley J, Hitzemann B, Rasmussen E, Sanderson S, Silverman S, Hitzemann R (1996) Mapping the genes for haloperidol‐induced catalepsy. J Pharmacol Exp Ther 277:1016–1025]. Drd2 expression was measured using the Affymetrix oligoarray system. Immunocytochemical techniques were used to determine the number of midbrain DA neurons [Hitzemann B, Dains K, Hitzemann R (1994) Further studies on the relationship between dopamine cell density and haloperidol response. J Pharmacol Exp Ther 271:969–976].Results and Conclusions: The range of difference in receptor binding for the RI strains was approximately 2‐fold in all regions examined, the core, the shell of the nucleus accumbens (NAc) and the dorsomedial caudate‐putamen (CPu); heritability in all regions was moderate—(h 2∼0.35). Drd2 expression in forebrain samples from the RI and parental strains ranged 1.5‐ to 2‐fold and h2 was moderate—0.47. Variation in the number of tyrosine hydroxylase (TH) positive neurons was moderate, 41% and 26% and h2 was low—0.19 and 0.15 for the ventral tegmental area (VTA) and substantia nigra compacta (SNc), respectively. Significant correlations were found between D2 DA receptor binding and the low dose (1.33 g/kg) ethanol stimulant response. (p &lt; 0.002) and between Drd2 expression and conditioned place preference (CPP) (p &lt; 0.0005). No significant correlations were detected between ethanol preference and either receptor binding or Drd2 expression; however, a significant correlation was found between preference and Ncam expression. Ncam is approximately 0.2 Mb from Drd2. Overall, the data suggest ethanol preference and CPP are associated with the expression of Drd2 or closely linked genetic loci.

Combinations of nondiabetic parental genomes elicit impaired glucose tolerance in mouse SMXA recombinant inbred strains.

Type 2 diabetes in humans is not a single gene disorder but a multifactorial disease caused by the interaction of multiple genes and environmental factors. Recombinant inbred (RI) strains are a powerful tool for analyzing not only single genetic traits but also multifactorial genetic traits. By using the SMXA RI mice, we genetically dissected diabetes-related traits (BMI, nonfasting blood glucose concentration, and blood glucose concentration during intraperitoneal glucose tolerance tests). For minimizing the variation of glucose tolerance in each strain, all mice were fed the high-carbohydrate diet and subjected to phenotypic and genetic analyses. The parental strains, SM/J and A/J, were nondiabetic, and the differences of the mean values of diabetes-related traits were small. In contrast, an impaired glucose tolerance was observed in (SM x A)F1 mice, and marked differences in diabetes-related traits were observed in 19 SMXA RI strains. In particular, several SMXA RI strains showed markedly impaired glucose tolerance and hyperglycemia. Quantitative trait locus (QTL) analysis revealed a locus on chromosome (Chr) 10 contributing significant effect on nonfasting blood glucose concentration, as well as six diabetes-related loci on four chromosomes with suggestive evidence of linkage with diabetes-related phenotypes. The A/J-derived QTLs on Chr 2 and 18 and an SM/J-derived QTL on Chr 10 contributed to the impairment of glucose tolerance and/or the increase of blood glucose concentration. The present study indicates that QTLs derived from parental SM/J and A/J genomes, both of which are nondiabetic, interact in the RI genomes, leading to the development of hyperglycemia and diabetic phenotypes. Genetic dissection of this kind of diabetogenesis will increase our understanding of the complex gene-gene interaction and mode of inheritance in human type 2 diabetes.

Genetics of Seed Abortion and Reproductive Traits in Soybean

In soybean [Glycine max (L.) Merr.], yield or seed number is determined by the number of seeds per pod, the number of pods per plant, and the number of plants per row. Seeds per pod is a function of the number of ovules per pod and the success of seed set (lack of seed abortion). The objective of this study was to define the genetic basis for seed set. In this study, recombinant inbred (RI) segregants of soybean have been used to identify genetic components, quantitative trait loci (QTLs) that regulate different parameters of seed set. The numbers of ovules per pod and abortions were measured in RI segregants of soybean, as were positions and developmental stages of abortions within pods. Quantitative trait loci were identified from segregants of the Minsoy-Noir 1 RI population grown in Utah and Minnesota. These were confirmed in Minsoy-Archer or Noir 1-Archer RI populations grown in Minnesota. The average abortion frequency in the three RI populations ranged from 10 to 29%. Abortions occurred most frequently in the basal position of the pod and embryo development ceased most often at one of two developmental stages: embryos failed to develop (or ovules were not fertilized), or embryos were partially developed and ceased growth just after cotyledon differentiation. Quantitative trait loci were found on several linkage groups, including U11, U13, and U22. The QTLs in U11 were linked to QTLs for flowering date, reproductive period (RP), and maturity. Two separate QTLs on U13 were linked to genes for male and female sterility (Ms1, Ms6, or St5) and to genes for disease resistance, respectively. One of two distinct QTLs on U22 was associated with a previously identified QTL for water use efficiency. Also of interest was a QTL on U3 linked to Lf1 that determined the number of ovules per pod, suggesting a common regulation of leaf and flower primordia.

Comparisons of quantitative trait locus mapping properties between two methods of recombinant inbred line development

Summary Theoretical comparisons for quantitative trait loci (QTL) mapping properties were conducted among simulated recombinant inbred (RI) populations developed by single-hill (SH), complete bulk, and single seed descent (SSD) procedures by Monte Carlo simulations based on various population sizes, heritabilities, and QTL effects. Our simulations included estimation of QTL effects, QTL positions, and statistical testing power in the RI populations by comparing the estimates with preset values. The simulation results showed that the single hill (SH) bulk and single seed descent RI populations were generally not significantly different with respect to quality of estimated QTL effects and positions. Furthermore, when each RI population had 150 lines, each could provide desirable properties for QTL mapping. The results implied that a SH RI population consisting of 75 or more F2-derived families with two lines per family (corresponding population size of 150 or above) was appropriate for QTL mapping and was not significantly different than a SSD RI population of 150. Thus, the SH method could be used to develop large numbers of RI lines for achieving better results in QTL mapping. Simulations also showed that there was no significant difference between means using SH methods with 10 and 100 fruits per family. However, RI populations developed by the complete bulk method where F2 identities are lost were not suitable for QTL mapping.

Genetic Variation and Relationships among Seedling Vigor Traits in Sorghum

Seedling vigor in sorghum [Sorghum bicolor (L.) Moench] is important for improving stand establishment of the crop, particularly in arid regions and in areas where low soil temperatures prevail at planting time. This study was conducted to examine the genetic variation, heritability, and relationships among seedling vigor traits in a recombinant inbred (RI) sorghum population developed from two contrasting inbreds. One hundred RI lines and their parents [‘SRN39’, an African caudatum and ‘Shan Qui Red’ (SQR), a Chinese kaoliang] were evaluated for seedling vigor in experiments conducted in the field, in an incubator, and in a greenhouse. Data on 100-kernel weight, visual seedling vigor scores, percentage germination at 12 and 22°C, percentage emergence, seedling height, and shoot dry weight were collected. Genotypic differences were significant for many of these seedling vigor traits. Significant genetic and additive variances were observed for field vigor scores as well as for those traits measured in the more controlled environments. Heritability estimates for visual scores, percentage germination, emergence, and seedling height were high, while those for seedling dry weight were low to medium. Genetic correlation coefficients of visual seedling scores with the different estimates of vigor were significant except for 100-seed weight. Significant genetic interrelationships were revealed among traits measured in the greenhouse and incubator at 22°C. Visual scores taken in field experiments appeared effective in integrating germination, emergence at high temperatures, and shoot dry weight. The significant additive genetic variances obtained indicate that the superior seedling vigor observed in the kaoliang parent, SQR, can be effectively utilized for improving germination in cold temperature, as well as germination, emergence, seedling growth, and development at optimum temperature.

Quantitative Trait Loci Conditioning Resistance to Fusarium Head Blight in Wheat Line F201R

Fusarium head blight (FHB) of wheat (Triticum aestivum L.) is a devastating disease in wheat production worldwide. Identifying resistance genes and understanding the genetic basis of resistance to FHB are prerequisites to developing cultivars that can avoid losses from FHB. This investigation of quantitative trait loci (QTL) was performed in a recombinant inbred (RI) population derived from a cross between the FHB-moderately susceptible cv. Patterson and the FHB-resistant line Fundulea 201R (F201R). Bulk DNAs from the 11 most resistant and 12 most susceptible lines of the phenotypic distribution of the RI population, together with the parental lines, were screened with simple sequence repeat (SSR) markers. Regional QTL mapping identified four interval regions, located on chromosomes 1B, 3A, 3D, and 5A, that conferred resistance to FHB. The QTLs located on chromosomes 1B and 3A, contributed by F201R, had large effects and were consistently expressed in three environments. The four QTLs together accounted for 32.7% of the phenotypic variation, or 43.0% of the genotypic variation. The QTL on chromosome 3A is located in the same region as a QTL that was detected in wild tetraploid wheat T. dicoccoides (Koern. ex Asch. & Graebner) Aarons. The possibility that the FHB resistance QTLs of F201R and that of T. dicoccoides on chromosome 3A have the same origin is discussed.

Improved strain distribution patterns of SMXA recombinant inbred strains by microsatellite markers.

To develop SMXA recombinant inbred (RI) strains as more valuable genetic resources, 302 microsatellite (Mit) loci were added to the strain distribution patterns (SDP) reported previously. The improved SDP were constructed in a total of 1085 loci containing 484 Mit markers, 571 restriction landmark genomic scanning (RLGS) spot markers and 30 others. This substantially improved SDP can be freely accessed on our homepage (http://www.med.nagoya-u.ac.jp/sisetu/SDP.htm).

QTL analysis of Al tolerance in recombinant inbred lines of Arabidopsis thaliana.

Quantitative trait loci (QTLs) and epistasis for Arabidopsis thaliana aluminum (Al) tolerance were analyzed using a recombinant inbred (RI) population of 100 lines derived from a cross between Landsberg erecta and Columbia (Col). Root growth of the RI population was determined in hydroponics using solutions containing 0 or 4 micro M of AlCl(3 )and a series of nutrients, except P(i), at pH 5.0. Al tolerance was defined as relative root length [RRL: plus Al/minus Al (%)], and the RI lines ranged from 22.6 to 97.4% with a broad sense heritability of 0.99. Using the composite interval mapping method, two significant single factor QTLs (P<0.05) were detected by RRL on chromosomes 1 and 4, where the Col allele showed positive and negative effects on the Al tolerance. These QTLs could explain about 43% of the total variation of Al tolerance among the RI population. On the other hand, five epistatic loci pairs were identified by the complete pair-wise search method (P<0.0005). No single factor QTL and epistatic loci pairs were shared by the root length in the control and the RRL, suggesting that the loci identified by the RRL would be specific for Al treatment and controlling Al tolerance among the RI population.

Mapping quantitative trait loci that influence femoral cross-sectional area in mice.

Size and shape are critical determinants of the mechanical properties of skeletal elements and can be anticipated to be highly heritable. Moreover, the genes responsible may be independent of those that regulate bone mineral density (BMD). To begin to identify the heritable determinants of skeletal geometry, we have examined femoral cross-sectional area (FCSA) in male and female mice from two inbred strains of mice with divergent FCSA (C57BL/6 [B6] and DBA/2 [D2]), a large genetically heterogeneous population (n = 964) of B6D2F2 mice and 18 BXD recombinant inbred (RI) strains derived from their F2 cross. Femora were harvested from 16-week-old mice and FCSA (bone and marrow space enclosed within the periosteum) was measured at the midshaft by digital image analysis. In all mouse populations examined, FCSA was positively correlated with body weight and weight-corrected FCSA (WC-FCSA) values were normally distributed in the BXD-RI and F2 populations, suggesting polygenic control of this trait. Genome-wide quantitative trait locus (QTL) analysis of the B6D2F2 population revealed regions on four different chromosomes that were very strongly linked to WC-FCSA (chromosomes 6, 8, 10, and X) in both genders. Evidence of gender-specific genetic influences on femoral geometry was also identified at three other chromosomal sites (chromosomes 2, 7, and 12). Supporting evidence for the WC-FCSA QTLs on chromosomes 2, 7, 8, 10, and 12 also was present in the RI strains. Interestingly, none of these WC-FCSA QTLs were identified in our previous QTL analysis of whole body BMD in the same B6D2F2 population. Thus, the genetic determinants of bone size appear to be largely, if not entirely, distinct from those that regulate BMD attainment. The identification of the genes responsible for geometric differences in bone development should reveal fundamentally important processes in the control of skeletal integrity.

Genetic analysis of metabolic defects in the spontaneously hypertensive rat.

Abnormalities in carbohydrate and lipid metabolism are common in patients with essential hypertension and in the spontaneously hypertensive rat (SHR). To identify chromosome regions contributing to this clustering of cardiovascular risk factors in the SHR, we searched for quantitative trait loci (QTL) associated with insulin resistance, glucose intolerance, and dyslipidemia by using the HXB/BXH recombinant inbred (RI) strains. Analysis of variance in RI strains suggested significant effects of genetic factors. A genome screening of the RI strains with more than 700 markers revealed QTL significantly associated with insulin resistance on Chromosomes (Chrs) 3 and 19. The Chr 19 QTL was confirmed by testing a previously derived SHR-19 congenic strain: transfer of a Chr 19 segment delineated by markers D19Rat57 and D19Mit7 from the Brown Norway (BN/Cr) strain onto the genetic background of the SHR/Ola was associated with decreased insulin and glucose concentrations and ameliorated insulin resistance at the tissue level. These findings suggest that closely linked genes on Chr 19, or perhaps even a single gene with pleiotropic effects, influence the clustering of metabolic disturbances in the SHR-BN model.

A Personal History of the Mouse Genome

The chapter describes some personal reminiscences of various stages in the growth of knowledge of the mouse genome in the past 50 years. Initially mapping was done by crossing new mutants with linkage testing stocks, a slow and laborious method. In the 1950s major mutagenesis experiments led to spin-offs in terms of new mutants, new knowledge of phenomena including sex determination and X-chromosome inactivation, and further understanding of the t-complex. The 1970s saw the development of recombinant inbred (RI) strains and the use of biochemical variants for mapping. In addition the linkage groups were assigned to chromosomes. Techniques of embryo surgery were developed, leading to work with embryonic stem (ES) cells and hence to the identification of gene functioning by knockouts and transgenesis. Another major advance in the 1970s and 1980s was the beginning of comparative mapping, which is now so important. With the advent of DNA technology, progress in mapping increased considerably. Progress became even faster with the use of interspecific backcrosses and with the development of microsatellite markers. The completion of the mouse DNA sequence is now imminent, opening fascinating prospects for the analysis of gene function.

Variability in response to nicotine in the LSxSS RI strains: potential role of polymorphisms in alpha4 and alpha6 nicotinic receptor genes.

Several studies have shown that genetic factors influence the effects of nicotine on respiration, acoustic startle, Y-maze crosses and rears, heart rate and body temperature in the mouse. Recently, we identified restriction fragment length polymorphisms (RFLPs) associated with the alpha4 (Chrna4) and alpha6 (Chrna6) nicotinic cholinergic receptor genes in the recombinant inbred (RI) strains derived from the Long-Sleep (LS) and Short-Sleep (SS) mouse lines. The alpha4 polymorphism has been identified as a point-mutation at position 529 (threonine to alanine) and the alpha6 polymorphism has not yet been identified. The studies described here evaluated the potential role of these polymorphisms in regulating sensitivity to nicotine by constructing dose-response curves for the effects of nicotine on six responses in the LSxSS RI strains. The results obtained suggest that both of the polymorphisms may play a role in regulating variability in sensitivity to nicotine. Those RI strains carrying the LS-like alpha4 RFLP were significantly more sensitive to the effects of nicotine on Y-maze crosses and rears, temperature and respiration and were less sensitive to the effects of nicotine on acoustic startle than those strains carrying the SS-like alpha4 RFLP. Those RI strains carrying the LS-like alpha6 RFLP were more sensitive to the effects of nicotine on respiration and acoustic startle, and less sensitive to the effects of nicotine on Y-maze crosses than those strains carrying the SS-like alpha6 RFLP. These results suggest that genetically determined differences in sensitivity to nicotine may be explained, in part, by variability associated with at least two of the neuronal nicotinic receptor genes, alpha4 and alpha6.

Molecular mapping and genetic analysis of a rice brown planthopper (Nilaparvata lugens Stål) resistance gene.

The brown planthopper (BPH), Nilaparvata lugens Stål, is a serious insect pest of rice (Oryza saliva L.). We have determined the chromosomal location of a BPH resistance gene in rice using SSR and RFLP techniques. A rice line 'B14', derived from the wild rice Oryza latifolia, showed high resistance to BPH. For tagging the resistance gene in 'B14X', an F2 population and a recombinant inbred (RI) population from a cross between Taichung Native 1 and 'B14' were developed and evaluated for BPH resistance. The results showed that a single dominant gene controlled the resistance of 'B14' to BPH. Bulked segregant SSR analysis was employed for identification of DNA markers linked to the resistance gene. From the survey of 302 SSR primer pairs, three SSR (RM335, RM261, RM185) markers linked to the resistance gene were identified. The closest SSR marker RM261 was linked to the resistance gene at a distance of 1.8 cM. Regions surrounding the resistance gene and the SSR markers were examined with additional RFLP markers on chromosome 4 to define the location of the resistance gene. Linkage of RFLP markers C820, R288, C946 with the resistance gene further confirmed its location on the short arm of chromosome 4. Closely linked DNA markers will facilitate selection for resistant lines in breeding programs and provide the basis for map-based cloning of this resistance gene.

CDNA sequence of five mouse guanine deaminase (Gda) alleles and mapping to mouse chromosome 19.

Guanine deaminase catalyses the conversion of guanine to xanthine and ammonia, thereby irreversibly removing the guanine base from the pool of guanine-containing metabolites. We have identified five alleles at the mouse guanine deaminase locus by cDNA sequencing. These alleles were defined by single-nucleotide polymorphisms at a total of 19 positions. For each allele the representative strains are as follows: Gda(a), C57BL/6J and DBA/2J; Gda(b), A/J; Gda(c), MOLF/Ei; Gda(d), CAST/Ei; and Gda(e), SPRET-1. The only codon change resulting in an amino acid substitution was found at nucleotide 523, where GAT was replaced by AAT in Mus spretus resulting in the deduced substitution of Asp-174 by Asn. The single-nucleotide difference between the a and b alleles was also typed by allele-specific oligonucleotide amplification for 17 common strains of Mus musculus susbp. musculus. By typing the AxB and BxA recombinant inbred (RI) strain sets, Gda was mapped to mouse chromosome 19, a region syntenic with human chromosome 9q11-q22.

Parental genetic contributions in the AXB and BXA recombinant inbred mouse strains.

Recombinant inbred (RI) strains are a valuable tool in mouse genetics to rapidly map the location of a new locus. Because RI strains have been typed for hundreds of genetic markers, the genotypes of individual strains within an RI set can be examined to identify specific strain(s) containing the desired region(s) of interest (e.g., one or more quantitative trait loci, QTLs) for subsequent phenotype testing. Specific RI strains might also be identified for use as progenitors in the construction of consomic (chromosome substitution strains or CSSs) or congenic lines or for use in the RI strain test (RIST). To quickly identify the genetic contributions of the parental A/J (A) and C57BL/6J (B) strains, we have generated chromosome maps for each commercially available AXB and BXA RI strain, in which the genetic loci are color-coded to signify the parent of origin. To further assist in strain selection for further breeding schemes, the percentages of A and B parental contributions were calculated, based on the total number of typed markers in the database for each strain. With these data, one can rapidly select the RI strain(s) carrying the desired donor and recipient strain region(s). Because points of recombination are known, starting with RI mice to generate CSSs or congenic lines immediately reduces genomewide screening to those donor-strain regions not already homozygous in the recipient strain. Two examples are presented to demonstrate potential uses of the generated chromosome maps: to select RI strains to construct congenic lines and to perform an RIST for Aliq1, a QTL linked to ozone-induced acute lung injury survival.