Breeding designs for recombinant inbred advanced intercross lines

Recombinant inbred lines derived from an advanced intercross, in which multiple generations of mating have increased the density of recombination breakpoints, are powerful tools for mapping the loci underlying complex traits. We investigated the effects of intercross breeding designs on the utility of such lines for mapping. The simplest design, random pair mating with each pair contributing exactly two offspring to the next generation, performed as well as the most extreme inbreeding avoidance scheme at expanding the genetic map, increasing fine-mapping resolution, and controlling genetic drift. Circular mating designs offer negligible advantages for controlling drift and exhibit greatly reduced map expansion. Random-mating designs with variance in offspring number are also poor at increasing mapping resolution. Given equal contributions of each parent to the next generation, the constraint of monogamy has no impact on the qualities of the final population of inbred lines. We find that the easiest crosses to perform are well suited to the task of generating populations of highly recombinant inbred lines.     

The genomes of recombinant inbred lines

Recombinant inbred lines (RILs) can serve as powerful tools for genetic mapping. Recently, members of the Complex Trait Consortium proposed the development of a large panel of eight-way RILs in the mouse, derived from eight genetically diverse parental strains. Such a panel would be a valuable community resource. The use of such eight-way RILs will require a detailed understanding of the relationship between alleles at linked loci on an RI chromosome. We extend the work of Haldane and Waddington on two-way RILs and describe the map expansion, clustering of breakpoints, and other features of the genomes of multiple-strain RILs as a function of the level of crossover interference in meiosis.     

IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains

Intermated Recombinant Inbred Lines (IRILs) in plants, or Advanced Recombinant Inbred Strains in animals, are constructed by carrying out generations of intermating between F2 individuals before starting recurrent inbreeding generations by selfing or sib-mating. IRILs are powerful for high-resolution genetic mapping because they have undergone more recombination than usual Recombinant Inbred Lines (RILs). However, there is no mapping software able to generate actual centiMorgan distances from the segregation data obtained with IRILs. IRILmap software converts genetic distances computed with any linkage mapping program designed for RILs, so that IRIL-derived data can be used to get actual centiMorgan distances, directly comparable to F2, backcross or RIL-derived maps.     

Two- and three-locus tests for linkage analysis using recombinant inbred lines

We consider fixed recombinant inbred lines (RILs) derived either by selfing or by full-sib mating; when applicable, we also consider intermated recombinant inbreds (IRIs). First, we show that the usual estimate of recombination fraction based on RIL data is biased, and we provide an estimate where the major part of that bias is removed. Second, we derive simple formulas to compute the frequencies of genotypes at three loci in RILs. We describe the nonindependence of multiple recombinations arising in RIL recombination data even though there may be no interference in each meiosis. Finally, we give formulas for interference tests, gene mapping, or QTL detection in RIL populations.     

Performance prediction of F1 hybrids between recombinant inbred lines derived from two elite maize inbred lines

Selection of recombinant inbred lines (RILs) from elite hybrids is a key method in maize breeding especially in developing countries. The RILs are normally derived by repeated self-pollination and selection. In this study, we first investigated the accuracy of different models in predicting the performance of F₁ hybrids between RILs derived from two elite maize inbred lines Zong3 and 87-1, and then compared these models through simulation using a wider range of genetic models. Results indicated that appropriate prediction models depended on genetic architecture, e.g., combined model using breeding value and genome-wide prediction (BV+GWP) has the highest prediction accuracy for high V _D/V _A ratio (>0.5) traits. Theoretical studies demonstrated that different components of genetic variance were captured by different prediction models, which in turn explained the accuracy of these models in predicting the F₁ hybrid performance. Based on genome-wide prediction model (GWP), 114 untested F₁ hybrids possibly having higher grain yield than the original F₁ hybrid Yuyu22 (the single cross between Zong3 and 87-1) have been identified and recommended for further field test.     

Distribution of parental genome blocks in recombinant inbred lines

We consider recombinant inbred lines obtained by crossing two given homozygous parents and then applying multiple generations of self-crossings or full-sib matings. The chromosomal content of any such line forms a mosaic of blocks, each alternatively inherited identically by descent from one of the parents. Quantifying the statistical properties of such mosaic genomes has remained an open challenge for many years. Here, we solve this problem by taking a continuous chromosome picture and assuming crossovers to be noninterfering. Using a continuous-time random walk framework and Markov chain theory, we determine the statistical properties of these identical-by-descent blocks. We find that successive block lengths are only very slightly correlated. Furthermore, the blocks on the ends of chromosomes are larger on average than the others, a feature understandable from the nonexponential distribution of block lengths.     

Variability for the in vitro culture response in tomato recombinant inbred lines

The aim of this work was to estimate genetic variability for in vitro culture response of recombinant inbred lines (RILs) of the genus Lycopersicon. The callus percentage (C), the regeneration percentage (R) and the productivity rate (PR) were evaluated 45 d after culture initiation in a set of 16 elite tomato RILs and their parents. The narrow sense heritability (h ²) values were 0.38 ± 0.04 for C, 0.46 ± 0.04 for R, and 0.28 ± 0.03 for R, while the genetic correlation (r _g ) values were −0.96 ± 0.07 between C and R, 0.81 ± 0.14 between PR and R, and −0.79 ± 0.16 between PR and C. Three AFLP markers associated to the in vitro traits were identified.     

Genotypic probabilities for pairs of inbred relatives

Expressions for the joint genotypic probabilities of two related individuals are used in many population and quantitative genetic analyses. These expressions, resting on a set of 15 probabilities of patterns of identity by descent among the four alleles at a locus carried by the relatives, are generally well known. There has been recent interest in special cases where the two individuals are both related and inbred, although there have been differences among published results. Here, we return to the original 15-probability treatment and show appropriate reductions for relatives when they are drawn from a population that itself is inbred or when the relatives have parents who are related. These results have application in affected-relative tests for linkage, and in methods for interpreting forensic genetic profiles.     

Generation and screening of recombinant inbred lines of rice for yellow stemborer resistance

Based on the results of studies on varietal screening, antixenosis (egg laying preference) and antibiosis (larval survival and adult emergence), rice varieties W1263 and CO43 were selected as resistant and susceptible parents, respectively, for yellow stemborer (YSB) infestation. A mapping population was developed using above parents following single seed descent method. Screening for YSB reaction in F1 and F2, generations under field and glasshouse conditions for both dead hearts and white ears, established the polygenic nature of inheritance for YSB resistance. Field screening for YSB resistance at F9 generation revealed the difference in the reactions among recombinant inbred lines (RILs) between vegetative and reproductive stages. The experiments under field and glasshouse screening of RILs for dead hearts showed significant positive association. However, the reaction was more towards susceptibility in glasshouse screening due to no choice test. Scoring of 250 RILs (F8) for various morphological traits showed wide range of variation indicating the suitability for QTL mapping.     

Marker-assisted recurrent selection for cumulating additive and interactive QTLs in recombinant inbred lines

A computer program has been designed to manage marker information in recombinant inbred-line populations. The objective is to select pairs of inbred lines (either recombinant-inbred or doubled-haploid) to be intercrossed, in order to accumulate all or most favourable alleles, either with additive effects or with interactive effects. The population size required to have a 95% chance of obtaining the best line from a given cross is computed, taking into account the number of QTLs and the probability that no recombination event occurs in any of the QTL confidence intervals. It is shown that the accuracy of QTL location greatly affects selection efficiency and that a recurrent selection scheme is highly preferable for pyramiding many QTLs. An application to the bread-making quality improvement of wheat is presented. Received: 25 September 1998 / Accepted: 29 July 1999     

Insect resistance in recombinant inbred soybean lines derived from non-resistant parents

Larval performance of Helicoverpa zea (Boddie) (corn earworm) (Lepidoptera: Noctuidae) was examined on 240 recombinant inbred (RI) soybean, Glycine max (L.) Merrill, lines. These homozygous RI were derived from an intraspecific cross of genetically distant, non-resistant, parents, Minsoy from China and Noir 1 from Hungary. Based upon a genetic map of more than 500 molecular markers, each RI line presented a unique genotype composed of a mixture of different parental alleles. The RI lines exhibited transgressive segregation with respect to their defensive effects on H. zea, such that the range of RI phenotypes far exceeded that of the parents. Similar effects were observed on the soybean looper, Pseudoplusia includens (Walker) (Lepidoptera: Noctuidae). We identified several independent quantitative trait loci (QTLs) linked to molecular markers that were associated with H. zea larval development parameters. Two QTLs affected several different traits including larval weight and developmental rate; other QTLs affected only a single trait each, i.e., larval weight, pupal weight, developmental rate, nutritional efficiency or survival. The results demonstrate that the increased range of defensive effects among the segregant RI lines is due to recombination among several parental genes that together quantitatively control plant defensive traits.Several alternative responses by herbivores have been proposed relative to plant hybrid swarms, hybrid avoidance due to higher hybrid resistance than either parent, hybrid preference due to lower resistance than either parent, hybrid equivalency to one or the other parent, or hybrid intermediacy. Within this RI population, we observed all of the proposed responses by H. zea, as might be expected when defensive traits are controlled by several genes.     

Model analysis of flowering phenology in recombinant inbred lines of barley

A generic model for flowering phenology as a function of daily temperature and photoperiod was applied to predict differences of flowering times among 96 individuals (including the two parents) of a recombinant inbred line population in barley (Hordeum vulgare L.). Because of the large number of individuals to study, there is a need for simple ways to derive model parameters for each genotype. Therefore the number of genotype-specific parameters was reduced to four, namely f(o) (the minimum number of days to flowering at the optimum temperature and photoperiod), (1) and (2) (the development stages for the start and the end of the photoperiod-sensitive phase, respectively), and delta (the photoperiod sensitivity). Values of these parameters were estimated using a newly described methodological framework based on data from a photoperiod-controlled experiment where plants were mutually transferred between long-day and short-day environments at regular intervals. This modelling approach was tested in eight independent field environments of different sowing dates in two growing seasons. The four-parameter model predicted 37-67% of observed phenotypic variation in an environment, 76% of variation in across-environment mean days to flowering among the genotypes, and 96% of variation in across-genotype mean among the eight environments. When all the observations of the 96 genotypes across the eight environments were pooled, the model explained 81% of the total variation. Sensitivity analysis showed that all four model parameters were important for predicting differences in flowering time among the genotypes; but their relative importance differed and the ranking was in the order of f(o), delta, theta1, and theta2. This study highlighted the potential of using ecophysiological models to assist the genetic analysis of quantitative crop traits whose phenotype is often environment-dependent.     

Quantitative trait mapping in a diallel cross of recombinant inbred lines

A recombinant inbred intercross (RIX) is created by generating diallel F₁ progeny from one or more panels of recombinant inbred (RI) strains. This design was originally introduced to extend the power of small RI panels for the confirmation of quantitative trait loci (QTL) provisionally detected in a parental RI set. For example, the set of 13 C × B (C57BL/6ByJ × BALB/cByJ) RI strains can, in principle, be supplemented with 156 isogenic F₁s. We describe and test a method of analysis, based on a linear mixed model, that accounts for the correlation structure of RIX populations. This model suggests a novel permutation algorithm that is needed to obtain appropriate threshold values for genome-wide scans of an RIX population. Despite the combinational multiplication of unique genotypes that can be generated using an RIX design, the effective sample size of the RIX population is limited by the number of progenitor RI genomes that are combined. When using small RI panels such as the C × B there appears to be only modest advantage of the RIX design when compared with the original RI panel for detecting QTLs with additive effects. The RIX, however, does have an inherent ability to detect dominance effects, and, unlike RI strains, the RIX progeny are genetically reproducible but are not fully inbred, providing somewhat more natural genetic context. We suggest a breeding strategy, the balanced partial RIX, that balances the advantage of RI and RIX designs. This involves the use of a partial RIX population derived from a large RI panel in which the available information is maximized by minimizing correlations among RIX progeny.     

Detection of quantitative trait Loci influencing recombination using recombinant inbred lines

The genetic basis of variation in recombination in higher plants is polygenic and poorly understood, despite its theoretical and practical importance. Here a method of detecting quantitative trait loci (QTL) influencing recombination in recombinant inbred lines (RILs) is proposed that relies upon the fact that genotype data within RILs carry the signature of past recombination. Behavior of the segregational genetic variance in numbers of chromosomal crossovers (recombination) over generations is described for self-, full-sib-, and half-sib-generated RILs with no dominance in true crossovers. This genetic variance, which as a fraction of the total phenotypic variance contributes to the statistical power of the method, was asymptotically greatest with half sibbing, less with sibbing, and least with selfing. The statistical power to detect a recombination QTL declined with diminishing QTL effect, genome target size, and marker density. For reasonably tight marker linkage power was greater with less intense inbreeding for later generations and vice versa for early generations. Generational optima for segregation variance and statistical power were found, whose onset and narrowness varied with marker density and mating design, being more pronounced for looser marker linkage. Application of this method to a maize RIL population derived from inbred lines Mo17 and B73 and developed by selfing suggested two putative QTL (LOD > 2.4) affecting certain chromosomes, and using a canonical transformation another putative QTL was detected. However, permutation tests failed to support their presence (experimentwise alpha = 0.05). Other populations with more statistical power and chosen specifically for recombination QTL segregation would be more effective.     

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.     

Segregation analysis of heading traits in hexaploid wheat utilizing recombinant inbred lines

The purpose of this study was to analyze the genetic segregation of heading traits in wheat using recombinant inbred lines (RILs) of hexaploid wheat, derived from Triticum aestivum cv. Chinese Spring and T. spelta var. duhameliamum. The population was examined under controlled environmental conditions as well as in the field. This strategy differentiated the effect of three genetic factors (vernalization requirement, photoperiod sensitivity and narrow-sense earliness) and identified their interactions. Correlation analysis showed that photoperiod sensitivity and narrow-sense earliness are critical for heading time in the field. Single-marker analysis using 322 molecular markers segregating among RIL detected a total of 38 linked markers for each genetic factor and heading in the field. In interval analysis, two Vrn genes (Vrn-B1 and Vrn-D1) and Ppd-B1 were mapped on chromosomes 5B, 5D and 2B, respectively. It was noticed that Vrn-B1 on 5B from the spelt wheat conferred a strong-spring habit equivalent to the homologous Vrn-A1. Quantitative trait locus analysis also showed that Ppd-B1 was not detected under the short-day condition without vernalization treatment, and that there were two types of genes for photoperiod sensitivity, dependent on and independent of vernalization treatment.     

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

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

QTLs for grain dry milling properties, composition and vitreousness in maize recombinant inbred lines

Vitreousness and kernel hardness are important properties for maize processing and end-product quality. In order to examine the genetic basis of these traits, a recombinant inbred line population resulting from a cross between a flint line (F-2) and a semident line (Io) was used to search for vitreousness and kernel composition QTLs. Vitreousness was measured by image processing from a kernel section, while NIR spectroscopy was used to estimate starch, protein, cellulose, lipid and semolina yield. In addition, thousand-grain weight and grain weight per ear were measured. The MQTL method was used to map the QTLs for the different traits. An additional program allowed for the detection of interaction QTLs between markers. The total number of main-effect and interaction QTLs was similar. The QTLs were not evenly distributed but tended to cluster. Such clusters, mixing main-effect and interaction QTLs, were observed at six positions : on chromosomes 1, 2, 3, 6, 8 and 9. Two of them, on chromosomes 6 and 9, concerned both QTLs for kernel-weight traits and QTLs for kernel-composition traits (protein and cellulose). Technological-trait QTLs (vitreousness or semolina yield) were located less than 16 cM from a protein-content QTL on chromosome 2, and were co-located with lipid- and starch-content QTLs on chromosome 8. The co-location of a vitreousness and a semolina-yield QTL at the telomeric end of the chromosome 2 (Bin 2.02) is likely to be meaningful since measurement of these related traits, made by completely different methods (NIRS vs image processing), yielded very close QTLs. A similar location was previously reported independently for a kernel-friability QTL. Comparing the map location of the numerous loci for known-function genes it was shown that three zein loci were closely linked to QTLs for vitreousness on chromosome 3, for semolina yield and starch on chromosome 4, and for protein, cellulose and grain weight on chromosome 9. Some other candidate genes linked to starch precursor metabolism were also suggested on chromosomes 6 and 8. Received: 27 April 2000 / Accepted: 3 July 2000