Identification of quantitative trait loci influencing aerial morphogenesis in the model legume <Emphasis Type="Italic">Medicago truncatula</Emphasis>

In many legume crops, especially in forage legumes, aerial morphogenesis defined as growth and development of plant organs, is an essential trait as it determines plant and seed biomass as well as forage quality (protein concentration, dry matter digestibility). Medicago truncatula is a model species for legume crops. A set of 29 accessions of M. truncatula was evaluated for aerial morphogenetic traits. A recombinant inbred lines (RILs) mapping population was used for analysing quantitative variation in aerial morphogenetic traits and QTL detection. Genes described to be involved in aerial morphogenetic traits in other species were mapped to analyse co-location between QTLs and genes. A large variation was found for flowering date, morphology and dynamics of branch elongation among the 29 accessions and within the RILs population. Flowering date was negatively correlated to main stem and branch length. QTLs were detected for all traits, and each QTL explained from 5.2 to 59.2% of the phenotypic variation. A QTL explaining a large part of genetic variation for flowering date and branch growth was found on chromosome 7. The other chromosomes were also involved in the variation detected in several traits. Mapping of candidate genes indicates a co-location between a homologue of Constans gene or a flowering locus T (FT) gene and the QTL of flowering date on chromosome 7. Other candidate genes for several QTLs are described. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Multi-population QTL detection for aerial morphogenetic traits in the model legume <Emphasis Type="Italic">Medicago truncatula</Emphasis>

Medicago truncatula, as a model species, is useful to study the genetic control of traits of agronomic interest in legumes species. Aerial morphogenesis is a key component of forage and seed yield. It was measured in four mapping populations originating from five parental lines. Single and multi-population quantitative trait locus (QTL) detections were carried out. A large variation was observed within populations and transgressive segregation was noted. Most traits showed high heritabilities in all seasons. Length of primary branches (LPB, cm) was positively correlated to branch elongation rate (BER, cm day⁻¹) and aerial dry matter (ADM, g). Flowering time (FT, °C day⁻¹) showed negative correlations with length of main stem (LMS, cm) and BER. One hundred and forty-one QTLs for BER, LMS, FT, LPB, diameter of primary branches (DPB), number of primary branches (NPB), number of nodes (NI) and ADM were identified and localized over all eight chromosomes. Single and multi-population analyses showed that the most important regions for aerial morphogenetic traits were chromosomes 1, 2, 7 and 8. Multi-population analysis revealed three regions of major QTLs affecting aerial morphogenetic traits (LPB, LMS, NPB, BER and FT). A region involved in flowering time variation was revealed on chromosome 6 on a single population. These results were used to identify candidate genes that could control variation for aerial morphogenesis traits in this species and in related crop legume species.     

Joint linkage QTL analyses for partial resistance to Phytophthora sojae in soybean using six nested inbred populations with heterogeneous conditions

Partial resistance to Phytophthora sojae in soybean is controlled by multiple quantitative trait loci (QTL). With traditional QTL mapping approaches, power to detect such QTL, frequently of small effect, can be limited by population size. Joint linkage QTL analysis of nested recombinant inbred line (RIL) populations provides improved power to detect QTL through increased population size, recombination, and allelic diversity. However, uniform development and phenotyping of multiple RIL populations can prove difficult. In this study, the effectiveness of joint linkage QTL analysis was evaluated on combinations of two to six nested RIL populations differing in inbreeding generation, phenotypic assay method, and/or marker set used in genotyping. In comparison to linkage analysis in a single population, identification of QTL by joint linkage analysis was only minimally affected by different phenotypic methods used among populations once phenotypic data were standardized. In contrast, genotyping of populations with only partially overlapping sets of markers had a marked negative effect on QTL detection by joint linkage analysis. In total, 16 genetic regions with QTL for partial resistance against P. sojae were identified, including four novel QTL on chromosomes 4, 9, 12, and 16, as well as significant genotype-by-isolate interactions. Resistance alleles from PI 427106 or PI 427105B contributed to a major QTL on chromosome 18, explaining 10–45 % of the phenotypic variance. This case study provides guidance on the application of joint linkage QTL analysis of data collected from populations with heterogeneous assay conditions and a genetic framework for partial resistance to P. sojae.     

Genetic determinism of reproductive fitness traits under drought stress in the model legume <Emphasis Type="Italic">Medicago truncatula</Emphasis>

Fitness traits that determine the reproductive ability of individuals and the persistence of populations are affected by drought stress. Medicago truncatula that commonly encounters drought stress in its natural area, and for which large natural diversity and genetic tools are available, is a suitable species to investigate genetic determinism of fitness traits under stress. In a common garden, three successive cycles of short drought stress were applied after flowering, during the reproductive stage that is the most susceptible to drought for that species. Ten genotypes derived from natural populations and a mapping population were used to investigate the genetic determinism of vegetative and reproductive traits as components of fitness. A large genetic variation was observed and transgressive genotypes (more resistant or more susceptible than the parental genotypes) were found in the mapping population. Fitness traits were reduced by 5–74% in drought condition compared to well-watered condition. The most affected characters were total pod number per plant and total pod weight per plant. A total of 49 QTL, explaining between 6 and 38% of phenotypic variation for vegetative and reproductive fitness traits, were detected on all chromosomes except chromosome 6. A major QTL for flowering date (R ² of 19 and 38%) that co-located with QTL for reproductive fitness traits were found on chromosome 7. In this study, no major QTL specific to drought-stressed or well-watered conditions were detected. We, thus, showed that QTL explaining fitness traits were numerous with small effects, in accordance with the genetic determinism of a complex trait.     

Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

Background

Cotton fibers (produced by Gossypium species) are the premier natural fibers for textile production. The two tetraploid species, G. barbadense (Gb) and G. hirsutum (Gh), differ significantly in their fiber properties, the former having much longer, finer and stronger fibers that are highly prized. A better understanding of the genetics and underlying biological causes of these differences will aid further improvement of cotton quality through breeding and biotechnology. We evaluated an inter-specific Gh × Gb recombinant inbred line (RIL) population for fiber characteristics in 11 independent experiments under field and glasshouse conditions. Sites were located on 4 continents and 5 countries and some locations were analyzed over multiple years.

Results

The RIL population displayed a large variability for all major fiber traits. QTL analyses were performed on a per-site basis by composite interval mapping. Among the 651 putative QTLs (LOD > 2), 167 had a LOD exceeding permutation based thresholds. Coincidence in QTL location across data sets was assessed for the fiber trait categories strength, elongation, length, length uniformity, fineness/maturity, and color. A meta-analysis of more than a thousand putative QTLs was conducted with MetaQTL software to integrate QTL data from the RIL and 3 backcross populations (from the same parents) and to compare them with the literature. Although the global level of congruence across experiments and populations was generally moderate, the QTL clustering was possible for 30 trait x chromosome combinations (5 traits in 19 different chromosomes) where an effective co-localization of unidirectional (similar sign of additivity) QTLs from at least 5 different data sets was observed. Most consistent meta-clusters were identified for fiber color on chromosomes c6, c8 and c25, fineness on c15, and fiber length on c3.

Conclusions

Meta-analysis provided a reliable means of integrating phenotypic and genetic mapping data across multiple populations and environments for complex fiber traits. The consistent chromosomal regions contributing to fiber quality traits constitute good candidates for the further dissection of the genetic and genomic factors underlying important fiber characteristics, and for marker-assisted selection.     

Detection of partial resistance quantitative trait loci against Didymella pinodes in Medicago truncatula

Ascochyta blight caused by Didymella pinodes (formerly Mycosphaerella pinodes) is one of the most important fungal diseases of pea (Pisum sativum) worldwide that can also infect the model legume Medicago truncatula. The objective of this study was to identify quantitative trait loci (QTLs) controlling resistance to D. pinodes in M. truncatula. Response to D. pinodes was studied under controlled conditions in seedlings of a population derived from the cross J6 × F83005.5, two M. truncatula lines that are, respectively, resistant and susceptible to D. pinodes. A combined map using two different recombinant inbred line populations was then used to identify the genomic regions bearing putative QTLs and to improve the position of the QTLs. A single QTL associated with resistance to D. pinodes was detected on linkage group 2, explaining up to 13 % of the total phenotypic variation for relative disease severity against the pathogen. Two simple sequence repeat markers, MTE80 and mtic890 (3 cM apart) were the ones most significantly associated with the QTL. These markers are located in bacterial artifical chromosomes AC119409 and AC125474, respectively, both of them overlapping on M. truncatula chromosome 2. The integration of QTL analysis and genomics in M. truncatula will contribute to the development of new markers and facilitate the identification of candidate genes for Ascochyta blight resistance.     

Genetic variability and QTL mapping of freezing tolerance and related traits in Medicago truncatula

Freezing is a major environmental limitation to crop productivity for a number of species including legumes. We investigated the genetic determinism of freezing tolerance in the model legume Medicago truncatula Gaertn (M. truncatula). After having observed a large variation for freezing tolerance among 15 M. truncatula accessions, the progeny of a F6 recombinant inbred line population, derived from a cross between two accessions, was acclimated to low above-freezing temperatures and assessed for: (a) number of leaves (NOL), leaf area (LA), chlorophyll content index (CCI), shoot and root dry weights (SDW and RDW) at the end of the acclimation period and (b) visual freezing damage (FD) during the freezing treatment and 2 weeks after regrowth and foliar electrolyte leakage (EL) 2 weeks after regrowth. Consistent QTL positions with additive effects for FD were found on LG1, LG4 and LG6, the latter being the most explanatory (R ² ≈ 40 %). QTL for NOL, QTL for EL, NOL and RDW, and QTL for EL and CCI colocalized with FD QTL on LG1, LG4 and LG6, respectively. Favorable alleles for these additive effects were brought by the same parent suggesting that this accession contributes to superior freezing tolerance by affecting plants’ capacity to maintain growth at low above-freezing temperatures. No epistatic effects were found between FD QTL, but for each of the studied traits, 3–6 epistatic effects were detected between loci not detected directly as QTL. These results open the way to the assessment of syntenic relationships between QTL for frost tolerance in M. truncatula and cultivated legume species.     

A high-density genetic map of the Medicago truncatula major freezing tolerance QTL on chromosome 6 reveals colinearity with a QTL related to freezing damage on Pisum sativum linkage group VI

Freezing is one of the most serious abiotic stress factors that affect cool-season legumes. It limits species geographic distribution and causes severe yield losses. Improving tolerance to freezing has long been a main concern for legume breeders. Medicago truncatula Gaertn. has been selected as a model species for legume biology. Various studies have shown significant macrosynteny between M. truncatula and agronomically important crop legumes. A major freezing tolerance quantitative trait locus (QTL), herein referred to as Mt-FTQTL6, was previously identified on M. truncatula chromosome 6. The physical location of this QTL was determined in this study and its corresponding chromosomal interval was enriched with additional markers. Markers were first developed using the draft sequence of M. truncatula euchromatin (release versions Mt3.0 and Mt3.5). Because Mt-FTQTL6 was found to coincide with an assembly gap, the Glycine max (L.) Merr. genome sequence was also used to generate markers. Five Mt-FTQTL6-linked markers were found to be common to a region on Pisum sativum L. linkage group VI harboring a QTL for freezing damage. A subset of markers was tested for transferability across 11 additional legume species. This study lays the groundwork for identifying the molecular basis of Mt-FTQTL6. Cross-legume markers will be useful in future efforts aiming to investigate the conservation of Mt-FTQTL6 in cool-season legumes and subsequently the existence of common mechanisms for response to freezing between M. truncatula and crop legumes.     

Identification of QTL for flag leaf length in common wheat and their pleiotropic effects

Leaf size is an important factor contributing to the photosynthetic capability of wheat plants. It also significantly affects various agronomic traits. In particular, the flag leaves contribute significantly to grain yield in wheat. A recombinant inbred line (RIL) population developed between varieties with significant differences in flag leaf traits was used to map quantitative trait loci (QTL) of flag leaf length (FLL) and to evaluate its pleiotropic effects on five yield-related traits, including spike length (SL), spikelet number per spike (SPN), kernel number per spike (KN), kernel length (KL), and thousand-kernel weight (TKW). Two additional RIL populations were used to validate the detected QTL and reveal the relationships in different genetic backgrounds. Using the diversity arrays technology (DArT) genetic linkage map, three major QTL for FLL were detected, with single QTL in different environments explaining 8.6–23.3% of the phenotypic variation. All the QTL were detected in at least four environments, and validated in two related populations based on the designed primers. These QTL and the newly developed primers are expected to be valuable for fine mapping and marker-assisted selection in wheat breeding programs.     

QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate rapid introgression of waterlogging tolerance in tropical maize breeding programs.     

Association of a CONSTANS-LIKE gene to flowering and height in autotetraploid alfalfa

In alfalfa (Medicago sativa), an autotetraploid forage legume, stem length is a major component of forage yield, quality and competing ability. In this species, flowering date is not a breeding criterion. Association mapping based on a candidate gene approach has given good results in plants, including autotetraploid species for which genetic analyses are complex. The role of a CONSTANS-LIKE gene, identified as a candidate for stem elongation and flowering date in the model legume M. truncatula, was tested for association with the same traits in alfalfa. Four hundred genotypes from ten cultivars were evaluated for stem height and flowering date in two locations during 4 years. They were genotyped with simple sequence repeat markers and a low structuration was noticed. Primers were designed to amplify and sequence two regions of the alfalfa gene homologous to CONSTANS-LIKE. Single nucleotide polymorphisms (SNPs) were detected and their allelic dose in each genotype was scored. Linkage disequilibrium within CONSTANS-LIKE rapidly decreased as expected. Eight SNPs with a frequency above 10% were detected over 1,010 bp (one SNP every 126 bp on average) in the 400 genotypes. This number was lower than observed in a neutral gene (a SNP every 31 bp on average). Highly significant associations of three SNPs to flowering date and stem height were identified. Each SNP explained up to 4.2% of the genetic variance. Thus, as in the model species, the CONSTANS-LIKE gene was shown to be involved in flowering date and stem height in alfalfa.     

Identification of novel quantitative trait loci for increased lycopene content and other fruit quality traits in a tomato recombinant inbred line population

Epidemiological and clinical studies indicate that a steady dietary intake of bioavailable lycopene, a C₄₀ carotenoid and potent natural antioxidant, may be associated with a decreased incidence of prostate cancer in humans. Since fresh tomatoes and processed tomato products represent approximately 85% of the average human??s dietary lycopene intake, the identification of novel genetic factors which regulate high fruit lycopene content in tomato is imperative for the improvement of nutritional quality in this commercially valuable specialty crop. To understand the genetic control of the extraordinarily high fruit lycopene content in an accession (LA2093) of the tomato wild species Solanum pimpinellifolium, a quantitative trait locus (QTL) mapping study was conducted using a recombinant inbred line (RIL) population of a cross between LA2093 and a cultivated tomato (S. lycopersicum) breeding line, NCEBR-1. The parental lines, F1 progeny, and F7-F10 RIL populations were grown in replicated field trials in four successive years and evaluated for lycopene content as well as several other traits, including fruit fresh weight, soluble solids content, pH of puree, and plant maturity. The lycopene content of ripe fruit was estimated using three methods: high-performance liquid chromatography (HPLC), spectrophotometry, and colorimetric assays. Based on these measurements, QTL were identified and compared across generations. Among the QTL identified for lycopene, two QTL, located on chromosomes 7 and 12, had very large effects and were consistent across generations. The genomic intervals in which these two QTL reside do not correspond to known map positions of carotenoid biosynthetic genes, indicating that these QTL may represent novel alleles with potentially important implications for tomato breeding as well as increased understanding of carotenoid accumulation in tomato. Several QTL were also identified for fruit weight, soluble solids content and plant maturity. The potential implications of these results for tomato crop improvement are discussed.     

Construction of two genetic linkage maps in cultivated tetraploid alfalfa (<Emphasis Type="Italic">Medicago sativa</Emphasis>) using microsatellite and AFLP markers

Background  

Alfalfa (Medicago sativa) is a major forage crop. The genetic progress is slow in this legume species because of its autotetraploidy and allogamy. The genetic structure of this species makes the construction of genetic maps difficult. To reach this objective, and to be able to detect QTLs in segregating populations, we used the available codominant microsatellite markers (SSRs), most of them identified in the model legume Medicago truncatula from EST database. A genetic map was constructed with AFLP and SSR markers using specific mapping procedures for autotetraploids. The tetrasomic inheritance was analysed in an alfalfa mapping population.     

Comparison of Mating Designs for Establishing Nested Association Mapping Populations in Maize and Arabidopsis thaliana

The nested association mapping (NAM) strategy promises to combine the advantages of linkage mapping and association mapping. The objectives of my research were to (i) investigate by computer simulations the power and type I error rate for detecting quantitative trait loci (QTL) with additive effects using recombinant inbred line (RIL) populations of maize derived from various mating designs, (ii) compare these estimates to those obtained for RIL populations of Arabidopsis thaliana, (iii) examine for both species the optimum number of inbreds used as parents of the NAM populations, and (iv) provide on the basis of the results of these two model species a general guideline for the design of NAM populations in other plant species. The computer simulations were based on empirical data of a set of 26 diverse maize inbred lines and a set of 20 A. thaliana inbreds both representing a large part of the genetic diversity of the corresponding species. I observed considerable differences in the power for QTL detection between NAM populations of the same size but created on the basis of different crossing schemes. This finding illustrated the potential to improve the power for QTL detection without increasing the total resources necessary for a QTL mapping experiment. Furthermore, my results clearly indicated that it is advantageous to create NAM populations from a large number of parental inbreds.MANY traits that are important for fitness and agricultural value of plants are quantitative traits. Such traits are affected by many genes, the environment, and interactions between genes and the environment (Holland 2007). In plants, quantitative trait locus (QTL) mapping is a key tool for studying the genetic architecture of quantitative traits (Yano 2001). This method enables the estimation of (i) the number of genome regions affecting a trait, (ii) the distribution of gene effects, and (iii) the relative importance of additive and nonadditive gene action.Until now, most of the plant QTL mapping studies have been based on linkage mapping methods using individual biparental populations. The major limitations of such approaches are a poor resolution in detecting QTL and that with biparental crosses of inbred lines only two alleles at any given locus can be studied simultaneously (Flint-Garcia et al. 2005). Association mapping methods, which are successfully applied in human genetics to detect genes coding for human diseases (e.g., Willer et al. 2008), promise to overcome these limitations (Kraakman et al. 2004). However, in comparison with linkage mapping approaches, association mapping approaches have only a low power to detect QTL in genomewide scans (Yu and Buckler 2006).The nested association mapping (NAM) strategy proposed by Yu et al. (2008) uses recombinant inbred line (RIL) populations derived from several crosses of parental inbreds. Due to diminishing chances of recombination over short genetic distance and a given number of generations, the genomes of these RILs are mosaics of chromosomal segments of their parental genomes. Consequently, within the chromosomal segments, the linkage disequilibrium (LD) information across the parental inbreds is maintained. Thus, if diverse parental inbreds are used, LD decays within the chromosomal segments of the RILs over a short physical distance (Wilson et al. 2004). Therefore, the NAM strategy allows to exploit both recent and ancient recombination and, thus, will show a high mapping resolution (Yu et al. 2008). Furthermore, due to the balanced design underlying the proposed mapping strategy as well as the systematic reshuffling of the genomes of the parental inbreds during RIL development, NAM populations are expected to show a high power to detect QTL in genomewide approaches (Buckler et al. 2009).Exploitation of the advantages of the NAM strategy requires developing, genotyping, and phenotyping of RIL populations from several crosses of diverse parental inbreds. This, however, requires large financial resources (cf. Yu et al. 2008). Therefore, it is mandatory that the available resources are spent in an optimum way.Stich et al. (2009) examined the optimum allocation of resources for NAM in maize with respect to the number of RILs derived from the reference design as well as the number of environments and replications per environment used for phenotypic evaluation. The power for QTL detection, however, is expected to be influenced not only by these factors but also by the crossing scheme from which RIL populations are derived. To my knowledge, no study has so far compared RIL populations derived from various mating designs regarding the power for detecting QTL with additive effects. Furthermore, no information is available on the optimum number of inbreds used as parents of the NAM populations.For Arabidopsis thaliana, more advanced genomic tools are available than for most other plant species (e.g., Alonso et al. 2003; Clark et al. 2007). This fact increases the prospects of success of NAM approaches. However, A. thaliana differs from maize with respect to the genome size and the allele frequency, which both have the potential to influence the power for QTL detection. Nevertheless, to my knowledge, no study has so far examined the power of NAM in A. thaliana.The objectives of my research were to (i) investigate by computer simulations the power and type I error rate for detecting QTL with additive effects using RIL populations of maize derived from various mating designs, (ii) compare these estimates to those obtained for RIL populations of A. thaliana, (iii) examine for both species the optimum number of inbreds used as parents of the NAM populations, and (iv) provide on the basis of the results of these two model species a general guideline for the design of NAM populations in other plant species.     

Quantitative trait locus analysis of a recombinant inbred line population derived from a Lycopersicon esculentum x Lycopersicon cheesmanii cross

Quantitative trait loci influencing fruit traits were identified by restriction fragment length polymorphism (RFLP) analysis in a population of recombinant inbred lines (RIL) derived from a cross of the cultivated tomato, Lycopersicon esculentum with a related wild species Lycopersicon cheesmanii. One hundred thirty-two polymorphic RFLP loci spaced throughout the tomato genome were scored for 97 F₈ RIL families. Fruit weight and soluble solids were measured in replicated trials during 1991 and 1992. Seed weight was measured in 1992. Significant (P<0.01 level) quantitative trait locus (QTL) associations of marker loci were identified for each trait. A total of 73 significant marker locus-trait associations were detected for the three traits measured. Fifty-three of these associations were for fruit weight and soluble solids, many of which involved marker loci signficantly associated with both traits. QTL with large effects on all three traits were detected on chromosome 6. Greater homozygosity at many loci in the RIL population as compared to F₂ populations and greater genomic coverage resulted in increased precision in the estimation of QTL effects, and large proportions of the total phenotypic variance were explained by marker class variation at significant marker loci for many traits. The RIL population was effective in detecting and discriminating among QTL for these traits previously identified in other investigations despite skewed segregation ratios at many marker loci. Large additive effects were measured at significant marker loci. Lower fruit weight, higher soluble solids, and lower seed weight were generally associated with RFLP alleles from theL. cheesmanii parent.     

Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy

Epistatic interactions among quantitative trait loci (QTL) contribute substantially to the variation in complex traits. The main objectives of this study were to (i) compare three- vs. four-step genome scans to identify three-way epistatic interactions among QTL belonging to a metabolic pathway, (ii) investigate by computer simulations the power and proportion of false positives (PFP) for detecting three-way interactions among QTL in recombinant inbred line (RIL) populations derived from a nested mating design, and (iii) compare these estimates to those obtained for detecting three-way interactions among QTL in RIL populations derived from diallel and different partial diallel mating designs. The single-nucleotide polymorphism haplotype data of B73 and 25 diverse maize inbreds were used to simulate the production of various RIL populations. Compared to the three-step genome scan, the power to detect three-way interactions was higher with the four-step genome scan. Higher power to detect three-way interactions was observed for RILs derived from optimally allocated distance-based designs than from nested designs or diallel designs. The power and PFP to detect three-way interactions using a nested design with 5000 RILs were for both the 4-QTL and the 12-QTL scenario of a magnitude that seems promising for their identification.     

QTL analysis of canning quality and color retention in black beans (Phaseolus vulgaris L.)

Black bean (Phaseolus vulgaris L.) consumption is increasing in the USA. One of the major challenges faced by breeders is to develop superior black bean cultivars to meet the demands of the canning industry. Processors require beans that take up water quickly during pre-canning soak and beans that retain their black color after canning. To properly assess canning quality requires expensive and detailed measurements of the canned product, often not possible for bean breeders. The objective of this research was identify quantitative trait loci (QTL) in a black bean recombinant inbred line (RIL) population for canning quality traits related to water uptake, color retention, and anthocyanin concentration. The parental lines from which the population was developed, Black Magic and Shiny Crow, contrasted in water uptake and color retention. These cultivars also differed in seed coat luster, controlled by a single gene, Asp. A medium-density linkage map of 1,449 markers and a distance of 1,660 cM was developed from this RIL population. The map was aligned to the bean genome sequence V1.0 by using sequence information associated with the Diversity Arrays Technology markers. QTL analysis revealed that the region near the Asp gene on chromosome Pv 07 is the major determinant of water uptake, explaining up to 49 % of the phenotypic variation. A group of QTL for color retention-related traits was found at the upper region of Pv 11, explaining up to 30 % of the phenotypic variation. A smaller effect QTL clustered on Pv 5 co-localized with a QTL for canned bean anthocyanin concentration and explained less than 10 % of the phenotypic variation. These color-related QTL have marker-assisted selection potential for bean breeders interested in enhancing color retention and anthocyanin concentration of processed black beans.     

A multiparental cross population for mapping QTL for agronomic traits in durum wheat (Triticum turgidum ssp. durum)

Multiparental cross designs for mapping quantitative trait loci (QTL) provide an efficient alternative to biparental populations because of their broader genetic basis and potentially higher mapping resolution. We describe the development and deployment of a recombinant inbred line (RIL) population in durum wheat (Triticum turgidum ssp. durum) obtained by crossing four elite cultivars. A linkage map spanning 2664 cM and including 7594 single nucleotide polymorphisms (SNPs) was produced by genotyping 338 RILs. QTL analysis was carried out by both interval mapping on founder haplotype probabilities and SNP bi‐allelic tests for heading date and maturity date, plant height and grain yield from four field experiments. Sixteen QTL were identified across environments and detection methods, including two yield QTL on chromosomes 2BL and 7AS, with the former mapped independently from the photoperiod response gene Ppd‐B1, while the latter overlapped with the vernalization locus VRN‐A3. Additionally, 21 QTL with environment‐specific effects were found. Our results indicated a prevalence of environment‐specific QTL with relatively small effect on the control of grain yield. For all traits, functionally different QTL alleles in terms of direction and size of genetic effect were distributed among parents. We showed that QTL results based on founder haplotypes closely matched functional alleles at known heading date loci. Despite the four founders, only 2.1 different functional haplotypes were estimated per QTL, on average. This durum wheat population provides a mapping resource for detailed genetic dissection of agronomic traits in an elite background typical of breeding programmes.