Association mapping in multiple segregating populations of sugar beet (<Emphasis Type="Italic">Beta vulgaris</Emphasis> L.)

Association mapping in multiple segregating populations (AMMSP) combines high power to detect QTL in genome-wide approaches of linkage mapping with high mapping resolution of association mapping. The main objectives of this study were to (1) examine the applicability of AMMSP in a plant breeding context based on segregating populations of various size of sugar beet (Beta vulgaris L.), (2) compare different biometric approaches for AMMSP, and (3) detect markers with significant main effect across locations for nine traits in sugar beet. We used 768 F _n (n = 2, 3, 4) sugar beet genotypes which were randomly derived from 19 crosses among diploid elite sugar beet clones. For all nine traits, the genotypic and genotype × location interaction variances were highly significant (P < 0.01). Using a one-step AMMSP approach, the total number of significant (P < 0.05) marker-phenotype associations was 44. The identification of genome regions associated with the traits under consideration indicated that not only segregating populations derived from crosses of parental genotypes in a systematic manner could be used for AMMSP but also populations routinely derived in plant breeding programs from multiple, related crosses. Furthermore, our results suggest that data sets, whose size does not permit analysis by the one-step AMMSP approach, might be analyzed using the two-step approach based on adjusted entry means for each location without losing too much power for detection of marker-phenotype associations.     

Dynamic gene action at QTLs for resistance to Setosphaeria turcica in maize

 Cultivars with quantitative resistance are widely used to control Setosphaeria turcica (Luttrell) Leonard & Suggs, the causal organism of northern corn leaf blight (NCLB). Here the effectiveness of quantitative trait loci (QTLs) for NCLB resistance was investigated over the course of host plant development in inoculated field trials. A population of 194–256 F_2:3 lines derived from a cross between a susceptible Italian (Lo951) and a highly resistant African inbred line (CML202) was tested in three environments in Kenya. The traits assessed were the incubation period (IP), the percentage disease severity (DS 1 to 5, taken biweekly), and the area under the disease progress curve (AUDPC). Considering all resistance traits and environments, a total of 19 putative QTLs were detected by composite interval mapping using a linkage map with 110 RFLP markers. In the combined analysis across environments, nine QTLs were significant (LOD >3.0) for DS 3, recorded around flowering time, explaining 71% of the genotypic variance. Four of these nine QTLs displayed significant (P<0.05) QTL×environment (QTL×E) interaction. Most QTLs were already significant in the juvenile stage (IP) and became less effective after flowering. Across environments, three QTLs conditioned adult-plant resistance, in the sense that they were only significant after flowering. Six QTL alleles on chromosomes 2, 4, 5, 8, and 9 of CML202 should be useful for marker-assisted backcrossing. Received: 24 August 1998 / Accepted: 29 September 1998     

Genetic basis of agronomically important traits in sugar beet (Beta vulgaris L.) investigated with joint linkage association mapping

Epistatic interactions may contribute substantially to the hybrid performance of sugar beet. The main goal of our study was to dissect the genetic basis of eight important physiological and agronomic traits using two different biometrical models for joint linkage association mapping. A total of 197 genotypes of an elite breeding population were evaluated in multi-location trials and fingerprinted with 194 SNP markers. Two different statistical models were used for the genome-wide scan for marker–trait associations: Model A, which corrects for the genetic background with markers as cofactors and Model B, which additionally models a population effect. Based on the extent of linkage disequilibrium in the parental population, we estimated that for a genome-wide scan at least 100 equally spaced markers are necessary. We mapped across the eight traits 39 QTL for Model A and 22 for Model B. Only 11% of the total number of QTL were identified based on Models A and B, which indicates that both models are complementary. Epistasis was detected only for two out of the eight traits, and contributed only to a minor extent to the genotypic variance. This low relevance of epistasis implies that in sugar beet breeding the prediction of performance of three-way hybrids is feasible with high accuracy based on the means of their single crosses.     

Comparison of biometrical models for joint linkage association mapping

Joint linkage association mapping (JLAM) combines the advantages of linkage mapping and association mapping, and is a powerful tool to dissect the genetic architecture of complex traits. The main goal of this study was to use a cross-validation strategy, resample model averaging and empirical data analyses to compare seven different biometrical models for JLAM with regard to the correction for population structure and the quantitative trait loci (QTL) detection power. Three linear models and four linear mixed models with different approaches to control for population stratification were evaluated. Models A, B and C were linear models with either cofactors (Model-A), or cofactors and a population effect (Model-B), or a model in which the cofactors and the single-nucleotide polymorphism effect were modeled as nested within population (Model-C). The mixed models, D, E, F and G, included a random population effect (Model-D), or a random population effect with defined variance structure (Model-E), a kinship matrix defining the degree of relatedness among the genotypes (Model-F), or a kinship matrix and principal coordinates (Model-G). The tested models were conceptually different and were also found to differ in terms of power to detect QTL. Model-B with the cofactors and a population effect, effectively controlled population structure and possessed a high predictive power. The varying allele substitution effects in different populations suggest as a promising strategy for JLAM to use Model-B for the detection of QTL and then to estimate their effects by applying Model-C.     

A gene for resistance to the maize streak virus in the African CIMMYT maize inbred line CML202

Resistance to maize streak virus (MSV) is an essential trait of improved maize varieties in sub-Saharan Africa. We mapped quantitative trait loci (QTL) for resistance to MSV in a population of 196 F_2:3 lines derived from a cross between the maize inbred lines CML202 (resistant) from CIMMYT-Zimbabwe and Lo951 (susceptible) from Italy. Field tests were planted at two locations in Zimbabwe, inoculated with viruliferous leaf hoppers (Cicadulina mbila), and scored twice (21 and 83 days after infesting, DAI) on a 1–5 scale. The mean final streak intensity (score 2) of the parent lines was 2.2 (CML202) and 4.8 (Lo951). Genotype × location interaction was large for score 1 but negligible for score 2. Consequently, the heritability was higher for score 2 (0.93) than for score 1 (0.62). By composite interval mapping across locations, using a linkage map with 110 RFLP loci, four significant (LOD 3.0) QTL were identified for score 1 on chromosomes (C) 1, 2, 3, and 4, respectively. All four were contributed by CML202. For score 2, only the QTL on C 1 was significant (LOD =37), explaining 59% of the phenotypic and 64% of the genotypic variance. The QTL's partially dominant gene action was consistent with the nearly intermediate resistance of the F₁ generation (relative heterosis for resistance 12%). The presence of one major QTL is consistent with the bimodal frequency distribution of the mapping population showing a clear 3:1 segregation. This gene seems to be allelic or identical to Msv1, a major resistance gene which was previously identified in the same genomic region in Tzi4, an inbred line from IITA. Inbred CML202 had lower final disease ratings than Tzi4. The greater resistance of CML202 may be due to allelic differences at the msv1 locus or due to the minor QTL on C 2, 3, and 4 which were not detected in Tzi4.z y Trigo (International Maize and Wheat Improvement Center); IITA, International Institute of Tropical Agriculture; IRAT, Institute de Recherches Agronomiques Tropicales et des Cultures Vivrières; KARI, Kenya Agricultural Research Institute; MSV, maize streak virus; QTL, quantitative trait locus/loci     

Interval mapping of genes for quantitative resistance of maize to Setosphaeria turcica,cause of northern leaf blight,in a tropical environment

Quantitative trait loci (QTL) involved in the resistance of maize to Setosphaeria turcica, the causal agent of northern leaf blight, were located by interval mapping analysis of 121 F_2:3 lines derived from a cross between Mo17 (moderately resistant) and B52 (susceptible). A linkage map spanning 112 RFLP loci with 15 cM mean interval length was constructed, based on marker data recorded in a previous study. Field tests with artificial inoculation were conducted at three sites in tropical mid- to high-altitude regions of Kenya, East Africa. Host-plant response was measured in terms of incubation period, disease severity (five scoring dates), and the area under the disease progress curve (AUDPC). Heritability of all traits was high (around 0.75). QTL associated with the incubation period were located on chromosomes 2S and 8L. For disease severity and AUDPC, significant QTL were detected in the putative centromeric region of chromosome 1 and on 2S, 3L, 5S, 6L, 7L, 8L and 9S. On 2S the same marker interval which carried a gene enhancing latent period was also associated with reduced disease severity of juvenile plants. QTL on chromosomes 3L, 5S, 7L and 8L were significant across environments but all other QTL were affected by a large genotype x environment interaction. Partially dominant gene action for resistance as well as for susceptibility was prevailing. Single QTL explained 10 to 38% of the phenotypic variation of the traits. All but the QTL on chromosomes 1, 6 and 9 were contributed by the resistant parent Mo17. On chromosome 8L a QTL mapped to the same region as the major race-specific gene Ht2, supporting the hypothesis that some qualitative and quantitative resistance genes may be allelic.Abbreviations AUDPC area under the disease progress curve - CIMMYT International Maize and Wheat Improvement Center - KARI Kenya Agricultural Research Institute - NCLB northern corn leaf blight - QTL quantitative trait locus/loci     

The role of a pseudo-response regulator gene in life cycle adaptation and domestication of beet

Life cycle adaptation to latitudinal and seasonal variation in photoperiod and temperature is a major determinant of evolutionary success in flowering plants. Whereas the life cycle of the dicotyledonous model species Arabidopsis thaliana is controlled by two epistatic genes, FLOWERING LOCUS C and FRIGIDA, three unrelated loci (VERNALIZATION) determine the spring and winter habits of monocotyledonous plants such as temperate cereals. In the core eudicot species Beta vulgaris, whose lineage diverged from that leading to Arabidopsis shortly after the monocot-dicot split 140 million years ago, the bolting locus B is a master switch distinguishing annuals from biennials. Here, we isolated B and show that the pseudo-response regulator gene BOLTING TIME CONTROL 1 (BvBTC1), through regulation of the FLOWERING LOCUS T genes, is absolutely necessary for flowering and mediates the response to both long days and vernalization. Our results suggest that domestication of beets involved the selection of a rare partial loss-of-function BvBTC1 allele that imparts reduced sensitivity to photoperiod that is restored by vernalization, thus conferring bienniality, and illustrate how evolutionary plasticity at a key regulatory point can enable new life cycle strategies.