Quantitative trait loci for plant height in four maize populations and their associations with qualitative genetic loci

Summary We report that plant height quantitative trait loci (QTLs) identified in a given small population are not consistent with QTLs identified in other small populations, and that most QTLs are in close proximity to mapped qualitative genetic loci. These observations provide evidence to support the hypothesis that qualitative genetic loci are the same loci that affect quantitative traits, and affirm that these modest experiments probably identify real QTLs.     

Quantitative trait loci influencing protein and starch concentration in the Illinois Long Term Selection maize strains

A study was initiated to determine the number, chromosomal location, and magnitude of effect of QTL (quantitative trait loci or locus depending on context) controlling protein and starch concentration in the maize (Zea mays L.) kernel. Restriction fragment length polymorphism (RFLP) analysis was performed on 100 F₃ families derived from a cross of two strains, Illinois High Protein (IHP), X Illinois Low Protein (ILP), which had been divergently selected for protein concentration for 76 generations as part of the Illinois Long Term Selection Experiment. These families were analyzed for kernel protein and starch in replicated field trials during 1990 and 1991. A series of 90 genomic and cDNA clones distributed throughout the maize genome were chosen for their ability to detect RFLP between IHP and ILP. These clones were hybridized with DNA extracted from the 100 F₃ families, revealing 100 polymorphic loci. Single factor analysis of variance revealed significant QTL associations of many loci with both protein and starch concentration (P < 0.05 level). Twenty-two loci distributed on 10 chromosome arms were significantly associated with protein concentration, 19 loci on 9 chromosome arms were significantly associated with starch concentration. Sixteen of these loci were significant for both protein and starch concentration. Clusters of 3 or more significant loci were detected on chromosome arms 3L, 5S, and 7L for protein concentration, suggesting the presence of QTL with large effects at these locations. A QTL with large additive effects on protein and starch concentration was detected on chromosome arm 3L. RFLP alleles at this QTL were found to be linked with RFLP alleles at the Shrunken-2 (Sh2) locus, a structural gene encoding the major subunit of the starch synthetic enzyme ADP-glucose pyrophosphorylase. A multiple linear regression model consisting of 6 significant RFLP loci on different chromosomes explained over 64 % of the total variation for kernel protein concentration. Similar results were detected for starch concentration. Thus, several chromosomal regions with large effects may be responsible for a significant portion of the changes in kernel protein and starch concentration in the Illinois Long Term Selection Experiment.     

Molecular-marker-facilitated studies of morphological traits in maize. II: Determination of QTLs for grain yield and yield components

Genetic factors controlling quantitative inheritance of grain yield and its components have not previously been investigated by using replicated lines of an elite maize (Zea mays L.) population. The present study was conducted to identify quantitative trait loci (QTLs) associated with grain yield and grain-yield components by using restriction fragment length polymorphism (RFLP) markers. A population of 150 random F₂₃ lines was derived from the single cross of inbreds Mo17 and H99, which are considered to belong to the Lancaster heterotic group. Trait values were measured in a replicated trial near Ames, Iowa, in 1989. QTLs were located on a linkage map constructed with one morphological and 103 RFLP loci. QTLs were found for grain yield and all yield components. Partial dominance to overdominance was the primary mode of gene action. Only one QTL, accounting for 35% of the phenotypic variation, was identified for grain yield. Two to six QTLs were identified for the other traits. Several regions with pleiotropic or linked effects on several of the yield components were detected.     

Genetic analysis of tolerance to low-phosphorus stress in maize using restriction fragment length polymorphisms

Summary An understanding of the genetic nature underlying tolerance to low-phosphorus (low-P) stress could aid in the efficient development of tolerant plant strains. The objective of this study was to identify the number of loci in a maize (Zea mays L.) population segregating for tolerance to low-P stress, their approximate location, and the magnitude of their effect.Seventy-seven restriction fragment length polymorphisms (RFLPs) were identified and scored in a maize F₂ population derived from a cross between line NY821 and line H99. The F₂ individuals were self-pollinated to produce F₃ families. Ninety F₃ families were grown in a sand-alumina system, which simulated diffusion-limited, low-P soil conditions. The F₃ families were evaluated for vegetative growth in a controlled-environment experiment. To identify quantitative trait loci (QTLs) underlying tolerance to low-P stress, the mean phenotypic performances of the F₃ families were contrasted based on genotypic classification at each of 77 RFLP marker loci.Six RFLP marker loci were significantly associated with performance under low-P stress (P<0.01). One marker locus accounted for 25% of the total phenotypic variation. Additive gene action was predominant for all of the QTLs identified. Significant marker loci were located on four separate chromosomes representing five unlinked genomic regions. Two marker loci were associated with an additive by additive epistatic interaction. A multiple regression model including three marker loci and the significant epistatic interaction accounted for 46% of the total phenotypic variation. Heterozygosity per se was not predictive of phenotypic performance.     

The suitability of restriction fragment length polymorphisms as genetic markers in maize

Summary Strain identification in Zea mays by restriction fragment length polymorphism should be feasible due to the high degree of polymorphism found at many loci. The polymorphism in maize is apparently higher than that currently known for any other organism. Five randomly selected maize inbred lines were examined by Southern filter hybridization with probes of cloned low copy sequences. Typically, several alleles could be distinguished among the inbred lines with any one probe and an appropriately selected restriction enzyme. Despite considerable polymorphism at the DNA level, 16 RFLP markers in three inbred lines of maize were examined for six to 11 generations and found be stable. Mapping of RFLP markers in maize can be accelerated by the use of B-A translocation stocks, which enable localization of a marker to chromosome arm in one generation. The use of recombinant inbred lines in further refinement of the map is discussed.     

RFLP mapping of QTLs conferring cold tolerance during seed germination in an interspecific cross of tomato

Most cultivars of tomato, Lycopersicon esculentum, are sensitive to low (chilling) temperatures (0–15 °C) during seed germination; however, genetic sources of cold (chilling) tolerance have been identified within the related wild species. The purpose of this study was to identify quantitative trait loci (QTLs) that contribute to cold tolerance during germination in tomato using a backcross population of an interspecific cross between a cold-sensitive tomato line (NC84173, recurrent parent) and a L. pimpinellifolium accession (LA722) that germinates rapidly under low temperatures. A total of 119 BC1 individuals were genotyped for 151 restriction fragment length polymorphism (RFLP) markers and a genetic linkage map was constructed. The parental lines and 119 BC1S1 families (self-pollinated progeny of the BC1 individuals) were evaluated for germination at a low temperature (11±0.5 °C). Germination was scored visually as radicle protrusion at 8 h intervals for 28 consecutive days. Germination response was analyzed by the survival analysis and the times to 25, 50 and 75% germination were calculated. In addition, a germination index (GI) was calculated as the weighted mean of the time from imbibition to germination for each family/line. Two QTL mapping techniques, interval mapping (using MAPMAKER/QTL) and single-point analysis (using QGENE), were used to identify QTLs. The results of both methods were similar and two chromosomal locations (3–5 putative QTLs) with significant effects on low temperature germination were identified. The L. pimpinellifolium accession had favorable QTL alleles on chromosomes 1 and NC84173 had favorable QTL alleles on chromosome 4. The percentage of phenotypic variation explained (PVE) by individual QTLs ranged from 11.9% to 33.4%. Multilocus analysis indicated that the cumulative action of all significant QTLs accounted for 43.8% of the total phenotypic variance. Digenic epistatic interactions were evident between two of the QTL-linked markers and two unlinked markers. Transgressive phenotypes were observed in the direction of cold sensitivity. The results indicate that low temperature germination of tomato seed can be improved by marker-assisted selection.     

Genetic analysis and mapping of genes controlling freezing tolerance in oilseedBrassica

Freezing tolerance is the ability of plants to survive subfreezing temperatures and is a major component of winter survival. In order to study the genetic regulation of freezing tolerance, an F2 population ofBrassica rapa and a doubled haploid population ofBrassica napus were assayedin vitro for relative freezing tolerance of acclimated and nonacclimated plants. Linkage maps developed previously were used to identify putative quantitative trait loci (QTL). Genomic regions with significant effects on freezing tolerance were not found for theB. napus population, but forB. rapa four regions were associated with acclimated freezing tolerance (FTA) and acclimation ability (FTB), and two unliked regions were associated with nonacclimated freezing tolerance (FTN). Acclimation ability was regulated by genes with very small additive effects and both positive and negative dominance effects. The allele from the winter parent at the FTN QTL had positive additive effects, but negative dominance effects. RFLP loci detected by a cold-induced and a stress-related cDNA fromArabidopsis thaliana mapped near two QTL for FTA/FTB. Further tests are needed to determine if alleles at these loci are responsible for the QTL effects we detected.     

Mapping QTLs conferring salt tolerance during germination in tomato by selective genotyping

This study was conducted to identify genomic regions (quantitative trait loci, QTLs) affecting salt tolerance during germination in tomato. Germination response of an F2 population of a cross between UCT5 (Lycopersicon esculentum, salt-sensitive) and LA716 (L. pennellii, salt-tolerant) was evaluated at a salt-stress level of 175 mM NaCl + 17.5 mM CaCl2 (water potential ca. –950 kPa). Germination was scored visually as radicle protrusion at 6 h intervals for 30 consecutive days. Individuals at both extremes of the response distribution (i.e., salt-tolerant and salt-sensitive individuals) were selected. The selected individuals were genotyped at 84 genetic markers including 16 isozymes and 68 restriction fragment length polymorphisms (RFLPs). Trait-based marker analysis (TBA) which measures changes (differences) in marker allele frequencies in selected lines was used to identify marker-linked QTLs. Eight genomic regions were identified on seven tomato chromosomes bearing genes (QTLs) with significant effects on this trait. The results confirmed our previous suggestion that salt tolerance during germination in tomato is polygenically controlled. The salt-tolerant parent contributed favorable QTL alleles on chromosomes 1, 3, 9 and 12 whereas the salt sensitive parent contributed favorable QTL alleles on chromosomes 2, 7 and 8. The identification of favorable alleles in both parents suggests the likelihood of recovering transgressive segregants in progeny derived from these parental genotypes. The results can be used for marker-assisted selection and breeding of salt-tolerant tomatoes.     

Identification of quantitative trait loci controlling resistance to gray leaf spot disease in maize

Breeding maize for gray leaf spot (GLS) resistance has been hindered by the quantitative nature of the inheritance of GLS resistance and by the limitations of selection under less than optimumal disease pressure. In order to identify the quantitative trait loci (QTLs) controlling GLS resistance, a cross was made between B73 (susceptible) and Va14 (resistant) to generate a large F₂ population. Six GLS disease assessments were made throughout the disease season for over 1000 F₂ plants in 1989, and for 600 F₂-derived F₃ lines replicated in two blocks in 1990. RFLP analysis for78 marker loci representing all ten maize chromosomes was conducted in 239 F₂ individuals including those with the extreme GLS disease phenotypes. The GLS disease scores of the three field evaluations, each averaged over six ratings, were separately used for the interval mapping in order to determine the consistency of the QTL effects. The heavy GLS disease pressure, meticulous disease ratings, and large population size of this study afforded us the sensitivity for detecting QTL effects. QTLs located on three chromosomes (1, 4, and 8) had large effects on GLS resistance, each explaining 35.0–56.0%, 8.8–14.3%, and 7.7–11.0% of the variance, respectively. These three QTL effects were remarkably consistent across three disease evaluations over 2 years and two generations. Smaller QTL effects were also found on chromosomes 2 and 5, but the chromosome-5 effect might be a false positive because it was not repeatable even in the same location. The chromosome-1 QTLs had the largest effect or highest R² reported for any quantitative trait to-date. Except for the chromosome-4 gene, which was from the susceptible parent B73, the resistance alleles at all QTL were derived from Va14. The resistance QTLs on chromosomes 1 and 2 appear to have additive effects, but those on chromosomes 4 and 8 are dominant and recessive, respectively. Significant interaction between the QTLs on chromosomes 1 and 4 was detected in all three evaluations. Cumulatively, the four QTLs identified in this study explained 44, 60, and 68% of the variance in F₂, and in F₃ replications 1 and 2, respectively.     

Restriction fragment length polymorphism analysis of loci associated with disease resistance genes and developmental traits in Pisum sativum L.

An F₂ population of pea (Pisum sativum L.) consisting of 174 plants was analysed by restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) techniques. Ascochyta pisi race C resistance, plant height, flowering earliness and number of nodes were measured in order to map the genes responsible for their variation. We have constructed a partial linkage map including 3 morphological character genes, 4 disease resistance genes, 56 RFLP loci, 4 microsatellite loci and 2 RAPD loci. Molecular markers linked to each resistance gene were found: Fusarium wilt (6 cM from Fw), powdery mildew (11 cM from er) and pea common Mosaic virus (15 cM from mo). QTLs (quantitative traits loci) for Ascochyta pisi race C resistance were mapped, with most of the variation explained by only three chromosomal regions. The QTL with the largest effect, on chromosome 4, was also mapped using a qualitative, Mendelian approach. Another QTL displayed a transgressive segregation, i.e. the parental line that was susceptible to Ascochyta blight had a resistance allele at this QTL. Analysis of correlations between developmental traits in terms of QTL effects and positions suggested a common genetic control of the number of nodes and earliness, and a loose relationship between these traits and height.     

Comparison between responses to gametophytic and sporophytic recurrent selection in maize (Zea mays L.)

Summary Experiments were conducted to determine the chromosomal location of the gene conditioning overproduction of a methionine-rich, 10-K zein in maize kernels of line BSSS53. In addition, the chromosomal location of the structural gene encoding the overproduced protein was determined. Whereas the structural gene, designated Zps10/(22), was found to be located on the long arm of chromosome 9 near the centromere, the locus regulating overproduction of the zein protein was mapped to the short arm of chromosome 4. This regulatory gene has been designated Zpr10/(22). Regulation of 10-K zein production by Zpr10/(22) is, therefore, via a trans-acting mechanism.     

Mapping of QTLs for lycopene and other fruit traits in a Lycopersicon esculentum × L. pimpinellifolium cross and comparison of QTLs across tomato species

Quantitative trait loci (QTLs) for several fruit traits in tomato were mapped and characterized in a backcross population of an interspecific cross between Lycopersicon esculentum fresh-marker breeding line NC84173 and L. pimpinellifolium accession LA722. A molecular linkage map of this cross that was previously constructed based on 119 BC1 individuals and 151 RFLP markers was used for the QTL mapping. The parental lines and 119 BC1S1 families (self-pollinated progeny of BC1 individuals) were grown under field conditions at two locations, Rock Spring, PA, and Davis, CA, and fruits were scored for weight (FW), polar (PD) and equatorial diameters (ED), shape (FS), total soluble solids content (SSC), pH and lycopene content (LYC). For each trait, between 4 and 10 QTLs were identified with individual effects ranging between 4.4% and 32.9% and multilocus QTL effects ranging between 39% and 75% of the total phenotypic variation. Most QTL effects were predictable from the parental phenotypes, and several QTLs were identified that affected more than one trait. A few pairwise epistatic interactions were detected between QTL-linked and QTL-unlinked markers. Despite great differences between PA and CA growing conditions, the majority of FW QTLs (78%) and SSC QTLs (75%) in the two locations shared similar genomic positions. Almost all of the QTLs that were identified in the present study for FW and SSC were previously identified in six other studies that used different interspecific crosses of tomato; this indicates conservation of QTLs for fruit traits across tomato species. Altogether, the seven studies identified at least 28 QTLs for FW and 32 QTLs for SSC on the 12 tomato chromosomes. However, for each trait a few major QTLs were commonly identified in 4 or more studies; such ‘popular’ QTLs should be of considerable interest for breeding purposes as well as basic research towards cloning of QTLs. Notably, a majority of QTLs for increased SSC also contributed to decreased fruit size. Therefore, to significantly increase SSC of the cultivated tomato, some compromise in fruit size may be unavoidable. This revised version was published online in June 2006 with corrections to the Cover Date.     

Mapping QTLs for root traits under different nitrate levels at the seedling stage in maize (Zea mays L.)

Nitrogen (N) loss is a worldwide problem in crop production. Apart from reasonable N fertilizer application, breeding N efficient cultivars provides an alternative way. Root architecture is an important factor determining N acquisition. However, little is known about the molecular genetic basis for root growth in relation to N supply. In the present study, an F₈ maize (Zea may L.) recombinant inbred (RI) population consisting of 94 lines was used to identify the QTLs for root traits under different nitrate levels. The lateral root length (LRL), axial root length (ARL), maximal axial root length (MARL), axial root number (ARN) and average axial root length (AARL) were evaluated under low N (LN) and high N (HN) conditions in a hydroponics system. A total of 17 QTLs were detected among which 14 loci are located on the same chromosome region as published QTLs for root traits. A major QTL on chromosome 1 (between bnlg1025 and umc2029) for the AARL under LN could explain 43.7% of the phenotypic variation. This QTL co-localizes with previously reported QTLs that associate with root traits, grain yield, and N uptake. Our results indicate that longer axial roots are important for efficient N acquisition and the major QTL for AARL may be used as a marker in breeding N efficient maize genotypes.     

Isozymes as Genetic Markers in Maize Breeding

The major objective of the research is to identify and locate quantitative trait loci (QTL_s) in the Yugoslav maize population. The plants (F2) were selected for the analysis at seedling stage and were selfed to obtain F3 generation. The analysis covered about 15 enzymes controlled by about 30 loci. The seeds of F3 family planted in the greenhouse for measuring some quantitative traits, recorded tasselling and silking during vegetation. At the end of vegetation grain yield, and some other quantitative traits of grain in F3 family were assessed. The relationship between marker loci and the loci for quantitative traits (QTL_s) were estimated by computerized statistical method.     

RFLP mapping of major and minor genes for important agronomic characters in rice

A molecular genetic map with 233 RFLP markers which covered about 2070 cM of rice genome was constructed based on a doubled haploid (DH) population derived from anther culture of a cross between an indica variety Gui630 and a japonica variety 02428. Quantitative trait loci (QTLs) for agronomic characters such as number of panides, heading date, plant height, number of spikelets, number of grains, fertility and 1 000-grain weight were analyzed using interval mapping approach. 8 major genes and 29 minor genes were identified associating with these traits. The results also indicated that great phenotypic difference between parents was profitable in detection of major genes.     

Molecular markers locate genes for resistance to the Colorado potato beetle,Leptinotarsa decemlineata,in hybrid Solanum tuberosum x S. berthaultii potato progenies

The wild Bolivian potato, Solanum berthaultii Hawkes, has been used as a source of resistance to the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say, one of the most significant pests of potato. In this study, two reciprocal backcross S. tuberosum x S. berthaultii potato progenies, BCB and BCT, were mapped with RFLP markers and screened for resistance to CPB consumption, oviposition and defoliation. The genotypic and phenotypic data were combined and analysed to locate quantitative trait loci (QTLs) for resistance to CPB. Three QTLs on three chromosomes in BCB, and two QTLs on two chromosomes in BCT influenced resistance. The QTLs were generally additive but one instance of epistasis was noted. Each QTL accounted for 4–12% of the phenotypic variation observed in resistance. In the more resistant BCB population, a three QTL model explained ca. 20% of the variation in CPB oviposition. When alleles at the three QTLs were homozygous S. berthaultii, oviposition was reduced ca. 60% compared to the heterozygotes. The QTLs for resistance to CPB were compared to those previously identified for the type A and B glandular trichomes, which have been implicated in resistance in the same progenies. Generally, the QTLs for resistance to CPB coincided with loci associated with the glandular trichomes confirming the importance of the glandular trichomes in mediating resistance. However, a relatively strong and consistent QTL for insect resistance in both BCB and BCT on chromosome 1 was observed that was not associated with any trichome traits, suggesting the trichomes may not account for all of the resistance observed in these progenies.     

Epistatic interaction is an important genetic basis of grain yield and its components in maize

A population of 294 recombinant inbred lines (RIL) derived from Yuyu22, an elite maize hybrid extending broadly in China, has been constructed to investigate the genetic basis of grain yield, and associated yield components in maize. The main-effect quantitative trait loci (QTL), digenic epistatic interactions, and their interactions with the environment for grain yield and its three components were identified by using the mixed linear model approach. Thirty-two main-effect QTL and forty-four pairs of digenic epistatic interactions were detected for the four measured traits in four environments. Our results suggest that both additive effects and epistasis (additive × additive) effects are important genetic bases of grain yield and its components in the RIL population. Only 30.4% of main-effect QTL for ear length were involved in epistatic interactions. This implies that many loci in epistatic interactions may not have significant effects for traits alone but may affect trait expression by epistatic interaction with the other loci.     

Isozyme marker loci associated with cold tolerance and maturity in maize

Summary Two maize (Zea mays L.) populations, AS1(S) and ECR-A, were evaluated for allozyme frequency changes associated with selection for improved seedling emergence, early season vigor and early maturity. Eleven marker loci were examined and four loci were used for indirect selection in an attempt to modify cold tolerance and maturity. Allozyme-selected divergent subpopulations were produced by compositing selected S₁ progeny from cycle one (C1) of AS1(S) and from C2 of ECR-A. These subpopulations and S₁ generations from all cycles resulting from phenotypic selection, ECR-A C1 through C7 and AS1(S) CO through C6, were tested in cold tolerance and agronomic performance trials over five environments in 1986. Seedling emergence and seedling dry weight did not improve with phenotypic selection in ECR-A, while plant height, ear height, grain yield, grain moisture, days to mid-silk and days to mid-pollen were reduced significantly. Contrasts between divergent allozyme-selected subpopulations from ECR-A were significant for grain moisture and mid-pollen date. For AS1(S), seeding emergence increased, while plant and ear height decreased with phenotypic selection. Contrasts between allozyme-selected subpopulations were significant for plant and ear height. Changes associated with marker-based selection for AS1(S) were not in the same direction as with phenotypic selection. Selection for favorable allozyme genotypes may be effective in changing certain traits in populations that have been modified by direct selection, however results may not be predictable.Contribution from the Department of Agronomy, Wisconsin Agric. Exp. Stn., Madison, WI. Part of a thesis submitted by the senior author in partial fulfillment of the requirements for a Ph. D. received June, 1987. Research supported by the College of Agric. and Life Sci., University of Wisconsin-Madison, Dekalb-Pfizer Genetics, Garst Seed Company, and Pioneer Hi-Bred.     

Restriction fragment length polymorphism differences among Illinois long-term selection oil strains

Restriction fragment length polymorphism (RFLP) analysis was used to characterize variability in the Illinois Long-Term Selection Experiment oil strains. Considerable polymorphism was detected within each oil strain and among oil strains. Fifty-two individual plants from each of the Illinois High Oil (IHO), Illinois Low Oil (ILO), Reverse High Oil (RHO) and Reverse Low Oil (RLO) strains were sampled to determine RFLP allele/variant frequencies. Generation 90 was sampled for IHO, RHO, and RLO whereas generation 87 was sampled for ILO. Forty-nine RFLP probes distributed throughout the maize genome were used. Chi-square analysis was performed to determine if RFLP genotypes at each of the 49 RFLP loci were significantly different among strains. Oil strains that have been separated for 90 generations showed high levels of significantly-different RFLP genotypic frequencies. The comparison of ILO vs RHO gave only significant chi-square values while the comparisons of IHO vs RLO and RHO vs RLO had 111 ratios of significant to non-significant chi-square values. Strains that have been separated for only 42 generations showed a lower level of significantly-different RFLP genotypic frequencies. The comparisons of IHO vs RHO and ILO vs RLO both had only a 32 ratio of significant to non-significant chi-squares values. Detection of multiple RFLP alleles/variants among the oil strains was common with 59% of the RFLP loci examined exhibiting multiple variants. A number of RFLP loci in RHO (3) and RLO (11) were associated with a trend in RFLP allele/variant frequencies consistent with a response to reverse selection for oil concentration.