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An informative linkage map of soybean reveals QTLs for flowering time, leaflet morphology and regions of segregation distortion.

A genetic linkage map covering a large region of the genome with informative markers is essential for plant genome analysis, including identification of quantitative trait loci (QTLs), map-based cloning, and construction of a physical map. We constructed a soybean genetic linkage map using 190 F2 plants derived from a single cross between the soybean varieties Misuzudaizu and Moshidou Gong 503, based on restriction-fragment-length polymorphisms (RFLPs) and simple-sequence-repeat polymorphisms (SSRPs). This linkage map has 503 markers, including 189 RFLP markers derived from expressed sequence tag (EST) clones, and consists of 20 major linkage groups that may correspond to the 20 pairs of soybean chromosomes, covering 2908.7 cM of the soybean genome in the Kosambi function. Using this linkage map, we identified 4 QTLs--FT1, FT2, FT3, and FT4--for flowering time, the QTLs for the 5 largest principal components determining leaflet shape, 6 QTLs for single leaflet area, and 18 regions of segregation distortion. All 503 analyzed markers identified were located on the map, and almost all phenotypic variations in flowering time were explained by the detected QTLs. These results indicate that this map covers a large region of the soybean genome.

Chromosome Mapping↗

Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population.

Correspondence among QTLs affecting height and/or flowering was investigated across the five races of sorghum, an interspecific sorghum F2 population, and 32 previously published sorghum, maize, rice, wheat, and barley populations revealing 185 QTLs or discrete mutants. Among nine QTLs mapped in the interspecific sorghum population (six affecting height and three affecting flowering), at least seven (78%) are associated with "conversion," backcross-introgression of alleles imparting reduced height or earlier flowering from cultivated sorghums into one or more exotic Sorghum bicolor races. One chromosomal region was "converted" in all S. bicolar races--in the interspecific F2, this region explained 54.8% of height variation (putatively the Dw2 gene) and 85.7% of flowering time variation (putatively Ma1). Comparative data suggest that Ma1 and Dw2 orthologs influence height and flowering of other Poaceae taxa and support classical dogma that the sorghum phenotypes attributed to Ma1 and Dw2 (respectively) are due to different genetic loci. Other sorghum QTLs also showed correspondence with those in other Poaceae, more frequently than would be expected by chance. Possible homoeologous QTLs were found within both the maize and sorghum genomes. Comparative QTL mapping provides a means to unify, and thereby simplify, molecular analysis of complex phenotypes.

Chromosome Mapping↗

Identification of QTLs for serum lipid levels in a female sib-pair cohort: a novel application to improve the power of two-locus linkage analysis.

Using a novel approach for a two-locus model that provides a greatly increased power to detect multiple quantitative trait loci (QTLs) in simulated data, we identified in a sample of 961 female sib-pairs, three genome-wide significant QTLs for apolipoprotein A1 on chromosomes 8p21.1-q13.1 (LOD score 3.71), 9q21.32-33.1 (LOD score 3.28) and 10p15.1-p13 (LOD score 5.51), two for lipoprotein (a) on chromosomes 6q25.2-q27 (LOD score 10.18) and 21q21.1-q21.3 (LOD score 4.57) and two for triglycerides on chromosomes 4q28.3-32.1 (LOD score 3.71) and 5q23.1-q32 (LOD score 3.60). The two-locus ordered-subset analysis has led to the confirmation of known and likely identification of novel regions linked to serum lipid levels that would have otherwise been missed and deserves wider application in linkage analyses of quantitative traits. Given the relative lack of power for the sample sizes commonly used in human genetics linkage studies, minor QTL effects often go undetected and those that are detected will be upwardly biased. We show through simulation that the discrepancy between the real and estimated QTL-effects is often likely to generate an unpredictable source of false-negative errors, using multi-locus models, reducing the power to detect multiple QTLs through oligogenic linkage analysis. The successful simultaneous modelling of the identified QTLs in a multi-locus context helps to eliminate false positives and increases the power to detect linkages, adding compelling evidence that they are likely to be reliable QTLs for these lipid traits.

Chromosome Mapping↗

QTLs for enzyme activities and soluble carbohydrates involved in starch accumulation during grain filling in maize.

ADPglucose, the essential substrate for starch synthesis, is synthesized in maize by a pathway involving at least invertases, sucrose synthase, and ADPglucose pyrophosphorylase, as shown by the starch-deficient mutants, mn1, sh1, and bt2 or sh2, respectively. To improve understanding of the relationship between early grain-filling traits and carbohydrate composition in mature grain, QTLs linked to soluble invertase, sucrose synthase, and ADPglucose pyrophosphorylase activities and to starch, sucrose, fructose, and glucose concentrations were investigated. In order to take into account the specific time-course of each enzyme activity during grain filling, sampling was carried out at three periods (15, 25, and 35 d after pollination) on 100 lines from a recombinant inbred family, grown in the field. The MQTL method associated with QTL interaction analysis revealed numerous QTLs for all traits, but only one QTL was consistently observed at the three sampling periods. Some chromosome zones were heavily labelled, forming clusters of QTLs. Numerous possible candidate genes of the starch synthetic pathway co-located with QTLs. Four QTLs were found close to the locus Sh1 (bin 9.01) coding for the sucrose synthase. In order to confirm the importance of this locus, the CAPS polymorphism of the Sh1 gene was analysed in 45 genetically unrelated maize lines from various geographical origins. The DNA polymorphism was significantly associated with phenotypic traits related to grain filling (starch and amylose content, grain matter, and ADPglucose pyrophosphorylase activity at 35 DAP). Thus, the Sh1 locus could provide a physiologically pertinent marker for maize selection.

Carbohydrate Metabolism↗

Comparative analysis of QTLs affecting plant height and flowering among closely-related diploid and polyploid genomes.

Quantitative trait loci (QTLs) affecting plant height and flowering were studied in the two Saccharum species from which modern sugarcane cultivars are derived. Two segregating populations derived from interspecific crosses between Saccharum officinarum and Saccharum spontaneum were genotyped with 735 DNA markers. Among the 65 significant associations found between these two traits and DNA markers, 35 of the loci were linked to sugarcane genetic maps and 30 were unlinked DNA markers. Twenty-one of the 35 mapped QTLs were clustered in eight genomic regions of six sugarcane homologous groups. Some of these could be divergent alleles at homologous loci, making the actual number of genes implicated in these traits much less than 35. Four QTL clusters controlling plant height in sugarcane corresponded closely to four of the six plant-height QTLs previously mapped in sorghum. One QTL controlling flowering in sugarcane corresponded to one of three flowering QTLs mapped in sorghum. The correspondence in locations of QTLs affecting plant height and flowering in sugarcane and sorghum reinforce the notion that the simple sorghum genome is a valuable "template" for molecular dissection of the much more complex sugarcane genome.

Chromosome Mapping↗

Genome-wide scan identifies novel QTLs for cholesterol and LDL levels in F2[Dahl RxS]-intercross rats.

Hypercholesterolemia is a significant risk factor for coronary artery disease development. Genes influencing nonmonogenic hypercholesterolemia susceptibility in humans remain to be identified. Animal models are key investigative systems because major confounding variables such as diet, activity, and genetic background can be controlled. We performed a 121-marker, total genome-analysis of an F2[Dahl RxS]-intercross selected for contrasting parental strain susceptibilities for hyperlipidemia on regular rat diets at 6 months of age. Quantitative traits studied were plasma total cholesterol, triglyceride, HDL, and LDL levels adjusted for obesity. Genome-wide analysis of 200 F2-intercross male rats detects two QTLs with highly significant linkage for total cholesterol (TC) on chromosome (chr) 5-133.3 Mbp (LOD 5.8), and chr5-54.2 Mbp (LOD 4.8), and two QTLs with significant linkage for TC: on chromosome 8, chr8-60.4 Mbp (LOD 3.8), and chromosome 2, chr2-243.5 Mbp (LOD 3.4). A QTL for LDL with significant linkage is detected on chromosome 5, chr5-104 Mbp (LOD 3.7). These QTLs contribute from 7% to 12% of total trait variance, respectively, with Dahl-S allele effects resulting in increased TC and LDL levels consistent with hyperlipidemia susceptibility in the parental Dahl-S rat strain. Predicted QTL-peaks do not coincide with previous genome scans. Human homologues of two TC-QTLs span genes listed in a LocusLink profile for cholesterol. Only suggestive loci were detected for HDL and total triglyceride levels. Altogether, the data demonstrates the contribution of multiple QTLs to hypercholesterolemia making a multipathway pathogenic framework imperative. QTL-peak candidate genes delineated are syntenic between rat and human genomes, increasing clinical relevance and mandating further study.

Animals↗

Apolipoprotein gene polymorphisms as cause of cholesterol QTLs in mice.

Quantitative trait locus (QTL) analyses of plasma cholesterol levels were carried out in three sets of F(2) mice that were formed in a 'round-robin' manner from C57BL/6J, KK (-A(y)), and RR strains. Six QTLs were identified on chromosomes 1 (Cq1, Cq2, and Cq6), 3 (Cq3), and 9 (Cq4 and Cq5); of these, Cq2 colocalized with Cq6, and Cq4 colocalized with Cq5. The major candidate gene for Cq2 and Cq6 is Apoa2, and that for Cq4 and Cq5 is Apoa4. The adequacy of polymorphisms in candidate genes as cause of QTLs was investigated in this study. For Apoa2, three different alleles (Apoa2(a), Apoa2(b), and Apoa2(c)) are known. Since there was no significant physiologic difference between Apoa2(a) and Apoa2(c) alleles, previous hypothesis that Apoa2(b) was different from Apoa2(a) and Apoa2(c) in the ability to increase cholesterol levels was further supported. Presumably, G-to-A substitution at nucleotide 84 and/or C-to-T substitution at nucleotide 182 are crucial to make the Apoa2(b) unique. On the other hand, for Apoa4, the most striking polymorphism was the number of Glu-Gln-Ala/Val-Gln repeats in carboxyl end; however, this might not be responsible for QTLs. Instead, a silent mutation, C-to-T substitution at nucleotide 771, was shown to be completely correlated with the occurrence of QTLs in a total of six F(2) intercrosses. Provisionally, but reasonably, these base substitutions are qualified as primary causes that constitute QTL effect. The potential strategy for identifying genes and base substitutions underlying QTLs is discussed.

Alleles↗

[Mapping QTLs controlling vascular bundle and panicle-related traits from Yuanjiang common wild rice (Oryza rufipogon Griff.)].

An advanced backcross population (BC3F2), derived from the cross between Yuanjiang common wild rice as the donor parent and Teqing as recurrent parent, was used to map QTLs controlling the number of vascular bundle and panicle-related traits from Yuanjiang common wild rice. Seven QTLs controlling the number of large vascular bundles in peduncle were detected on chromosome 1, 2, 3, 4, 7 and 10. Five QTLs for the number of small vascular bundles in peduncle were mapped on chromosome 1, 2, 3, 4 and 8. A total of 15 QTLs for the number of primary and secondary rachis branches and spikelets per panicle were identified on all chromosomes except chromosome 11 and 12. Most of alleles derived from O. rufipogon Griff. showed negative effect that reduced significantly vascular bundle, rachis branches and spikelets per panicle, suggesting that during the evolution from common wild rice to cultivated rice, favorable alleles were retained while removed undesirable ones. Most of QTLs controlling vascular bundle, rachis branches and spikelets per panicle showed cluster form or close linkage on chromosomes. The directions of their additive effects were consistent, which explained the genetic basis of significant correlation of their phenotypic characters. All the information suggested parallel evolution relationship among these traits.

Chromosomes, Plant↗

Mapping QTLs for alpha-amylase activity in rye grain.

Genetic control of alpha-amylase activity in rye grain was investigated by QTL mapping based on DS2 x RXL10 intercross consisting of 99 F5-6 families propagated at one location during four vegetation seasons. A wide range of variation in alpha-amylase activity and transgression effects were found among families and parental lines. This variation was shown to be determined in 40.1% by 7 significant (LOD score not less than 2.5) and 2 putative QTLs (2 < LOD < 2.5) distributed on all rye chromosomes except 4R. Two significant QTLs located on 3RL and 5RL chromosome arms were expressed each year. The third significant QTL was detected in three years (1RL). The other four significant QTLs (2RL, 5RS, 6RL, 7RL) were found in one year of study. The number and composition of QTLs were specific for a given year varying from three to six. QTLs were not correlated with isoenzyme polymorphisms at the structural alpha-Amy1 loci. A QTL associated with a region containing the alpha-Amy3 locus was detected on chromosome 5RL. Both high- and low-activity QTL alleles were found in each parental line, which explains the appearance of transgressive recombinants in the segregating population.

Chromosome Mapping↗

QTLs associated with phenolic acid accumulation and antioxidant activity in tropical maize.

Maize represents a significant source of phytochemicals, with phenolic acids standing out as one of the most extensively studied functional compound families. These bioactive molecules have gained attention for their potent antioxidant properties and potential contributions to human health improvement. To evaluate the segregation of phenolic compounds in maize and its genetic basis, this study was conducted to identify quantitative trait loci (QTLs) associated with major phenolic compounds and their antioxidant capacity. The mapping population comprised 100 recombinant inbred lines (RILs) derived from the cross between P84 and Kilima. Twelve traits were analyzed: free and cell wall-bound antioxidant capacity, total phenolic content, and contents of p-coumaric acid, ferulic acid, three isomers of di-ferulic acid, and three isomers of tri-ferulic acid. The RILs exhibited substantial diversity in phenolic compound profiles. In total, 19 QTLs were identified for nine traits, with the number of associated regions ranging from 1 to 5 and explaining between 2.95% and 37.48% of the phenotypic variation. This research provides substantial evidence for the co-localization of major QTLs for principal phenolic acids in maize with genomic regions harboring genes putatively related to their biosynthesis and biotic resistance. This is the first study to report QTLs associated with triferulic acids in maize. The identified regions co-localizing with biotic stress resistance genes represent targets for marker-assisted selection toward the improvement of phenolic acid accumulation in maize breeding programs.

QTLs↗

Obesity QTLs on mouse chromosomes 2 and 17.

The inheritance of obesity has been analyzed in an intercross between the mouse strains AKR/J and C57L/J. Two novel obesity quantitative trait loci (QTLs) have been identified using the strategy of selective DNA pooling. One QTL affecting adiposity, Obq3, was mapped to a 39-cM segment near the middle of Chromosome 2, with a peak lod score (5.1) just distal to the D2Mit15 locus. The AKR/J Obq3 allele confers increased adiposity in a nearly additive manner, and males are more affected than females. A second obesity QTL (Obq4) maps to the centromeric end of Chromosome 17, with a lod score peak of 4.6 at D17Mit143. The obesity-conferring allele is contributed by C57L/J and acts in a recessive or an additive manner. Obq4 also has more influence in males and affects the inguinal fat depot differentially. Obq3 and Obq4 account for 7.0 and 6.1% of the phenotypic variance in adiposity (gender-merged data), respectively. The possible relationships between these QTLs and previously described obesity QTLs and candidate genes are discussed. The large number of different obesity QTLs that have been described in mice and the relatively small effects contributed by individual loci suggest considerable genetic complexity.

Adipose Tissue↗

Genetic mapping of grapevine ( Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight.

Parental and consensus genetic maps of Vitis vinifera L. (2n = 38) were constructed using a F(1) progeny of 139 individuals from a cross between two partially seedless genotypes. The consensus map contained 301 markers [250 amplification fragment length polymorphisms (AFLPs), 44 simple sequence repeats (SSRs), three isozymes, two random amplified polymorphic DNAs (RAPDs), one sequence-characterized amplified region (SCAR), and one phenotypic marker, berry color] mapped onto 20 linkage groups, and covered 1,002 cM. The maternal map consisted of 157 markers covering 767 cM (22 groups). The paternal map consisted of 144 markers covering 816 cM (23 groups). Differences in recombination rates between these maps and another unpublished map are discussed. The major gene for berry color was mapped on both the paternal and consensus maps. Quantitative trait loci (QTLs) for several quantitative subtraits of seedlessness in 3 successive years were searched for, based on parental maps: berry weight, seed number, seed total fresh and dry weights, seed percent dry matter, and seed mean fresh and dry weights. QTLs with large effects (R(2) up to 51%) were detected for all traits and years at the same location on one linkage group, with some evidence for the existence of a second linked major QTL for some of them. For these major QTLs, differences in relative parental effects were observed between traits. Three QTLs with small effects (R(2) from 6% to 11%) were also found on three other linkage groups, for berry weight and seed number in a single year, and for seed dry matter in 2 different years.

Journal Article↗

Identification of QTLs controlling tissue-culture traits in barley ( Hordeum vulgare L.).

Quantitative trait loci (QTLs) controlling callus growth (CG), subsequent shoot differentiation ratio (SD) and green shoot ratio (GS) in immature embryo culture were identified in barley. A base map was developed from 99 recombinant inbred lines (RILs) of 'Azumamugi' x 'Kanto Nakate Gold'. The tissue-culture traits were evaluated at the F(7) and F(10) generations of the RILs. The RILs showed wide and continuous variations in each of the three tissue-culture traits. Three QTLs for CG, three QTLs for SD and two QTLs for GS were detected by using composite interval mapping. A QTL for SD on chromosome 3H had a large effect, and 'Kanto Nakate Gold', which has a high differentiation ability, contributed to this QTL. The location of this QTL is identical to, or very close to, the uzu locus. We discuss the relationships between tissue-culture loci in 'Azumamugi' x 'Kanto Nakate Gold' and those in other mapping populations.

Journal Article↗

QTLs for grain carbon isotope discrimination in field-grown barley.

In several crops including cereals, carbon isotope discrimination (Delta) has been associated with drought tolerance in terms of water-use efficiency and yield stability in drought-prone environments. By using a complete genetic map generated from 167 recombinant inbred lines from a cross between Tadmor and Er/Apm, QTLs associated with grain Delta have been detected in barley grown in three Mediterranean field environments, two differing only in water availability. Ten QTLs were identified: one was specific to one environment, two presented interaction with the environment, six presented main effects across three or two environments and one presented both effects. Heading date did not contribute to the environment (E) and G x E effects acting on Delta. Seasonal rainfall and the ratio of rainfall to evapo-transpiration made large contributions to the environmental effect, but their influence on G x E was weaker. Eight QTLs for Delta co-located with QTLs for physiological traits related to plant water status and/or osmotic adjustment, and/or for agronomic traits previously measured on the same population. Some perspectives in terms of characterising drought tolerance are evoked.

Biomarkers↗

QTLs conferring cold tolerance at the booting stage of rice using recombinant inbred lines from a japonica x indica cross.

Low temperature stress is common for rice grown in temperate regions and at high elevations in the tropics. The most senstive stage to this stress is booting, about 11 days before heading. Japonica cultivars are known to be more tolerant than indicas. We constructed a genetic map using 191 recombinant inbred lines derived from a cross between a temperate japonica, M-202, and a tropical indica, IR50, in order to locate quantitative trait loci (QTLs) conferring cold tolerance. The map with a total length of 1,276.8 cM and an average density of one marker every 7.1 cM was developed from 181 loci produced by 175 microsatellite markers. Cold tolerance was measured as the degree of spikelet sterility of treated plants at a 12 degrees C temperature for 5 days in the growth chamber. QTLs on chromosomes 1, 2, 3, 5, 6, 7, 9 and 12 were identified to confer cold tolerance at the booting stage. The QTL contribution to the phenotypic variation ranged from 11 to 17%. The two QTLs with the highest contribution to variation, designated qCTB2a and qCTB3, were derived from the tolerant parent, M-202, each explaining approximately 17% of the phenotypic variance. Two of the eight QTLs for cold tolerance were contributed by IR50.

Chromosome Mapping↗

A molecular linkage map with associated QTLs from a hulless x covered spring oat population.

In spring-type oat ( Avena sativa L.), quantitative trait loci (QTLs) detected in adapted populations may have the greatest potential for improving germplasm via marker-assisted selection. An F(6) recombinant inbred (RI) population was developed from a cross between two Canadian spring oat varieties: 'Terra', a hulless line, and 'Marion', an elite covered-seeded line. A molecular linkage map was generated using 430 AFLP, RFLP, RAPD, SCAR, and phenotypic markers scored on 101 RI lines. This map was refined by selecting a robust set of 124 framework markers that mapped to 35 linkage groups and contained 35 unlinked loci. One hundred one lines grown in up to 13 field environments in Canada and the United States between 1992 and 1997 were evaluated for 16 agronomic, kernel, and chemical composition traits. QTLs were localized using three detection methods with an experiment-wide error rate of approximately 0.05 for each trait. In total, 34 main-effect QTLs affecting the following traits were identified: heading date, plant height, lodging, visual score, grain yield, kernel weight, milling yield, test weight, thin and plump kernels, groat beta-glucan concentration, oil concentration, and protein. Several of these correspond to QTLs in homologous or homoeologous regions reported in other oat QTL studies. Twenty-four QTL-by-environment interactions and three epistatic interactions were also detected. The locus controlling the covered/hulless character ( N1) affected most of the traits measured in this study. Additive QTL models with N1 as a covariate were superior to models based on separate covered and hulless sub-populations. This approach is recommended for other populations segregating for major genes. Marker-trait associations identified in this study have considerable potential for use in marker-assisted selection strategies to improve traits within spring oat breeding programs.

Agriculture↗

Haplotype diversity at fusarium head blight resistance QTLs in wheat.

Fusarium head blight (FHB) reduces grain yield and quality in common and durum wheat. Host FHB resistance is an effective control measure that is achieved by stacking multiple resistance genes into a wheat line. Therefore, breeders would benefit from knowing which resistance sources carry different resistance genes. A diverse collection of FHB-resistant and -susceptible wheat lines was characterized with microsatellite markers linked to FHB resistance quantitative trait loci (QTLs) on chromosomes 2DL, 3BS (distal to the centromere), 3BSc (proximal to the centromere), 4B, 5AS and 6BS identified in wheat lines Maringa, Sumai 3 and Wuhan 1. Putative Sumai 3 QTLs were commonly observed in advanced breeding lines, whereas putative Maringa and Wuhan 1 QTLs were relatively rare. Marker data suggested the 3BS, 3BSc and 5AS QTLs in the Brazilian cv. Maringa were derived from Asian germplasm and not from Frontana or other Brazilian lines. Haplotype diversity was reduced near the 5AS QTL, which might impact the deployment of this QTL. Finally, Brazilian germplasm was not closely related to other resistance sources and might be useful for pyramiding with Asian wheat-derived FHB resistance.

Agriculture↗

Analysis of QTLs for yield, yield components, and malting quality in a BC3-DH population of spring barley.

Advanced backcross (AB)-quantitative trait locus (QTL) analysis has been successfully applied for detecting and transferring QTLs from unadapted germplasm into elite breeding lines in various plant species. Here, we describe the application of a modified AB breeding scheme to spring barley. A BC3-doubled haploid (DH) population consisting of 181 lines derived from the German spring barley cultivar 'Brenda' (Hordeum vulgare subsp. vulgare) as the recurrent parent and the wild species line 'HS213' (H. vulgare subsp. spontaneum) as the donor line was evaluated for yield and its components as well as malting quality traits. A set of 60 microsatellite markers was used to genotype the population, and phenotypic data were collected at two locations in Germany in continuous years. Altogether, 25 significant QTLs were detected by single-marker regression analysis and interval mapping. Most positive QTLs originated from the recurrent parent 'Brenda'. A QTL, Qhd2.1, on chromosome 2HS from 'Brenda' explained 18.3% and 20.7% of the phenotypic variation for yield and heading date, respectively. Due to the small percentage of donor-parent genome of 6.25%, the BC3-DH lines could be directly used for the extraction of near-isogenic lines (NILs) for Qhd2.1. Consequently, it was possible to determine the precise location of the locus hd2.1 within a region of 6.5 cM, using an F2 population consisting of 234 individuals developed from a cross between an NIL containing a defined donor segment at this locus and 'Brenda'. The location of this QTL was consistent with the presence of a major photoperiod response gene, Ppd-H1, previously reported in this region, which is associated with pleiotropic effects on yield components. In summary, the analysis of a BC3-DH population in barley provides a compromise between the analysis of QTLs by means of an AB scheme and the generation of defined substitution lines. Several lines carrying defined different donor segments for only one single chromosome or trait in the genetic background of 'Brenda' could be selected for further genetic studies.

Breeding↗