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QTL mapping of grain quality traits from the interspecific cross Oryza sativa x O. glaberrima.

International rice export markets are increasing demands for rapid improvements in grain quality characteristics. The African rice Oryza glaberrima is a new potential source of genes that will enhance the eating, cooking, and milling properties of the rice grain. The objective of this research was to identify and characterize quantitative trait loci (QTLs) among 312 doubled haploid lines derived from the BC3F1 of an interspecific cross of O. sativa x O. glaberrima. Genetic material was planted in replicated plots and evaluated for ten grain quality traits in 2001 in Colombia. A linkage map was constructed with 100 polymorphic microsatellite markers using the mapdisto software program to adjust for segregation distortion. Transgressive segregation was observed for all traits. Interval and composite interval analyses identified 27 QTLs for nine characters located on 11/12 chromosomes. The chromosomal positions of QTLs for percentage amylose, alkali-spreading score, and percentage protein were in agreement with data reported by others, whereas QTL markers for percentage head rice, percentage milled rice, percentage protein, and percentage brown rice were different in our mapping population. Five major QTLs were found to be associated with improved percentage rice bran, percentage amylose, and alkali-spreading score. Seven QTLs for improved percentage rice bran, percentage milled rice, alkali-spreading score, percentage protein, and grain length/width ratio were derived from the O. glaberrima accession. Three new QTLs for percentage rice bran are reported here for the first time. Results from this study suggest that the African rice might be a valuable new source for introgression and improvement of several traits that affect quality traits demanded by the different rice export markets.

Chromosome Mapping↗

The mapping of QTLS for chlorophyll content and responsiveness to gibberellic (GA3) and abscisic (ABA) acids in rye.

Genetic maps containing molecular markers are useful tools for the identification of genes underlying quantitative traits (QTLs). Three traits important for plant physiology, i.e. chlorophyll content, sensitivity to GA and sensitivity to ABA, were evaluated for 99 F2 families of the DS2 x RXL10 rye mapping population. The observed variation in the chlorophyll content in rye leaves was shown to be under the genetic control of four independent QTLs. They were located on the following chromosome arms: 1RL (QChc-1R.1), 3RS (QChc-3R.1), 4RL (QChc-4R.1) and 5RL (QChc-5R.1) The marker-assisted selection of recombinants comprising positively-acting alleles at these loci may significantly increase the chlorophyll content in rye leaves, which should result in a higher efficiency of photosynthesis. A decreasing of plant height in rye is one of the major aims of breeders selecting for lodging resistance. The polymorphism of genes controlling sensitivity to gibberellic acid may be the basis for a potential selection strategy. Three QTLs underlying the sensitivity of rye seedlings to GA were located on chromosomes 5RL (QGar-5R.1), 1RL (QGar-1R.1) and on 7RL (QGar-7R.1). The dwarfing allele of a Dw1 locus present in line RXL10 was mapped in the same position as the QGar-5R.1 gene. Sensitivity to ABA plays an important role in imposing dormancy in rye grain. Three QTLs affecting sensitivity to ABA were found. They were mapped on chromosomes 1RS (QAbr-1R.1), 2R in the centromeric region (QAbr-2R.1) and on 5RL (QAbr-5R.1). QAbr-5R.1, Dw1 and QGar-5R.1 are located in the same position on the distal part of the 5RL chromosome arm, which suggests that they belong to a single locus for a major regulatory gene controlling the development of rye plants.

Abscisic Acid↗

Mapping and characterisation of QTL x E interactions for traits determining grain and stover yield in pearl millet.

A mapping population of 104 F(3) lines of pearl millet, derived from a cross between two inbred lines H 77/833-2 x PRLT 2/89-33, was evaluated, as testcrosses on a common tester, for traits determining grain and stover yield in seven different field trials, distributed over 3 years and two seasons. The total genetic variation was partitioned into effects due to season (S), genotype (G), genotype x season interaction (G x S), and genotype x environment-within-season interaction [G x E(S)]. QTLs were determined for traits for their G, G x S, and G x E(S) effects, to assess the magnitude and the nature (cross over/non-crossover) of environmental interaction effects on individual QTLs. QTLs for some traits were associated with G effects only, while others were associated with the effects of both G and G x S and/or G, G x S and G x E(S) effects. The major G x S QTLs detected were for flowering time (on LG 4 and LG 6), and mapped to the same intervals as G x S QTLs for several other traits (including stover yield, harvest index, biomass yield and panicle number m(-2)). All three QTLs detected for grain yield were unaffected by G x S interaction however. All three QTLs for stover yield (mapping on LG 2, LG 4 and LG 6) and one of the three QTLs for grain yield (mapping on LG 4) were also free of QTL x E(S) interactions. The grain yield QTLs that were affected by QTL x E(S) interactions (mapping on LG 2 and LG 6), appeared to be linked to parallel QTL x E(S) interactions of the QTLs for panicle number m(-2) on (LG 2) and of QTLs for both panicle number m(-2) and harvest index (LG 6). In general, QTL x E(S) interactions were more frequently observed for component traits of grain and stover yield, than for grain or stover yield per se.

Chromosome Mapping↗

Standardization of cage techniques to screen chickpeas for resistance to Helicoverpa armigera (Lepidoptera: Noctuidae) in greenhouse and field conditions.

Because of variations in insect populations and staggered flowering of chickpea, Cicer arietinum L., genotypes, it is difficult to compare the genotypic performance across seasons and locations. We standardized a cage technique to screen chickpeas for resistance to Helicoverpa armigera (Hübner). Leaf feeding by the larvae was significantly lower on ICC 506 than on ICCC 37 when the seedlings were infested with 20 neonates per five plants at 15 d after seedling emergence or 10 neonates per three plants at the flowering stage. Maximum differences in pod damage were observed when the plants were infested with six third-instar larvae per three plants in the greenhouse, and with eight larvae per plant under field conditions. Larval weights were significantly lower on ICC 506 than on ICCC 37 across growth stages and infestation levels. At the podding stage, percentage of reduction in grain yield was significantly greater on ICCC 37 and Annigeri than on ICCV 2 and ICC 506. The no-choice test can be used to screen segregating breeding material and mapping populations for resistance to H. armigera. It also provides useful information on antibiosis mechanism of resistance to H. armigera.

Agriculture↗

Mapping of Fhb2 on chromosome 6BS: a gene controlling Fusarium head blight field resistance in bread wheat (Triticum aestivum L.).

Fusarium head blight (FHB) is one of the most important fungal wheat diseases worldwide. Understanding the genetics of FHB resistance is key to facilitate the introgression of different FHB resistance genes into adapted wheat. The objective of this project was to study the FHB resistance QTL on chromosome 6B, quantify the phenotypic variation, and qualitatively map the resistance gene as a Mendelian factor. The FHB resistant parent BW278 (AC Domain*2/Sumai 3) was used as the source of the resistance allele. A large recombinant inbred line (RIL) mapping population was developed from the cross BW278/AC Foremost. The population segregated for three known FHB resistance QTL located on chromosomes 3BSc, 5A, and 6B. Molecular markers on chromosome 6B (WMC104, WMC397, GWM219), 5A (GWM154, GWM304, WMC415), and 3BS (WMC78, GWM566, WMC527) were amplified on approximately 1,440 F2:7 RILs. The marker information was used to select 89 RILs that were fixed homozygous susceptible for the 3BSc and 5A FHB QTLs and were recombinant in the 6B interval. Disease response was evaluated on 89 RILs and parental checks in the greenhouse and field nurseries. Dual floret injection (DFI) was used in greenhouse trials to evaluate disease severity (DS). Macroconidial spray inoculations were used in field nurseries conducted at two locations in southern Manitoba (Carman and Glenlea) over two years 2003 and 2004, to evaluate disease incidence, disease severity, visual rating index, and Fusarium-damaged kernels. The phenotypic distribution for all five-disease infection measurements was bimodal, with lines resembling either the resistant or susceptible checks and parents. All of the four field traits for FHB resistance mapped qualitatively to a coincident position on chromosome 6BS, flanked by GWM133 and GWM644, and is named Fhb2. The greenhouse-DS trait mapped 2 cM distal to Fhb2. Qualitative mapping of Fhb2 in wheat provides tightly linked markers that can reduce linkage drag associated with marker assisted selection of Fhb2 and aid the pyramiding of different resistance loci for wheat improvement.

Analysis of Variance↗

Development of sequence characterized amplified region (SCAR) primers for the detection of Phyto.5.2, a major QTL for resistance to Phytophthora capsici Leon. in pepper.

Phytophthora capsici causes devastating disease on many crop species, including Capsicum. Resistance in Capsicum annuum is genetically and physiologically complex. A panel of Capsicum germplasm that included genotypes from both C. annuum and C. chinense showing highly resistant, highly susceptible and intermediate or tolerant responses to the pathogen, respectively, was screened with a series of randomly amplified polymorphic sequence primers to determine which genomic regions contribute to the highest level of resistance. One primer, OpD04, amplified a single band only in those C. annuum and C. chinense genotypes showing the highest level of resistance. The amplified product was cloned, sequenced and used to design longer primers in order to generate a sequence characterized amplified region marker which was then mapped in a reference mapping population and a screened population segregating for resistance to P. capsici. These primers were observed to define a locus on pepper chromosome 5 tightly linked to Phyto.5.2, one of six quantitative trait loci (QTL) previously reported to contribute to P. capsici resistance. These results indicate that the Phyto.5.2 QTL may be widely distributed in highly resistant germplasm and provide improved resolution for this QTL. This work also defines the first breeding tools for this system, allowing for the rapid selection of genotypes likely to be highly resistant to P. capsici.

Capsicum↗

Quantitative trait loci for component physiological traits determining salt tolerance in rice.

Rice (Oryza sativa) is sensitive to salinity, which affects one-fifth of irrigated land worldwide. Reducing sodium and chloride uptake into rice while maintaining potassium uptake are characteristics that would aid growth under saline conditions. We describe genetic determinants of the net quantity of ions transported to the shoot, clearly distinguishing between quantitative trait loci (QTL) for the quantity of ions in a shoot and for those that affect the concentration of an ion in the shoot. The latter coincide with QTL for vegetative growth (vigor) and their interpretation is therefore ambiguous. We distinguished those QTL that are independent of vigor and thus directly indicate quantitative variation in the underlying mechanisms of ion uptake. These QTL independently govern sodium uptake, potassium uptake, and sodium:potassium selectivity. The QTL for sodium and potassium uptake are on different linkage groups (chromosomes). This is consistent with the independent inheritance of sodium and potassium uptake in the mapping population and with the mechanistically different uptake pathways for sodium and potassium in rice under saline conditions (apoplastic leakage and membrane transport, respectively). We report the chromosomal location of ion transport and selectivity traits that are compatible with agronomic needs and we indicate markers to assist selection in a breeding program. Based upon knowledge of the underlying mechanisms of ion uptake in rice, we argue that QTL for sodium transport are likely to act through the control of root development, whereas QTL for potassium uptake are likely to act through the structure or regulation of membrane-sited transport components.

Analysis of Variance↗

The use of phenotypic markers to identify Brassica oleracea genotypes for routine high-throughput Agrobacterium-mediated transformation.

Doubled haploid (DH) genotypes from a genetic mapping population of Brassica oleracea were screened for ease of transformation. Candidate genotypes were selected based on prior knowledge of three phenotypic markers: susceptibility to Agrobacterium tumefaciens, shoot regeneration potential and mode of shoot regeneration. Mode of regeneration was found to be the most significant of the three factors. Transgenic plants were successfully obtained from genotypes that regenerated multiple shoots via a distinct swelling or callus phase. The absence of tissue culture blackening (associated with genotypes that formed callus) was found to be critical for transformation success. Transgenic shoots were obtained from genotypes that regenerated via an indirect callus mode, even when susceptibility to Agrobacterium was low. The most efficient genotype (DH AG1012) produced transgenic shoots at an average rate of 15% (percentage of inoculated explants giving rise to transgenic plants). The speed and efficiency of regeneration enabled the isolation of transgenic shoots 5-6 weeks after inoculation with A. tumefaciens. This line was also self-compatible, enabling the production of seed without the need for hand-pollination. A genetically uniform DH genotype, with an associated genetic map, make DH AG1012 highly desirable as a potential model B. oleracea genotype for studying gene function. The possibility of applying the same phenotypic tissue culture markers to other Brassica species is discussed.

Biomarkers↗

Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map.

Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of AzucenaxIR64 and AzucenaxBala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319 on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175 annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23 pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.

Disasters↗

The contribution of epistasis to species differences in annual sunflowers.

The contribution of epistasis to 15 morphological traits differentiating two annual sunflowers (Helianthus annuus and H. debilis ssp. cucumerifolius) and to hybrid pollen sterility was estimated in a first generation backcross (BC1) mapping population. Analysis of digenic interactions among quantitative trait loci (QTLs) with significant main effects revealed significant interaction effects for six of the 15 morphological traits and for pollen sterility. Likewise, a genome-wide scan of all possible two-locus combinations detected additional significant interactions for three of the traits with significant epistasis in the original analysis: stem pigmentation, phyllary pubescence, and pollen viability. However, these were the only traits of the 16 examined in which detected interactions explained more than 5% of phenotypic variance. The implications of these findings for adaptive evolution and for the introgression of advantageous morphological QTLs across a natural hybrid zone between these taxa are discussed.

Adaptation, Biological↗

Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat.

Wild emmer wheat, Triticum dicoccoides, is the progenitor of modern tetraploid and hexaploid cultivated wheats. Our objective was to map domestication-related quantitative trait loci (QTL) in T. dicoccoides. The studied traits include brittle rachis, heading date, plant height, grain size, yield, and yield components. Our mapping population was derived from a cross between T. dicoccoides and Triticum durum. Approximately 70 domestication QTL effects were detected, nonrandomly distributed among and along chromosomes. Seven domestication syndrome factors were proposed, each affecting 5-11 traits. We showed: (i) clustering and strong effects of some QTLs; (ii) remarkable genomic association of strong domestication-related QTLs with gene-rich regions; and (iii) unexpected predominance of QTL effects in the A genome. The A genome of wheat may have played a more important role than the B genome during domestication evolution. The cryptic beneficial alleles at specific QTLs derived from T. dicoccoides may contribute to wheat and cereal improvement.

Alleles↗

AFLP targeting of the 1-cM region conferring the vrs1 gene for six-rowed spike in barley, Hordeum vulgare L.

Spike morphology is a key characteristic in the study of barley domestication, yield, and use. Multiple alleles at the vrs1 locus control the development and fertility of the lateral spikelets of barley. We developed five amplified fragment length polymorphism (AFLP) markers tightly linked to the vrs1 locus using well-characterized near-isogenic lines as plant materials. The AFLP markers were integrated into three different maps, in which 'Azumamugi' was used as the maternal parent. Of the three maps, Hordeum vulgare L. 'Azumamugi' x H. vulgare 'Golden Promise' showed recombination of the AFLP markers and the vrs1 locus (closest, 0.05 cM), providing the best mapping population for positional cloning of alleles at the vrs1 locus. Conversion of AFLP bands into polymorphic sequence-tagged sites (STSs) is necessary for further high-throughput genotype scoring and for bacterial artificial chromosome (BAC) library screening. We cloned and sequenced the five AFLP bands and synthesized primer pairs. PCR amplification generated DNAs of the same size from all four parental lines for each marker. Restriction endonuclease treatment of e40m36-1110/AccIII, e34m13-260/Psp1406I, e52m32-270/FokI, and e31m26-520/MnlI revealed fragment length polymorphisms between 'Azumamugi' and all the two-rowed parents. Allelism between the AFLPs and corresponding STS markers was confirmed genetically, indicating the usefulness of the STSs as genetic markers.

Alleles↗

Mapping of a spontaneous mutation for early flowering time in maize highlights contrasting allelic series at two-linked QTL on chromosome 8.

Only a few mutations affecting flowering time have been detected in maize. We analyzed a spontaneous early mutation, vgt-f7p, which appeared during production of the inbred line F7. This mutation shortens the time from planting to flowering by about 100 growing degree days (GDD), and reduces the number of nodes. It therefore seems to affect the timing of meristem differentiation from a vegetative to a reproductive state. It was mapped to a 6 cM confidence interval on chromosome 8, using a QTL mapping approach. QTL analysis of a mapping population generated by crossing the mutant F7 line (F7p) and the Gaspé flint population showed that vgt-f7p is probably allelic to vgt1, a QTL described in previous studies, and affects earliness more strongly than the Gaspé allele at vgt1. Global analysis of the QTL in the region suggested that there may be two consensus QTL, vgt1 and vgt2. These two QTL have contrasting allelic effects: rare alleles conferring extremely early flowering at vgt1 vs. greater diversity and milder effects at locus vgt2. Finally, detailed syntenic analysis showed that the vgt1 region displays a highly conserved duplicated region on chromosome 6, which also plays an important role in maize flowering time variation. The cloning of vgt1 should, therefore, also facilitate the analysis of the molecular basis of variation due to this second region.

Alleles↗

The genetic basis of chloride exclusion in grapevines.

Mediterranean regions are among the most important areas for global grape production, characterized by dry climates and frequent challenges associated with soil salinity. In these environments, chloride toxicity is a major factor limiting vine growth and fruit quality. Despite the critical role of chloride exclusion in salinity tolerance, the genetic mechanisms underlying this trait remain poorly understood. In this study, we analyzed natural variation in chloride exclusion using a diverse panel of 335 accessions representing 18 wild and cultivated Vitis species. This panel, comprising accessions from the southwestern United States and Mexico, captures a broad range of evolutionary adaptations to abiotic stress and provides a valuable genetic resource for breeding efforts aimed at introducing novel traits. Using genome-wide association and quantitative trait loci (QTL) mapping, we identified a major QTL on chromosome 8, now designated qClEx8.1, containing candidate genes encoding cation/H⁺ exchangers (CHXs), which are involved in ion transport and homeostasis. To validate these findings, we analyzed a mapping population derived from Vitis acerifolia longii 9018 and the commercial rootstock GRN3, confirming the chromosome 8 locus as a major determinant of chloride exclusion. Structural variant analysis revealed nonsynonymous substitutions within CHX genes that may influence protein function and salinity tolerance. Additionally, we discovered a novel QTL on chromosome 19 enriched with G-type lectin S-receptor-like serine/threonine-protein kinases, known regulators of stress signaling. By integrating phenotypic and genomic data across a diverse Vitis collection, this study advances our understanding of the genetic architecture underlying chloride exclusion and highlights candidate genes for breeding salt-tolerant rootstocks.

Vitis↗

QTL for yield and its components responded to elevated CO2 in rice (Oryza sativa L.).

FACE (free air carbon dioxide enrichment) technology may provide a means by which the environment around growing plants can be modified to realistically simulate the concentration of atmospheric CO2 in the future. The plant growth and its yield of plant species can be enhanced under FACE. Identification of genomic regions influencing the response of yield and its components to elevated CO2 will be useful for understanding the genetics of active response to changed CO2 environment and developing higher yield cultivars, which will be adapted to future enriched atmospheric CO2 environment. A mapping population of 65 indica (IR24) chromosome segment substitution lines (CSSLs) in japonica (Asominori) background and their parents were used to detect QTLs for yield and its components, e. g. number of fertile tillers per plant (FT), 1000-grain weight (TGW), number of grains per panicle (GP) and grain yield per plant (GY) under FACE (200 micromol CO2/mol above current levels) and current CO2 concentration (Ambient, about 370 micromol CO2/mol) in the field experiment. The results showed that, GY, GP and FT of two parents under FACE were significant greater than that under Ambient. The transgressive segregation of the four traits was observed in the CSSLs population under both FACE and Ambient. A total of 20 QTLs for the four traits were detected on chromosome 1, 2, 4, 6, 7, 9 and 12 with LOD (Log10-likelihood ratio) of QTLs ranging from 2.5 to 5.7. Three QTLs were detected under both FACE and Ambient. However,other QTLs were detected only under one level of CO2, which indicated that these loci were sensitive to CO2 concentration. Additionally, two QTLs qFT12 and qGP4 were found for the QTL x Environment (QE) interaction effects. It is suggested that there is a high possibility to improve the yield of rice under elevated CO2 through marker-assisted selection.

Biomass↗

The biological basis of epistasis between quantitative trait loci for flavone and 3-deoxyanthocyanin synthesis in maize (Zea mays L.).

A major weakness in our understanding of the genetic basis of complex traits has been that of defining the extent and biological basis of epistasis. Our research group has been studying the genetic control of the accumulation of maysin, a C-glycosyl flavone, in maize, Zea mays (L.), silks. Previously, we demonstrated the importance of the p1 locus as a QTL for maysin synthesis. The p1 locus often exhibits significant epistatic interactions with other loci. We developed a mapping population, (W23al x GT119)F2, specifically designed to test whether genes in an intersecting pathway might be detected as QTLs for maysin synthesis and result in epistatic interaction effects. The a1 gene is not required for the synthesis of flavones but is required for the synthesis of 3-deoxyanthocyanins, an intersecting pathway, in maize silks. The p1 locus (P < 0.0001) was a QTL for both flavones and 3-deoxyanthocyanins. The a1 locus was also highly significant (P < 0.0001) for both traits, as was the p1 x a1 epistatic interaction (P < 0.0001). Our results demonstrate that altering the flux of biochemical intermediates between pathways may be the biological basis of major QTL effects and epistatic interactions.

Alleles↗

Genetic architecture of variation in sex-comb tooth number in Drosophila simulans.

The sex comb on the forelegs of Drosophila males is a secondary sexual trait, and the number of teeth on these combs varies greatly within and between species. To understand the relationship between the intra- and interspecific variation, we performed quantitative trait locus (QTL) analyses of the intraspecific variation in sex-comb tooth number. We used five mapping populations derived from two inbred Drosophila simulans strains that were divergent in the number of sex-comb teeth. Although no QTLs were detected on the X chromosome, we identified four QTLs on the second chromosome and three QTLs on the third chromosome. While identification and estimated effects of the second-chromosome QTLs depend on genetic backgrounds, significant and consistent effects of the two third-chromosome QTLs were found in two genetic backgrounds. There were significant epistatic interactions between a second-chromosome QTL and a third-chromosome QTL, as well as between two second-chromosome QTLs. The third-chromosome QTLs are concordant with the locations of the QTLs responsible for the previously observed differences in sex-comb tooth number between D. simulans and D. mauritiana.

Animals↗

Genetic mapping and functional analysis of the tomato Bs4 locus governing recognition of the Xanthomonas campestris pv. vesicatoria AvrBs4 protein.

Xanthomonas campestris pv. vesicatoria is the causal agent of bacterial spot disease on pepper (Capsicum spp.) and tomato (Lycopersicon spp.). Analysis of 17 different Lycopersicon accessions with avrBs4-expressing X. campestris pv. vesicatoria strains identified 15 resistant and two susceptible tomato genotypes. Genetic analysis revealed that AvrBs4 recognition in tomato is governed by a single locus, designated Bs4 (bacterial spot resistance locus no. 4). Amplified fragment length polymorphism and bulked DNA templates from resistant and susceptible plants were used to define a 2.6-cM interval containing the Bs4 locus. A standard tomato mapping population was employed to localize Bs4-linked markers on the short arm of chromosome 5. Investigation of X. campestris pv. vesicatoria hrp mutant strains revealed that AvrBs4 secretion and avirulence activity are hrp dependent. Agrobacterium-based delivery of the avrBs4 gene into tomato triggered a plant response that phenotypically resembled the hypersensitive response induced by avrBs4-expressing X. campestris pv. vesicatoria strains, suggesting symplastic perception of the avirulence protein. Mutations in the avrBs4 C-terminal nuclear localization signals (NLSs) showed that NLSs are dispensable for Bs4-mediated recognition. Our data suggest that tomato Bs4 and pepper Bs3 employ different recognition modes for detection of the highly homologous X. campestris pv. vesicatoria avirulence proteins AvrBs4 and AvrBs3.

Bacterial Proteins↗