Minor Quantitative Trait Loci Research Articles

Mapping of QTL for Tolerance to Cereal Yellow Dwarf Virus in Two-rowed Spring Barley.

Cereal yellow dwarf virus (CYDV-RPV) causes a serious viral disease affecting small grain crops around the world. In the United States, it frequently is present in California where it causes significant yield losses, and when infections start early in development, plant death. CYDV is transmitted by aphids, and it has been a major impediment to developing malting barley in California. To identify chromosome locations associated with tolerance/resistance to CYDV, a segregating population of 184 recombinant inbred lines (RIL) from a cross of the California adapted malting barley line Butta 12 with the CYDV tolerant Madre Selva was used to construct a genetic map including 180 polymorphic markers mapping to 163 unique loci. Tolerance to CYDV was evaluated in replicated experiments where plants were challenged by aphid mediated inoculation with the isolate CYDV-RPV in a controlled environment. Quantitative trait loci (QTL) analysis revealed the presence of two major QTL for CYDV tolerance from Madre Selva on chromosomes 2H (Qcyd.MaBu-1) and 7H (Qcyd.MaBu-2), and 4 minor QTL from Butta 12 on chromosomes 3H, 4H, and 2H. This paper discusses the contribution of each QTL and their potential value to improve barley tolerance to CYDV.

Quantitative trait analysis of flowering time in spring rapeseed (B. napus L.)

The inheritance of flowering time trait in spring-type rapeseed (Brassica napus L.) is poorly understood, and the investigations on mapping of quantitative trait loci (QTL) for the trait are only few. We identified QTL underlying variation for flowering time in a doubled haploid (DH) mapping population of nonvernalization-responsive canola (B. napus L.) cultivar 465 and line 86 containing introgressions from Houyou11, a Chinese early-flowering cultivar in Brassica rapa L. Significant genetic variation in flowering time and response to photoperiod were observed among the DH lines from 465/86. A molecular linkage map was generated comprising three types of markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 4 major loci, localized on four different linkage groups A6, A7, C8 and C9. These loci each accounted for between 9.2 and 12.56 % of the total genotypic variation for first flowering. The published high-density maps for flowering time mapping used different marker systems, and the parents of our crosses have different genetic origins, with either spring-type B. napus or B. rapa. So we cannot determine whether the QTL on the same linkage groups were in the same region or not. There was evidence of additive × additive epistatic effects for flowering time in the DH population. Epistasis existed not only between main-effect QTLs, but also between QTLs with minor effects. Four pair of epistasis effects between minor QTLs explained about 20 % of the genetic variance observed in the DH population. The results indicated that minor QTLs for flowering time should not be ignored. Significant genotypes × environment interactions were also found for the quantitative traits, and with significant change in the ranking of the DH lines in different environments. The results implied that FQ3 was a non-environment-specific QTL and may control flowering time by autonomous pathway. FQ4 were winter-environment-specific QTL and may control flowering time by photoperiod-pathway. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for high altitude areas, via marker-assisted selection.

Quantitative trait locus analysis of resistance to panicle blast in the rice cultivar Miyazakimochi.

BackgroundRice blast is a destructive disease caused by Magnaporthe oryzae, and it has a large impact on rice production worldwide. Compared with leaf blast resistance, our understanding of panicle blast resistance is limited, with only one panicle blast resistance gene, Pb1, isolated so far. The japonica cultivar Miyazakimochi shows resistance to panicle blast, yet the genetic components accounting for this resistance remain to be determined.ResultsIn this study, we evaluated the panicle blast resistance of populations derived from a cross between Miyazakimochi and the Bikei 22 cultivar, which is susceptible to both leaf and panicle blast. The phenotypic analyses revealed no correlation between panicle blast resistance and leaf blast resistance. Quantitative trait locus (QTL) analysis of 158 recombinant inbred lines using 112 developed genome-wide and 35 previously reported polymerase chain reaction (PCR) markers revealed the presence of two QTLs conferring panicle blast resistance in Miyazakimochi: a major QTL, qPbm11, on chromosome 11; and a minor QTL, qPbm9, on chromosome 9. To clarify the contribution of these QTLs to panicle blast resistance, 24 lines homozygous for each QTL were selected from 2,818 progeny of a BC2F7 backcrossed population, and characterized for disease phenotypes. The panicle blast resistance of the lines harboring qPbm11 was very similar to the resistant donor parental cultivar Miyazakimochi, whereas the contribution of qPbm9 to the resistance was small. Genotyping of the BC2F7 individuals highlighted the overlap between the qPbm11 region and a locus of the panicle blast resistance gene, Pb1. Reverse transcriptase PCR analysis revealed that the Pb1 transcript was absent in the panicles of Miyazakimochi, demonstrating that qPbm11 is a novel genetic component of panicle blast resistance.ConclusionsThis study revealed that Miyazakimochi harbors a novel panicle blast resistance controlled mainly by the major QTL qPbm11. qPbm11 is distinct from Pb1 and could be a genetic source for breeding panicle blast resistance, and will improve understanding of the molecular basis of host resistance to panicle blast.

Dw2, a New Dwarfing Locus in Apple Rootstocks and Its Relationship to Induction of Early Bearing in Apple Scions

The ability of certain apple rootstocks to dwarf their scions has been known for centuries and their use revolutionized apple (Malus ×domestica) production systems. In this investigation, several apple rootstock breeding populations, planted in multiple replicated field and pot experiments, were used to ascertain the degree of dwarfing when grafted with multiple scions. A previous genetic map of a breeding population derived from parents ‘Ottawa 3’ (O.3) and ‘Robusta 5’ (R5) was used for quantitative trait locus (QTL) analysis of traits related to scion vigor suppression, induction of early bearing, and other tree size measurements on own-rooted and grafted trees. The analysis confirmed a previously reported QTL that imparts vigor control [Dw1, log of odds (LOD) = 7.2] on linkage group (LG) 5 and a new QTL named Dw2 (LOD = 6.4) on LG11 that has a similar effect on vigor. The data from this population were used to study the interaction of these two loci. To validate these findings, a new genetic map comprised of 1841 single-nucleotide polymorphisms was constructed from a cross of the dwarfing, precocious rootstocks ‘Geneva 935’ (G.935) and ‘Budagovsky 9’ (B.9), resulting in the confirmation and modeling of the effect of Dw1 and Dw2 on vigor control of apple scions. Flower density and fruit yield data allowed the identification of genetic factors Eb1 (LOD = 7.1) and Eb2 (LOD = 7.6) that cause early bearing of scions, roughly colocated with the dwarfing factors. The major QTL for mean number of fruit produced per tree colocated with Dw2 (LOD = 7.0) and a minor QTL was located on LG16 (LOD = 3.5). These findings will aid the development of a marker-assisted breeding strategy, and the discovery of additional sources for dwarfing and predictive modeling of new apple rootstocks in the Geneva® apple rootstock breeding program.

QTL mapping of fire blight resistance in Malus ×robusta 5 after inoculation with different strains of Erwinia amylovora

Fire blight caused by Erwinia amylovora is one of the most disastrous diseases in apple production. Whereas most apple cultivars are susceptible to fire blight, several wild apple species accessions like Malus ×robusta 5 (Mr5) bear significant resistance. The resistance of Mr5 is mainly inherited by a major quantitative trait locus (QTL) on linkage group 3. QTL mapping was performed after inoculation of the population 04208 (Idared × Mr5) using strains differing in their virulence to Mr5. The QTL mapping approach demonstrated that the major QTL on linkage group 3 could be confirmed after inoculation with strains non-virulent to Mr5. In contrast, the major QTL disappeared after inoculation with strains virulent to Mr5. Only after inoculation with the resistance breaking strain Ea 3049 was a minor QTL with a LOD >3 found on linkage group 3. Additionally, several minor QTLs were detected on linkage groups 5, 7, 11 and 14 of Mr5 after inoculation with virulent strains able to overcome the major resistance QTL of Mr5. Their usefulness for further breeding activities will be discussed. The strain-specific results obtained in the present study provide further evidence for the existence of gene-for-gene relationships in the host–pathogen system Mr5–E. amylovora. Of the newly discovered minor QTLs, the one detected on LG7 contributes significantly to fire blight resistance in the presence of the major QTL, independently of the strain used.

Mapping quantitative trait loci associated with blush in peach [Prunus persica (L.) Batsch

Blush is an important trait for marketing peaches. The red skin pigmentation develops through the flavonoid and anthocyanin pathways, and both genetic and environmental stimuli, and their interaction, control the regulation of these pathways. The molecular basis of blush development in peach is yet to be understood. An F2 blush population (ZC2) derived from a cross between two peach cultivars with contrasting phenotypes for blush, “Zin Dai” (∼30 % red) and “Crimson Lady” (∼100 % red), was used for linkage map construction and quantitative trait loci (QTLs) mapping. The segregating population was phenotyped for blush for 4 years using a visual rating scale and quantified using a colorimeter (L*, a*, and b*) 1 year. The ZC2 population was genotyped with the IPSC 9 K peach single-nucleotide polymorphism (SNP) array v1, and a high-density ZC2 genetic linkage map was constructed. The map covers genetic a distance of ∼452.51 cM with an average marker spacing of 2.38 cM/marker. Four QTLs were detected: one major QTL on LG3 (Blush.Pp.ZC-3.1) and three minor QTLs on LG 4 and 7 (Blush.Pp.ZC-4.1; Blush.Pp.ZC-4.2; Blush.Pp.ZC-7.1), indicating the presence of major and minor genes involved in blush development. Candidate genes involved in skin and flesh coloration of peach (PprMYB10), cherry (PavMYB10), and apple (MdMYB1/MdMYBA/MdMYB10) are located within the interval of the major QTL on LG3, suggesting the same genetic control for color development in the Rosaceae family. Marker-assisted selection (MAS) for blush is discussed.

Molecular mapping of the brace root traits in sorghum (Sorghum bicolor L. Moench).

The presence and morphology of plant brace roots are important root architecture traits. Brace roots contribute significantly to effective anchorage and water and nutrient uptake during late growth and development, and more importantly, have a substantial influence on grain yield under soil flooding or water limited conditions. However, little is known about the genetic mechanisms that underlie brace root traits. In this study, quantitative trait loci (QTLs) for presence of brace roots from the sorghum landrace “Sansui” were mapped and associated molecular markers were identified. A linkage map was constructed with 109 assigned simple sequence repeat markers using a F2 mapping population derived from the cross Sansui/Jiliang 2. Two QTLs associated with presence of brace roots were localized on chromosomes 6 and 7. The major QTL on chromosome 7 between markers Dsenhsbm7 and Xcup 70 explained about 52.5% of the phenotypic variation, and the minor QTL on chromosome 6 was flanked by Xtxp127 and Xtxp6 and accounted for 7.0% of phenotypic variation. These results will provide information for the improvement of sorghum root architecture associated with brace roots.

Mapping of Seed Shattering Loci Provides Insights into Origin of Weedy Rice and Rice Domestication

Seed shattering is an important trait that distinguishes crop cultivars from the wild and weedy species. The genetics of seed shattering was investigated in this study to provide insights into rice domestication and the evolution of weedy rice. Quantitative trait locus (QTL) analysis, conducted in 2 recombinant inbred populations involving 2 rice cultivars and a weedy rice accession of the southern United States, revealed 3-5 QTLs that controlled seed shattering with 38-45% of the total phenotypic variation. Two QTLs on chromosomes 4 and 10 were consistent in both populations. Both cultivar and weedy rice contributed alleles for increased seed shattering. Genetic backgrounds affected both QTL number and the magnitude of QTL effects. The major QTL qSH4 and a minor QTL qSH3 were validated in near-isogenic lines, with the former conferring a significantly higher degree of seed shattering than the latter. Although the major QTL qSH4 overlapped with the sh4, the presence of the nonshattering single nucleotide polymorphism allele in the weedy rice accession suggested involvement of a linked locus or an alternative molecular genetic mechanism. Overlapping of several QTLs with those from earlier studies indicated that weedy rice may have been derived from the wild species Oryza rufipogon. Natural hybridization of rice cultivars with the highly variable O. rufipogon present in different geographic regions might be responsible for the evolution of a wide range of phenotypic and genotypic variabilities seen in weedy rice populations worldwide.

Conditional QTL Mapping of Sedimentation Volume on Seven Quality Traits in Common Wheat

To evaluate the possible genetic interrelationships between flour components and the sedimentation volume (SD), a doubled haploid (DH) population comprising 168 lines were used to identify the conditional quantitative trait loci (QTLs) for SD in three environments. Ten additive QTLs and 15 pairs of epistatic QTLs were detected for SD through unconditional and conditional QTL mapping. Three major additive QTLs were detected for SD conditioned on the seven quality traits. Two additive QTLs were found to be independent of these traits. Three additive QTLs were suppressed by three of the seven traits because of non-detection in unconditional mapping. Three pairs of epistatic QTLs were completely affected by the seven traits because of detection in unconditional mapping but no-detection in conditional mapping. Twelve pairs of epistatic QTLs were detected in conditional mapping. Our results indicated that conditional mapping could contribute to a better understanding of the interdependence of different and closely correlated traits at the QTL molecular level, especially some minor QTLs were found. The conditional mapping approach provides new insights that will make it possible to avoid the disadvantages of different traits by breeding through molecular design.

Unlinked genetic loci control the reduced transcription of aminopeptidase N 1 and 3 in the European corn borer and determine tolerance to Bacillus thuringiensis Cry1Ab toxin

Transgenic expression of Bacillus thuringiensis (Bt) crystalline (Cry) toxins by crop plants result in reduced insect feeding damage, but sustainability is threatened by the development of resistance traits in target insect populations. We investigated Bt toxin resistance trait in a laboratory colony of the European corn borer, Ostrinia nubilalis, selected for increased survival when exposed to Cry1Ab and correlated survival on Cry1Ab toxin with a constitutive ∼146.2 ± 17.3-fold reduction in midgut aminopeptidase N1 (apn1) transcript levels. A 7.1 ± 1.9-fold reduction apn3 transcript level was also correlated with Cry1Ab resistance. Quantitative trait locus (QTL) mapping identified a single major genome region controlling Cry1Ab resistance on linkage group 24 (LG24), and a minor QTL on LG27. Both QTL were independent of apn1 and apn3 loci on LG02. Positional mapping identified genetic markers that may assist in the identification of causal gene(s) within QTL intervals. This study indicates that genetic factor(s) may act in trans to reduce both apn1 and apn3 expression in Cry1Ab resistant O. nubilalis larvae, and suggest that gene regulatory pathways can influence Bt resistance traits. These findings show that gene interactions (epistasis) may influence Bt resistance in target insect populations.

Characterization of Yr54 and other genes associated with adult plant resistance to yellow rust and leaf rust in common wheat Quaiu 3

Leaf rust (LR) and yellow rust (YR), caused by Puccinia triticina and Puccinia striiformis f. sp. tritici, respectively, are important diseases of wheat. Quaiu 3, a common wheat line developed at the International Maize and Wheat Improvement Center (CIMMYT), is immune to YR in Mexico despite seedling susceptibility to predominant races. Quaiu 3 also shows immunity to LR in field trials and is known to possess the race-specific gene Lr42. A mapping population of 182 recombinant inbred lines (RILs) was developed by crossing Quaiu 3 with susceptible Avocet-YrA and phenotyped with LR and YR in field trials for 2 years in Mexico. Quantitative trait loci (QTL) associated with YR and LR resistance in the RILs were identified using Diversity Arrays Technology and simple sequence repeat markers. A large-effect QTL on the long arm of chromosome 2D explained 49–54 % of the phenotypic variation in Quaiu 3 and was designated as Yr54. Two additional loci on 1BL and 3BS explained 8–17 % of the phenotypic variation for YR and coincided with previously characterized adult plant resistance (APR) genes Lr46/Yr29 and Sr2/Yr30, respectively. QTL on 1DS and 1BL corresponding to Lr42 and Lr46/Yr29, respectively, contributed 60–71 % of the variation for LR resistance. A locus on 3D associated with APR to both diseases explained up to 7 % of the phenotypic variance. Additional Avocet-YrA-derived minor QTL were also detected for YR on chromosomes 1A, 3D, 4A, and 6A. Yr54 is a newly characterized APR gene which can be combined with other genes by using closely linked molecular markers.

Mapping of flag smut resistance in common wheat

Flag smut, caused by Urocystis agropyri, has been a problem in wheat production, but its incidence has declined with the use of resistant varieties and seed dressing. Diamondbird, an Australian wheat cultivar that carries high levels of resistance to flag smut, was crossed with susceptible Chinese landrace TH3929 and a doubled haploid (DH) population was developed. A linkage map comprising 386 markers was used for detection of genomic regions controlling flag smut resistance. Composite interval mapping identified five quantitative trait loci (QTL) with significant effects for flag smut resistance. QTL QFs.sun-3AL, QFs.sun-6AS, QFs.sun-1BL and QFs.sun-5BS were contributed by Diamondbird. Although TH3929 was susceptible, it contributed a minor QTL QFs.sun-3AS. QTL QFs.sun-3AL and QFs.sun-6AS were detected in both seasons and each explained more than 17 % of the variation in flag smut response. Other QTL QFs.sun-3AS, QFs.sun-1BL and QFs.sun-5BS explained 5–10 % of the phenotypic variation. DH lines that showed low flag smut levels carried combinations of three or more QTL. This is the first report on chromosomal location of flag smut resistance in a modern common wheat cultivar.

Identification of multiple interacting alleles conferring low glycerol and high ethanol yield in Saccharomyces cerevisiae ethanolic fermentation

BackgroundGenetic engineering of industrial microorganisms often suffers from undesirable side effects on essential functions. Reverse engineering is an alternative strategy to improve multifactorial traits like low glycerol/high ethanol yield in yeast fermentation. Previous rational engineering of this trait always affected essential functions like growth and stress tolerance. We have screened Saccharomyces cerevisiae biodiversity for specific alleles causing lower glycerol/higher ethanol yield, assuming higher compatibility with normal cellular functionality. Previous work identified ssk1E330N…K356N as causative allele in strain CBS6412, which displayed the lowest glycerol/ethanol ratio.ResultsWe have now identified a unique segregant, 26B, that shows similar low glycerol/high ethanol production as the superior parent, but lacks the ssk1E330N…K356N allele. Using segregants from the backcross of 26B with the inferior parent strain, we applied pooled-segregant whole-genome sequence analysis and identified three minor quantitative trait loci (QTLs) linked to low glycerol/high ethanol production. Within these QTLs, we identified three novel alleles of known regulatory and structural genes of glycerol metabolism, smp1R110Q,P269Q, hot1P107S,H274Y and gpd1L164P as causative genes. All three genes separately caused a significant drop in the glycerol/ethanol production ratio, while gpd1L164P appeared to be epistatically suppressed by other alleles in the superior parent. The order of potency in reducing the glycerol/ethanol ratio of the three alleles was: gpd1L164P > hot1P107S,H274Y ≥ smp1R110Q,P269Q.ConclusionsOur results show that natural yeast strains harbor multiple specific alleles of genes controlling essential functions, that are apparently compatible with survival in the natural environment. These newly identified alleles can be used as gene tools for engineering industrial yeast strains with multiple subtle changes, minimizing the risk of negatively affecting other essential functions. The gene tools act at the transcriptional, regulatory or structural gene level, distributing the impact over multiple targets and thus further minimizing possible side-effects. In addition, the results suggest polygenic analysis of complex traits as a promising new avenue to identify novel components involved in cellular functions, including those important in industrial applications.

Fine mapping and identification of candidate genes controlling the resistance to southern root-knot nematode in PI 96354

Meloidogyne incognita (Kofoid and White) Chitwood (Mi) is the most economically damaging species of the root-knot nematode to soybean and other crops in the southern USA. PI 96354 was identified to carry a high level of resistance to galling and Mi egg production. Two Quantitative Trait Locus(QTLs) were found to condition the resistance in PI 96354 including a major QTL and a minor QTL on chromosome 10 and chromosome 18, respectively. To fine map the major QTL on chromosome 10, F5:6 recombinant inbred lines from the cross between PI 96354 and susceptible genotype Bossier were genotyped with Simple Sequence Repeats(SSR) markers to identify recombinational events. Analysis of lines carrying key recombination events placed the Mi-resistant allele on chromosome 10 to a 235-kb region of the 'Williams 82' genome sequence with 30 annotated genes. Candidate gene analysis identified four genes with cell wall modification function that have several mutations in promoter, exon, 5', and 3'UTR regions. qPCR analysis showed significant difference in expression levels of these four genes in Bossier compared to PI 96354 in the presence of Mi. Thirty Mi-resistant soybean lines were found to have same SNPs in these 4 candidate genes as PI 96354 while 12 Mi-susceptible lines possess the 'Bossier' genotype. The mutant SNPs were used to develop KASP assays to detect the resistant allele on chromosome 10. The four candidate genes identified in this study can be used in further studies to investigate the role of cell wall modification genes in conferring Mi resistance in PI 96354.

Quantitative trait locus mapping reveals conservation of major and minor loci for powdery mildew resistance in four sources of resistance in mungbean [Vigna radiata (L.) Wilczek

Powdery mildew (PM) is a common and serious disease of mungbean [Vigna radiata (L.) Wilczek]. A few quantitative trait loci (QTL) for PM resistance in mungbean have been reported. The objective of this study was to locate QTL for PM resistance in two resistant accessions V4718 and RUM5. Simple sequence repeat markers were analyzed in an F2 population from a cross between Kamphaeng Saen 1 (KPS1; susceptible to PM) and V4718 (resistant to PM), and in F2 and BC1F1 populations from a cross between Chai Nat 60 (CN60; susceptible to PM) and RUM5 (resistant to PM). Progenies of 134 F2:3 and F2:4 lines derived from KPS1 × V4718, and 190 F2:3 and 74 BC1F1:2 lines derived from CN60 × RUM5 and CN60 × (CN60 × RUM5), respectively, were evaluated for response to PM under field conditions. Multiple interval mapping identified a major QTL on linkage group (LG) 9 and two minor QTL on LG4 for the resistance in V4718, and detected two major QTL on LG6 and LG9 and one minor QTL on LG4 for the resistance in RUM5. Comparative linkage analysis of the QTL for PM resistance in this study and in previous reports suggests that the resistance QTL on LG9 in V4718, RUM5, ATF3640 and VC6468-11-1A are the same locus or linked. One QTL on LG4 is the same in three sources (V4718, RUM5 and VC1210A). Another QTL on LG6 is the same in two sources (RUM5 and VC6468-11-1A). In addition, one QTL in V4718 on LG4 appears to be a new resistance locus. These different resistance loci will be useful for breeding durably PM-resistant mungbean cultivars.

Identification of genomic loci associated with crown rust resistance in perennial ryegrass (Lolium perenne L.) divergently selected populations

The inheritance of crown rust resistance in perennial ryegrass is complex with both major and minor quantitative trait loci (QTL) being detected on all seven linkage groups. However, QTL mapping populations have only few segregating alleles, limiting the transferability of results to other materials. In this study, a synthetic population was developed from four crown rust resistant and susceptible parents as starting material for a divergent selection experiment of crown rust resistance to be closer to practice in plant breeding programs, and to identify genome regions relevant across a broader range of genotypes. Following three cycles of directional selection, perennial ryegrass populations were produced with a two-fold difference in average rust resistance. Divergently selected populations were genotyped at 7 resistance gene analog-derived expressed sequence tag (RGA-derived EST) as well as 15 simple sequence repeat (SSR) loci. A test for selective neutrality (Waples test), which tests the hypothesis of genetic drift versus selection, identified significant differences in allele frequencies for 7 loci (32%). The selection effect was bidirectional with the same loci showing significant response in both positively and negatively selected populations. A region under selection represented by markers LpSSR006 and EST13 on linkage group (LG) 4 was further confirmed by colocation with two separate QTL for crown rust resistance in a VrnA, a two-way pseudo-testcross mapping population. This suggests suitability of alleles identified for introgression into perennial ryegrass germplasm, where quantitative resistance to crown rust is desired.

Genetic mapping of three quantitative trait loci for soybean aphid resistance in PI 567324.

Host-plant resistance is an effective method for controlling soybean aphid (Aphis glycines Matsumura), the most damaging insect pest of soybean (Glycine max (L.) Merr.) in North America. Recently, resistant soybean lines have been discovered and at least four aphid resistance genes (Rag1, Rag2, Rag3 and rag4) have been mapped on different soybean chromosomes. However, the evolution of new soybean aphid biotypes capable of defeating host-plant resistance conferred by most single genes demonstrates the need for finding germplasm with multigenic resistance to the aphid. This study was conducted to map quantitative trait loci (QTL) for aphid resistance in PI 567324. We identified two major QTL (QTL_13_1 and QTL_13_2) for aphid resistance on soybean chromosome 13 using 184 recombinant inbred lines from a 'Wyandot' × PI 567324 cross. QTL_13_1 was located close to the previously reported Rag2 gene locus, and QTL_13_2 was close to the rag4 locus. A minor QTL (QTL_6_1) was also detected on chromosome 6, where no gene for soybean aphid resistance has been reported so far. These results indicate that PI 567324 possesses oligogenic resistance to the soybean aphid. The molecular markers closely linked to the QTL reported here will be useful for development of cultivars with oligogenic resistance that are expected to provide broader and more durable resistance against soybean aphids compared with cultivars with monogenic resistance.

Inheritance of field resistance to Septoria tritici blotch in the wheat doubled-haploid population Solitär × Mazurka

Breeding for field resistance to Septoria tritici blotch (STB), caused by Mycosphaerella graminicola (anamorph: Septoria tritici), is the most suitable strategy for controlling this important disease of wheat. Although many Stb genes for resistance to single pathogen isolates have been identified in wheat, knowledge of their efficiency against natural fungal populations is lacking. In a quantitative-trait-locus (QTL) mapping approach in six environments and four locations, field resistance to STB was studied in a doubled-haploid population derived from a cross between the field-resistant cultivar Solitar and the susceptible cultivar Mazurka. After plant height as a disease escape trait was accounted for, five QTL with effects on STB response on chromosomes 5A, 6D and 7D explained 20 % of the genotypic variance; QTL × environment interactions were minor. Field resistance was conferred exclusively by alleles from Solitar, which was previously shown to carry the isolate-specific genes Stb6 and Stb11 as well as minor QTL detected with seven fungal isolates. Surprisingly, neither the Stb6 nor Stb11 isolate-specific genes nor minor QTL previously detected in Solitar were found to be involved in its field resistance. The study suggests that resistance breeding for STB should not rest solely on the deployment of Stb genes. Field tests are indispensable to show their efficacy and durability and to identify genes conferring partial field resistance to STB.

Identification and QTL mapping of whitefly resistance components in Solanum galapagense

Solanum galapagense is closely related to the cultivated tomato and can show a very good resistance towards whitefly. A segregating population resulting from a cross between the cultivated tomato and a whitefly resistant S. galapagense was created and used for mapping whitefly resistance and related traits, which made it possible to study the genetic basis of the resistance. Quantitative trait loci (QTL) for adult survival co-localized with type IV trichome characteristics (presence, density, gland longevity and gland size). A major QTL (Wf-1) was found for adult survival and trichome characters on Chromosome 2. This QTL explained 54.1 % of the variation in adult survival and 81.5 % of the occurrence of type IV trichomes. A minor QTL (Wf-2) for adult survival and trichome characters was identified on Chromosome 9. The major QTL was confirmed in F3 populations. Comprehensive metabolomics, based on GCMS profiling, revealed that 16 metabolites segregating in the F2 mapping population were associated with Wf-1 and/or Wf-2. Analysis of the 10 most resistant and susceptible F2 genotypes by LCMS showed that several acyl sugars were present in significantly higher concentration in the whitefly resistant genotypes, suggesting a role for these components in the resistance as well. Our results show that whitefly resistance in S. galapagense seems to inherit relatively simple compared to whitefly resistance from other sources and this offers great prospects for resistance breeding as well as elucidating the underlying molecular mechanism(s) of the resistance.

QTL mapping and epistatic interaction analysis in asparagus bean for several characterized and novel horticulturally important traits

BackgroundAsparagus bean (Vigna. unguiculata. ssp sesquipedalis) is a subspecies and special vegetable type of cowpea (Vigna. unguiculata L. Walp.) important in Asia. Genetic basis of horticulturally important traits of asparagus bean is still poorly understood, hindering the utilization of targeted, DNA marker-assisted breeding in this crop. Here we report the identification of quantitative trait loci (QTLs) and epistatic interactions for four horticultural traits, namely, days to first flowering (FLD), nodes to first flower (NFF), leaf senescence (LS) and pod number per plant (PN) using a recombinant inbred line (RIL) population of asparagus bean.ResultsA similar genetic mode of one major QTL plus a few minor QTLs was found to dominate each of the four traits, with the number of QTLs for individual traits ranging from three to four. These QTLs were distributed on 7 of the 11 chromosomes. Major QTLs for FLD, NFF and LS were co-localized on LG 11, indicative of tight linkage. Genome wide epistasis analysis detected two and one interactive locus pairs that significantly affect FLD and LS, respectively, and the epistatic QTLs for FLD appeared to work in different ways. Synteny based comparison of QTL locations revealed conservation of chromosome regions controlling these traits in related legume crops.ConclusionMajor, minor, and epistatic QTLs were found to contribute to the inheritance of the FLD, NFF, LS, and PN. Positions of many of these QTLs are conserved among closely related legume species, indicating common mechanisms they share. To our best knowledge, this is the first QTL mapping report using an asparagus bean × asparagus bean intervarietal population and provides marker-trait associations for marker-assisted approaches to selection.