Mapping of QTL for tiller number at different stages of growth in wheat using double haploid and immortalized F<Subscript>2</Subscript> populations

Effective tiller number is one of the most important traits for wheat (Triticum aestivum L.) yield, but the inheritance of tillering is poorly understood. A set of 168 doubled haploid (DH) lines derivatives of a cross between two winter wheat cultivars (Huapei 3 and Yumai 57), and an immortalized F₂ (IF₂) population generated by randomly permutated intermating of these DHs were investigated, and QTLs of tillering related to the maximum tillering of pre-winter (MTW), maximum tillering in spring (MTS), and effective tillering in harvest (ETH) were mapped. Phenotypic data were collected for the two populations from two different environments. Using inclusive composite interval mapping (ICIM), a total of 9 and 18 significant QTL were detected across environments for tillering in the DH and IF₂ populations, respectively. Four QTLs were common between two populations. A major QTL located on the 5D chromosome with the allele originating from Yumai 57 was detected and increased 1.92 and 3.55 tillers in MTW and MTS, respectively. QTLs (QMts6D, QEth6D) having a neighbouring marker interval at Xswes679.1 and Xcfa2129 on chromosome 6D was detected in MTS and ETH. These results provide a better understanding of the genetic factors for selectively expressing the control of tiller number in different growth stages and facilitate marker-assisted selection strategy in breeding.     

Mapping of yield influencing QTL in <Emphasis Type="Italic">Brassica juncea</Emphasis>: implications for breeding of a major oilseed crop of dryland areas

Quantitative trait loci (QTL) analysis of yield influencing traits was carried out in Brassica juncea (AABB) using a doubled haploid (DH) mapping population of 123 lines derived from a cross between Varuna (a line representing the Indian gene pool) and Heera (representing the east European gene pool) to identify potentially useful alleles from both the parents. The existing AFLP based map of B. juncea was further saturated with RFLP and SSR markers which led to the identification of the linkage groups belonging to the A (B. rapa) and B (B. nigra) genome components of B. juncea. For QTL dissection, the DH lines were evaluated at three different environments and phenotyped for 12 quantitative traits. A total of 65 QTL spread over 13 linkage groups (LG) were identified from the three environments. QTL analysis showed that the A genome has contributed more than the B genome to productivity (68% of the total QTL detected) suggesting a more prominent role of the A genome towards domestication of this crop. The east European line, Heera, carried favorable alleles for 42% of the detected QTL and the remaining 58% were in the Indian gene pool line, Varuna. We observed clustering of major QTL in a few linkage groups, particularly in J7 and J10 of the A genome, with QTL of different traits having agronomically antagonistic allelic effects co-mapping to the same genetic interval. QTL analysis also identified some well-separated QTL which could be readily transferred between the two pools. Based on the QTL analysis, we propose that improvement in yield could be achieved more readily by heterosis breeding rather than by pure line breeding. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Multi-trait and multi-environment QTL analysis reveals the impact of seed colour on seed composition traits in <Emphasis Type="Italic">Brassica napus</Emphasis>

Brassica napus seed composition traits (fibre, protein, oil and fatty acid profiles), seed colour and yield-associated traits are regulated by a complex network of genetic factors. Although previous studies have attempted to dissect the underlying genetic basis for these traits, a more complete picture of the available quantitative trait loci (QTL) variation and any interaction between the different traits is required. In this study, QTL mapping for eleven seed composition traits, seed colour and a yield-related trait (TSW) was conducted in a spring-type canola-quality B. napus doubled haploid (DH) population from a cross between black-seeded (DH12075) and yellow-seeded (YN01-429) lines across five environments. A major QTL associated with fibre traits (acid detergent fibre, acid detergent lignin and neutral detergent fibre) and seed colour (whiteness index) was mapped on chromosome N9 across the five environments. Multi-trait analysis identified QTL which had pleiotropic effect for seed colour and other composition traits. Multi-environment analysis revealed genetic (QTL) × environment effects on most QTL. These findings provide a more detailed insight into the complex QTL networks controlling seed composition and yield-associated traits in canola-quality B. napus.     

Mapping QTLs with digenic epistasis under multiple environments and predicting heterosis based on QTL effects

Mixed linear model approach was proposed for mapping QTLs with the digenic epistasis and QTL by environment (QE) interaction as well as additive and dominant effects. Monte Carlo simulations indicated that the proposed method could provide unbiased estimations for both positions and genetic main effects of QTLs, as well as unbiased predictions for QE interaction effects. A method was suggested for predicting heterosis based on individual QTL effects. The immortalized F₂ (IF₂) population constructed by random mating among RI or DH lines is appropriate for mapping QTLs with epistasis and their QE interaction. Based on the models and methodology proposed, we developed a QTL mapping software, QTLMapper 2.0 on the basis of QTLmapper 1.0, which is suitable for analyzing populations of DH, RIL, F₂ and IF₂. Data of thousand grain weight of IF₂ population with 240 lines derived from elite hybrid rice Shanyou 63 were analyzed as a worked example.     

Comparative QTL analysis of salinity tolerance in terms of fruit yield using two solanum populations of F<Subscript>7</Subscript> lines

Salt tolerance has been analysed in two populations of F₇ lines developed from a salt sensitive genotype of Solanum lycopersicum var. cerasiforme, as female parent, and two salt tolerant lines, as male parents, from S. pimpinellifolium, the P population (142 lines), and S. cheesmaniae, the C population (116 lines). Salinity effects on 19 quantitative traits including fruit yield were investigated by correlation, principal component analysis, ANOVA and QTL analysis. A total of 153 and 124 markers were genotyped in the P and C populations, respectively. Some flowering time and salt tolerance candidate genes were included. Since most traits deviated from a normal distribution, results based on the Kruskal–Wallis non-parametric test were preferred. Interval mapping methodology and ANOVA were also used for QTL detection. Eight out of 15 QTLs at each population were detected for the target traits under both control and high salinity conditions, and among them, only average fruit weight (FW) and fruit number (FN) QTLs (fw1.1, fw2.1 and fn1.2) were detected in both populations. The individual contribution of QTLs were, in general, low. After leaf chloride concentration, flowering time is the trait most affected by salinity because different QTLs are detected and some of their QTL×E interactions have been found significant. Also reinforcing the interest on information provided by QTL analysis, it has been found that non-correlated traits may present QTL(s) that are associated with the same marker. A few salinity specific QTLs for fruit yield, not associated with detrimental effects, might be used to increase tomato salt tolerance. The beneficial allele at two of them, fw8.1 (in C) and tw8.1 (for total fruit weight in P) corresponds to the salt sensitive parent, suggesting that the effect of the genetic background is crucial to breed for wide adaptation using wild germplasm.     

Identification of a major QTL for silique length and seed weight in oilseed rape (Brassica napus L.)

Silique length (SL) and seed weight (SW) are two important yield-related traits controlled by quantitative trait loci (QTL) in oilseed rape (Brassica napus L.). The genetic bases underlying these two traits are largely unknown at present. In this study, we conducted QTL analyses for SL and SW using 186 recombinant inbred lines (RILs) derived from a cross between S1, an EMS mutant with extremely long siliques and large seeds, and S2, an inbred line with regular silique length and seed size. RILs were grown in Wuhan in the 2008/09 (SS09) and 2009/10 (SS10) growing seasons, and mean SL and SW for each line were investigated. Ten non-redundant QTL were identified for SL. Of these, a major QTL, cqSLA9, consistently explained as much as 53.4% of SL variation across environments. The others are minor QTL and individually explained less than 10% of the SL variation. Nine non-redundant QTL were identified for SW. Of which, one major QTL, cqSWA9, explained as much as 28.2% of the total SW variation in the SS09 and SS10 environments. In addition, three additive by additive interactions with small effects were detected for SL, and no interactions were detected for SW. Interestingly, the two major QTL, cqSLA9 for SL and cqSWA9 for SW colocalized in the same chromosomal region and were integrated into a unique QTL, uqA9. The S1 allele at this locus increases both SL and SW, suggesting that uqA9 has pleiotropic effects on both SL and SW. The existence and effect of uqA9 was confirmed in genetically different RILs derived from the cross between S1 and No2127, a resynthesized DH line having regular silique length and seed size. Individuals in one residual heterozygous line for cqSLA9 showed significant difference in silique length. The results in this study revealed that silique length in the S1 mutant is mainly controlled by the cqSLA9 locus, which will be suitable for fine mapping and marker-assisted selection in rapeseed breeding for high yield.     

Identification of a Conserved Calmodulin-Binding Motif &;#x220A; the Sequence of F<Subscript>0</Subscript>F<Subscript>1</Subscript>ATPsynthase Inhibitor Protein

The natural inhibitor proteins IF₁ regulate mitochondrial F₀F₁ATPsynthase in a wide range of species. We characterized the interaction of CaM with purified bovine IF₁, two bovine IF₁ synthetic peptides, as well as two homologous proteins from yeast, namely IF₁ and STF₁. Fluorometric analyses showed that bovine and yeast inhibitors bind CaM with a 1:1 stoichiometry in the pH range between 5 and 8 and that CaM-IF₁ interaction is Ca²⁺-dependent. Bovine and yeast IF₁ have intermediate binding affinity for CaM, while the K_d (dissociation constant) of the STF₁-CaM interaction is slightly higher. Binding studies of CaM with bovine IF₁ synthetic peptides allowed us to identify bovine IF₁ sequence 33–42 as the putative CaM-binding region. Sequence alignment revealed that this region contains a hydrophobic motif for CaM binding, highly conserved in both yeast IF₁ and STF₁ sequences. In addition, the same region in bovine IF₁ has an IQ motif for CaM binding, conserved as an IQ-like motif in yeast IF₁ but not in STF₁. Based on the pH and Ca²⁺ dependence of IF₁ interaction with CaM, we suggest that the complex can be formed outside mitochondria, where CaM could regulate IF₁ trafficking or additional IF₁ roles not yet clarified.     

Population-based resequencing analysis of improved wheat germplasm at wheat leaf rust resistance locus Lr21

Little is known about the genetic control of heterosis in the complex polyploid crop species oilseed rape (Brassica napus L.). In this study, two large doubled-haploid (DH) mapping populations and two corresponding sets of backcrossed test hybrids (THs) were analysed in controlled greenhouse experiments and extensive field trials for seedling biomass and yield performance traits, respectively. Genetic maps from the two populations, aligned with the help of common simple sequence repeat markers, were used to localise and compare quantitative trait loci (QTL) related to the expression of heterosis for seedling developmental traits, plant height at flowering, thousand seed mass, seeds per silique, siliques per unit area and seed yield. QTL were mapped using data from the respective DH populations, their corresponding TH populations and from mid-parent heterosis (MPH) data, allowing additive and dominance effects along with digenic epistatic interactions to be estimated. A number of genome regions containing numerous heterosis-related QTL involved in different traits and at different developmental stages were identified at corresponding map positions in the two populations. The co-localisation of per se QTL from the DH population datasets with heterosis-related QTL from the MPH data could indicate regulatory loci that may also contribute to fixed heterosis in the highly duplicated B. napus genome. Given the key role of epistatic interactions in the expression of heterosis in oilseed rape, these QTL hotspots might harbour genes involved in regulation of heterosis (including fixed heterosis) for different traits throughout the plant life cycle, including a significant overall influence on heterosis for seed yield.     

Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F<Subscript>1</Subscript> hybrids of tomato

Key message

Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato.

Abstract

So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F₂ population derived from a cross between two commercial F₁ cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F₁ cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F₂ plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.

     

QTL for phytosterol and sinapate ester content in <Emphasis Type="Italic">Brassica napus</Emphasis> L. collocate with the two erucic acid genes

Improving oil and protein quality for food and feed purposes is an important goal in rapeseed (Brassica napus L.) breeding programs. Rapeseed contains phytosterols, used to enrich food products, and sinapate esters, which are limiting the utilization of rapeseed proteins in the feed industry. Increasing the phytosterol content of oil and lowering sinapate ester content of meal could increase the value of the oilseed rape crop. The objective of the present study was to identify quantitative trait loci (QTL) for phytosterol and sinapate ester content in a winter rapeseed population of 148 doubled haploid lines, previously found to have a large variation for these two traits. This population also segregated for the two erucic acid genes. A close negative correlation was found between erucic acid and phytosterol content (Spearman’s rank correlation, r _s = −0.80^**). For total phytosterol content, three QTL were detected, explaining 60% of the genetic variance. The two QTL with the strongest additive effects were mapped on linkage groups N8 and N13 within the confidence intervals of the two erucic acid genes. For sinapate ester content four QTL were detected, explaining 53% of the genetic variance. Again, a close negative correlation was found between erucic acid and sinapate ester content (r _s = −0.66^**) and the QTL with the strongest additive effects mapped on linkage groups N8 and N13 within the confidence intervals of the two erucic acid genes. The results suggests, that there is a pleiotropic effect of the two erucic acid genes on phytosterol and sinapate ester content; the effect of the alleles for low erucic acid content is to increase phytosterol and sinapate ester content. Possible reasons for this are discussed based on known biosynthetic pathways. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Conditional QTL mapping of oil content in rapeseed with respect to protein content and traits related to plant development and grain yield

Oil content in rapeseed (Brassica napus L.) is generally regarded as a character with high heritability that is negatively correlated with protein content and influenced by plant developmental and yield related traits. To evaluate possible genetic interrelationships between these traits and oil content, QTL for oil content were mapped using data on oil content and on oil content conditioned on the putatively interrelated traits. Phenotypic data were evaluated in a segregating doubled haploid population of 282 lines derived from the F₁ of a cross between the old German cultivar Sollux and the Chinese cultivar Gaoyou. The material was tested at four locations, two each in Germany and in China. QTLMapper version 1.0 was used for mapping unconditional and conditional QTL with additive (a) and locus pairs with additive × additive epistatic (aa) effects. Clear evidence was found for a strong genetic relationship between oil and protein content. Six QTL and nine epistatic locus pairs were found, which had pleiotropic effects on both traits. Nevertheless, two QTL were also identified, which control oil content independent from protein content and which could be used in practical breeding programs to increase oil content without affecting seed protein content. In addition, six additional QTL with small effects were only identified in the conditional mapping. Some evidence was apparent for a genetic interrelationship between oil content and the number of seeds per silique but no evidence was found for a genetic relationship between oil content and flowering time, grain filling period or single seed weight. The results indicate that for closely correlated traits conditional QTL mapping can be used to dissect the genetic interrelationship between two traits at the level of individual QTL. Furthermore, conditional QTL mapping can reveal additional QTL with small effects that are undetectable in unconditional mapping.     

QTL detection for stover yield and quality traits using two connected populations in high-oil maize

Both yield and quality traits for stover portion were important for forage and biofuel production utility in maize. A high-oil maize inbred GY220 was crossed with two normal-oil dent maize inbred lines 8984 and 8622 to generate two connected F_2:3 populations with 284 and 265 F_2:3 families. Seven yield and quality traits were evaluated under two environments. The variance components of genotype (σ_g²), environment (σ_e²) and genotype × environment interactions (σ_ge²) were all significant for most traits in both populations. Different levels of correlations were observed for all traits. QTL mapping was conducted using composite interval mapping (CIM) for data under each environment and in combined analysis in both populations. Totally, 45 and 42 QTL were detected in the two populations. Only five common QTL across the two populations, and one and three common QTL across the two environments in the two populations were detected, reflecting substantial influence of genetic backgrounds and environments on the results of QTL detection for stover traits. Combined analysis across two environments failed to detect most QTL mapped using individual environmental data in both populations. Few of the detected QTL displayed digenic epistatic interactions. Common QTL among all traits were consistent with their correlations. Some QTL herein have been detected in previous researches, and linked with candidate genes for enzymes postulated to have direct and indirect roles in cell wall components biosynthesis.     

Identification of plant architecture and yield-related QTL in <Emphasis Type="Italic">Vicia faba</Emphasis> L.

Low and unstable yields across seasons and environments are among the main reasons which make profitability for farmers too low. Along with resistance/tolerance to biotic and abiotic stresses, plant architecture and yield-related traits are the main determinants of yield stability. The current study was conducted to identify and validate quantitative trait loci (QTL) for plant architecture and yield-related traits in faba bean; our results provide novel information about the genetics of plant architecture traits in this crop. An equina × paucijuga recombinant inbred line population was derived and submitted to field experiments at Córdoba (Spain) over a period of four seasons. Stable QTL were identified for eight of the traits evaluated. QTL clusters were identified on almost each chromosome. The high inter-trait correlations between some of the traits controlled by a cluster of QTL might reflect either a set of closely linked loci or, more likely, pleiotropic effects. The stability of many of these major QTL in different years offers the possibility of exploiting them via marker-assisted selection. Further fine mapping of these target regions will help to identify potential candidate genes using synteny.     

Identification of trait-improving quantitative trait loci for grain yield components from a dent corn inbred line in an advanced backcross BC<Subscript>2</Subscript>F<Subscript>2</Subscript> population and comparison with its F<Subscript>2:3</Subscript> population in popcorn

Normal maize germplasm could be used to improve the grain yield of popcorn inbreds. Our first objective was to locate genetic factors associated with trait variation and make first assessment on the efficiency of advanced backcross quantitative trait locus (AB-QTL) analysis for the identification and transfer of favorable QTL alleles for grain yield components from the dent corn inbred. A second objective was to compare the detection of QTL in the BC₂F₂ population with results using F_2:3 lines of the same parents. Two hundred and twenty selected BC₂F₂ families developed from a cross between Dan232 and an elite popcorn inbred N04 were evaluated for six grain yield components under two environments, and genotyped by means of 170 SSR markers. Using composite interval mapping (CIM), a total of 19 significant QTL were detected. Eighteen QTL had favorable alleles contributed by the dent corn parent Dan232. Sixteen of these favorable QTL alleles were not in the same or near marker intervals with QTL for popping characteristics. Six QTL were also detected in the F_2:3 population. Improved N04 could be developed from 210 and 208 families with higher grain weight per plant and/or 100-grain weight, respectively, and 35 families with the same or higher popping expansion volume than N04. In addition, near isogenic lines containing detected QTL (QTL-NILs) for grain weight per plant and/or 100-grain weight could be obtained from 12 families. Our study demonstrated that the AB-QTL method can be applied to identify and manipulate favorable QTL alleles from normal corn inbreds and combine QTL detection and popcorn breeding efficiently.     

Molecular detection of QTLs for agronomic and quality traits in a doubled haploid population derived from two Canadian wheats (Triticum aestivum L.)

Development of high-yielding wheat varieties with good end-use quality has always been a major concern for wheat breeders. To genetically dissect quantitative trait loci (QTLs) for yield-related traits such as grain yield, plant height, maturity, lodging, test weight and thousand-grain weight, and for quality traits such as grain and flour protein content, gluten strength as evaluated by mixograph and SDS sedimentation volume, an F₁-derived doubled haploid (DH) population of 185 individuals was developed from a cross between a Canadian wheat variety “AC Karma” and a breeding line 87E03-S2B1. A genetic map was constructed based on 167 marker loci, consisting of 160 microsatellite loci, three HMW glutenin subunit loci: Glu-A1, Glu-B1 and Glu-D1, and four STS-PCR markers. Data for investigated traits were collected from three to four environments in Manitoba, Canada. QTL analyses were performed using composite interval mapping. A total of 50 QTLs were detected, 24 for agronomic traits and 26 for quality-related traits. Many QTLs for correlated traits were mapped in the same genomic regions forming QTL clusters. The largest QTL clusters, consisting of up to nine QTLs, were found on chromosomes 1D and 4D. HMW glutenin subunits at Glu-1 loci had the largest effect on breadmaking quality; however, other genomic regions also contributed genetically to breadmaking quality. QTLs detected in the present study are compared with other QTL analyses in wheat.     

QTL analysis reveals context-dependent loci for seed glucosinolate trait in the oilseed <Emphasis Type="Italic">Brassica juncea</Emphasis>: importance of recurrent selection backcross scheme for the identification of ‘true’ QTL

Seed glucosinolate content in Brassica juncea is a complex quantitative trait. A recurrent selection backcross (RSB) method with a doubled haploid (DH) generation interspersing backcross generations was used for the introgression of low glucosinolate alleles from an east European gene pool B. juncea line, Heera into an Indian gene pool variety, Varuna. Phenotypic comparisons among the DH populations derived from early to advanced backcrosses revealed a shift in the mean values for various glucosinolates with the advancement of backcrossing, indicating a change in the selective values of the alleles with change in the genetic background due to the existence of epistasis and context dependencies. QTL mapping for various seed glucosinolates from early (F₁DH) and advanced generation (BC₄DH) populations confirmed the presence of epistasis and context dependency. The common QTL detected in both F₁DH and BC₄DH changed their R ² values from the former to the later generation. Some of the QTL detected in the F₁DH became irrelevant in the BC₄DH population. Further, new QTL were detected in the BC₄DH population for various glucosinolates. A validation study on a population of low glucosinolate DH lines derived from all the backcross generations of the RSB breeding programme revealed that the QTL detected in BC₄DH were the ‘true’ QTL. Using glucosinolate as an example, the study provides strong evidence for the importance of the RSB method for the identification of the ‘true’ QTL which would be significant for marker assisted introgression of a complex quantitative trait whose expression is influenced by epistatic interactions. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Authors N. Ramchiary, N. C. Bisht, V. Gupta, A. Mukhopadhyay and N. Arumugam have contributed equally to this work.     

甘蓝型油菜遗传图谱的构建及单株产量构成因素的QTL分析

采用常规品系04-1139与高产多角果品系05-1054构建的F2代群体为作图群体, 运用SSR(Simple sequence repeat)和SRAP(Sequence-related amplified polymorphism)构建分子标记遗传图谱并对甘蓝型油菜单株产量构成因素进行QTL分析。遗传图谱包含200个分子标记, 分布于19个连锁群上, 总长度1 700.23 cM, 标记间的平均距离8.50 cM。采用复合区间作图法(Composite interval mapping, CIM)对单株产量构成因素(单株有效角果数、每果粒数和千粒重)进行QTL分析, 共检测到12个QTL: 其中单株有效角果数4个QTL, 分别解释表型变异为35.64%、12.96%、28.71%和34.02%; 每果粒数获得5个QTL, 分别解释表型变异为8.41%、7.87%、24.37%、8.57%和14.31%; 千粒重获得３个QTL, 分别解释表型变异为2.33%、1.81%和1.86%。结果表明: 同一性状的等位基因增效作用可以同时来自高值亲本和低值亲本; 文章中与主效QTL连锁的标记可用于油菜产量性状的分子标记辅助选择和聚合育种。     

Association mapping of<Emphasis Type="Italic"> Stagonospora nodorum</Emphasis> blotch resistance in modern European winter wheat varieties

Association mapping in populations relevant for wheat breeding has a large potential for validating and fine-mapping QTLs identified in F2- or DH (double haploid)-derived populations. In this study, associations between markers in the region of QSng.sfr-3BS, a major QTL for resistance to Stagonospora nodorum glume blotch (SNG), and SNG resistance were investigated by linkage and association analyses. After increasing marker density in 240 F_5:7 recombinant inbred lines (RILs), QSng.sfr-3BS explained 43% of the genetic variance and peaked 0.6 cM proximal from the marker SUN2-3B. Association between SNG resistance and markers mapped in the region of QSng.sfr-3BS was investigated in a population of 44 modern European winter wheat varieties. Two genetically distinct subpopulations were identified within these lines. In agreement with linkage analyses, association mapping by a least squares general linear model (GLM) at marker loci in the region of QSng.sfr-3BS revealed the highest association with SNG resistance for SUN2-3B (p < 0.05). Association mapping can provide an effective mean of relating genotypes to complex quantitative phenotypes in hexaploid wheat. Linkage disequilibrium (r ²) in chromosome 3B extended less than 0.5 cM in 44 varieties, while it extended about 30 cM in 240 RILs, based on 91 SSR and STS marker-pair comparisons. This indicated that the association mapping population had a marker resolution potential at least 390-fold higher compared to the RIL population. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

QTL mapping of anthracnose (<Emphasis Type="Italic">Colletotrichum</Emphasis> spp.) resistance in a cross between <Emphasis Type="Italic">Capsicum annuum</Emphasis> and <Emphasis Type="Italic">C. chinense</Emphasis>

Anthracnose fruit rot is an economically important disease that affects pepper production in Indonesia. Strong resistance to two causal pathogens, Colletotrichum gloeosporioides and C. capsici, was found in an accession of Capsicum chinense. The inheritance of this resistance was studied in an F₂ population derived from a cross of this accession with an Indonesian hot pepper variety (Capsicum annuum) using a quantitative trait locus (QTL) mapping approach. In laboratory tests where ripe fruits were artificially inoculated with either C. gloeosporioides or C. capsici, three resistance-related traits were scored: the infection frequency, the true lesion diameter (averaged over all lesions that actually developed), and the overall lesion diameter (averaged over all inoculation points, including those that did not develop lesions). One main QTL was identified with highly significant and large effects on all three traits after inoculation with C. gloeosporioides and on true lesion diameter after inoculation with C. capsici. Three other QTL with smaller effects were found for overall lesion diameter and true lesion diameter after inoculation with C. gloeosporioides, two of which also had an effect on infection frequency. Interestingly, the resistant parent carried a susceptible allele for a QTL for all three traits that was closely linked to the main QTL. The results with C. capsici were based on less observations and therefore less informative. Although the main QTL was shown to have an effect on true lesion diameter after inoculation with C. capsici, no significant QTL were identified for overall lesion diameter or infection frequency.