Detection and verification of malting quality QTLs using wild barley introgression lines

A malting quality quantitative trait locus (QTL) study was conducted using a set of 39 wild barley introgression lines (hereafter abbreviated with S42ILs). Each S42IL harbors a single marker-defined chromosomal segment from the wild barley accession ‘ISR 42-8’ (Hordeum vulgare ssp. spontaneum) within the genetic background of the elite spring barley cultivar ‘Scarlett’ (Hordeum vulgare ssp. vulgare). The aim of the study was (1) to verify genetic effects previously identified in the advanced backcross population S42, (2) to detect new QTLs, and (3) to identify S42ILs exhibiting multiple QTL effects. For this, grain samples from field tests in three different environments were subjected to micro malting. Subsequently, a line × phenotype association study was performed with the S42ILs in order to localize putative QTL effects. A QTL was accepted if the trait value of a particular S42IL was significantly (P < 0.05) different from the recurrent parent as a control, either across all tested environments or in a particular environment. For eight malting quality traits, altogether 40 QTLs were localized, among which 35 QTLs (87.5%) were stable across all environments. Six QTLs (15.0%) revealed a trait improving wild barley effect. Out of 36 QTLs detected in a previous advanced backcross QTL study with the parent BC₂DH population S42, 18 QTLs (50.0%) could be verified with the S42IL set. For the quality parameters α-amylase activity and Hartong 45°C, all QTLs assessed in population S42 were verified by S42ILs. In addition, eight new QTL effects and 17 QTLs affecting two newly investigated traits were localized. Two QTL clusters harboring simultaneous effects on eight and six traits, respectively, were mapped to chromosomes 1H and 4H. In future, fine-mapping of these QTL regions will be conducted in order to shed further light on the genetic basis of the most interesting QTLs.     

Identification and verification of QTLs for agronomic traits using wild barley introgression lines

A set of 39 wild barley introgression lines (hereafter abbreviated with S42ILs) was subjected to a QTL study to verify genetic effects for agronomic traits, previously detected in the BC₂DH population S42 (von Korff et al. 2006 in Theor Appl Genet 112:1221–1231) and, in addition, to identify new QTLs and favorable wild barley alleles. Each line within the S42IL set contains a single marker-defined chromosomal introgression from wild barley (Hordeum vulgare ssp. spontaneum), whereas the remaining part of the genome is exclusively derived from elite spring barley (H. vulgare ssp. vulgare). Agronomic field data of the S42ILs were collected for seven traits from three different environments during the 2007 growing season. For detection of putative QTLs, a two-factorial mixed model ANOVA and, subsequently, a Dunnett test with the recurrent parent as a control were conducted. The presence of a QTL effect on a wild barley introgression was accepted, if the trait value of a particular S42IL was significantly (P < 0.05) different from the control, either across all environments and/or in a particular environment. A total of 47 QTLs were localized in the S42IL set, among which 39 QTLs were significant across all tested environments. For 19 QTLs (40.4%), the wild barley introgression was associated with a favorable effect on trait performance. Von Korff et al. (2006 in Theor Appl Genet 112:1221–1231) mapped altogether 44 QTLs for six agronomic traits to genomic regions, which are represented by wild barley introgressions of the S42IL set. Here, 18 QTLs (40.9%) revealed a favorable wild barley effect on the trait performance. By means of the S42ILs, 20 out of the 44 QTLs (45.5%) and ten out of the 18 favorable effects (55.6%) were verified. Most QTL effects were confirmed for the traits days until heading and plant height. For the six corresponding traits, a total of 17 new QTLs were identified, where at six QTLs (35.3%) the exotic introgression caused an improved trait performance. In addition, eight QTLs for the newly studied trait grains per ear were detected. Here, no QTL from wild barley exhibited a favorable effect. The introgression line S42IL-107, which carries an introgression on chromosome 2H, 17–42 cM is an example for S42ILs carrying several QTL effects simultaneously. This line exhibited improved performance across all tested environments for the traits days until heading, plant height and thousand grain weight. The line can be directly used to transfer valuable Hsp alleles into modern elite cultivars, and, thus, for breeding of improved varieties.     

Genomic regions determining resistance to leaf stripe (Pyrenophora graminea) in barley.

Leaf stripe is a seed-borne disease of barley (Hordeum vulgare) caused by Pyrenophora graminea. Little is known about the genetics of resistance to this pathogen. In the present work, QTL analysis was applied on two recombinant inbred line (RIL) populations derived from two- and six-rowed barley genotypes with different levels of partial resistance to barley leaf stripe. Quantitative trait loci for partial resistance were identified using the composite interval mapping (CIM) method of PLABQTL software, using the putative QTL markers as cofactors. In the L94 x 'Vada' mapping population, one QTL for resistance was detected on chromosome 2H; the same location as the leaf-stripe resistance gene Rdg1 mapped earlier in 'Alf', where it confers complete resistance to the pathogen. An additional minor-effect QTL was identified by further analyses in this segregating population on chromosome 7H. In L94 x C123, two QTLs for resistance were mapped, one each on chromosomes 7H and 2H.     

Genetic architecture of quantitative trait loci associated with morphological and agronomic trait differences in a wild by cultivated barley cross.

Hordeum vulgare subsp. spontaneum is the progenitor of cultivated barley (Hordeum vulgare L.). Domestication combined with plant breeding has led to the morphological and agronomic characteristics of modern barley cultivars. The objective of this study was to map the genetic factors that morphologically and agronomically differentiate wild barley from modern barley cultivars. To address this objective, we identified quantitative trait loci (QTLs) associated with plant height, flag leaf width, spike length, spike width, glume length in relation to seed length, awn length, fragility of ear rachis, endosperm width and groove depth, heading date, flag leaf length, number of tillers per plant, and kernel color in a Harrington/OUH602 advanced backcross (BC2F8) population. This population was genotyped with 113 simple sequence repeat markers. Thirty QTLs were identified, of which 16 were newly identified in this study. One to 4 QTLs were identified for each of the traits except glume length, for which no QTL was detected. The portion of phenotypic variation accounted for by individual QTLs ranged from about 9% to 54%. For traits with more than one QTL, the phenotypic variation explained ranged from 25% to 71%. Taken together, our results reveal the genetic architecture of morphological and agronomic traits that differentiate wild from cultivated barley.     

Identification of proteins associated with malting quality in a subset of wild barley introgression lines

Malted barley is an important ingredient used in the brewing and distilling industry worldwide. In this study, we used a proteomics approach to investigate the biochemical function of previously identified quantitative trait loci (QTLs) on barley chromosomes 1H and 4H that influence malting quality. Using a subset of barley introgression lines containing wild barley (Hordeum vulgare ssp. spontaneum) alleles at these QTLs, we validated that wild barley alleles at the chromosome 1H QTL reduced overall malting quality, whereas wild barley alleles at the chromosome 4H QTL improved the malting quality parameters α-amylase activity, VZ45, and Kolbach index compared to the control genotype Scarlett. 2DE was used to detect changes in protein expression during the first 72 h of micromalting associated with these QTLs. In total, 16 protein spots showed a significant change in expression between the introgression lines and Scarlett, of which 14 were successfully identified with MS. Notably, the wild barley alleles in the line containing the chromosome 4H QTL showed a sixfold increased expression of a limit dextrinase inhibitor. The possible role of the identified proteins in malting quality is discussed. The knowledge gained will assist ongoing research toward cloning the genes underlying these important QTL.     

Effectiveness of selective genotyping for detection of quantitative trait loci: an analysis of grain and malt quality traits in three barley populations.

Marker genotype data and grain and malt quality phenotype data from three barley (Hordeum vulgare L.) mapping populations were used to investigate the feasibility of selective genotyping for detection of quantitative trait loci (QTLs). With selective genotyping, only individuals with high and low phenotypic values for the trait of interest are genotyped. Here, genotyping of 10 to 70% of each population (i.e., 5 to 35% in each tail of the phenotypic distribution) was considered. Genomic positions detected by selective genotyping were compared to QTL position estimates from interval mapping analysis using marker genotype data from the entire population. Selective genotyping reliably detected almost all of the mapped QTLs, often with only 10% of the population genotyped. Selective genotyping also detected spurious QTLs in regions of the genome where no significant QTL had been mapped. Even with additional genotyping to verify putative QTLs, the total genotyping effort for detection of QTLs for a single trait by selective genotyping was usually less than 30% of that required for conventional interval mapping. Simultaneous investigation of two or more traits by selective genotyping would require additional genotyping effort, but could still be worthwhile.     

标记基因型中QTL基因型条件概率分布

随着分子数量遗传学的发展,人们提出了很多统计模型用于QTL定位分析。在这些模型中,首先得确定QTL在标记基因型中的条件概率分布,然后利用适当的统计方法对QTL在基因组中所处的位置进行估计。本文讨论了常见作图群体（如F2和回交群体）中在给定标记基因型下QTL的条件概率分布,提出了用Mathematics软件推导QTL基因型条件概率分布的方法。用该方法能够快速地、准确地推导出比较复杂的标记基因型中QTL基因型的条件概率分布。     

Advanced backcross QTL analysis for the identification of quantitative trait loci alleles from wild relatives of wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Advanced backcross QTL (AB-QTL) analysis was used to identify quantitative trait loci (QTLs) for yield and yield components in a BC(2)F(2) population derived from a cross between the German winter wheat variety 'Prinz' and the synthetic wheat line W-7984 developed by CIMMYT. Two hundred and ten microsatellite markers were employed to genotype 72 pre-selected BC(2)F(2) plants and phenotypic data were collected for five agronomic traits from corresponding BC(2)F(3) families that were grown at four locations in Germany. Using single-marker regression and interval mapping, a total of 40 putative QTLs derived from W-7984 were detected, of which 11 were for yield, 16 for yield components, eight for ear emergence time and five for plant height. For 24 (60.0%) of them, alleles from the synthetic wheat W-7984 were associated with a positive effect on agronomic traits, despite the fact that synthetic wheat was overall inferior with respect to agronomic appearance and performance. The present study indicated that favorable QTL alleles could be transferred from wild relatives of wheat into an elite wheat variety for improvement of quantitative trait loci like yield by the advanced backcross QTL strategy and molecular breeding. To our knowledge, the results presented here were the first report on AB-QTL analysis in wheat.     

Experimental designs and statistical methods for mapping quantitative trait loci underlying triploid endosperm traits without maternal genetic variation

Many endosperm traits are related to grain quality in cereal crops. Endosperm traits are mainly controlled by the endosperm genome but may be affected by the maternal genome. Studies have shown that maternal genotypic variation could greatly influence the estimation of the direct effects of quantitative trait loci (QTLs) underlying endosperm traits. In this paper, we propose methods of interval mapping of endosperm QTLs using seeds of F2 or BC1 (an equal mixture of F1 x P1 and F1 x P2 with F1 as the female parent) derived from a cross between 2 pure lines (P1 x P2). The most significant advantage of our experimental designs is that the maternal effects do not contribute to the genetic variation of endosperm traits and therefore the direct effects of endosperm QTLs can be estimated without the influence of maternal effects. In addition, the experimental designs can greatly reduce environmental variation because a few F1 plants grown in a small block of field will produce sufficient F2 or BC1 seeds for endosperm QTL analysis. Simulation studies show that the methods can efficiently detect endosperm QTLs and unbiasedly estimate their positions and effects. The BC1 design is better than the F2 design.     

江西东乡野生稻苗期抗旱基因定位

普通野生稻是栽培稻的祖先种,其遗传多样性远远大于栽培稻,蕴涵着栽培品种中难以找到的重要性状.以江西东乡普通野生稻为供体、以桂朝2号为遗传背景的野生稻基因渗入系（BC4F5、BC4F6）为材料,利用30%的PEG人工模拟干旱环境,对渗入系二叶一心苗期进行抗旱鉴定,共定位了12个与抗旱有关的QTL,其中在第2、6和12染色体上发现了4个QTL的加性效应值为正,来自东乡野生稻的等位基因能使渗入系的抗旱性增强,特别是位于第12染色体RM17附近的qSDT12-2在多次重复中均被检测到,在PEG处理后1-8 d能稳定表达.通过对抗旱性QTL的动态分析,发现不同QTL表达时间不同.     

Mapping of yield-related QTLs in pepper in an interspecific cross of <Emphasis Type="Italic">Capsicum annuum</Emphasis> and <Emphasis Type="Italic">C. frutescens</Emphasis>

An advanced backcross QTL study was performed in pepper using a cross between the cultivated species Capsicum annuum cv. Maor and the wild C. frutescens BG 2816 accession. A genetic map from this cross was constructed, based on 248 BC(2) plants and 92 restriction fragment length polymorphism (RFLP) markers distributed throughout the genome. Ten yield-related traits were analyzed in the BC(2) and BC(2)S(1) generations, and a total of 58 quantitative trait loci (QTLs) were detected; the number of QTLs per trait ranged from two to ten. Most of the QTLs were found in 11 clusters, in which similar QTL positions were identified for multiple traits. Unlike the high percentage of favorable QTL alleles discovered in wild species of tomato and rice, only a few such QTL alleles were detected in BG 2816. For six QTLs (10%), alleles with effects opposite to those expected from the phenotype were detected in the wild species. The use of common RFLP markers in the pepper and tomato maps enabled possible orthologous QTLs in the two species to be determined. The degree of putative QTL orthology for the two main fruit morphology traits-weight and shape-varied considerably. While all eight QTLs identified for fruit weight in this study could be orthologous to tomato fruit weight QTLs, only one out of six fruit shape QTLs found in this study could be orthologous to tomato fruit shape QTLs.     

Comparative AB-QTL analysis in barley using a single exotic donor of Hordeum vulgare ssp. spontaneum.

This paper reports on the first comparative advanced backcross quantitative trait locus (AB-QTL) study in barley. The BC₂F₂ population H×101 was generated from crossing var. Harry [H; Hordeum vulgare ssp. vulgare (Hv)] with ISR101-23 [101; H. v. ssp. spontaneum (Hsp)]. The results of the AB-QTL analysis for 13 quantitative traits are presented and, subsequently, compared with the AB-QTL study of the barley cross Apex × ISR101-23 (A×101; Pillen et al., Theor Appl Genet 107:340–352). Both AB populations share the exotic Hsp donor accession ISR101-23. In H×101, 108 putative QTLs (17%) were identified among the 650 marker×trait combinations tested. Altogether 52 (48 %) favorable effects were identified from the exotic parent. At these marker loci, the homozygous Hsp genotype was associated with an improvement in the trait compared to the homozygous Hv genotype. The percentage of QTLs detected in H×101 was comparable to that in A×101 (17% vs. 15%), however more favorable exotic QTL alleles were located in H×101 than in A×101 (48% vs. 34%). In H×101, the Hsp QTL allele at EBmac0679_[4H] was associated with a yield increase of 5.9% averaged across the six environments tested. A comparison of putative QTLs between H×101 and A×101 was based on 26 shared SSR markers. In total, 26% of the putative QTLs could be detected simultaneously in both AB populations. This finding indicates that only a portion of the QTL effects of the donor allele can be transferred from one elite recipient to the next.Communicated by G. WenzelThis work is dedicated to the 65th birthday of Prof. Dr. H.H. Geiger, Department of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Germany.     

Analysis of QTLs for yield components, agronomic traits, and disease resistance in an advanced backcross population of spring barley.

Hordeum vulgare subsp. spontaneum, the wild progenitor of barley, is a potential source of useful genetic variation for barley breeding programs. The objective of this study was to map quantitative trait loci (QTLs) in an advanced backcross population of barley. A total of 207 BC3 lines were developed using the 2-rowed German spring cultivar Hordeum vulgare subsp. vulgare 'Brenda' as a recurrent parent and the H. vulgare subsp. spontaneum accession HS584 as a donor parent. The lines were genotyped by 108 simple-sequence repeat (SSR) markers and evaluated in field tests for the measurement of grain yield and its components, such as ear length, spikelet number per spike, grain number per spike, spike number, and 1000-grain mass, as well as heading date and plant height. A total of 100 QTLs were detected. Ten QTLs with increasing effects were found for ear length, spikelet number, and grain number per spike. Three QTLs contributed by HS584 were found to significantly decrease days to heading across all years at 2 locations. In addition, 2 QTLs from HS584 on chromosomes 2H and 3H were associated with resistance to leaf rust. Based on genotypic data obtained from this population, 55 introgression lines carrying 1 or 2 donor segments were selected to develop a set of doubled-haploid lines, which will be used to reconfirm and investigate the effects of 100 QTLs for future genetic studies.     

Inheritance of the number and thickness of cell layers in barley aleurone tissue (<Emphasis Type="Italic">Hordeum vulgare </Emphasis>L.): an approach using F2–F3 progeny

The aleurone tissue of cereal grains, nutritionally rich in minerals and vitamins, is an important target for the improvement of cereals. Inheritance of the thickness and the number of cell layers in barley aleurone was studied on the F2–F3 progeny of an Erhard Frederichen × Criolla Negra cross in which the parental lines have three or two aleurone layers, respectively. F3 grain was sampled from each F2 plant and 96.8% of the entire F3 grain population was classified as being either the 2- or 3-layer type. Using microsatellite, single nucleotide polymorphism (SNP) and morphological markers on 190 F2 plants, a linkage map was built. Three quantitative trait loci (QTLs) affecting aleurone traits were revealed on chromosome 5H (max. LOD = 5.83) and chromosome 7H (max. LOD = 4.45) by interval mapping, and on chromosome 2H by marker analysis with an unmapped marker. These QTLs were consistent with genetic sub-models involving either 2-cell type dominance for 7H and 2H, or putative partial dominance for 5H where 2-cell-layer dominance and additivity gave similar LODs. The number of aleurone cell layers and aleurone thickness were strongly correlated and QTL results for these traits were alike. An SNP marker of sal1, an orthologue of the maize multilayer aleurone gene was mapped to the 7HL chromosome arm. However, the 7H QTL did not co-locate with the barley sal1 SNP, suggesting that an additional gene is involved in determining aleurone traits. These new mapping data allow comparisons to be made with related studies.     

Localisation of genes for resistance against Blumeria graminis f.sp. hordei and Puccinia graminis in a cross between a barley cultivar and a wild barley (Hordeum vulgare ssp. spontaneum) line

The aims of this investigation have been to map new (quantitative) resistance genes against powdery mildew, caused by Blumeria graminis f.sp. hordei L., and leaf rust, caused by Puccinia hordei L., in a cross between the barley ( Hordeum vulgare ssp. vulgare) cultivar "Vada" and the wild barley ( Hordeum vulgare ssp. spontaneum) line "1B-87" originating from Israel. The population consisted of 121 recombinant inbred lines. Resistance against leaf rust and powdery mildew was tested on detached leaves. The leaf rust isolate "I-80" and the powdery mildew isolate "Va-4", respectively, were used for the infection in this experiment. Moreover, powdery mildew disease severity was observed in the field at two different epidemic stages. In addition to other DNA markers, the map included 13 RGA (resistance gene analog) loci. The structure of the data demanded a non-parametric QTL-analysis. For each of the four observations, two QTLs with very high significance were localised. QTLs for resistance against powdery mildew were detected on chromosome 1H, 2H, 3H, 4H and 7H. QTLs for resistance against leaf rust were localised on 2H and 6H. Only one QTL was common for two of the powdery mildew related traits. Three of the seven QTLs were localised at the positions of the RGA-loci. Three of the five powdery mildew related QTLs are sharing their chromosomal position with known qualitative resistance genes. All detected QTLs behaved additively. Possible sources of the distorted segregation observed, the differences between the results for the different powdery mildew related traits and the relation between qualitative and quantitative resistance are discussed.     

Mapping QTLs for root morphological traits inBrassica rapa L. based on AFLP and RAPD markers

Root growth and thickening plays a key role in the final productivity and even the quality of storage roots in root crops. This study was conducted to identify and map quantitative trait loci (QTLs) affecting root morphological traits in Brassica rapa by using molecular markers. An F2 population was developed from a cross between Chinese cabbage (Brassica rapa ssp. chinensis) and turnip (B. rapa ssp. rapifera), which differed greatly in root characters. A genetic map covering 1837.1 cM, with 192 marker loci and 11 linkage groups, was constructed by using this F2 population. The F3 families derived from F2 plants were grown in the field and evaluated for taproot traits (thickness, length, and weight). QTL analysis via simple interval mapping detected 18 QTLs for the 3 root traits, including 7 QTLs for taproot thickness, 5 QTLs for taproot length, and 6 QTLs for taproot weight. Individually, the QTLs accounted for 8.4-27.4% of the phenotypic variation. The 2 major QTLs, qTRT4b for taproot thickness and qTRW4 for taproot weight, explained 27.4% and 24.8% of the total phenotypic variance, respectively. The QTLs for root traits, firstly detected in Brassica crops, may provide a basis for marker-assisted selection to improve productivity in root-crop breeding.     

Molecular mapping of a gene responsible for Al-activated secretion of citrate in barley

Aluminium (Al) toxicity is an important limitation to barley (Hordeum vulgare L.) on acid soil. Al-resistant cultivars of barley detoxify Al externally by secreting citrate from the roots. To link the genetics and physiology of Al resistance in barley, genes controlling Al resistance and Al-activated secretion of citrate were mapped. An analysis of Al-induced root growth inhibition from 100 F2 seedlings derived from an Al-resistant cultivar (Murasakimochi) and an Al-sensitive cultivar (Morex) showed that a gene associated with Al resistance is localized on chromosome 4H, tightly linked to microsatellite marker Bmag353. Quantitative trait locus (QTL) analysis from 59 F4 seedlings derived from an F3 plant heterozygous at the region of Al resistance on chromosome 4H showed that a gene responsible for the Al-activated secretion of citrate was also tightly linked to microsatellite marker Bmag353. This QTL explained more than 50% of the phenotypic variation in citrate secretion in this population. These results indicate that the gene controlling Al resistance on barley chromosome 4H is identical to that for Al-activated secretion of citrate and that the secretion of citrate is one of the mechanisms of Al resistance in barley. The identification of the microsatellite marker associated with both Al resistance and citrate secretion provides a valuable tool for marker-assisted selection of Al-resistant lines.     

Identification of Hordeum spontaneum QTL alleles improving field performance of barley grown under rainfed conditions

Advanced backcross QTL (AB-QTL) analysis was deployed to identify allelic variation in wild barley (Hordeum vulgare ssp. spontaneum) of value in the improvement of grain yield and other agronomically important traits in barley (Hordeum vulgare ssp. vulgare) grown under conditions of water deficit in Mediterranean countries. A population of 123 double haploid (DH) lines obtained from BC₁F₂ plants derived from a cross between Barke (European two-row cultivar) and HOR11508 (wild barley accession) were tested in replicated field trials, under varying conditions of water availability in Italy, Morocco and Tunisia, for seven quantitative traits. Significant QTL effects at one (P 0.001) or more trial sites (P 0.01) were identified for all traits. At 42 (52%) of the 80 putative QTLs identified, the allele increasing a “traits' value” was contributed by H. spontaneum. For example, though the majority (67%) of QTL alleles increasing grain yield were contributed by H. vulgare, H. spontaneum contributed the alleles increasing grain yield at six regions on chromosomes 2H, 3H, 5H and 7H. Among them, two QTLs (associated to Bmac0093 on chromosome 2H and to Bmac0684 on chromosome 5H) were identified in all three locations and had the highest additive effects. The present study shows the validity of deploying AB-QTL analysis for identifying favourable QTL alleles from wild germplasm and indicates its potential as an enhancement strategy for the genetic improvement of cultivars better adapted to drought-prone environments.     

Advanced backcross QTL analysis of a Lycopersicon esculentum ×Lycopersicon parviflorum cross

Lycopersicon parviflorum is a sexually compatible, wild tomato species which has been largely unutilized in tomato breeding. The Advanced Backcross QTL (AB-QTL) strategy was used to explore this genome for QTLs affecting traits of agronomic importance in an interspecific cross between a tomato elite processing inbred, Lycopersicon esculentum E6203, and the wild species L. parviflorum (LA2133). A total of 170 BC2 plants were genotyped by means of 133 genetic markers (131 RFLPs; one PCR-based marker, I-2, and one morphological marker, u, uniform ripening). Approximately 170 BC3 families were grown in replicated field trials, in California, Spain and Israel, and were scored for 30 horticultural traits. Significant putative QTLs were identified for all traits, for a total of 199 QTLs, ranging from 1 to 19 QTLs detected for each trait. For 19 (70%) traits (excluding traits for which effects of either direction are not necessarily favourable or unfavourable) at least one QTL was identified for which the L. parviflorum allele was associated with an agronomically favourable effect, despite the overall inferior phenotype of the wild species. Received: 14 September 1999 / Accepted: 7 October 1999