QTL analysis of tolerance to a German strain of BYDV-PAV in barley (Hordeum vulgare L.)

One hundred and forty six barley doubled-haploid lines (DH lines) were tested for variation in grain yield, yield components, plant height, and heading date after artificial infection with a German isolate of barley yellow dwarf virus (BYDV-PAV-Braunschweig). Of these 146 lines 76 were derived from the cross of the barley yellow dwarf virus (BYDV) tolerant cultivar ’Post’ to cv ’Vixen’ (Ryd2) and 70 from the cross of Post to cv ’Nixe’. Phenotypic measurements were gathered on both non-infected plants and plants artificially inoculated with BYDV-PAV by viruliferous aphids in pot and field experiments for three years at two locations. For all traits a continuous variation was observed suggesting a quantitative mode of inheritance for tolerance against BYDV-PAV. Using skeleton maps constructed using SSRs, AFLPs and RAPDs, two QTLs for relative grain yield per plant after BYDV infection, explaining about 47% of the phenotypic variance, were identified in Post × Vixen at the telomeric region of chromosome 2HL and at a region containing the Ryd2 gene on chromosome 3HL. In Post × Nixe, a QTL was found in exactly the same chromosome 2HL marker interval. In this cross, additional QTL were mapped on chromosomes 7H and 4H and together these explained about 40% of the phenotypic variance. QTL for effects of BYDV infection on yield components, plant height, and heading date generally mapped to the same marker intervals, or in the vicinity of the QTL for relative grain yield, on chromosomes 2HL and 3HL, suggesting that these regions are of special importance for tolerance to the Braunschweig isolate of BYDV-PAV. Possible applications of marker-assisted selection for BYDV tolerance based on these results are discussed. Received: 1 December 2000 / Accepted: 9 March 2001     

An RFLP map of diploid Hordeum bulbosum L. and comparison with maps of barley (H. vulgare L.) and wheat (Triticum aestivum L.)

This paper describes the first extensive genetic map of Hordeum bulbosum, the closest wild relative of cultivated barley. H. bulbosum is valuable for haploid production in barley breeding, and because of desirable agronomic characteristics, it also has potential for trait introgression into barley. A H. bulbosum map will assist introgression and provide a basis for the identification of QTLs for crossability with barley and other potentially useful genes. The present study used a population of 111 individuals from a PB1×PB11 cross to develop a genetic linkage map of diploid H. bulbosum (2n=2x=14) based on barley, wheat and other ”anchor” cereal RFLP markers previously mapped in other species. Because of the cross-pollinating and highly polymorphic nature of H. bulbosum, up to four alleles showed segregation at any one locus, and five different segregation types were found. This enabled maps to be developed for the PB1 and PB11 parents, as well as a combined map. In total, 136 RFLP loci were mapped with a marker coverage of 621 cM. The markers were generally colinear with barley but H. bulbosum had less recombination in the centromeric regions and similar or more in the distal regions. Cytological studies on pollen mother cells at metaphase-I showed marked distal localization of chiasmata and a frequency consistent with the genetic map length. This study showed that H. bulbosum was highly polymorphic, making it suitable for trait analysis and supplementing maps of barley. Received: 20 November 2000 / Accepted: 5 January 2001     

Verification of yield QTL through realized molecular marker- assisted selection responses in a barley cross

Verification of putative quantitative trait loci (QTL) is an essential step towards implementing the use of marker-assisted selection (MAS) in cultivar improvement. In a previous study with 150 doubled haploid lines derived from the 6-row cross Steptoe/Morex (S/M), four regions (QTL1–4) of the barley genome were associated with differential genotypic expression for grain yield across environments. The objectives of this study were to verify the value of these four QTL for selection and to compare the efficiency of alternative MAS strategies using these QTL vs. conventional phenotypic selection for grain yield. A total of 92 DHLs derived from the S/M cross that were not used in the original mapping efforts were used for QTL verification. Confirmation of QTL effects was first accomplished by assessing yield differences between individuals carrying alternative alleles at each putative locus in three environments. QTL1 on chromosome 3 was confirmed as the most important and consistent locus to determine yield across sites, with the S allele being favorable. The M allele at QTL3 on chromosome 6 was beneficial for grain yield across sites, but to a lesser degree than QTL1. Magnitudes of allele effects at QTL2 (chromosome 2) and QTL4 (chromosome 7) were highly influenced by the environment where the genotypes were grown. Verification of QTL effects was best achieved by comparing realized selection response. Genotypic (MAS) and tandem genotypic and phenotypic selection were at least as good as phenotypic selection. Consistent selection responses were detected for QTL1 alone and together with QTL3. Genotypic selection for lines carrying the S allele at QTL1 resulted in the identification of high-yielding genotypes. Selection responses increased when the M allele at QTL3 was combined with the S allele at QTL1. Significant qualitative QTL × environment interactions for QTL2 and QTL4 were detected through differential realized selection responses at different sites. Without a thorough understanding of the physiological and agronomic particulars of any QTL and the target environment, MAS for QTL showing qualitative interactions should be minimized This revised version was published online in June 2006 with corrections to the Cover Date.     

应用二种定位法比较不同世代水稻产量性状QTL的检测结果

应用珍汕97B／密阳46的F2和重组自交系（RIL）群体,建立RFLP连锁图,检测控制稻谷产量及其5个构成因子的QTL。结果表明,具有较大加性效应者,能同时在F2和RIL群体中检测到。而且,在重组自交系群体中,发现设重复的表型鉴定与基于单株的表型鉴定,对效应较高的QTL的检测影响不大。     

Identification of two key genes controlling chill haze stability of beer in barley (Hordeum vulgare L)

Background

In bright beer, haze formation is a serious quality problem, degrading beer quality and reducing its shelf life. The quality of barley (Hordeum vulgare L) malt, as the main raw material for beer brewing, largely affects the colloidal stability of beer.

Results

In this study, the genetic mechanism of the factors affecting beer haze stability in barley was studied. Quantitative trait loci (QTL) analysis of alcohol chill haze (ACH) in beer was carried out using a Franklin/Yerong double haploid (DH) population. One QTL, named as qACH, was detected for ACH, and it was located on the position of about 108 cM in chromosome 4H and can explain about 20 % of the phenotypic variation. Two key haze active proteins, BATI-CMb and BATI-CMd were identified by proteomics analysis. Bioinformatics analysis showed that BATI-CMb and BATI-CMd had the same position as qACH in the chromosome. It may be deduced that BATI-CMb and BATI-CMd are candidate genes for qACH, controlling colloidal stability of beer. Polymorphism comparison between Yerong and Franklin in the nucleotide and amino acid sequence of BATI-CMb and BATI-CMd detected the corresponding gene specific markers, which could be used in marker-assisted selection for malt barley breeding.

Conclusions

We identified a novel QTL, qACH controlling chill haze of beer, and two key haze active proteins, BATI-CMb and BATI-CMd. And further analysis showed that BATI-CMb and BATI-CMd might be the candidate genes associated with beer chill haze.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1683-1) contains supplementary material, which is available to authorized users.     

Improving QTL Mapping Resolution Based on Genotypic Sampling—a Case Using a RIL Population

The QTL mapping results were compared with the genotypically selected and random samples of the same size on the base of a RIL population. The results demonstrated that there were no obvious differences in the trait distribution and marker segregation distortion between the genotypically selected and random samples with the same population size. However, a significant increase in QTL detection power, sensitivity, specificity, and QTL resolution in the genotypically selected samples were observed. Moreover, the highly significant effect was detected in small size of genotypically selected samples. In QTL mapping, phenotyping is a more sensitive limiting factor than genotyping so that the selection of samples could be an attractive strategy for increasing genome-wide QTL mapping resolution. The efficient selection of samples should be more helpful for QTL maker assistant selection, fine mapping, and QTL cloning.     

Marker-assisted analysis of three grain yield QTL in barley (Hordeum vulgare L.) using near isogenic lines

Three previously identified grain yield quantitative trait loci (QTL) on chromosomes 2S(2HS), 3C(3HC) and 5L(1HL), designated QTL-2S, QTL-3 and QTL-5L, respectively, were evaluated for their potential to increase yields of high-quality malting barley without disturbing their favorable malting quality profile. QTL mapping of yield related traits was performed and near-isogenic lines (NILs) were developed. QTL for plant height, head shattering, seed weight and number of rachis nodes/spike were detected in the QTL-3 region. NILs developed by introgressing QTL-3 from the high-yielding cv. Steptoe to the superior malting quality, moderate-yielding cv. Morex acquired reduced height, lodging and head shattering features of Steptoe without major changes in malting quality. The yield of NILs, measured by minimizing the losses due to lodging and head shattering, did not exceed that of Morex. Steptoe NILs, with the Morex QTL-2S region, flowered 10 days later than Steptoe but the grain yield was not changed. None of the 3 QTL studied altered the measured yield of the recipient genotype, per se, although QTL 2S and QTL-3 affected yield-related traits. We conclude that these yield QTL must interact with other genes for full expression. Alternatively, they affect the harvestable yield through reduced lodging, head shattering, and/or altered flowering time.     

水稻生物学产量及其构成性状的QTL定位

QTL的加性效应、加性×加性上位性效应及它们与环境的互作效应是数量性状的重要遗传分量.利用IR64/Azucena的125个DH品系为群体,分析了水稻生物学产量及其两个构成性状干草产量和谷粒产量的遗传组成.用基于混合模型的复合区间作图(MCIM)方法进行QTL定位.检测到12个位点有加性主效应,27个位点涉及双位点互作,18个位点存在环境互作.结果表明水稻生物学产量和它的两个构成性状普遍存在上位性效应和QE互作效应.此外,还探讨了性状间相关的遗传基础.发现4个QTLs和一对上位性QTLs可能与生物学产量与干草产量之间的正相关有关.3个QTL可能与干草产量与谷粒产量之间的负相关有关.这些结果可能部分地解释了这3个性状相关的遗传原因.通过对水稻生物学产量及其两个构成性状所定位QTL的分析,加深了对数量性状QTL的认识.首先,QTL的上位性效应和QE互作效应是普遍存在的;其次,QTL的多效性或紧密连锁可能是遗传相关的原因,当QTL对两个性状作用的方向相同时可导致正向遗传相关,反之则为负向遗传相关,当有些QTL表现为同向作用而另一些QTL表现为反向作用时,则可削弱性状间的遗传相关性;第三,复合性状的QTL效应可分解为其组成性状的QTL效应,如果QTL对各组成性状的效应方向相反而相互抵消,可使复合性状的QTL效应不易被检测;第四,加性效应的QTL常参预构成上位性效应,而具有上位性效应的QTL并非都有加性主效应,表明忽略上位性的QTL定位方法会降低检测QTL的功效;最后,鉴别不同类型的QTL效应有利于指导育种实践,选择主效QTL适用于多环境,QE互作QTL适用于特定环境,对上位性QTL应强调选择基因组合而并非单个基因.     

Localization of quantitative trait loci (QTL) for agronomic important characters by the use of a RFLP map in barley (Hordeum vulgare L.)

Two hundred and fifty doubled haploid lines were studied from a cross between two 2-row winter barley varieties. The lines were evaluated for several characters in a field experiment for 3 years on two locations with two replications. From a total of 431 RFLP probes 50 were found to be polymorphic and subsequently used to construct a linkage map. Quantitative trait loci (QTLs) were determined and localized for resistance against Rhynchosporium secalis and Erysiphe graminis, for lodging, stalk breaking and ear breaking tendency, for the physical state before harvest, plant height, heading date, several kernel parameters and kernel yield. The heritability of the traits ranged from 0.56 to 0.89. For each trait except for kernel thickness, QTLs have been localized that explain 5–52% of the genetic variance. Transgressive segregation occurred for all of the traits studied.     

Mapping of chromosome regions conferring boron toxicity tolerance in barley (Hordeum vulgare L.)

 Boron toxicity has been recognised as an important problem limiting production in the low-rainfall regions of southern Australia, West Asia and North Africa. Genetic variation for boron toxicity tolerance in barley has been characterised but the mode of inheritance and the location of genes controlling tolerance were not previously known. A population of 150 doubled-haploid lines from a cross between a boron toxicity tolerant Algerian landrace, Sahara 3771, and the intolerant Australian cultivar Clipper was screened in four tolerance assays. An RFLP linkage map of the Clipper×Sahara population was used to identify chromosomal regions associated with boron tolerance in barley. Interval regression-mapping allowed the detection of four chromosomal regions involved in the boron tolerance traits measured. A region on chromosome 2H was associated with leaf-symptom expression, a region on chromosome 3H was associated with a reduction of the affect of boron toxicity on root growth suppression, a region on chromosome 6H was associated with reduced boron uptake, and a region on chromosome 4H was also associated with the control of boron uptake as well as being associated with root-length response, dry matter production and symptom expression. The benefits and potential of marker-assisted selection for boron toxicity tolerance are discussed. Received: 18 December 1997 / Accepted: 28 November 1998     

Mapping loci associated with milling yield in wheat (Triticum aestivum L.)

A partial genetic linkage map constructed using 150 single seed descent (SSD) lines generated from a cross between the hexaploid wheat varieties Schomburgk and Yarralinka was used to identify loci controlling milling yield. Milling yield data were obtained using seed collected from field trials conducted at different sites over two seasons. The estimated broad-sense heritability of milling yield in this population was calculated as 0.48. In the preliminary analysis, two regions were identified on chromosomes 3A and 7D, which were significantly associated with milling yield and accounted for 22% and 19% of the genetic variation, respectively. Bulked segregant analysis in combination with AFLP identified other markers linked to these loci, as well as an additional region on chromosome 5A, which accounted for 19% of the genetic variation. The applicability of these markers as selection tools for breeding purposes is discussed.     

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。     

Map construction of sequence-tagged sites (STSs) in barley (Hordeum vulgare L.)

 In order to identify sequence-tagged sites (STSs) appropriate for recombinant inbred lines (RILs) of barley cultivars ‘Azumamugi’ × ‘Kanto Nakate Gold’, a total of 43 STS primer pairs were generated on the basis of the terminal sequences of barley restriction fragment length polymorphism (RFLP) clones. Forty one of the 43 primer pairs amplified PCR products in Azumamugi, Kanto Nakate Gold, or both. Of these, two showed a length polymorphism and two showed the presence or absence of polymorphism between the parents. PCR products of the remaining 37 primers were digested with 46 restriction endonucleases, and polymorphisms were detected for 15 primers. A 383.6-cM linkage map of RILs of Azumamugi×Kanto Nakate Gold was constructed from the 19 polymorphic STS primer pairs (20 loci) developed in this study, 45 previously developed STS primer pairs (47 loci), and two morphological loci. Linkage analysis and analysis of wheat-barley chromosome addition lines showed that with three exceptions, the chromosome locations of the STS markers were identical with those of the RFLP markers. Received: 4 August 1998 / Accepted: 8 October 1998     

Drought‐related secondary metabolites of barley (Hordeum vulgare L.) leaves and their metabolomic quantitative trait loci

Determining the role of plant secondary metabolites in stress conditions is problematic due to the diversity of their structures and the complexity of their interdependence with different biological pathways. Correlation of metabolomic data with the genetic background provides essential information about the features of metabolites. LC‐MS analysis of leaf metabolites from 100 barley recombinant inbred lines (RILs) revealed that 98 traits among 135 detected phenolic and terpenoid compounds significantly changed their level as a result of drought stress. Metabolites with similar patterns of change were grouped in modules, revealing differences among RILs and parental varieties at early and late stages of drought. The most significant changes in stress were observed for ferulic and sinapic acid derivatives as well as acylated glycosides of flavones. The tendency to accumulate methylated compounds was a major phenomenon in this set of samples. In addition, the polyamine derivatives hordatines as well as terpenoid blumenol C derivatives were observed to be drought related. The correlation of drought‐related compounds with molecular marker polymorphisms resulted in the definition of metabolomic quantitative trait loci in the genomic regions of single‐nucleotide polymorphism 3101‐111 and simple sequence repeat Bmag0692 with multiple linkages to metabolites. The associations pointed to genes related to the defence response and response to cold, heat and oxidative stress, but not to genes related to biosynthesis of the compounds. We postulate that the significant metabolites have a role as antioxidants, regulators of gene expression and modulators of protein function in barley during drought.     

Confirmation of QTL controlling seed yield in spring canola (Brassica napus L.) hybrids

Allelic effects observed in QTL discovery experiments must be confirmed to be useful in subsequent breeding efforts. Two QTL affecting seed yield of spring hybrid canola (Brassica napus L.) were previously identified in two populations of inbred backcross lines (IBLs) containing germplasm introgressed from a winter cultivar. The effects of favorable alleles at these QTL were retested by crossing two selected IBLs (M5 and M31) to three spring canola lines having different genetic backgrounds. Doubled haploid (DH) lines derived from each F₁ were genotyped with RFLP markers flanking the QTL and grouped into the four possible QTL genotypes. For the first field experiment, DH lines derived by crossing the M5 line to one spring line were crossed to two female testers and evaluated as individual testcross progenies in one environment. QTL genotypes had large variances and were not significantly different. A second field experiment was conducted using the DH lines from the first experiment and two other sets of DH lines derived from the M31 line crossed to two different spring canola lines. Individual lines within each QTL genotype of each set were bulked and crossed to the same testers used in Experiment 1. Bulked hybrid seeds of each QTL genotype were planted in a split-split plot randomized block design and 12 replicates. QTL genotypes had smaller variances in this experiment, and the effects of one QTL were confirmed in some genetic backgrounds. These results suggest that bulking of QTL genotypes and use of an appropriate experimental design with many replicates are needed to detect small differences between QTL genotypes.     

与水稻籼粳分化有关的穗颈维管束性状基因的分子标记定位

水稻穗颈维管束数及其与穗一次枝梗数之比（V／R）是与籼粳分化有关的重要性状,采用籼粳交（圭630／02428）杂种F1花药培养获得的DH群体,对水稻穗颈维管束数,穗一次枝梗数及V／R比进行了QTL分析,检测到3个控制穗颈维管束数的QTL;其中,效应最大的qVB-8的贡献率为31．1％,加性效应值为1．96％,增效等位基因来自灿稻亲本圭630,2个控制一次枝梗数的QTL效应较小,但分别与控制穗颈维管束数的2个QTL同位,检测到影响V／R比的3个QTL,其中,效应最大的qV/R-1的贡献率为25．3％,被定位于第1染色体上,与落粒性基因sh-2紧密连锁（亦或为一因多效）。此外,还检测到4对和2对分别控制穗颈维管束数和V／R比的互作QTL。结果分析表明,水稻穗颈维管束数与穗一次枝梗数受不同的多基因系统控制,但这2个多基因系统的某些位点在基因组中具有同位性;在第1染色体上,控制V／R比,且效应最大的qV/R-1所在的染色体区段在水稻籼粳分化过程中可能具有重要作用。     

水稻纹枯病抗性QTL分析

对灿稻窄叶青8号（ZYQ8）和粳稻京系17（JX17）以及由它们构建的加倍单倍体（DH）群体,分别在杭州和海南岛,采用注射器接种法进行纹枯病抗性鉴定,并使用该群体的分子链锁图谱进行数量性状座位（QTL）分析。共检测到4个抗纹枯病的QTL（qSBR-2、qSBR-3、qSBR-7和qSBR-11）,分别位于第2、第3、第7和第11染色体。其中qSBR-2、qSBR-3、qSBR-7的抗性基因由抗病亲本ZYQ8贡献,而qSBR-11的抗性基因来自感病亲本JX17。qSBR-2、qSBR-3、qSBR-7在杭州和海南岛都能检测到,而qSBR-11只在杭州检测到。在杭州的实验中,纹枯病病级与秆长和抽穗期呈显著负相关;在控制秆长和抽穗期的QTL中,控制秆长的qCL-3与qSBR-3位于同一染色体区域,其余QTL与抗纹枯病的QTL之间无连锁关系。     

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.     

Intergeneric somatic hybridization of rice (Oryza sativa L.) and barley (Hordeum vulgare L.) by protoplast fusion

An intergeneric somatic hybrid was obtained upon fusion of protoplasts of rice and barley. Protoplasts isolated from suspension cultures of rice cells were fused by electrofusion with protoplasts that had been isolated from young barley leaves. Some of the resultant calli formed green spots and shoots. Only one shoot formed roots, and it was subsequently successfully transferred to soil in a greenhouse. Its morphology closely resembled that of the parental rice plant. Cytological analysis indicated that the plant had both small chromosomes from rice and large chromosomes from barley. Southern hybridization analysis with a fragment of the tryptophan B (trpB) gene revealed both a rice-specific band and a barley-specific band. Mitochondrial (mt) and chloroplast (cp) DNAs were also analyzed using the same method. The plant was shown to contain novel mitochondrial and chloroplast sequence rearrangements that were not detected in either of the parents. Received: 5 March 1997 / Revision received: 4 September 1997 / Accepted: 13 September 1997