QTL analysis of a cross between European and North American malting barleys reveals a putative candidate gene for β-glucan content on chromosome 1H

To determine the genetic factors influencing grain β-glucan content, that were effective in a population of two-row barley grown in very contrasting environments, 102 doubled haploid lines from the cross Beka × Logan were sown at two sites, Lleida (N.E. Spain) and Dundee (E. Scotland) in 2002. Following harvest, grain samples were assessed for total β-glucan content. Beka had lower β-glucan content than Logan at both sites but, while there was transgressive segregation among the DH lines, this was primarily amongst lines with higher β-glucan than Logan. In addition to differences between DH lines, there were differences between the sites and there was also genotype × site interaction. Three QTLs for β-glucan content were detected at both sites, but their contribution to β-glucan content was, in all cases, higher at Lleida compared to Dundee. One QTL was located in the distal end of the long arm of chromosome 1H, in the same region as a gene for UDP-glucose-4-epimerase, an enzyme known to be involved in the synthesis of cell wall polysaccharides, while another was located in the same area of chromosome 5H as a genetic factor shown previously, in the same cross, to influence grain protein content. The third was in the centromeric region of chromosome 7H, close to the gene for naked (hulless) grain. These findings will be important in designing crosses and devising selection strategies in breeding of both low β-glucan, malting barley and high β-glucan, hulless barley for human food use.     

水稻F2不育和抽穗期QTL分析

对台中65（粳稻）/Bhadua（籼稻）杂交F2代群体构建了RFLP连锁图谱,含94个分布较为均匀的标记。对F2小穗不育性状进行单点分析和区间分析的结果基本一致：有两个F2小穗不育QTL座位分别位于染色体1的XNpb113～XNpb346之间和染色体8的G187～XNpb397之间,而且该两个QTL均为新检测出的座位;检测出5个抽穗期TQL,其中3个座位在单点分析和区间分析中的结果一致,分别位于染色体1的XNpb113～XNpb346,染色体4的C891～C335,染色体的8的C166～C1121,另外,染色体6的XNpb27为单点分析结果,染色体10的R716～C405为区间分析结果。由于染色体1上的F2不育QTL和抽穗期QTL重叠,该QTL座位是由于遗传效应所至还是由于环境因素（迟抽穗）所至有待构建近等基因系进一步研究。;位于染色体1和10上的抽穗期QTL座位为新检测的座位。对新检测的F2不育和抽穗期QTL座位正在建立相应的近等基因系以精确定位和克隆上述基因。     

QTLs for earliness and yield-forming traits in the Lubuski × CamB barley RIL population under various water regimes

Drought has become more frequent in Central Europe causing large losses in cereal yields, especially of spring crops. The development of new varieties with increased tolerance to drought is a key tool for improvement of agricultural productivity. Material for the study consisted of 100 barley recombinant inbred lines (RILs) (LCam) derived from the cross between Syrian and European parents. The RILs and parental genotypes were examined in greenhouse experiments under well-watered and water-deficit conditions. During vegetation the date of heading, yield and yield-related traits were measured. RIL population was genotyped with microsatellite and single nucleotide polymorphism markers. This population, together with two other populations, was the basis for the consensus map construction, which was used for identification of quantitative trait loci (QTLs) affecting the traits. The studied lines showed a large variability in heading date. It was noted that drought-treatment negatively affected the yield and its components, especially when applied at the flag leaf stage. In total, 60 QTLs were detected on all the barley chromosomes. The largest number of QTLs was found on chromosome 2H. The main QTL associated with heading, located on chromosome 2H (Q.HD.LC-2H), was identified at SNP marker 5880–2547, in the vicinity of Ppd-H1 gene. SNP 5880–2547 was also the closest marker to QTLs associated with plant architecture, spike morphology and grain yield. The present study showed that the earliness allele from the Syrian parent, as introduced into the genome of an European variety could result in an improvement of barley yield performance under drought conditions.     

Development and molecular characterization of wheat--Aegilops kotschyi addition and substitution lines with high grain protein, iron, and zinc

Over two billion people, depending largely on staple foods, suffer from deficiencies in protein and some micronutrients such as iron and zinc. Among various approaches to overcome protein and micronutrient deficiencies, biofortification through a combination of conventional and molecular breeding methods is the most feasible, cheapest, and sustainable approach. An interspecific cross was made between the wheat cultivar 'Chinese Spring' and Aegilops kotschyi Boiss. accession 396, which has a threefold higher grain iron and zinc concentrations and about 33% higher protein concentration than wheat cultivars. Recurrent backcrossing and selection for the micronutrient content was performed at each generation. Thirteen derivatives with high grain iron and zinc concentrations and contents, ash and ash micronutrients, and protein were analyzed for alien introgression. Morphological markers, high molecular weight glutenin subunit profiles, anchored wheat microsatellite markers, and GISH showed that addition and substitution of homoeologous groups 1, 2, and 7 chromosomes of Ae. kotschyi possess gene(s) for high grain micronutrients. The addition of 1U/1S had high molecular weight glutenin subunits with higher molecular weight than those of wheat, and the addition of 2S in most of the derivatives also enhanced grain protein content by over 20%. Low grain protein content in a derivative with a 2S-wheat translocation, waxy leaves, and absence of the gdm148 marker strongly suggests that the gene for higher grain protein content on chromosome 2S is orthologous to the grain protein QTL on the short arm of group 2 chromosomes.     

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.     

Localising QTLs for leaf rust resistance and agronomic traits in barley (Hordeum vulgare L.)

The Hordeum vulgare accession ’HOR 1063’ was crossed with the barley cultivar Krona, and 220 doubled haploid lines were produced based on this cross. A molecular map was constructed based on RFLP markers. Field trials were performed over 2 years and at two locations. In field trials, resistance to leaf rust by means of artificial infection, heading date, plant height and Kernel weight were assessed. For leaf rust resistance, 4 QTLs were localised, that explained 96.1% of the genetic variation. One QTL on chromosome 4H confirmed a position found in another genetic background and one mapped to the same position as Rph16 on chromosome 2H. All digenic effects decreased the effects of the respective QTLs. In addition to the denso-locus and the hex-v locus, other QTLs influencing heading date, plant length and kernel weight were found in this cross. Received: 16 July 1999 / Accepted: 7 September 1999     

水稻抗褐飞虱种质Swarnalata抽穗期和休眠性相关QTL检测

为有效利用抗褐飞虱水稻Swarnalata,对2013年南京种植的Swarnalata/02428 F2分离群体进行抽穗期和种子休眠性考察,利用172个分子标记构建了Swarnalata/02428 F2的分子遗传连锁图谱,图谱全长为3311.4c M,标记间平均图距为19.22c M。利用Windows QTL Cartographer V2.5软件对该分离群体进行抽穗期和种子休眠性相关QTL检测,共检测到7个抽穗期相关QTL,分别位于第2、3、6、11染色体,其中位于第11染色体的q HD-11-1贡献率最高,为28.85%;检测到3个种子休眠性相关QTL,分别位于第3、6、9染色体,其中位于第9染色体的q Sd-9贡献率最高,为22.11%。分析表明,本研究检测到的抽穗期QTL与种子休眠QTL所在位置不同,说明该群体中种子休眠与抽穗期没有直接关系,它们分别由不同基因控制。本研究不仅为水稻休眠基因的精细定位及克隆奠定基础,也为更有效利用Swarnalata中的抗褐飞虱基因提供基础和一些优良的中间材料。     

The role of chromosomes from homeologous group 5 in regulation of grain hardness and protein content in substitution lines of common wheat cultivar Saratovskaya 29

Genetic regulation of grain hardness and protein content in intervarietal substitution lines for chromosomes of homeologous group 5 was examined. Common wheat cultivar Saratovskaya 29 with high bread-backing properties served as the recipient. Donors of chromosomes 5A and 5D were 18 cultivars with variable traits examined, including high-protein cultivars (Atlas 66 and Diamant 2), and soft-grain cultivars (Ul’yanovka and Chinese Spring). Analysis of substitution lines pointed to a substantial effect of chromosome 5D on the regulation of both traits. It was demonstrated that as a result of intervarietal substitution for chromosome 5D from donor cultivars Ul’yanovka and Chinese Spring, the endosperm softness was increased compared to the recipient cultivar Saratovskaya 29. Substitution lines Saratovskaya 29/Atlas 66 5D and Saratovskaya 29/Diamant 2 5D were characterized by high grain protein content, as well as by high endosperm hardness. In addition, the line Saratovskaya 29/Novosibirskaya 67 5D, characterized by grain hardness higher than in Saratovskaya 29, was isolated. In the lines with intervarietal substitution of chromosome 5A, grain protein content was found to be lower than in recipient cultivar Saratovskaya 29.     

Genetic analysis and molecular mapping of a stripe rust resistance gene derived from Psathynrostachys huashanica Keng in wheat line H9014-121-5-5-9

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases worldwide and is also an important disease in China. The wheat translocation line H9014-121-5-5-9 was originally developed from interspecific hybridization between wheat (Triticum aestivum L.) line 7182 and Psathyrostachys huashanica Keng. This translocation line showed resistance to predominant stripe rust races in China when it was tested with nine races of Pst. To determine the inheritance and map the resistance gene, segregating populations were developed from the cross between H9014-121-5-5-9 and the susceptible cultivar Mingxian 169. The seedlings of the F1, F2, and F2:3 generations were tested with race CYR31. The results showed that the resistance in H9014-121-5-5-9 was conferred by a single dominant gene. Bulked segregant analysis and simple sequence repeat (SSR) markers were used to identify polymorphic markers associated with the resistance gene locus. Seven polymorphic SSR markers were linked to the resistance gene. A linkage map was constructed according to the genotypes of the seven SSR markers and the resistance gene. Based on the SSR marker positions on the wheat chromosome, the resistance gene was assigned on chromosome 1AL, temporarily designated YrHA. Based on chromosomal location, reaction patterns and pedigree analysis, YrHA should be a novel resistance gene to stripe rust. The molecular markers of the new resistance gene in H9014-121-5-5-9 could be useful for marker-assisted selection in breeding programs against stripe rust.     

QTLs for cell membrane stability and flag leaf area under drought stress in a wheat RIL population

A population of 206 recombinant inbred lines (RILs F₉–F₁₀) derived from wheat cross WL711/C306 was phenotyped for morpho-physiological traits such as flag leaf area (FLA), flag leaf length (FLL), flag leaf width (FLW), and cell membrane stability (CMS) under water deficit stress (WDS) environment. High yielding cultivar, WL711 had higher FLA than the medium yielding cultivar C306 across trials under both environments. Parent cultivar C306 maintained membrane integrity while WL711 showed higher membrane damage under WDS. The RIL population showed considerable variation, normal distribution and transgressive segregation for FLA, FLL, FLW and CMS under WDS. The genetic linkage map of WL711/C306 RIL population was constructed comprising of 346 markers. The total map distance was 4526.8 cM with an averaged interval of 12.9 cM between adjacent markers. Major consistent QTL for FLA, FLL, FLW, and CMS were identified on chromosomes 2DS and 3BS respectively in the WL711/C306 RIL population under WDS. The major QTL for FLA, qFLAWD.2D.1 which expressed in multiple environments and for CMS, qCMSWD.3B.3 and qCMSWD.3B.4, accounted for a large proportion of phenotypic variance (PV) with positive allele being contributed by C306, a drought resistant (DR) parent. QTL qFLAWD.2D.1 for FLA co-located with QTL for grain number (GN) and days to flowering (DTF) while QTL qCMSWD.3B.3 and qCMS.3B.4 co-located with QTL for grain yield and its components, days to flowering, canopy temperature and coleoptiles length as reported in our previous publications on the WL711/C306 population (Shukla et al. in Euphytica 203:449–467, 2015; Singh et al. in J Plant Biochem Biotechnol 24:324–330, 2015). Two candidate genes Ghd7 for grain yield and heading date and OsCDK4 for calcium dependent protein kinases were identified in the 2DS and 3BS QTL regions respectively on comparison with gene content of rice chromosomes 7 and 1 respectively. Hence, QTLs qFLAWD.2D.1 and qCMSWD.3B.3 are potential target regions for fine mapping and marker assisted selection for FLA and CMS respectively in wheat under water deficit environments.

     

Rph22: mapping of a novel leaf rust resistance gene introgressed from the non-host Hordeum bulbosum L. into cultivated barley (Hordeum vulgare L.)

A resistance gene (Rph22) to barley leaf rust caused by Puccinia hordei was introgressed from the non-host species Hordeum bulbosum into cultivated barley. The H. bulbosum introgression in line ‘182Q20’ was located to chromosome 2HL using genomic in situ hybridisation (GISH). Using molecular markers it was shown to cover approximately 20 % of the genetic length of the chromosome. The introgression confers a very high level of resistance to P. hordei at the seedling stage that is not based on a hypersensitive reaction. The presence of the resistance gene increased the latency period of the leaf rust fungus and strongly reduced the infection frequency relative to the genetic background cultivar ‘Golden Promise’. An F₂ population of 550 individuals was developed and used to create a genetic map of the introgressed region and to determine the map position of the underlying resistance gene(s). The resistance locus, designated Rph22, was located to the distal portion of the introgression, co-segregating with markers H35_26334 and H35_45139. Flanking markers will be used to reduce the linkage drag, including gene(s) responsible for a yield penalty, around the resistance locus and to transfer the gene into elite barley germplasm. This genetic location is also known to harbour a QTL (Rphq2) for non-hypersensitive leaf rust resistance in the barley cultivar ‘Vada’. Comparison of the ‘Vada’ and H. bulbosum resistances at this locus may lead to a better understanding of the possible association between host and non-host resistance mechanisms.     

Advanced backcross QTL analysis of a hard winter wheat × synthetic wheat population

Advanced backcross quantitative trait locus (AB-QTL) analysis was used to identify QTLs for yield and yield components in a backcross population developed from a cross between hard red winter wheat (Triticum aestivum L.) variety Karl 92 and the synthetic wheat line TA 4152-4. Phenotypic data were collected for agronomic traits including heading date, plant height, kernels per spike, kernel weight, tiller number, biomass, harvest index, test weight, grain yield, protein content, and kernel hardness on 190 BC₂F_2:4 lines grown in three replications in two Kansas environments. Severity of wheat soilborne mosaic virus (WSBMV) reaction was evaluated at one location. The population was genotyped using 151 microsatellite markers. Of the ten putative QTLs identified, seven were located on homoeologous group 2 and group 3 chromosomes. The favorable allele was contributed by cultivated parent Karl 92 at seven QTLs including a major one for WSBMV resistance, and by the synthetic parent at three QTLs: for grain hardness, kernels per spike, and tiller number. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.     

Genetic mapping in pea. 1. RAPD-based genetic linkage map of Pisum sativum

 A genetic linkage map of Pisum sativum L. was constructed based primarily on RAPD markers that were carefully selected for their reproducibility and scored in a population of 139 recombinant inbred lines (RILs). The mapping population was derived from a cross between a protein-rich dry-seed cultivar ‘Térèse’ and an increased branching mutant (K586) obtained from the pea cultivar ‘Torsdag’. The map currently comprises nine linkage groups with two groups comprising only 6 markers (n=7 in pea) and covers 1139 cM. This RAPD-based map has been aligned with the map based on the (JI281×JI399) RILs population that currently includes 355 markers in seven linkage groups covering 1881 cM. The difference in map lengths is discussed. For this alignment 7 RFLPs, 23 RAPD markers, the morphological marker le and the PCR marker corresponding to the gene Uni were used as common markers and scored in both populations. Received: 13 March 1998 / Accepted: 29 April 1998     

Identification and characterization of a major QTL responsible for erect panicle trait in <Emphasis Type="Italic">japonica</Emphasis> rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Panicle erectness (PE) is one of the most important traits for high-yielding japonica cultivars. Although several cultivars with PE trait have been developed and released for commercial production in China, there is little information on the inheritance of PE traits in rice. In the present study, 69 widely cultivated japonica cultivars and a double haploid (DH) population derived from a cross between a PE cultivar (Wuyunjing 8) and a drooping panicle cultivar (Nongken 57) were utilized to elucidate the mechanisms of PE formation and to map PE associated genes. Our data suggested that panicle length (PL) and plant height (PH) significantly affected panicle curvature (PC), with shorter PL and PH resulting in smaller PC and consequently more erect. A putative major gene was identified on chromosome 9 by molecular markers and bulk segregant analysis in DH population. In order to finely map the major gene, all simple sequence repeats (SSR) markers on chromosome 9 as well as 100 newly developed sequence-tagged site (STS) markers were used to construct a linkage group for quantitative trait locus (QTL) mapping. A major QTL, qPE9-1, between STS marker H90 and SSR marker RM5652, was detected, and accounted for 41.72% of PC variation with pleiotropic effect on PH and PL. another QTL, qPE9-2, was also found to be adjacent to qPE9-1. In addition, we found that H90, the nearest marker to qPE9-1, used for genotyping 38 cultivars with extremely erect and drooping panicles, segregated in agreement with PC, suggesting the H90 product was possibly part of the qPE9-1 gene or closely related to it. These data demonstrated that H90 could be used for marker-aided selection for the PE trait in breeding and in the cloning of qPE9-1.     

Development of wild barley (Hordeum chilense)-derived DArT markers and their use into genetic and physical mapping

Diversity arrays technology (DArT) genomic libraries were developed from H. chilense accessions to support robust genotyping of this species and a novel crop comprising H. chilense genome (e.g., tritordeums). Over 11,000 DArT clones were obtained using two complexity reduction methods. A subset of 2,209 DArT markers was identified on the arrays containing these clones as polymorphic between parents and segregating in a population of 92 recombinant inbred lines (RIL) developed from the cross between H. chilense accessions H1 and H7. Using the segregation data a high-density map of 1,503 cM was constructed with average inter-bin density of 2.33 cM. A subset of DArT markers was also mapped physically using a set of wheat-H. chilense chromosome addition lines. It allowed the unambiguous assignment of linkage groups to chromosomes. Four segregation distortion regions (SDRs) were found on the chromosomes 2H(ch), 3H(ch) and 5H(ch) in agreement with previous findings in barley. The new map improves the genome coverage of previous H. chilense maps. H. chilense-derived DArT markers will enable further genetic studies in ongoing projects on hybrid wheat, seed carotenoid content improvement or tritordeum breeding program. Besides, the genetic map reported here will be very useful as the basis to develop comparative genomics studies with barley and model species.     

Mapping and validation of chromosome regions conferring boron toxicity tolerance in wheat (Triticum aestivum)

Boron is an essential plant micro-nutrient which can be phytotoxic to plants if present in soils in high concentration. Boron toxicity has been recognised as an important problem limiting production in the low rainfall areas of southern Australia, West Asia and North Africa. Genetic variation for boron toxicity tolerance in wheat has been well-characterised. The efficiency of breeding for boron toxicity tolerance could be greatly enhanced by the development of molecular markers associated with QTLs for tolerance in wheat. A population of 161 doubled haploids from a cross between the tolerant cultivar Halberd and the moderately sensitive cultivar Cranbrook was used to identify chromosomal regions involved in boron tolerance. A combined RFLP and AFLP linkage map of the Cranbrook x Halberd population was used to identify chromosomal regions involved in the boron tolerance traits measured. Regions on chromosome 7B and 7D were associated with leaf symptom expression. The region on chromosome 7B was also associated with the control of boron uptake and with a reduction in the effect of boron toxicity on root-growth suppression. RFLP markers at the chromosome 7B and 7D loci were shown to be effective in selecting for improved boron tolerance in an alternative genetic background. Halberd alleles at the chromosome 7B locus were associated with the concentration of boron in whole shoots and grain. The concentration of boron in whole shoots and in grain were both related to grain yield in a field trial conducted on soil containing toxic levels of boron. Implications relating to marker-assisted selection for boron toxicity tolerance in wheat are discussed. Received: 3 September 1999 / Accepted: 12 February 2000     

Identification of RFLP markers linked to the H1 gene conferring resistance to the potato cyst nematode Globodera rostochiensis.

The H1 gene from Solanum tuberosum ssp. andigena confers high levels of resistance to the potato cyst nematode Globodera rostochiensis and is used extensively in potato breeding. Using a dihaploid segregating population, a search was conducted for linkage between this gene and markers on the potato/tomato RFLP map. A total of 60 RFLP markers covering the entire genome were screened on bulk resistant and susceptible segregants. Linkage was indicated for eight markers on chromosome 5. Individual plant analysis placed the closest marker, CD78, at a maximum map distance of 2.7 cM from H1. A molecular marker for the H1 should be useful both as a correlative screening tool for incorporation of resistance into new cultivars and as starting point for map-based cloning of this important gene.     

Single nucleotide polymorphism mapping and alignment of recombinant chromosome substitution lines in barley

Single nucleotide polymorphism (SNP) genotyping is useful for assessing genetic variation in germplasm collections, genetic map development and detection of alien chromosome substitutions. In this study, a diversity analysis using 1,301 SNPs on a set of 37 barley accessions was conducted. This analysis showed a high polymorphism rate between the malting barley cultivar 'Haruna Nijo' and the food barley cultivar 'Akashinriki'. Haruna Nijo and Akashinriki are donors of the barley expressed sequence tag (EST) collections. A doubled haploid (DH) population derived from the cross between Haruna Nijo and Akashinriki was genotyped with 1,448 SNPs. Of these 1,448 SNPs, 734 were polymorphic and distributed on barley linkage groups (chromosomes) as follows: 1H (86), 2H (125), 3H (120), 4H (100), 5H (127), 6H (88) and 7H (88). By using cMAP, we integrated the SNP markers across high-density maps. The SNPs were also used to genotype 98 BC(3)F(4) recombinant chromosome substitution lines (RCSLs) developed from the same cross (Haruna Nijo/Akashinriki). These data were used to create graphical genotypes for each line and thus estimate the location, extent and total number of introgressions from Akashinriki in the Haruna Nijo background. The 35 selected RCSLs sample most of the Akashinriki food barley genome, with only a few missing segments. These resources bring new alleles into the malting barley gene pool from food barley.