Chromosome 2H Research Articles

Wild barley shows a wider diversity in genes regulating heading date compared with cultivated barley

Heading date (HD) is an important agronomic trait that influences plant adaptability to varying environment and, ultimately, grain yield. In this study, two doubled haploid (DH) populations were used to identify new QTL for HD. One of the DH populations is originated from a cross between an Australian malting barley cv. Franklin and a wild barley accession TAM407227 and the other one is from the cross between a Syrian wild barley SYR01 and an Australian malting barley cv. Gairdner. Using three times of sowing (TOS) differing in daylength and temperature, we investigated quantitative trait loci (QTL) controlling HD from both populations. Fourteen QTL were identified for HD from different populations and sowing dates. The expression of HD related genes varied with the TOS, suggesting a significant QTL × environment interaction. By comparing the positions of previously mapped HD genes and those of QTL detected in this population, we found that eleven of the fourteen QTL identified in this study were located at similar positions to those reported genes for HD. Among the three new potential QTL, one was located at 73.5 cM on chromosome 2H, explaining 19.2% and 4.6% HD of DH lines in spring and summer growing, respectively. The wild barley parent TAM407227 contributed the early maturity allele. HORVU2Hr1G088460 within the interval of QTL could be the candidate gene. The second new QTL was identified on chromosome 3H from a summer sowing trial and the third one on chromosome 4H affected HD of DH lines only under spring sowing condition. These new QTL identified will provide alternative genetic resources for plant breeders developing barley varieties with improved HD adaptability to varying environments.

Identification of QTL underlying the leaf length and area of different leaves in barley

Leaf is the main organ of photosynthesis, which significantly impacts crop yield. A high-density linkage map containing 1894 single nucleotide polymorphism (SNP) and 68 simple sequence repeats (SSR) markers was used to identify quantitative trait locus (QTL) for flag leaf length (FLL), second leaf length (SLL), third leaf length (TLL), fourth leaf length (FOLL), flag leaf area (FLA), second leaf area (SLA), third leaf area (TLA) and fourth leaf area (FOLA). In total, 57 QTLs underlying the top four leaf length and area traits were identified and mapped on chromosome 2H, 3H, 4H and 7H. Individual QTL accounted for 5.17% to 37.11% of the phenotypic variation in 2015 and 2016. A major stable QTL qFLL2-2 close to the marker 2HL_25536047 was identified on the long arm of chromosome 2H. The most important QTL clustered region at M_256210_824 - 2HL_23335246 on chromosome 2H was associated with FLL, SLL, FLA and SLA and explained high phenotypic variation. These findings provide genetic basis for improving the leaf morphology of barley. In addition, our results suggested that the top four leaves were significantly positively correlated with plant height and some yield-related traits.

Proposal of updated XYZ system for the production of hybrid wheat seed

The following updates have been proposed for the XYZ system for the production of hybrid wheat: The waxy characteristics of the grain were used as a classifying mark. The candidate pollen sterility gene TIP2 was detected in silico based on similarity to known pollen sterility genes in rice. In order to maintain a sterile maternal component, the addition chromosome 7H was proposed, carrying wild-type alleles Waxy-H and TIP2-H. The concept of practical production of the commercial F<sub>1 </sub>seed was designed.

A tiered approach to genome-wide association analysis for the adherence of hulls to the caryopsis of barley seeds reveals footprints of selection

BackgroundSeeds of domesticated barley are grouped into two distinct types, which differ in morphology. Caryopses covered by adaxial (palea) and abaxial (lemma) hulls that tightly adhere to the pericarp at maturity give rise to hulled seeds whereas caryopses without adhering hulls give rise to naked seeds. The naked caryopsis character is an essential trait regarding the end use of barley.ResultsTo uncover the genetic basis of the trait, a genome-wide association study (GWAS) has been performed in a panel comprising 222 2-rowed and 303 6-rowed spring barley landrace accessions. In addition to the well-described Nud locus on chromosome 7H, three novel loci showed strong associations with the trait: the first locus on 2H was specifically detected in 6-rowed accessions, the second locus on 3H was found in 2-rowed accessions from Eurasia and the third locus on 6H was revealed in 6-rowed accessions from Ethiopia. PCR analysis of naked accessions also confirmed the absence of a 17 kb region harboring the Nud gene on chromosome 7H for all but one naked accession. The latter was characterized by a slightly variant phenotype of the caryopsis.ConclusionOur findings provide evidence of the pervasiveness of the 17 kb deletion in spring barley from different geographic regions and at the same time reveal genomic footprints of selection in naked barley, which follow both geographic and morphological patterns.

High-throughput 3D modelling to dissect the genetic control of leaf elongation in barley (Hordeum vulgare).

SummaryTo optimize shoot growth and structure of cereals, we need to understand the genetic components controlling initiation and elongation. While measuring total shoot growth at high throughput using 2D imaging has progressed, recovering the 3D shoot structure of small grain cereals at a large scale is still challenging. Here, we present a method for measuring defined individual leaves of cereals, such as wheat and barley, using few images. Plant shoot modelling over time was used to measure the initiation and elongation of leaves in a bi‐parental barley mapping population under low and high soil salinity. We detected quantitative trait loci (QTL) related to shoot growth per se, using both simple 2D total shoot measurements and our approach of measuring individual leaves. In addition, we detected QTL specific to leaf elongation and not to total shoot size. Of particular importance was the detection of a QTL on chromosome 3H specific to the early responses of leaf elongation to salt stress, a locus that could not be detected without the computer vision tools developed in this study.

Identification of QTL Related to ROS Formation under Hypoxia and Their Association with Waterlogging and Salt Tolerance in Barley.

Waterlogging is a serious environmental problem that limits agricultural production in low-lying rainfed areas around the world. The major constraint that plants face in a waterlogging situation is the reduced oxygen availability. Accordingly, all previous efforts of plant breeders focused on traits providing adequate supply of oxygen to roots under waterlogging conditions, such as enhanced aerenchyma formation or reduced radial oxygen loss. However, reduced oxygen concentration in waterlogged soils also leads to oxygen deficiency in plant tissues, resulting in an excessive accumulation of reactive oxygen species (ROS) in plants. To the best of our knowledge, this trait has never been targeted in breeding programs and thus represents an untapped resource for improving plant performance in waterlogged soils. To identify the quantitative trait loci (QTL) for ROS tolerance in barley, 187 double haploid (DH) lines from a cross between TX9425 and Naso Nijo were screened for superoxide anion (O2•−) and hydrogen peroxide (H2O2)—two major ROS species accumulated under hypoxia stress. We show that quantifying ROS content after 48 h hypoxia could be a fast and reliable approach for the selection of waterlogging tolerant barley genotypes. The same QTL on chromosome 2H was identified for both O2•− (QSO.TxNn.2H) and H2O2 (QHP.TxNn.2H) contents. This QTL was located at the same position as the QTL for the overall waterlogging and salt tolerance reported in previous studies, explaining 23% and 24% of the phenotypic variation for O2•− and H2O2 contents, respectively. The analysis showed a causal association between ROS production and both waterlogging and salt stress tolerance. Waterlogging and salinity are two major abiotic factors affecting crop production around the globe and frequently occur together. The markers associated with this QTL could potentially be used in future breeding programs to improve waterlogging and salinity tolerance.

Introgression of resistance to Rhopalosiphum padi L. from wild barley into cultivated barley facilitated by doubled haploid and molecular marker techniques

Key messageLong-term pre-breeding using Hordeum vulgare ssp. spontaneum as a donor of bird cherry-oat aphid resistance has resulted in agronomically improved resistance sources of barley along with easy-to-use molecular markers.Bird cherry-oat aphid (Rhopalosiphum padi L.) is a pest and a virus vector in barley to which there are no bred-resistant cultivars. The present study describes how resistance from Hordeum vulgare ssp. spontaneum has been introgressed in cultivated barley via five successive crosses with the same cultivar Lina (BC) and in parallel with other more modern barley cultivars. Most of the selections for resistance are based on measurements of individual aphid growth in the laboratory. This very slow phenotyping method has been complemented by molecular marker evaluation and application in part of the breeding material. Doubled haploid production in each generation has been crucial for more precise selection of lines with the quantitatively expressed resistance. A field trial of selected “BC3”-generation lines essentially confirmed the laboratory results, so did genotyping of the whole pedigree of parents and selected “BC2” and “BC4” offspring lines. The Infinium iSelect 50 K SNP assay confirmed relationships between lines and discerned several new markers for a resistance QTL on chromosome 2H.

Fine mapping of Rha2 in barley reveals candidate genes for resistance against cereal cyst nematode

Key messageThe cereal cyst nematode resistance locus Rha2 was mapped to a 978 kbp region on the long arm of barley chromosome 2H. Three candidate genes are discussed.The cereal cyst nematode (CCN) Heterodera avenae is a soil-borne obligate parasite that can cause severe damage to cereals. This research involved fine mapping of Rha2, a CCN resistance locus on chromosome 2H of barley. Rha2 was previously mapped relative to restriction fragment length polymorphisms (RFLPs) in two mapping populations. Anchoring of flanking RFLP clone sequences to the barley genome assembly defined an interval of 5077 kbp. Genotyping-by-sequencing of resistant and susceptible materials led to the discovery of potentially useful single nucleotide polymorphisms (SNPs). Assays were designed for these SNPs and applied to mapping populations. This narrowed the region of interest to 3966 kbp. Further fine mapping was pursued by crossing and backcrossing the resistant cultivar Sloop SA to its susceptible ancestor Sloop. Evaluation of F2 progeny confirmed that the resistance segregates as a single dominant gene. Genotyping of 9003 BC2F2 progeny identified recombinants. Evaluation of recombinant BC2F3 progeny narrowed the region of interest to 978 kbp. Two of the SNPs within this region proved to be diagnostic of CCN resistance across a wide range of barley germplasm. Fluorescence-based and gel-based assays were developed for these SNPs for use in marker-assisted selection. Within the candidate region of the reference genome, there are nine high-confidence predicted genes. Three of these, one that encodes RAR1 (a cysteine- and histidine-rich domain-containing protein), one that is predicted to encode an acetylglutamate kinase and one that is predicted to encode a tonoplast intrinsic protein, are discussed as candidate genes for CCN resistance.

Undesired fertility restoration in msm1 barley associates with two mTERF genes

The novel Rfm3 locus causing undesired fertility restoration in the msm1 cytoplasm of winter barley is located on the short arm of chromosome 6H. Undesired fertility restoration of cytoplasmic male sterile (CMS) mother lines in absence of the functional Rfm1 restorer gene is a significant problem for hybrid breeding in winter barley. Here, we describe that a novel restorer locus on the short arm of chromosome 6H, designated Rfm3, is closely linked to two mitochondrial transcription termination factor family (mTERF) protein coding genes. Genome-wide association studies in a multiparental mapping population revealed that two of the most significantly associated markers are located very close to these genes, with one marker lying directly within one mTERF gene sequence. Sequences of the candidate genes in the parental lines, segregating individuals and an independent set of breeding lines clearly revealed haplotypes discriminating completely sterile, partially fertile and Rfm1-restorer lines. The haplotypes segregate for several single nucleotide polymorphisms, a 6bp insertion-deletion (InDel) polymorphism and another 2bp InDel. CMS-unstable genotypes carrying haplotypes associated with undesired fertility restoration showed significantly higher grain setting on bagged spikes when plants were subjected to elevated temperatures during anthesis, indicating a temperature influence on pollen fertility. SNPs associated with desirable Rfm3 haplotypes can be implemented in marker-assisted selection of stable CMS mother lines.

Novel loci and a role for nitric oxide for seed dormancy and preharvest sprouting in barley.

Barley is used for food and feed, and brewing. Nondormant seeds are required for malting, but the lack of dormancy can lead to preharvest sprouting (PHS), which is also undesired. Here, we report several new loci that modulate barley seed dormancy and PHS. Using genome-wide association mapping of 184 spring barley genotypes, we identified four new, highly significant associations on chromosomes 1H, 3H, and 5H previously not associated with barley seed dormancy or PHS. A total of 71 responsible genes were found mostly related to flowering time and hormone signalling. A homolog of the well-known Arabidopsis Delay of Germination 1 (DOG1) gene was annotated on the barley chromosome 3H. Unexpectedly, DOG1 appears to play only a minor role in barley seed dormancy. However, the gibberellin oxidase gene HvGA20ox1 contributed to dormancy alleviation, and another seven important loci changed significantly during after-ripening. Furthermore, nitric oxide release correlated negatively with dormancy and shared 27 associations. Origin and growth environment affected seed dormancy and PHS more than did agronomic traits. Days to anthesis and maturity were shorter when seeds were produced under drier conditions, seeds were less dormant, and PHS increased, with a heritability of 0.57-0.80. The results are expected to be useful for crop improvement.

Population Genetics Revealed a New Locus That Underwent Positive Selection in Barley.

Trait variation among natural populations and their cultivated relatives occurs due to evolutionary forces, including selection and drift. In the present study, we analyzed these forces at the locus level in a global barley diversity set using population genetics analysis. Genome-wide outlier loci detection found a locus on chromosome 2H at which a common single nucleotide polymorphism (SNP) marker SCRI_RS_170235 accounted for the highest diversity index (Fst) values between cultivars and landraces and between cultivars and wild accessions. For a population wide genetic analysis, we developed a Polymerase Chain Reaction (PCR)-based cleaved amplified polymorphic marker at the identified locus. Marker genotyping of 115 genotypes identified a characteristic distribution of polymorphisms among the cultivated, landraces, and wild barley accessions. Using this marker, we screened a library of wild barley introgression lines (IL) and selected IL S42IL-109 that carried the wild introgression of the outlier locus in cultivar ‘Scarlett’ background. A plethora of phenotypic evaluation was performed between the S42IL109 and ‘Scarlett’ to dissect the putative effect of the identified outlier locus. Comparison of S42IL109 and ‘Scarlett’ revealed significant difference in the development of phyllochron two (Phyl-2), phyllochron three (Phyl-3), and phyllochron four (Phyl-4). Across the three phyllochrons, it was consistently observed that S42IL109 developed successive leaves in a shorter time span, by one to two days, compared to ‘Scarlett’. These data suggest that outlier locus may influence phyllochron variation which underwent positive selection in barley.

Expression Analysis of Pyrenophora teres f. maculata-Responsive Loci in Hordeum vulgare

Abstract Pyrenophora teres f. maculata is the causal agent of barley spot form net blotch (SFNB), a major stubble-borne disease in many barley-growing areas worldwide. In plants, the Nucleotide-Binding Site-Leucine-Rich Repeat (NBS-LRR) gene family functions in immunity against a variety of pathogens and pests. From a pre-established set of NBS-type resistance gene candidates, we have selected three candidate genes, HvNBS10, HvNBS72 and HvNBS85, to analyze their possible involvement in P. teres f. maculata resistance. The studied genes were mapped on chromosomes 5H and 7H. Expression profiles using qRT-PCR, 48 hours after infection by P. teres. f. maculata, revealed that the transcription of all genes acted in the same direction (down-regulation) in both resistant and susceptible cultivars, although they showed a variation in transcript dosage. This result suggests that coordinated transcriptional responses of multiple barley NBS genes would be required to an efficient response against P. teres f. maculata. Moreover, the phylogenetic analysis revealed that the studied barley candidate R genes were characterized by a high homology with the barley Nbs2-Rdg2a gene conferring resistance to the fungus Pyrenophora graminea, suggesting a common origin of P. graminea and P. teres resistance genes in barley, following pathogens evolution. The genes characterized in the present study hold potential in elucidating the molecular pathways and developing novel markers associated with SFNB resistance in barley.

Mapping QTLs for Grain Protein Concentration and Agronomic Traits under Different Nitrogen Levels in Barley

Growing crops with improved N use efficiency (NUE) could decrease fertilizer inputs and the negative environmental effects of N overuse. We measured nine agronomic and yield component traits under N‐limiting and nonlimiting treatments for 250 two‐row and 250 six‐row barley (Hordeum vulgare L.) breeding lines. We calculated four stress indices to approximate NUE. To identify quantitative trait loci (QTLs), we conducted association mapping (AM) for these phenotypic data with 3072 single nucleotide polymorphism markers. All traits and two stress indices—the geometric mean and the stress tolerance index—exhibited significant genetic variation within the two‐row and six‐row panels. Of the 25 QTLs identified in the two‐row panel and 31 identified in the six‐row panel, only four were common to both. Four of the QTLs detected in the two‐row panel and 10 detected in the six‐row panel were identified under the N‐limiting treatment or for a stress index, but not under the nonlimiting treatment, signaling that they may be associated with NUE. We detected a QTL for grain protein concentration (GPC) on chromosome 6H that has been mapped previously in barley and is collinear with the well‐characterized Gpc‐B1 locus in wheat. Groups of lines defined by marker haplotypes at this locus exhibited significant differences in GPC but not in grain yield. These results support that breeding strategies for improving NUE include crossing between two‐ and six‐row parents with complementary alleles, phenotypic selection based on stress indices, marker‐assisted selection for desirable alleles, and genomic selection to capture small‐effect loci.

The identification of multiple SNP markers for scald resistance in spring barley through restriction-site associated sequencing

Leaf scald caused by Rhynchosporium commune (formerly R. secalis) is an important fungal disease in barley (Hordeum vulgare) in western Canada. Pyramiding multiple scald resistance qualitative trait loci (QTL) is considered an effective strategy for breeding durable scald resistance into barley. The objective of this study was to map QTLs with restriction site-associated (RAD) markers and identify single nucleotide polymorphism (SNP) markers for scald resistance. Two recombinant inbred line (RIL) populations (crosses Harrington/Seebe and Seebe/Shyri) with good resistance to local scald isolates were genotyped by RAD sequencing (RADseq). A total of 4203 SNPs were obtained from the RADseq analysis of 162 F7 RILs. Inclusive composite interval mapping identified multiple major QTLs for scald resistance on chromosomes 3H, 4H, and 5H in Shyri, and 2H and 6H in Seebe. SNP markers from Shyri were located in the same region as the previously reported 3H QTL Rrs1. Several SNP markers from Seebe clustered on chromosome 6H near a major scald resistance QTL. The 6H QTL appeared effective for both adult plant resistance and seedling resistance, and explained up to 70.9% of the phenotypic variation among the sequenced lines. A tightly linked SNP for the major 6H QTL was converted into an allele specific PCR marker. The QTLs and their genetic markers found in this study will be useful in barley breeding for the selection of resistance to barley leaf scald.

The Coiled-Coil NLR Rph1, Confers Leaf Rust Resistance in Barley Cultivar Sudan.

Unraveling and exploiting mechanisms of disease resistance in cereal crops is currently limited by their large repeat-rich genomes and the lack of genetic recombination or cultivar (cv)-specific sequence information. We cloned the first leaf rust resistance gene Rph1 (Rph1 a) from cultivated barley (Hordeum vulgare) using "MutChromSeq," a recently developed molecular genomics tool for the rapid cloning of genes in plants. Marker-trait association in the CI 9214/Stirling doubled haploid population mapped Rph1 to the short arm of chromosome 2H in a physical region of 1.3 megabases relative to the barley cv Morex reference assembly. A sodium azide mutant population in cv Sudan was generated and 10 mutants were confirmed by progeny-testing. Flow-sorted 2H chromosomes from Sudan (wild type) and six of the mutants were sequenced and compared to identify candidate genes for the Rph1 locus. MutChromSeq identified a single gene candidate encoding a coiled-coil nucleotide binding site Leucine-rich repeat (NLR) receptor protein that was altered in three different mutants. Further Sanger sequencing confirmed all three mutations and identified an additional two independent mutations within the same candidate gene. Phylogenetic analysis determined that Rph1 clustered separately from all previously cloned NLRs from the Triticeae and displayed highest sequence similarity (89%) with a homolog of the Arabidopsis (Arabidopsis thaliana) disease resistance protein 1 protein in Triticum urartu In this study we determined the molecular basis for Rph1-mediated resistance in cultivated barley enabling varietal improvement through diagnostic marker design, gene editing, and gene stacking technologies.

Association and genome analyses to propose putative candidate genes for malt quality traits.

We studied the genetics of nine malt quality traits using association genetics in a panel of North Dakota, ICARDA, and Ethiopian barley lines. Grain samples harvested from Bekoji in 2011 and 2012 were used. The mapping panel revealed strong population structure explained by inflorescence-type, geographic origin, and breeding history. North Dakota germplasm were superior in malt quality traits and they can be donors to improve malt quality properties. We identified 106 marker-trait associations (MTAs) for the nine traits, representing 81 genomic regions across all barley chromosomes. Chromosomes 3H, 5H, and 7H contained most of the MTAs (58.5%). Nearly 18.5% of these genomic regions contained two to three malt quality traits. Within ±250 kb of 81 genomic regions, we recovered 348 barley genes, with some potential impacting malt quality. These include invertase, β-fructofuranosidase, α-glucosidase, serine carboxypeptidase, and bidirectional sugar transporter SWEET14-like protein. Eighteen of these genes were also previously reported in the Hordeum Toolbox, and 17 of them highly expressed during the germination process. The results from this study invite further follow-up functional characterization experiments to relate the genes with individual malt quality traits with higher confidence. It also provides germplasm resources for malt barley improvement. © 2018 Society of Chemical Industry.

Characterisation of barley resistance to rhynchosporium on chromosome 6HS.

Major resistance gene to rhynchosporium, Rrs18, maps close to the telomere on the short arm of chromosome 6H in barley. Rhynchosporium or barley scald caused by a fungal pathogen Rhynchosporium commune is one of the most destructive and economically important diseases of barley in the world. Testing of Steptoe×Morex and CIho 3515×Alexis doubled haploid populations has revealed a large effect QTL for resistance to R. commune close to the telomere on the short arm of chromosome 6H, present in both populations. Mapping markers flanking the QTL from both populations onto the 2017 Morex genome assembly revealed a rhynchosporium resistance locus independent of Rrs13 that we named Rrs18. The causal gene was fine mapped to an interval of 660Kb using Steptoe×Morex backcross 1 S2 and S3 lines with molecular markers developed from Steptoe exome capture variant calling. Sequencing RNA from CIho 3515 and Alexis revealed that only 4 genes within the Rrs18 interval were transcribed in leaf tissue with a serine/threonine protein kinase being the most likely candidate for Rrs18.

Pyramiding rpg4- and Rpg1-Mediated Stem Rust Resistance in Barley Requires the Rrr1 Gene for Both to Function.

Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt) is an economically important disease of wheat and barley. Rpg1 is the only resistance gene deployed in Midwestern US barley varieties and provides remarkable resistance to most North American races, except Pgt race QCCJB. Rpg1 is also ineffective against Pgt race TTKSK and its lineage that originated in Africa. The barley rpg4-mediated resistance locus (RMRL) conferring resistance to Pgt races QCCJB and TTKSK was isolated from line Q21861, which is resistant to all known Pgt races due to Rpg1 and RMRL. To develop elite barley varieties RMRL was pyramided into the varieties, Pinnacle and Conlon (both contain Rpg1), producing the near isogenic lines (NILs), Pinnacle RMRL-NIL (PRN) and Conlon RMRL-NIL (CRN). The CRN was resistant to Pgt races QCCJB (RMRL specific) and HKHJC (Rpg1 specific) at the seedling stage and Pgt race TTKSK (RMRL specific) at the adult stage. In contrast, PRN was susceptible to QCCJB and HKHJC at the seedling stage and TTKSK at the adult stage. Interestingly, PRN’s susceptibility to QCCJB and HKHJC showed that RMRL was non-functional in the Pinnacle background but its presence also suppressed Rpg1-mediated resistance. Thus, in the absence of a gene/s found in the Q21861 background, Rpg1 becomes non-functional if RMRL is present, suggesting that another polymorphic gene, that we designated Rrr1 (required for rpg4-mediated resistance 1), is required for RMRL resistance and Rpg1-mediated resistance in the presence of RMRL. Utilizing a PRN/Q21861 derived recombinant inbred line (RIL) population, Rrr1 was delimited to a ∼0.5 MB physical region, slightly proximal (∼1.8 MB) of RMRL on barley chromosome 5H. A second gene, designated required for Rpg1-mediated resistance 2 (Rrr2), with duplicate gene action to Rrr1 in Rpg1-mediated resistance function, was genetically delimited to a physical region of ∼0.7 MB, slightly distal (∼3.1 MB) to Rpg1 on the short arm of barley chromosome 7H. Thus, Rrr1 is required for RMRL resistance and Rrr1 or Rrr2 is required for functional Rpg1-mediated resistance in the presence of the RMRL introgression. Candidate Rrr1 and Rrr2 genes were identified that need to be considered when pyramiding Rpg1 and RMRL in barley.

Development and genetic analysis of wheat double substitution lines carrying Hordeum vulgare 2H and Thinopyrum intermedium 2Ai#2 chromosomes

Thinopyrum intermedium and barley are two close relatives of wheat and carry many genes that are potentially valuable for the improvement of various wheat traits. In this study we created wheat double substitution lines by hybridizing different wheat–Th. intermedium and wheat–barley disomic alien substitution lines, with the aim of using genes in Th. intermedium and barley for wheat breeding and investigating the genetic behavior of alien chromosomes and their wheat homoeologs. As expected, we obtained two types of wheat double substitution lines, 2D2Ai#2(2B)2H(2A) and 2A2Ai#2(2B)2H(2D), in which different group 2 wheat chromosomes were replaced by barley chromosome 2H and Th. intermedium chromosome 2Ai#2. The new materials were characterized using molecular markers, genomic in situ hybridization (GISH), and fluorescent in situ hybridization (FISH). GISH and FISH experiments revealed that the double substitution lines harbor 42 chromosomes including 38 wheat chromosomes, a pair of barley chromosomes, and a pair of Th. intermedium chromosomes. Analysis using specific DNA markers showed that two pairs of wheat homoeologous group 2 chromosomes in the new lines were substituted by a pair of 2H and a pair of 2Ai#2 chromosomes. Chromosome 2H showed a higher transmission rate than 2Ai#2, and both chromosomes were preferentially transmitted between generations via female gametes. Evaluation of botanic and agronomic traits demonstrated that, compared with their parents, the new lines showed similar growth habits and plant type but differences in plant height, flowering date, and self-fertility. Cytological observations using different probes suggested that the double substitution lines showed nearly normal genetic behavior before and during meiosis. The novel substitution lines can potentially be used in wheat meiosis research and breeding programs.

Genome-wide Scan Using DArT Markers for Selection Footprints in Six-rowed Naked Barley from the Tibetan Plateau

As one of the world’s earliest domesticated crops, barley is a model species for the study of evolution and domestication. Domestication is an evolutionary process whereby a population adapts, through selection; to new environments created by human cultivation. We describe the genome-scanning of molecular diversity to assess the evolution of barley in the Tibetan Plateau. We used 667 Diversity Arrays Technology (DArT) markers to genotype 185 barley landraces and wild barley accessions from the Tibetan Plateau. Genetic diversity in wild barley was greater than in landraces at both genome and chromosome levels, except for chromosome 3H. Landraces and wild barley accessions were clearly differentiated genetically, but a limited degree of introgression was still evident. Significant differences in diversity between barley subspecies at the chromosome level were observed for genes known to be related to physiological and phenotypical traits, disease resistance, abiotic stress tolerance, malting quality and agronomic traits. Selection on the genome of six-rowed naked barley has shown clear multiple targets related to both its specific end-use and the extreme environment in Tibet. Our data provide a platform to identify the genes and genetic mechanisms that underlie phenotypic changes, and provide lists of candidate domestication genes for modified breeding strategies.