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Key message This study reported validation and fine mapping of a Fusarium crown rot resistant locus on chromosome arm 6HL in barley using near isogenic lines, transcriptome sequences, and a large near isogenic line-derived population. Abstract Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, is a chronic and serious disease affecting cereal production in semi-arid regions globally. The increasing prevalence of this disease in recent years is attributed to the widespread adoption of minimum tillage and stubble retention practices. In the study reported here, we generated eight pairs of near isogenic lines (NILs) targeting a putative QTL (Qcrs.caf-6H) conferring FCR resistance in barley. Assessing the NILs confirmed the large effect of this locus. Aimed to develop markers that can be reliably used in incorporating this resistant allele into breeding programs and identify candidate genes, transcriptomic analyses were conducted against three of the NIL pairs and a large NIL-derived population consisting of 1085 F7 recombinant inbred lines generated. By analyzing the transcriptomic data and the fine mapping population, Qcrs.caf-6H was delineated into an interval of 0.9 cM covering a physical distance of ~ 547 kb. Six markers co-segregating with this locus were developed. Based on differential gene expression and SNP variations between the two isolines among the three NIL pairs, candidate genes underlying the resistance at this locus were detected. These results would improve the efficiency of incorporating the targeted locus into barley breeding programs and facilitate the cloning of causal gene(s) responsible for the resistance.

In this first genetic study on assessing leaf thickness directly in cereals, major and environmentally stable QTL were detected in barley and candidate genes underlying a major locus were identified. Leaf thickness (LT) is an important characteristic affecting leaf functions which have been intensively studied. However, as LT has a small dimension in many plant species and technically difficult to measure, previous studies on this characteristic are often based on indirect estimations. In the first study of detecting QTL controlling LT by directly measuring the characteristic in barley, large and stable loci were detected from both field and glasshouse trials conducted in different cropping seasons by assessing a population of 201 recombinant inbred lines. Four loci (locating on chromosome arms 2H, 3H, 5H and 6H, respectively) were consistently detected for flag leaf thickness (FLT) in each of these trials. The one on 6H had the largest effect, with a maximum LOD 9.8 explaining up to 20.9% of phenotypic variance. FLT does not only show strong interactions with flag leaf width and flag leaf area but has also strong correlations with fertile tiller number, spike row types, kernel number per spike and heading date. Though with reduced efficiency, these loci were also detectable from assessing second last leaf of fully grown plants or even from assessing the third leaves of seedlings. Taking advantage of the high-quality genome assemblies for both parents of the mapping population used in this study, three candidate genes underlying the 6H QTL were predicted based on orthologous analysis. These results do not only broaden our understanding on genetic basis of LT and its relationship with other traits in cereal crops but also form the bases for cloning and functional analysis of genes regulating LT in barley.

Background Polyploids are common in flowering plants and they tend to have more expanded ranges of distributions than their diploid progenitors. Possible mechanisms underlying polyploid success have been intensively investigated. Previous studies showed that polyploidy generates novel changes and that subgenomes in allopolyploid species often differ in gene number, gene expression levels and levels of epigenetic alteration. It is widely believed that such differences are the results of conflicts among the subgenomes. These differences have been treated by some as subgenome dominance, and it is claimed that the magnitude of subgenome dominance increases in polyploid evolution. Scope In addition to changes which occurred during evolution, differences between subgenomes of a polyploid species may also be affected by differences between the diploid donors and changes which occurred during polyploidization. The variable genome components in many plant species are extensive, which would result in exaggerated differences between a subgenome and its progenitor when a single genotype or a small number of genotypes are used to represent a polyploid or its donors. When artificially resynthesized polyploids are used as surrogates for newly formed genotypes which have not been exposed to evolutionary selection, differences between diploid genotypes available today and those involved in the formation of the natural polyploid genotypes must also be considered. Conclusions Contrary to the now widely held views that subgenome biases in polyploids are the results of conflicts among the subgenomes and that one of the parental subgenomes generally retains more genes which are more highly expressed, available results show that subgenome biases mainly reflect legacy from the progenitors and that they can be detected before the completion of polyploidization events. Further, there is no convincing evidence that the magnitudes of subgenome biases have significantly changed during evolution for any of the allopolyploid species assessed.

Subgenome asymmetry (SA) has routinely been attributed to different responses between the subgenomes of a polyploid to various stimuli during evolution. Here, we compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, consistent differences were not detected between these two types of polyploid genotypes, although they differ in times exposed to evolutionary selection. The estimated ratio of shared genes between a subgenome and its diploid donor was invariably higher for the artificial allopolyploid genotypes than those for the natural genotypes, which is expected as it is now well-known that many genes in a species are not shared among all individuals. As the exact diploid parent for a given subgenome is unknown, the estimated ratios of shared genes for the natural genotypes would also include difference among individual genotypes of the diploid donor species. Further, we detected the presence of SA in genotypes before the completion of the polyploidization events as well as in those which were not formed via polyploidization. These results indicate that SA may, to a large degree, reflect differences between its diploid donors or that changes occurred during polyploid evolution are defined by their donor genomes.

Kernel weight (KW), together with kernel number per unit area, determines yield of cereal crops. Here, two barley recombinant inbred lines (RILs) populations with a shared parent were used to identify loci controlling KW. One is Baudin/AWCS276 (BA) for which a linkage map was available. Several large-effect QTL controlling KW were detected in this population. Another is Morex/AWCS276 (MA). A linkage map with 5273 makers formed 1454 clusters, was constructed by the genotyping by sequence (GBS) data of 201 RILs from this population. A single marker was selected to represent each of the clusters and the linkage map constructed with these markers covers a total length of 1022.4 cM with an average interval of approximately 0.7 cM between loci. Three of the large-effect loci controlling KW (located on 2HL, 6HL, and 7HL, respectively) identified from the BA population were also detected in the MA population under different environments. The locus on 6HL was detected in each of the experiments conducted for both populations thus was selected for developing near isogenic lines (NILs). Apart from KW, the two isolines for each pair of the putative NILs obtained showed no significant difference for any of the morphological characteristics assessed. The average difference in KW between the isolines for all the NILs obtained was about 15% based on assessments under both glasshouse and field conditions. Taken advantage that high quality genome assemblies for both Morex and AWCS276 are available, we identified candidate genes underlying two of the three loci based on an orthologous analysis. The NILs developed and the candidate genes identified in this study should facilitate the cloning and functional analysis of genes regulating KW in barley.

Fusarium crown rot (FCR), a chronic and severe disease caused by various Fusarium species, is prevalent in semi-arid cropping regions worldwide. One of the major QTL conferring FCR resistance was detected on chromosome arm 1HL (Qcrs.cpi-1H) in barley. To develop markers that can be reliably used to incorporate the resistance locus into breeding programs, we developed and assessed a near-isogenic line-derived population consisting of 1180 recombinant inbred lines targeting the locus. Using this population, we delineated Qcrs.cpi-1H into an interval of 0.4 cM covering a physical length of about 487 kb. Six markers co-segregating with this locus were generated. Co-linearity for genes located in this interval between the genome of barley and those of either rice or Brachypodium distachyon is poor. Three genes with non-synonymous variations between the resistant and susceptible lines were identified within the interval. The results reported in this study not only provide markers for integrating Qcrs.cpi-1H into breeding programs, but also form a solid foundation for cloning the causal gene(s) underlying this locus.

We identified 1.844 million barley pan-genome sequence anchors from 12,306 genotypes using genetic mapping and machine learning. There is increasing evidence that genes from a given crop genotype are far to cover all genes in that species; thus, building more comprehensive pan-genomes is of great importance in genetic research and breeding. Obtaining a thousand-genotype scale pan-genome using deep-sequencing data is currently impractical for species like barley which has a huge and highly repetitive genome. To this end, we attempted to identify barley pan-genome sequence anchors from a large quantity of genotype-by-sequencing (GBS) datasets by combining genetic mapping and machine learning algorithms. Based on the GBS sequences from 11,166 domesticated and 1140 wild barley genotypes, we identified 1.844 million pan-genome sequence anchors. Of them, 532,253 were identified as presence/absence variation (PAV) tags. Through aligning these PAV tags to the genome of hulless barley genotype Zangqing320, our analysis resulted in a validation of 83.6% of them from the domesticated genotypes and 88.6% from the wild barley genotypes. Association analyses against flowering time, plant height and kernel size showed that the relative importance of the PAV and non-PAV tags varied for different traits. The pan-genome sequence anchors based on GBS tags can facilitate the construction of a comprehensive pan-genome and greatly assist various genetic studies including identification of structural variation, genetic mapping and breeding in barley.

Leaf thickness (LT) is an important characteristic affecting leaf functions which have been intensively studied. However, as LT has a small dimension in many plant species and technically difficult to measure, previous studies on this characteristic are often based on indirectly estimations. In the first study of detecting QTL controlling LT by directly measuring the characteristic in barley, large and stable loci were detected from both field and glasshouse trials conducted in different cropping seasons. Four loci (locating on chromosome arms 2H, 3H, 5H and 6H, respectively) were consistently detected for flag leaf thickness (FLT) in each of these trials. The one on 6H had the largest effect, with a maximum LOD 9.8 explaining up to 20.9% of phenotypic variance. FLT does not only show strong interactions with flag leaf width and flag leaf area but has also strong correlations with fertile tiller number, spike row types, kernel number per spike, and heading date. Though with reduced efficiency, these loci were also detectable from assessing second last leaf of fully grown plants or even from assessing the third leaves of seedlings. Taken advantage of the high-quality genome assemblies for both parents of the mapping population used in this study, three candidate genes underlying the 6H QTL were identified based on orthologous analysis. These results do not only provide direct evidence showing the importance of LT in improving kernel yield of cereal crops but also form the bases for cloning and functional analysis of genes regulating LT in barley.

Background As one of the most important food crops in the world, increasing wheat (Triticum aestivum L.) yield is an urgent task for global food security under the continuous threat of stripe rust (caused by Puccinia striiformis f. sp. tritici) in many regions of the world. Molecular marker-assisted breeding is one of the most efficient ways to increase yield. Here, we identified loci associated to multi-environmental yield-related traits under stripe rust stress in 244 wheat accessions from Sichuan Province through genome-wide association study (GWAS) using 44,059 polymorphic markers from the 55 K single nucleotide polymorphism (SNP) chip. Results A total of 13 stable quantitative trait loci (QTLs) were found to be highly associating to yield-related traits, including 6 for spike length (SL), 3 for thousand-kernel weight (TKW), 2 for kernel weight per spike (KWPS), and 2 for both TKW and KWPS, in at least two test environments under stripe rust stress conditions. Of them, ten QTLs were overlapped or very close to the reported QTLs, three QTLs, QSL.sicau-1AL, QTKW.sicau-4AL, and QKWPS.sicau-4AL.1, were potentially novel through the physical location comparison with previous QTLs. Further, 21 candidate genes within three potentially novel QTLs were identified, they were mainly involved in the regulation of phytohormone, cell division and proliferation, meristem development, plant or organ development, and carbohydrate transport. Conclusions QTLs and candidate genes detected in our study for yield-related traits under stripe rust stress will facilitate elucidating genetic basis of yield-related trait and could be used in marker-assisted selection in wheat yield breeding. Electronic supplementary material The online version of this article (10.1186/s12864-019-6005-6) contains supplementary material, which is available to authorized users.

Background It has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications. Results In this study we constructed a pan-transcriptome for barley by de novo assembling 288 sets of RNA-seq data from 32 cultivated barley genotypes and 31 wild barley genotypes. The pan-transcriptome consists of 756,632 transcripts with an average N50 length of 1240 bp. Of these, 289,697 (38.2%) were not found in the genome of the international reference genotype Morex. The novel transcripts are enriched with genes associated with responses to different stresses and stimuli. At the pan-transcriptome level, genotypes of wild barley have a higher proportion of disease resistance genes than cultivated ones. Conclusions We demonstrate that the use of the pan-transcriptome dramatically improved the efficiency in detecting variation in barley. Analysing the pan-transcriptome also found that, compared with those in other categories, disease resistance genes have gone through stronger selective pressures during domestication. Electronic supplementary material The online version of this article (10.1186/s12864-018-5357-7) contains supplementary material, which is available to authorized users.

Trichomes are differentiated epidermal cells and can be found on above ground organs of nearly all land plants. Results from previous studies show that trichomes play important roles against a wide range of both biotic and abiotic stresses. By examining differences between parental genotypes of available populations, we identified a population of recombinant inbred lines showing clear segregation for trichome density and length. Assessing the F8 lines of the population growing in the field detected a major locus on chromosome arm 4BL. This locus was detected based the assessments of either fully expanded third leaves or flag leaves after anthesis. Based on the position of the QTL, an SSR marker was used to identify heterozygous plants at this locus from F5 lines derived from the same cross for the F8 population. Three pairs of near isogenic lines targeting this locus were obtained from these heterozygous plants. Difference in trichome length between the two lines with opposite alleles for each of these NIL pairs were similar to that between the two parental genotypes for the mapping populations, confirming that this single locus is mainly responsible for the trichome characteristics measured in this study. The allele with long and dense trichome is dominant as this characteristic was shown by the heterozygous individuals at this marker locus. Apart from the targeted locus, NIL pairs have highly homogeneous genetic backgrounds. Thus, the NILs could be invaluable in understanding the relationship between trichome density and resistance or tolerance to various biotic and abiotic stresses. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-021-01201-8.

Background: Fusarium crown rot is a chronic disease in cereal production worldwide. The impact of this disease is highly environmentally dependant and significant yield losses occur mainly in drought-affected crops. Results: In the study reported here, we evaluated possible relationships between genes conferring FCR resistance and drought tolerance using two approaches. The first approach studied FCR induced DEGs (differentially expressed genes) targeting two barley and one wheat loci against a panel of selected genes with known functions in drought tolerance. Of the 149 selected genes, 61% were responsive to FCR infection across the three loci. The second approach was an comparison of the global DEGs induced by FCR infection with the global transcriptomic responses under drought in wheat. This analysis found that approximately 48.0% percent of the DEGs detected one week following drought treatment and 74.4% of the DEGs detected three weeks following drought treatment were also differentially expressed between the susceptible and resistant isolines under FCR infection at one or more timepoints. As for the results from the first approach, the vast majority of common DEGs were downregulated under drought and expressed more highly in the resistant isoline than the sensitive isoline under FCR infection. Conclusions: Results from this study suggest that the resistant isoline in wheat was experiencing less drought stress, which could contribute to the stronger defence response than the sensitive isoline. However, most of the genes induced by drought stress in barley were more highly expressed in the susceptible isolines than the resistant isolines under infection, indicating that genes conferring drought tolerance and FCR resistance may interact differently between these two crop species. Nevertheless, the strong relationship between FCR resistance and drought responsiveness provide further evidence indicating the possibility to enhance FCR resistance by manipulating genes conferring drought tolerance.

Background: Brassica napus is one of the most important sources of vegetable oil for human nutrition and biofuel. It is an allotetraploid formed about 7500 years ago by hybridization between B. rapa and B. oleracea. Results from earlier studies show that the allopolyploidization process was accompanied by rapid and intensive changes and abundant homoeologous exchanges between the subgenomes have been accumulated during its short history of evolution. Results: By comparing differences between 19 artificially synthesized and 30 natural genotypes, we assessed possible changes in gene ratio, diversity and functional groups during the evolution and domestication of this species. This comparison revealed that gene ratio and diversity between the two subgenomes have hardly changed. However, large numbers of genes have been lost and many new genes gained. Compared with the artificial genotypes, the natural ones contain much lower proportions of genes conferring resistance and tolerance to biotic and abiotic stresses but much higher proportions of genes associated with seeds development and metabolic processes. The diploid donor for the A subgenome of B. napus contributed more genes involved in agronomic traits and the C subgenome donor contributed more genes related to cellular development and metabolic process. Conclusions: Our results show that genes conditioning resistance and tolerance to both biotic and abiotic stresses have suffered stronger selection during the evolution and domestication of B. napus, and that changes in different aspects including gene content and genome size in the allotetraploid are not random but dictated by its two diploid donors.

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A high-density genetic map constructed with a wheat 55 K SNP array was highly consistent with the physical map of this species and it facilitated the identification of a novel major QTL for productive tiller number. Productive tiller number (PTN) plays a key role in wheat grain yield. In this study, a recombinant inbred line population with 199 lines derived from a cross between '20828' and 'Chuannong16' was used to construct a high-density genetic map using wheat 55 K single nucleotide polymorphism (SNP) array. The constructed genetic map contains 12,109 SNP markers spanning 3021.04 cM across the 21 wheat chromosomes. The orders of the genetic and physical positions of these markers are generally in agreement, and they also match well with those based on the 660 K SNP array from which the one used in this study was derived. The ratios of SNPs located in each of the wheat deletion bins were similar among the wheat 9 K, 55 K, 90 K, 660 K and 820 K SNP arrays. Based on the constructed maps, a novel major quantitative trait locus QPtn.sau-4B for PTN was detected across multi-environments in a 0.55 cM interval on 4B and it explained 17.23-45.46% of the phenotypic variance. Twenty common genes in the physical interval between the flanking markers were identified on chromosome 4B of 'Chinese Spring' and wild emmer. These results indicate that wheat 55 K SNP array could be an ideal tool in primary mapping of target genes and the identification of QPtn.sau-4B laid a foundation for the following fine mapping and cloning work.

Crop productivity is highly dependent on successful seed germination and seedling establishment. This study evaluated two mapping populations, Batavia/Ernie (double haploid) and Synthetic/Opata (recombinant inbred lines), for early vigor under water stress and normal growing conditions. Significant gene, environment (water), and gene by environment interaction effects were observed. Broad sense heritability was 29 and 40% for the Batavia/Ernie and Synthetic/Opata populations, respectively. Quantitative trait loci (QTL) were analyzed based on single and multienvironment models. The two mapping populations differed in the number and locations of QTLs except qNev.uwa.4AL was identified in both populations under the non-stress condition, while qSev.uwa.3BL was specifically expressed under the stress condition in the Synthetic/Opata population. QTL by environment interaction (QEI) enabled identification of nine QTLs, including those identified by the single environment approach. Phenotypic variation expression (PVE) of QEIs ranged from 4.8 to 14.9% across the populations. Larger proportion of PVE of QEIs was explained by the additive components. Favorable alleles for three of the QTLs identified in the Synthetic/Opata population were derived from Synthetic, while Batavia contributed favorable alleles to a QTL on the long arm of chromosome 1D in the Batavia/Ernie population. QTL detected under water stress (qSev.uwa.3BL) co-located with the DREB 1 gene, which was mapped between markers Xmwg818 and Xfbb117 (58.1–77.6 cM). QTLs with high proportion of additive components can be validated for marker assisted gene pyramiding and selection.

Organic phosphorus (P) is an important component of the soil P pool, and it has been proven to be a potential source of P for plants. The phosphorus utilization efficiency (PUE) and PUE related traits (tiller number (TN), shoot dry weight (DW), and root dry weight) under different phytate-P conditions (low phytate-P, 0.05 mmol L−1 and normal phytate-P, 0.5 mmol L−1) were investigated using a population consisting of 128 recombinant inbred lines (RILs) at the vegetative stage in barley. The population was derived from a cross between a P-inefficient genotype (Baudin) and a P-efficient genotype (CN4027, a Hordeum spontaneum accession). A major locus (designated Qpue.sau-3H) conferring PUE was detected in shoots and roots from the RIL population. The quantitative trait locus (QTL) was mapped on chromosome 3H and the allele from CN4027 confers high PUE. This locus explained up to 30.3 and 28.4% of the phenotypic variance in shoots under low and normal phytate-P conditions, respectively. It also explains 28.3 and 30.7% of the phenotypic variation in root under the low and normal phytate-P conditions, respectively. Results from this study also showed that TN was not correlated with PUE, and a QTL controlling TN was detected on chromosome 5H. However, dry weight (DW) was significantly and positively correlated with PUE, and a QTL controlling DW was detected near the Qpue.sau-3H locus. Based on a covariance analysis, existing data indicated that, although DW may affect PUE, different genes at this locus are likely involved in controlling these two traits.

The phenomenon of overcompensation has been reported in various plant species although it has been treated by some as isolated incidents with only limited values. Reviewing reports on the extensive studies of defoliation in maize showed that different genotypes respond differently to defoliation, varying from phenomenal increase to significant loss in grain yield. The different responses of maize in kernel yield among genotypes to defoliation are confirmed in our experiments conducted in both China and Australia. Defoliated plants are likely to use less water during vegetative growth and that they also have better ability to extract water from the soil. We also found that defoliation dramatically delayed plant senescence under dry conditions, facilitating the production of high quality silage by widening the harvest window. As overcompensation occurs only in some genotypes, we believe that exploiting defoliation as a management practice directly for crop production can be risky. However, the fact that significant yield increase following defoliation does occur and that large genetic variation does exist meet the requirements for a successful breeding program. The detection of sizable quantitative trait locus (QTL) in the model plant species provides further evidence indicating the feasibility of exploiting this phenomenon through breeding. The stunning magnitudes of desirable responses reported in the literature suggest that overcompensation could become the most valuable breeding target in at least some species and its impact on crop production could be huge even if only a proportion of the reported variations could be captured.

This study demonstrates how identification of genes underpinning disease-resistance QTL based on differential expression and SNPs can be improved by performing transcriptomic analysis on multiple near isogenic lines. Transcriptomic analysis has been widely used to understand the genetic basis of a trait of interest by comparing genotypes with contrasting phenotypes. However, these approaches identify such large sets of differentially expressed genes that it proves difficult to isolate which genes underpin the phenotype of interest. This study tests whether using multiple near isogenic lines (NILs) can improve the resolution of RNA-seq-based approaches to identify genes underpinning disease-resistance QTL. A set of NILs for a major effect Fusarium crown rot-resistance QTL in barley on the 4HL chromosome arm were analysed under Fusarium crown rot using RNA-seq. Differential gene expression and single nucleotide polymorphism detection analyses reduced the number of putative candidates from thousands within individual NIL pairs to only one hundred and two genes, which were differentially expressed or contained SNPs in common across NIL pairs and occurred on 4HL. Our findings support the value of performing RNA-seq analysis using multiple NILs to remove genetic background effects. The enrichment analyses indicated conserved differences in the response to infection between resistant and sensitive isolines suggesting that sensitive isolines are impaired in systemic defence response to Fusarium pseudograminearum.

OsGW7 (also known as OsGL7) is homologous to the Arabidopsis thaliana gene that encodes LONGIFOLIA protein, which regulates cell elongation, and is involved in regulating grain length in rice. However, our knowledge on its ortholog in wheat, TaGW7, is limited. In this study, we identified and mapped TaGW7 in wheat, characterized its nucleotide and protein structures, predicted the cis-elements of its promoter, and analysed its expression patterns. The GW7 orthologs in barley (HvGW7), rice (OsGW7), and Brachypodium distachyon (BdGW7) were also identified for comparative analyses. TaGW7 mapped onto the short arms of group 2 chromosomes (2AS, 2BS, and 2DS). Multiple alignments indicated GW7 possesses five exons and four introns in all but two of the species analysed. An exon–intron junction composed of introns 3–4 and exons 4–5 was highly conserved. GW7 has a conserved domain (DUF 4378) and two neighbouring low complexity regions. GW7 was mainly expressed in wheat spikes and stems, in barley seedling crowns, and in rice anthers and embryo-sacs during early development. Drought and heat significantly increased and decreased GW7 expression in wheat, respectively. In barley, GW7 was significantly down-regulated in paleae and awns but up-regulated in seeds under drought treatment and down-regulated under Fusarium and stem rust inoculation. In rice, OsGW7 expression differed significantly under drought treatments. Collectively, these results provide insights into GW7 structure and expression in wheat, barley and rice. The GW7 sequence structure and expression data are the foundation for manipulating GW7 and uncovering its roles in plants.

Fusarium pseudograminearum is an important pathogen of wheat and barley, particularly in semi-arid environments. Previous genome assemblies for this organism were based entirely on short read data and are highly fragmented. In this work, a genetic map of F. pseudograminearum has been constructed for the first time based on a mapping population of 178 individuals. The genetic map, together with long read scaffolding of a short read-based genome assembly, was used to give a near-complete assembly of the four F. pseudograminearum chromosomes. Large regions of synteny between F. pseudograminearum and F. graminearum, the related pathogen that is the primary causal agent of cereal head blight disease, were previously proposed in the core conserved genome, but the construction of a genetic map to order and orient contigs is critical to the validation of synteny and the placing of species-specific regions. Indeed, our comparative analyses of the genomes of these two related pathogens suggest that rearrangements in the F. pseudograminearum genome have occurred in the chromosome ends. One of these rearrangements includes the transposition of an entire gene cluster involved in the detoxification of the benzoxazolinone (BOA) class of plant phytoalexins. This work provides an important genomic and genetic resource for F. pseudograminearum, which is less well characterized than F. graminearum. In addition, this study provides new insights into a better understanding of the sexual reproduction process in F. pseudograminearum, which informs us of the potential of this pathogen to evolve.

A wide range of differences between the subgenomes, termed as subgenome asymmetry or SA, has been reported in various polyploids and different species seem to have different responses to polyploidization. We compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, consistent differences in neither gene ratio nor relative diversity between the subgenomes were detected between these two types of polyploid genotypes although they differ in times exposed to evolutional selection. As expected, the estimated ratio of retained genes between a subgenome and its diploid donor was invariably higher for the artificial allopolyploid genotypes due likely to the presence of variable genome components (VGC). Clearly, the presence of VGC means that exaggerated differences between a donor and a subgenome in a polyploid are inevitable when random genotypes were used to represent species of either a polyploid or its donors. SA was also detected in genotypes before the completion of the polyploidization events as well as in those which were not formed via polyploidization. Considering that significant changes during and following polyploidization have been detected in previous studies, our results suggest that the influence of VGC needs to be considered in evaluating SA and that diploid donors may define changes in polyploid evolution.

BackgroundFusarium crown rot (FCR) is a chronic and severe disease in cereal production in semi-arid regions worldwide. One of the putative quantitative trait locus (QTL) designated as Qcrs.cpi-1H has been previously mapped on chromosome arm 1HL in barley.ResultsIn this study, five pairs of near-isogenic lines (NILs) targeting the 1HL locus were developed. Analysing the NILs found that the resistant allele at Qcrs.cpi-1H significantly reduced FCR severity. Transcriptomic analysis was then conducted against three of the NIL pairs, which placed the Qcrs.cpi-1H locus in an interval spanning about 11 Mbp. A total of 56 expressed genes bearing SNPs were detected in this interval, which would facilitate detailed mapping as well as cloning gene(s) underlying the resistance locus. Also, five differentially expressed genes (DEGs) bearing non-synonymous SNPs were identified in the interval. Differences in DEGs regulated by Qcrs.cpi-1H those by Qcrs.cpi-4H (another known locus conferring FCR resistance) indicate that different mechanisms could be involved in their resistance.ConclusionNILs developed in this study and the transcriptomic sequences obtained from them did not only allow the validation of the resistance locus Qcrs.cpi-1H and the identification of candidate genes underlying its resistance, they also allowed the delineation of the resistance locus and the development of SNPs markers which formed a solid base for detailed mapping as well as cloning gene(s) underlying the locus.

Homoploid hybrid speciation has been reported in a wide range of species since the exploitation of genome sequences in evolutionary studies. However, the interference of ancestral subdivision has not been adequately considered in many such investigations. Using the D lineage in wheat as an example, we showed clearly that ancestral subdivision has led to false detection of homoploid hybridization signals. We develop a novel statistical framework by examining the changes in shared ancestral variations and infer on the likelihood of speciation due to genuine homoploid hybridization or ancestral subdivisions. Applying this to wheat data, we found that homoploid hybridization was not involved in the origin of the D lineage contrary to the now widely held belief. This example indicates that the significance of homoploid hybrid speciation is likely exaggerated. The underlying methodology developed in this study should be valuable for clarifying whether homoploid hybridization has contributed to the speciation of many other species.