Structural and functional organization of the '1S0.8 gene-rich region' in the Triticeae

Genome-wide identification, expression analysis and evolutionary relationships of the IQ67-domain gene family in common wheat (Triticum aestivum L.) and its progenitors

BACKGROUND

The plant-specific IQ67-domain (IQD) gene family plays an important role in plant development and stress responses. However, little is known about the IQD family in common wheat (Triticum aestivum L), an agriculturally important crop that provides more than 20% of the calories and protein consumed in the modern human diet.

RESULTS

We identified 125 IQDs in the wheat genome and divided them into four subgroups by phylogenetic analysis. The IQDs belonging to the same subgroup had similar exon-intron structure and conserved motif composition. Polyploidization contributed significantly to the expansion of IQD genes in wheat. Characterization of the expression profile of these genes revealed that a few T. aestivum (Ta)IQDs showed high tissue-specificity. The stress-induced expression pattern also revealed a potential role of TaIQDs in environmental adaptation, as TaIQD-2A-2, TaIQD-3A-9 and TaIQD-1A-7 were significantly induced by cold, drought and heat stresses, and could be candidates for future functional characterization. In addition, IQD genes in the A, B and D subgenomes displayed an asymmetric evolutionary pattern, as evidenced by their different gain or loss of member genes, expression levels and nucleotide diversity.

CONCLUSIONS

This study elucidated the potential biological functions and evolutionary relationships of the IQD gene family in wheat and revealed the divergent fates of IQD genes during polyploidization.

Rye Pm8 and wheat Pm3 are orthologous genes and show evolutionary conservation of resistance function against powdery mildew

The improvement of wheat through breeding has relied strongly on the use of genetic material from related wild and domesticated grass species. The 1RS chromosome arm from rye was introgressed into wheat and crossed into many wheat lines, as it improves yield and fungal disease resistance. Pm8 is a powdery mildew resistance gene on 1RS which, after widespread agricultural cultivation, is now widely overcome by adapted mildew races. Here we show by homology-based cloning and subsequent physical and genetic mapping that Pm8 is the rye orthologue of the Pm3 allelic series of mildew resistance genes in wheat. The cloned gene was functionally validated as Pm8 by transient, single-cell expression analysis and stable transformation. Sequence analysis revealed a complex mosaic of ancient haplotypes among Pm3- and Pm8-like genes from different members of the Triticeae. These results show that the two genes have evolved independently after the divergence of the species 7.5 million years ago and kept their function in mildew resistance. During this long time span the co-evolving pathogens have not overcome these genes, which is in strong contrast to the breakdown of Pm8 resistance since its introduction into commercial wheat 70 years ago. Sequence comparison revealed that evolutionary pressure acted on the same subdomains and sequence features of the two orthologous genes. This suggests that they recognize directly or indirectly the same pathogen effectors that have been conserved in the powdery mildews of wheat and rye.

Construction of chromosomal recombination maps of three genomes of lilies (Lilium) based on GISH analysis

Chromosomal recombination maps were constructed for three genomes of lily (Lilium) using GISH analyses. For this purpose, the backcross (BC) progenies of two diploid (2n = 2x = 24) interspecific hybrids of lily, viz. Longiflorum x Asiatic (LA) and Oriental x Asiatic (OA), were used. Mostly the BC progenies of LA hybrids consisted of both triploid (2n = 3x = 36) and diploid (2n = 2x = 24) with some aneuploid genotypes and those of OA hybrids consisted of triploid (2n = 3x = 36) and some aneuploid genotypes. In all cases, it was possible to identify the homoeologous recombinant chromosomes as well as accurately count the number of crossover points, which are called "recombination sites". Recombination sites were estimated in the BC progeny of 71 LA and 41 OA genotypes. In the case of BC progenies of LA hybrids, 248 recombination sites were cytologically localized on 12 different chromosomes of each genome (i.e., L and A). Similarly, 116 recombinant sites were localized on the 12 chromosomes each from the BC progenies of OA hybrids (O and A genomes). Cytological maps were constructed on the basis of the percentages of distances (micrometres) of the recombination sites from the centromeres. Since an Asiatic parent was involved in both hybrids, viz. LA and OA, two maps were constructed for the A genome that were indicated as Asiatic (L) and Asiatic (O). The other two maps were Longiflorum (A) and Oriental (A). Remarkably, the recombination sites were highly unevenly distributed among the different chromosomes of all four maps. Because the recombination sites can be unequivocally identified through GISH, they serve as reliable landmarks and pave the way for assigning molecular markers or desirable genes to chromosomes of Lilium and also monitor introgression of alien segments.

Mapping barleyDsinsertions using wheat deletion lines reveals high insertion frequencies in gene-rich regions with high to moderate recombination rates

Gene distribution is highly uneven in the large genomes of barley and wheat; however, location, order, and gene density of gene-containing regions are very similar between the two genomes. Flanking sequences from 35 unique, single-copy, barley Ds insertion events were physically mapped using wheat nullisomic-tetrasomic, ditelosomic, and deletion lines. Of the 35 sequences, 23 (66%) detected 34 loci mapping on all 7 homoeologous wheat groups. Seven sequences were not mapped owing to lack of polymorphism and the remaining 5 (14%) were barley-specific. All 34 loci physically mapped to the previously identified gene-rich regions (GRRs) of wheat, making the contained genes candidates for targeted mutagenesis by remobilization. Transpositions occurred preferentially into GRRs with higher recombination rates. The GRRs containing 17 of the 23 Ds insertions accounted for 60%–89% of the respective arm’s recombination. The remaining 6 (17%) insertions mapped to GRRs with <15% of the arm’s recombination. Overall, kb/cM estimates for the Ds-containing GRRs were twofold higher than those for regions without insertions. These results suggest that all genes may be targeted by transposon-based gene cloning, although the transposition frequency for genes present in recombination-poor regions is significantly less than that present in highly recombinogenic regions.

High level of conservation between genes coding for the GAMYB transcription factor in barley (Hordeum vulgare L.) and bread wheat (Triticum aestivum L.) collections

The transcription factor GAMYB is involved in gibberellin signalling in cereal aleurone cells and in plant developmental processes. Nucleotide diversity of HvGAMYB and TaGAMYB was investigated in 155 barley (Hordeum vulgare) and 42 wheat (Triticum aestivum) accessions, respectively. Polymorphisms defined 18 haplotypes in the barley collection and 1, 7 and 3 haplotypes for the A, B, and D genomes of wheat, respectively. We found that (1) Hv- and TaGAMYB genes have identical structures. (2) Both genes show a high level of nucleotide identity (>95%) in the coding sequences and the distribution of polymorphisms is similar in both collections. At the protein level the functional domain is identical in both species. (3) GAMYB genes map to a syntenic position on chromosome 3. GAMYB genes are different in both collections with respect to the Tajima D statistic and linkage disequilibrium (LD). A moderate level of LD was observed in the barley collection. In wheat, LD is absolute between polymorphic sites, mostly located in the first intron, while it decays within the gene. Differences in Tajima D values might be due to a lower selection pressure on HvGAMYB, compared to its wheat orthologue. Altogether our results provide evidence that there have been only few evolutionary changes in Hv- and TaGAMYB. This confirms the close relationship between these species and also highlights the functional importance of this transcription factor.

Wheat cytogenetics in the genomics era and its relevance to breeding

Hexaploid wheat is a species that has been subjected to most extensive cytogenetic studies. This has contributed to understanding the mechanism of the evolution of polyploids involving diploidization through genetic restriction of chromosome pairing to only homologous chromosomes. The availability of a variety of aneuploids and the ph mutants (Ph1 and Ph2) in bread wheat also allowed chromosome manipulations leading to the development of alien addition/substitution lines and the introgression of alien chromosome segments into the wheat genome. More recently in the genomics era, molecular tools have been used extensively not only for the construction of molecular maps, but also for identification/isolation of genes/QTLs (including epistatic QTLs, eQTLs and PQLs) for several agronomic traits. It has also been possible to identify gene-rich regions and recombination hot spots in the wheat genome, which are now being subjected to sequencing at the genome level, through development of BAC libraries. In the EST database also, among all plants wheat ESTs are the highest in number, and are only next to those for human, mouse, Ciona intestinalis (a chordate), rat and zebrafish genomes. These ESTs and sequences of several genomic regions have been subjected to a variety of applications including development of perfect markers and establishment of microcollinearity. The technique of in situ hybridization (including FISH, GISH and McFISH) and the development of deletion stocks also facilitated the preparation of physical maps. Molecular markers are also used for marker-assisted selection in wheat breeding programs in several countries. Construction of a wheat DNA chip, which will also become available soon, may further facilitate wheat genomics research. These enormous resources, knowledge base and the fast development of additional molecular tools and high throughput approaches for genotyping will prove extremely useful in future wheat research and will lead to development of improved wheat cultivars.

Origin, structure, and behavior of a highly rearranged deletion chromosome 1BS-4 in wheat

Wheat (Triticum aestivum L.) deletion (del) stocks are valuable tools for the physical mapping of molecular markers and genes to chromosome bins delineated by 2 adjacent deletion breakpoints. The wheat deletion stocks were produced by using gametocidal genes derived from related Aegilops species. Here, we report on the origin, structure, and behavior of a highly rearranged chromosome 1BS-4. The cytogenetic and molecular marker analyses suggest that 1BS-4 resulted from 2 breakpoints in the 1BS arm and 1 breakpoint in the 1BL arm. The distal segment from 1BS, except for a small deleted part, is translocated to the long arm. Cytologically, chromosome 1BS-4 is highly stable, but shows a unique meiotic pairing behavior. The short arm of 1BS-4 fails to pair with a normal 1BS arm because of lack of homology at the distal ends. The long arm of 1BS-4 only pairs with a normal 1BS arm within the distal region translocated from 1BS. Therefore, using the 1BS-4 deletion stock for physical mapping will result in the false allocation of molecular markers and genes proximal to the breakpoint of 1BS-4.Key words: Triticum aestivum, wheat, deletion–translocation, physical mapping.

Analysis of recombination and gene distribution in the 2L1.0 region of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

Both wheat and barley belong to tribe Triticeae and are closely related. High-density detailed comparison of physical and genetic linkage maps revealed that wheat genes are present in physically small gene-rich regions (GRRs). One of the largest GRRs is located around fraction length 1.0 of the long arm of wheat homoeologous group 2 chromosomes termed the "2L1.0 region." The main objective of this study was to analyze the structural and functional organization of the 2L1.0 region in barley in comparison to wheat. Using the 29 physically mapped RFLP markers for the region, wheat and barley consensus genetic linkage maps of the 2L1.0 region were generated by combining information from 18 wheat and 7 barley genetic linkage maps. Comparative analysis using these consensus maps and other available wheat and barley mapping resources identified 227 DNA markers and ESTs for the region. The region accounted for 58% of the genes and 68% of the arm's recombination in wheat. However, the corresponding region in barley accounted for about 42% of the genes and 81% of the recombination. The kb/cM ratio for the region was 122 in barley compared to 244 in wheat. Distribution of genes and recombination varied between the two species even though the gene order and density were similar.

Linkage mapping of powdery mildew and greenbug resistance genes on recombinant 1RS from 'Amigo' and 'Kavkaz' wheat-rye translocations of chromosome 1RS.1AL

Cultivated rye (Secale cereale L., 2n = 2x = 14, RR) is an important source of genes for insect and disease resistance in wheat (Triticum aestivum L., 2n = 6x = 42). Rye chromosome arm 1RS of S. cereale 'Kavkaz' originally found as a 1BL.1RS translocation, carries genes for disease resistance (e.g., Lr26, Sr31, Yr9, and Pm8), while 1RS of the S. cereale 'Amigo' translocation (1RSA) carries a single resistance gene for greenbug (Schizaphis graminum Rondani) biotypes B and C and also carries additional disease-resistance genes. The purpose of this research was to identify individual plants that were recombinant in the homologous region of.1AL.1RSV and 1AL.1RSA using both molecular and phenotypic markers. Secale cereale 'Nekota' (1AL.1RSA) and S. cereale 'Pavon 76' (1AL.1RSV) were mated and the F1 was backcrossed to 'Nekota' (1AL.1AS) to generate eighty BC1F2:3 families (i.e., ('Nekota' 1AL.1RSA x 'Pavon 76' 1AL.1RSV) x 'Nekota' 1AL.1AS). These families were genotyped using the secalin-gliadin grain storage protein banding pattern generated with polyacrylamide gel electrophoresis to discriminate 1AL.1AS/1AL.1RS heterozygotes from the 1AL.1RSA+V and 1AL.1AS homozygotes. Segregation of the secalin locus and PCR markers based on the R173 family of rye specific repeated DNA sequences demonstrated the presence of recombinant 1AL.1RSA+V families. Powdery mildew (Blumeria graminis) and greenbug resistance genes on the recombinant 1RSA+V arm were mapped in relation to the Sec-1 locus, 2 additional protein bands, 3 SSRs, and 13 RFLP markers. The resultant linkage map of 1RS spanned 82.4 cM with marker order and spacing showing reasonable agreement with previous maps of 1RS. Fifteen markers lie within a region of 29.7 cM next to the centromere, yet corresponded to just 36% of the overall map length. The map position of the RFLP marker probe mwg68 was 10.9 cM distal to the Sec-1 locus and 7.8 cM proximal to the powdery mildew resistance locus. The greenbug resistance gene was located 2.7 cM proximal to the Sec-1 locus.

The integration of recombination and physical maps in a large-genome monocot using haploid genome analysis in a trihybrid allium population

Integrated mapping in large-genome monocots has been carried out on a limited number of species. Furthermore, integrated maps are difficult to construct for these species due to, among other reasons, the specific plant populations needed. To fill these gaps, Alliums were chosen as target species and a new strategy for constructing suitable populations was developed. This strategy involves the use of trihybrid genotypes in which only one homeolog of a chromosome pair is recombinant due to interspecific recombination. We used genotypes from a trihybrid Allium cepa x (A. roylei x A. fistulosum) population. Recombinant chromosomes 5 and 8 from the interspecific parent were analyzed using genomic in situ hybridization visualization of recombination points and the physical positions of recombination were integrated into AFLP linkage maps of both chromosomes. The integrated maps showed that in Alliums recombination predominantly occurs in the proximal half of chromosome arms and that 57.9% of PstI/MseI markers are located in close proximity to the centromeric region, suggesting the presence of genes in this region. These findings are different from data obtained on cereals, where recombination rate and gene density tends to be higher in distal regions.

Identification of wheat chromosomal regions containing expressed resistance genes

The objectives of this study were to isolate and physically localize expressed resistance (R) genes on wheat chromosomes. Irrespective of the host or pest type, most of the 46 cloned R genes from 12 plant species share a strong sequence similarity, especially for protein domains and motifs. By utilizing this structural similarity to perform modified RNA fingerprinting and data mining, we identified 184 putative expressed R genes of wheat. These include 87 NB/LRR types, 16 receptor-like kinases, and 13 Pto-like kinases. The remaining were seven Hm1 and two Hs1(pro-1) homologs, 17 pathogenicity related, and 42 unique NB/kinases. About 76% of the expressed R-gene candidates were rare transcripts, including 42 novel sequences. Physical mapping of 121 candidate R-gene sequences using 339 deletion lines localized 310 loci to 26 chromosomal regions encompassing approximately 16% of the wheat genome. Five major R-gene clusters that spanned only approximately 3% of the wheat genome but contained approximately 47% of the candidate R genes were observed. Comparative mapping localized 91% (82 of 90) of the phenotypically characterized R genes to 18 regions where 118 of the R-gene sequences mapped.

Demarcating the gene-rich regions of the wheat genome

By physically mapping 3025 loci including 252 phenotypically characterized genes and 17 quantitative trait loci (QTLs) relative to 334 deletion breakpoints, we localized the gene-containing fraction to 29% of the wheat genome present as 18 major and 30 minor gene-rich regions (GRRs). The GRRs varied both in gene number and density. The five largest GRRs physically spanning <3% of the genome contained 26% of the wheat genes. Approximate size of the GRRs ranged from 3 to 71 Mb. Recombination mainly occurred in the GRRs. Various GRRs varied as much as 128-fold for gene density and 140-fold for recombination rates. Except for a general suppression in 25-40% of the chromosomal region around centromeres, no correlation of recombination was observed with the gene density, the size, or chromosomal location of GRRs. More than 30% of the wheat genes are in recombination-poor regions thus are inaccessible to map-based cloning.

In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S

Comparative RFLP mapping has revealed extensive conservation of marker order in different grass genomes. However, microcolinearity studies at the sequence level have shown rapid genome evolution and many exceptions to colinearity. Most of these studies have focused on a limited size of genomic fragment and the extent of microcolinearity over large distances or across entire genomes remains poorly characterized in grasses. Here, we have investigated the microcolinearity between the rice genome and a total of 1,500 kb from physical BAC contigs on wheat chromosome 1AS. Using ESTs mapped in wheat chromosome bins as an additional source of physical data, we have identified 27 conserved orthologous sequences between wheat chromosome 1AS and a region of 1,210 kb located on rice chromosome 5S. Our results extend the orthology described earlier between wheat chromosome group 1S and rice chromosome 5S. Microcolinearity was found to be frequently disrupted by rearrangements which must have occurred after the divergence of wheat and rice. At the Lr10 orthologous loci, microrearrangements were due to the insertion of mobile elements, but also originated from gene movement, amplification, deletion and inversion. These mechanisms of genome evolution are at the origin of the mosaic conservation observed between the orthologous regions. Finally, in silico mapping of wheat genes identified an intragenomic colinearity between fragments from rice chromosome 1L and 5S, suggesting an ancestral segmental duplication in rice.

A large rearrangement involving genes and low-copy DNA interrupts the microcollinearity between rice and barley at the Rph7 locus

Grass genomes differ greatly in chromosome number, ploidy level, and size. Despite these differences, very good conservation of the marker order (collinearity) was found at the genetic map level between the different grass genomes. Collinearity is particularly good between rice chromosome 1 and the group 3 chromosomes in the Triticeae. We have used this collinearity to saturate the leaf rust resistance locus Rph7 on chromosome 3HS in barley with ESTs originating from rice chromosome 1S. Chromosome walking allowed the establishment of a contig of 212 kb spanning the Rph7 resistance gene. Sequencing of the contig showed an average gene density of one gene/20 kb with islands of higher density. Comparison with the orthologous rice sequence revealed the complete conservation of five members of the HGA gene family whereas intergenic regions differ greatly in size and composition. In rice, the five genes are closely associated whereas in barley intergenic regions are >38-fold larger. The size difference is due mainly to the presence of six additional genes as well as noncoding low-copy sequences. Our data suggest that a major rearrangement occurred in this region since the Triticeae and rice lineage diverged.