Homoeologous Segments Research Articles

Analysis of a global wheat panel reveals a highly diverse introgression landscape and provides evidence for inter-homoeologue chromosomal recombination

Key messageThis study highlights the agronomic potential of rare introgressions, as demonstrated by a major QTL for powdery mildew resistance on chromosome 7D. It further shows evidence for inter-homoeologue recombination in wheat.Agriculturally important genes are often introgressed into crops from closely related donor species or landraces. The gene pool of hexaploid bread wheat (Triticum aestivum) is known to contain numerous such “alien” introgressions. Recently established high-quality reference genome sequences allow prediction of the size, frequency and identity of introgressed chromosome regions. Here, we characterise chromosomal introgressions in bread wheat using exome capture data from the WHEALBI collection. We identified 24,981 putative introgression segments of at least 2 Mb across 434 wheat accessions. Detailed study of the most frequent introgressions identified T. timopheevii or its close relatives as a frequent donor species. Importantly, 118 introgressions of at least 10 Mb were exclusive to single wheat accessions, revealing that large populations need to be studied to assess the total diversity of the wheat pangenome. In one case, a 14 Mb introgression in chromosome 7D, exclusive to cultivar Pamukale, was shown by QTL mapping to harbour a recessive powdery mildew resistance gene. We identified multiple events where distal chromosomal segments of one subgenome were duplicated in the genome and replaced the homoeologous segment in another subgenome. We propose that these examples are the results of inter-homoeologue recombination. Our study produced an extensive catalogue of the wheat introgression landscape, providing a resource for wheat breeding. Of note, the finding that the wheat gene pool contains numerous rare, but potentially important introgressions and chromosomal rearrangements has implications for future breeding.

Engineered Durum Wheat Germplasm with Multiple Alien Introgressions: Agronomic and Quality Performance

If genetic gains in wheat yield are to be achieved in today’s breeding, increasing the genetic variability of cultivated genotypes is an essential requisite to meet. To this aim, alien gene transfer through chromosome engineering (CE) is a validated and sound strategy. Attempts to incorporate more than one alien segment into cultivated wheat have been rare, particularly for tetraploid durum wheat. Here, we present the agronomic and quality performance of the first successful CE-mediated multiple introgression into the latter species. By assembling into 7AL, 3BS, and 1AS arms of a single genotype homoeologous segments of Thinopyrum ponticum 7el1L, Aegilops longissima 3SlS, and Triticum aestivum 1DS arms, respectively, we have stacked several valuable alien genes, comprising Lr19+Sr25+Yp (leaf and stem rust resistance and a gene increasing semolina yellowness), Pm13 (powdery mildew resistance), and Gli-D1/Glu-D3 (genes affecting gluten properties), respectively. Advanced progenies of single, double, and triple recombinants were field-tested across three years in a typical durum wheat growing area of central Italy. The results showed that not only all recombinants had normal phenotype and fertility, but also that one of the triple recombinants had the highest yield through all seasons compared with all other recombinants and control cultivars. Moreover, the multiple introgressions enhanced quality traits, including gluten characteristics and semolina yellow index. The presence of effective disease resistance genes confers additional breeding value to the novel and functional CE products, which can greatly contribute to crop security and safety.

TCTAP C-048 Treatment of Distal Left Main True Bifurcation Involving LAD CTO Lesion by the Retrograde Approach and Culotte Stenting

With the advent of high-throughput sequencing, the availability of genomic sequence for comparative genomics is increasing exponentially. Numerous completed plant genome sequences enable characterization of patterns of the retention and evolution of genes within gene families due to multiple polyploidy events, gene loss and fractionation, and differential evolutionary pressures over time and across different gene families. In this report, we trace the changes that have occurred in 12 surviving homoeologous genomic regions from three rounds of polyploidy that contributed to the current Glycine max genome: a genome triplication before the origin of the rosids (~130 to 240 million years ago), a genome duplication early in the legumes (~58 million years ago), and a duplication in the Glycine lineage (~13 million years ago). Patterns of gene retention following the genome triplication event generally support predictions of the Gene Balance Hypothesis. Finally, we find that genes in networks with a high level of connectivity are more strongly conserved than those with low connectivity and that the enrichment of these highly connected genes in the 12 highly conserved homoeologous segments may in part explain their retention over more than 100 million years and repeated polyploidy events.

Identifying crossover-rich regions and their effect on meiotic homologous interactions by partitioning chromosome arms of wheat and rye

Chiasmata are usually formed in the distal half of cereal chromosomes. Previous studies showed that the crossover-rich region displays a more active role in homologous recognition at early meiosis than crossover-poor regions in the long arm of rye chromosome 1R, but not in the long arm of chromosome 5R. In order to determine what happens in other chromosomes of rye and wheat, we have partitioned, by wheat-rye translocations of variable-size, the distal fourth part of chromosome arms 1BS and 2BL of wheat and 1RS and 2RL of rye. Synapsis and chiasma formation in chromosome pairs with homologous (wheat-wheat or rye-rye) and homoeologous (wheat-rye) stretches, positioned distally and proximally, respectively, or vice versa, have been studied by rye chromatin labelling using fluorescence in situ hybridisation. Chromosome arm partitioning showed that the distal 12 % of 1BS form one crossover in 50 % of the cells, while the distal 6.7 % of 2RL and the distal 10.5 % of 2BL account for 94 % and 81 % of chiasmata formed in these arms. Distal homoeologous segments reduce the frequency of chiasmata and the possibility of interaction between the intercalary/proximal homologous segments. Such a reduction is related to the size of the homoeologous (translocated) segment. The effect on synapsis and chiasma formation was much lower in chromosome constructions with distal homology and proximal homoeology. All of these data support that among wheat and rye chromosomes, recombining regions are more often involved in homologous recognition and pairing than crossover-poor regions.

Changes in Twelve Homoeologous Genomic Regions in Soybean following Three Rounds of Polyploidy

With the advent of high-throughput sequencing, the availability of genomic sequence for comparative genomics is increasing exponentially. Numerous completed plant genome sequences enable characterization of patterns of the retention and evolution of genes within gene families due to multiple polyploidy events, gene loss and fractionation, and differential evolutionary pressures over time and across different gene families. In this report, we trace the changes that have occurred in 12 surviving homoeologous genomic regions from three rounds of polyploidy that contributed to the current Glycine max genome: a genome triplication before the origin of the rosids (~130 to 240 million years ago), a genome duplication early in the legumes (~58 million years ago), and a duplication in the Glycine lineage (~13 million years ago). Patterns of gene retention following the genome triplication event generally support predictions of the Gene Balance Hypothesis. Finally, we find that genes in networks with a high level of connectivity are more strongly conserved than those with low connectivity and that the enrichment of these highly connected genes in the 12 highly conserved homoeologous segments may in part explain their retention over more than 100 million years and repeated polyploidy events.

Comparative Analysis between Homoeologous Genome Segments ofBrassica napusand Its Progenitor Species Reveals Extensive Sequence-Level Divergence

Homoeologous regions of Brassica genomes were analyzed at the sequence level. These represent segments of the Brassica A genome as found in Brassica rapa and Brassica napus and the corresponding segments of the Brassica C genome as found in Brassica oleracea and B. napus. Analysis of synonymous base substitution rates within modeled genes revealed a relatively broad range of times (0.12 to 1.37 million years ago) since the divergence of orthologous genome segments as represented in B. napus and the diploid species. Similar, and consistent, ranges were also identified for single nucleotide polymorphism and insertion-deletion variation. Genes conserved across the Brassica genomes and the homoeologous segments of the genome of Arabidopsis thaliana showed almost perfect collinearity. Numerous examples of apparent transduplication of gene fragments, as previously reported in B. oleracea, were observed in B. rapa and B. napus, indicating that this phenomenon is widespread in Brassica species. In the majority of the regions studied, the C genome segments were expanded in size relative to their A genome counterparts. The considerable variation that we observed, even between the different versions of the same Brassica genome, for gene fragments and annotated putative genes suggest that the concept of the pan-genome might be particularly appropriate when considering Brassica genomes.

Detection and mapping of homologous and homoeologous segments in homoeologous groups of allotetraploid cotton by BAC-FISH

BackgroundCotton, as an allopolyploid species, contains homoeologous A and D subgenomes. The study of the homoeologous (duplicated) segments or chromosomes can facilitate insight into the evolutionary process of polyploidy and the development of genomic resources. Fluorescence in situ hybridization (FISH) using bacterial artificial chromosome (BAC) clones as probes has commonly been used to provide a reliable cytological technique for chromosome identification. In polyploids, it also presents a useful approach for identification and localization of duplicated segments. Here, two types of BACs that contained the duplicated segments were isolated and analyzed in tetraploid cotton by FISH.ResultsHomologous and homoeologous BACs were isolated by way of SSR marker-based selection and then used to develop BAC-FISH probes. Duplicated segments in homoeologous chromosomes were detected by FISH. The FISH and related linkage map results followed known reinforced the relationships of homoeologous chromosomes in allotetraploid cotton, and presented a useful approach for isolation of homoeologous loci or segments and for mapping of monomorphic loci. It is very important to find that the large duplicated segments (homologous BACs) do exist between homoeologous chromosomes, so the shot-gun approach for genome sequencing was unavailable for tetraploid cotton. However, without doubt, it will contain more information and promote the research for duplicated segments as well as the genome evolution in cotton.ConclusionThese findings and the analysis method by BAC-FISH demonstrated the powerful nature and wide use for the genome and genome evolutionary researches in cotton and other polyploidy species.

Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5

We constructed a bacterial artificial chromosome (BAC) library, designated as KBrH, from high molecular weight genomic DNA of Brassica rapa ssp. pekinensis (Chinese cabbage). This library, which was constructed using HindIII-cleaved genomic DNA, consists of 56,592 clones with average insert size of 115 kbp. Using a partially duplicated DNA sequence of Arabidopsis, represented by 19 and 9 predicted genes on chromosome 4 and 5, respectively, and BAC clones from the KBrH library, we studied conservation and microsynteny corresponding to the Arabidopsis regions in B. rapa ssp. pekinensis. The BAC contigs assembled according to the Arabidopsis homoeologues revealed triplication and rearrangements in the Chinese cabbage. In general, collinearity of genes in the paralogous segments was maintained, but gene contents were highly variable with interstitial losses. We also used representative BAC clones, from the assembled contigs, as probes and hybridized them on mitotic (metaphase) and/or meiotic (leptotene/pachytene/metaphase I) chromosomes of Chinese cabbage using bicolor fluorescence in situ hybridization. The hybridization pattern physically identified the paralogous segments of the Arabidopsis homoeologues on B. rapa ssp. pekinensis chromosomes. The homoeologous segments corresponding to chromosome 4 of Arabidopsis were located on chromosomes 2, 8 and 7, whereas those of chromosome 5 were present on chromosomes 6, 1 and 4 of B. rapa ssp. pekinensis.

Molecular cytogenetic characterization and seed storage protein analysis of 1A/1D translocation lines of durum wheat

Two durum wheat [Triticum turgidum L. ssp. durum (Desf.) Husn.] lines carrying the high-molecular-weight (HMW) glutenin subunits (GS) 1 D x 5 + 1Dy10 encoded by Glu-D1d, L252 and S99B34, were characterized using fluorescent genomic in-situ hybridization (FGISH) and microsatellite markers. These two durum lines were derived from the crosses in which the common wheat (T. aestivum L.) 'Len' and durum wheat 'Langdon' (LDN) and 'Renville' were involved. FGISH patterns of the mitotic chromosomes indicated that these two durum lines have one pair of 1AS.1AL-1DL translocated chromosomes in which the terminal region of 1AL was replaced by a homoeologous segment of 1DL. The 1DL segment spans approximately 31% of the long arm of the translocated chromosome. Microsatellite marker analysis confirmed the 1AS.1AL-1DL translocation and determined the translocation breakpoint to be distal to Xgwm357 on 1AL. Seed storage proteins (GS and gliadins) were analysed in these two 1AS.1AL-1DL translocation lines and three sib lines (L092, S99B19 and S99B33) using SDS-PAGE and A-PAGE. The SDS-PAGE and A-PAGE profiles demonstrated that the two low yielding lines (L252 and S99B19) had the low-molecular-weight (LMW) -1 GS encoded by Glu-A3k and Glu-B3s and 1B-encoded gliadins from LDN, and the other three lines (L092, S99B33 and S99B34) with higher yield had LMW-2 GS and 1B-encoded gliadins from Renville, suggesting that undesirable genetic components from LDN might limit substantial improvement of yield. Thus, the translocation lines with 1 D x 5 + 1Dy10 and LMW-2, which are associated with good bread-making and pasta qualities, respectively, in a good genetic background will be useful for developing durum cultivars with dual-purpose end-use. Results from this study demonstrate that the D-genome could play an important role in the genetic improvement of durum wheat and evolution of the A- and B-genomes in tetraploid wheat.

Construction of a Festuca pratensis BAC library for map-based cloning in Festulolium substitution lines

Introgression in Festulolium is a potentially powerful tool to isolate genes for a large number of traits which differ between Festuca pratensis Huds. and Lolium perenne L. Not only are hybrids between the two species fertile, but the two genomes can be distinguished by genomic in situ hybridisation and a high frequency of recombination occurs between homoeologous chromosomes and chromosome segments. By a programme of introgression and a series of backcrosses, L. perenne lines have been produced which contain small F. pratensis substitutions. This material is a rich source of polymorphic markers targeted towards any trait carried on the F. pratensis substitution not observed in the L. perenne background. We describe here the construction of an F. pratensis BAC library, which establishes the basis of a map-based cloning strategy in L. perenne. The library contains 49,152 clones, with an average insert size of 112 kbp, providing coverage of 2.5 haploid genome equivalents. We have screened the library for eight amplified fragment length polymorphism (AFLP) derived markers known to be linked to an F. pratensis gene introgressed into L. perenne and conferring a staygreen phenotype as a consequence of a mutation in primary chlorophyll catabolism. While for four of the markers it was possible to identify bacterial artificial chromosome (BAC) clones, the other four AFLPs were too repetitive to enable reliable identification of locus-specific BACs. Moreover, when the four BACs were partially sequenced, no obvious coding regions could be identified. This contrasted to BACs identified using cDNA sequences, when multiple genes were identified on the same BAC.

Linkage map positions and allelic diversity of two Mal d 3 (non-specific lipid transfer protein) genes in the cultivated apple (Malus domestica)

Non-specific lipid transfer proteins (nsLTPs) of Rosaceae fruits, such as peach, apricot, cherry, plum and apple, represent major allergens for Mediterranean atopic populations. As a first step in elucidating the genetics of nsLTPs, we directed the research reported here towards identifying the number and location of nsLTP (Mal d 3) genes in the apple genome and determining their allelic diversity. PCR cloning was initially performed on two cultivars, Prima and Fiesta, parents of a core apple mapping progeny in Europe, based on two Mal d 3 sequences (AF221502 and AJ277164) in the GenBank. This resulted in the identification of two distinct sequences (representing two genes) encoding the mature nsLTP proteins. One is identical to accession AF221502 and has been named Mal d 3.01, and the other is new and has been named Mal d 3.02. Subsequent genome walking in the upstream direction and DNA polymorphism analysis revealed that these two genes are intronless and that they could be mapped on two homoeologous segments of linkage groups 12 and 4, respectively. Further cloning and sequencing of the coding and upstream region of both Mal d 3 genes in eight cultivars was performed to identify allelic variation. Assessment of the deduced nsLTP amino acid sequences gave a total of two variants at the protein level for Mal d 3.01 and three for Mal d 3.02. The consequences of our results for allergen nomenclature and the breeding of low allergenic apple cultivars are discussed.

Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives

The cultivated Brassica species are the group of crops most closely related to Arabidopsis thaliana (Arabidopsis). They represent models for the application in crops of genomic information gained in Arabidopsis and provide an opportunity for the investigation of polyploid genome formation and evolution. The scientific literature contains contradictory evidence for the dynamics of the evolution of polyploid genomes. We aimed at overcoming the inherent complexity of Brassica genomes and clarify the effects of polyploidy on the evolution of genome microstructure in specific segments of the genome. To do this, we have constructed bacterial artificial chromosome (BAC) libraries from genomic DNA of B. rapa subspecies trilocularis (JBr) and B. napus var Tapidor (JBnB) to supplement an existing BAC library from B. oleracea. These allowed us to analyse both recent polyploidization (under 10,000 years in B. napus) and more ancient polyploidization events (ca. 20 Myr for B. rapa and B. oleracea relative to Arabidopsis), with an analysis of the events occurring on an intermediate time scale (over the ca. 4 Myr since the divergence of the B. rapa and B. oleracea lineages). Using the Arabidopsis genome sequence and clones from the JBr library, we have analysed aspects of gene conservation and microsynteny between six regions of the genome of B. rapa with the homoeologous regions of the genomes of B. oleracea and Arabidopsis. Extensive divergence of gene content was observed between the B. rapa paralogous segments and their homoeologous segments within the genome of Arabidopsis. A pattern of interspersed gene loss was identified that is similar, but not identical, to that observed in B. oleracea. The conserved genes show highly conserved collinearity with their orthologues across genomes, but a small number of species-specific rearrangements were identified. Thus the evolution of genome microstructure is an ongoing process. Brassica napus is a recently formed polyploid resulting from the hybridization of B. rapa (containing the Brassica A genome) and B. oleracea (containing the Brassica C genome). Using clones from the JBnB library, we have analysed the microstructure of the corresponding segments of the B. napus genome. The results show that there has been little or no change to the microstructure of the analysed segments of the Brassica A and C genomes as a consequence of the hybridization event forming natural B. napus. The observations indicate that, upon polyploid formation, these segments of the genome did not undergo a burst of evolution discernible at the scale of microstructure.

Structural divergence of chromosomal segments that arose from successive duplication events in the Arabidopsis genome.

Using the extensive segmental duplications of the Arabidopsis thaliana genome, a comparative study of homoeologous segments occurring in chromosomes 1, 2, 4 and 5 was performed. The gene-by-gene BLASTP approach was applied to identify duplicated genes in homoeologues. The levels of synonymous substitutions between duplicated coding sequences suggest that these regions were formed by at least two rounds of duplications. Moreover, remnants of even more ancient duplication events were recognised by a whole-genome study. We describe a subchromosomal organisation of genes, including the tandemly repeated genes, and the distribution of transposable elements (TEs). In certain cases, evidence of the possible mechanisms of structural rearrangements within the segments could be found. We provide a probable scenario of the rearrangements that took place during the evolution of the homoeologous regions. Furthermore, on the basis of the comparative analysis of the chromosomal segments in the Columbia and Landsberg erecta accessions, an additional structural variation in the A.thaliana genome is described. Analysis of the segments, spanning 7 Mb or 5.6% of the genome, permitted us to propose a model of evolution at the subchromosomal level.

Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana.

A growing body of research indicates that microsynteny is common among dicot genomes. However, most studies focus on just one or a few genomic regions, so the extent of microsynteny across entire genomes remains poorly characterized. To estimate the level of microsynteny between Medicago truncatula (Mt) and Glycine max (soybean), and also among homoeologous segments of soybean, we used a hybridization strategy involving bacterial artificial chromosome (BAC) contigs. A Mt BAC library consisting of 30,720 clones was screened with a total of 187 soybean BAC subclones and restriction fragment length polymorphism (RFLP) probes. These probes came from 50 soybean contig groups, defined as one or more related BAC contigs anchored by the same low-copy probe. In addition, 92 whole soybean BAC clones were hybridized to filters of HindIII-digested Mt BAC DNA to identify additional cases of cross-hybridization after removal of those soybean BACs found to be repetitive in Mt. Microsynteny was inferred when at least two low-copy probes from a single soybean contig hybridized to the same Mt BAC or when a soybean BAC clone hybridized to three or more low-copy fragments from a single Mt BAC. Of the 50 soybean contig groups examined, 54% showed microsynteny to Mt. The degree of conservation among 37 groups of soybean contigs was also investigated. The results indicated substantial conservation among soybean contigs in the same group, with 86.5% of the groups showing at least some level of microsynteny. One contig group was examined in detail by a combination of physical mapping and comparative sequencing of homoeologous segments. A TBLASTX similarity search was performed between 1,085 soybean sequences on the 50 BAC contig groups and the entire Arabidopsis genome. Based on a criterion of sequence homologues <100 kb apart, each with an expected value of < or =1e-07, seven of the 50 soybean contig groups (14%) exhibited microsynteny with Arabidopsis.

Genetic analysis of the Aegilops longissima 3S chromosome carrying the Pm13 resistance gene

The distal region of the short arm of chromosome 3S from Aegilopslongissima, which carries the powdery mildew resistance gene Pm13, was introgressed into common wheat. Due to suppression of recombination between this region and corresponding wheat homoeologous segments, a possible strategy to construct a genetic map around the Pm13 gene was based on crosses between a wheat addition line carrying the Ae.longissima 3S chromosome and the corresponding 3S addition lines of Ae.searsii and Ae. variabilis. The efficiency of this strategy was evaluated by scoring recombination frequencies inprogenies derived from these crosses. Recombination between 3S chromosomes fromAe. searsii and Ae. longissimawas very low, whereas 26.5% recombinant alien chromosomes were obtained from the cross involving the Ae. variabilisand Ae. longissima 3S addition lines. These data were used to construct a3S chromosome map that resulted largely colinear to the consensus map of the homoeologous group 3 of wheat.

Implementation of probes for tracing chromosome segments conferring barley yellow dwarf virus resistance

Two PCR-based assays were examined for tracing the presence of a Thinopyrum chromosome segment (Tc6 or Tc14) conferring barley yellow dwarf virus (BYDV) resistance in wheat breeding lines. The microsatellite gwm37 was used to assay the Thinopyrum chromosome segment or its wheat, Group 7, homoeologous segment, and was effective in characterising breeders material since heterozygous lines could be identified. A new set of primers derived from a Thinopyrum-specific DNA segment (csTiB1) provided a dominant marker that was readily scored by agarose gel electrophoresis. It was also demonstrated that the csTiB1 primers could be used to establish a solid phase PCR assay that avoided the requirement for gel electrophoresis and was amenable to use in a high-throughput, microtitre plate format. Depending on the number of DNA samples to be assayed, both primer pairs appear to have a place in breeding programs.

Introgression of Lilium rubellum Baker chromosomes into L. longiflorum Thunb.: a genome painting study of the F1 hybrid, BC1 and BC2 progenies.

Interspecific hybrids between Lilium longiflorum (L, 2n = 2x = 24) and Lilium rubellum (R, 2n = 2x = 24) were produced with the aim of transferring desirable horticultural traits from L. rubellum to L. longiflorum. All F1 hybrids (LR, 2n = 2x = 24) and BC1 individuals (LLR, 2n = 3x = 36) were phenotypically uniform for plant height, flowering time, leaf shape and flower colour. The BC1 plants were, in spite of their triploid nature, fertile and could be used as a female parent in backcrossings with autotetraploid L. longiflorum (LLLL, 2n = 4x = 48). Twelve BC2 individuals were obtained and three of them were selected for further chromosome analysis. As L. longiflorum and L. rubellum chromosomes were indistinguishable in the hybrids, genomic in-situ hybridization (GISH) was applied to establish the parentage of the chromosomes of the F1 hybrids and the BC1 and BC2 progenies. GISH confirmed the LLRR constitution of the doubled amphimonoploid (allodiploid), and the LLR constitution of all BC1 plants. The three selected BC2 plants were, as expected, aneuploid, containing three complete sets of L. longiflorum chromosomes and six, seven or eight L. rubellum chromosomes, respectively. However, L/R translocation or recombinant chromosomes could not be demonstrated in the mitotic metaphase complements of the F1, BC1 and BC2 plants. In spite of the high frequencies of homoeologous recombination in the F1 hybrids (LR) pollen was found to be sterile in all cases. At metaphase I of the pollen mother cells of the BC1 plants, genome painting did not reveal any cases of homoeologous pairing and recombination between L and R chromosomes. This lack of exchange between homoeologous chromosome segments indicates complete preferential pairing of the L and R chromosomes in the F1 (amphidiploid) and BC1 plants. It seems that the preferential pairing in the F1 and BC1 hybrids hinder the introgression of the chromosome segments or species-specific genes into the recipient for breeding purposes.

Identification and analysis of homoeologous segments of the genomes of rice andArabidopsis thaliana

Using contiguous genomic DNA sequences of Arabidopsis thaliana, we were able to identify a region of conserved structure in the genome of rice. The conserved, and presumptive homoeologous segments, are 194 kb and 219-300 kb in size in Arabidopsis and rice, respectively. They contain five homologous genes, distinguished in order by a single inversion. These represent the first homoeologous segments identified in the genomes of a dicot and a monocot, demonstrating that fine-scale conservation of genome structure exists and is detectable across this major divide in the angiosperms. The conserved framework of genes identified is interspersed with non-conserved genes, indicating that mechanisms beyond segmental inversions and translocations need to be invoked to fully explain plant genome evolution, and that the benefits of comparative genomics over such large taxonomic distances may be limited.

Identification and analysis of homoeologous segments of the genomes of rice and &lt;i&gt;Arabidopsis thaliana&lt;/i&gt;

Identification and analysis of homoeologous segments of the genomes of rice and &lt;i&gt;Arabidopsis thaliana&lt;/i&gt;

Aneuploid marker assignment in hexaploid oat with the C genome as a reference for determining remnant homoeology.

Nullisomic lines of hexaploid oat Avena sativa L. (2n = 6x - 2 = 40, AACCDD) cultivar Sun II were used to assign 134 DNA sequences to 10 chromosome-associated syntenic groups. A limited set of ditelosomic lines allowed localization of subsets of these sequences to six chromosome arms. Advantages of using such aneuploids in mapping are in the assignment of gene families, monomorphic RFLP sequences, and oat linkage groups to chromosomes. The published hexaploid oat RFLP linkage map has 38 linkage groups, 17 more than expected on the basis of the haploid chromosome number. Using nullisomics, eight linkage groups were assigned to five physical chromosomes; using ditelosomics, three of these linkage groups were assigned to their respective chromosome arms. The A- and D-genome chromosome sets of oat are indistinguishable from each other based on different staining and genomic in situ hybridization techniques, while C-genome chromosomes are distinct. Because chromosomal rearrangements such as translocations and inversions have played an important role in the evolution of hexaploid oat, the distinction of C-genome chromosomes can be used to determine remnant homoeologous segments that exist in the other two genomes. Among the 10 syntenic groups identified, six chromosomes showed sequence homoeology believed to represent segmental homoeologous regions. Owing to various evolutionary forces, segmental homoeology instead of whole chromosome homoeology appears to best describe the genome organization in hexaploid oat.