Linkage disequilibrium among modern sugarcane cultivars

Modern sugarcane cultivars are derived from a few interspecific hybrids created early in this century. Linkage disequilibrium was investigated in a population of 59 cultivars representing the most important commercial clones bred in Mauritius as well as a few old cultivars involved in their genealogy. Thirty-eight probes scattered over the sugarcane genome map were used to reveal RFLPs. Forty-two cases of bilocus associations were observed involving a total of 33 loci. Most of them are separated by less than 10 cM. All the corresponding allele couples were found in at least 1 of the originally created cultivars, suggesting that they depict ancient associations. This global disequilibrium is interpreted as the result of the foundation bottleneck related to the first interspecific crosses; the preferential allele associations thus created have been maintained through subsequent crosses when the loci were closely linked. This phenomenon is likely also to apply to genes of agricultural interest. A practical consequence is that markers can be used to track known QTLs in modern breeding materials without the necessity to repeatedly study segregating progenies. This structure gives high value to the correlation between molecular markers and agricultural traits among cultivars. Received: 6 March 1999 / Accepted: 25 March 1999     

Genome remodelling in three modern S. officinarumxS. spontaneum sugarcane cultivars

This study provides evidence that nuclear and chromosome remodelling has taken place in sugarcane, a vegetative crop with a complex genome derived from interspecific hybridizations between Saccharum officinarum and S. spontaneum. Detailed knowledge on the chromosomal compositions of the three clones analysed was acquired. (1) All hybrid cultivars were found to be aneuploid, affecting both parental genomes (having chromosomes in addition to full genomes), with chromosome numbers from 2n=102-106 in My5514 and up to 2n=113-117 in C236-51. (2) Comparative in situ hybridization showed that about 16% of these chromosomes are inherited from S. spontaneum and less than 5% are recombinant or translocated chromosomes containing sequences of both S. officinarum and S. spontaneum. (3) Differences between the observed DNA contents (estimated by flow cytometry) and those expected from the number of chromosomes, allowed the introgression of additional S. spontaneum or S. officinarum DNA pieces into the B42231 and C236-51 cultivars to be estimated. (4) Size heterogeneity between S. officinarum homologous chromosomes carrying the 18S-5.8S-25S and 5S ribosomal genes (identified by FISH with pTa71 and pTa794, respectively) confirms remodelling occurred by chromosomal interchange events, at least in these homologous chromosomes. (5) Simultaneous visualization of nucleoli and NORs showed that all 18S-5.8S-25S loci were potentially functional in the three clones, independent of their origin and size.     

Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics

Cultivated sugarcane clones (Saccharum spp., 2n=100 to 130) are derived from complex interspecific hybridizations between the speciesS. officinarum andS. spontaneum. Using comparative genomic DNA in situ hybridization, we demonstrated that it is possible to distinguish the chromosomes contributed by these two species in an interspecific F1 hybrid and a cultivated clone, R570. In the interspecific F1 studied, we observed n+n transmission of the parental chromosomes instead of the peculiar 2n+n transmission usually described in such crosses. Among the chromosomes of cultivar R570 (2n=107–115) about 10% were identified as originating fromS. spontaneum and about 10% were identified as recombinant chromosomes between the two speciesS. officinarum andS. spontaneum. This demonstrated for the first time the occurrence of recombination between the chromosomes of these two species. The rDNA sites were located by in situ hybridization in these two species and the cultivar R570. This supported different basic chromosome numbers and chromosome structural differences between the two species and provided a first bridge between physical and genetical mapping in sugarcane.     

Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics

Cultivated sugarcane clones (Saccharum spp., 2n=100 to 130) are derived from complex interspecific hybridizations between the speciesS. officinarum andS. spontaneum. Using comparative genomic DNA in situ hybridization, we demonstrated that it is possible to distinguish the chromosomes contributed by these two species in an interspecific F1 hybrid and a cultivated clone, R570. In the interspecific F1 studied, we observed n+n transmission of the parental chromosomes instead of the peculiar 2n+n transmission usually described in such crosses. Among the chromosomes of cultivar R570 (2n=107–115) about 10% were identified as originating fromS. spontaneum and about 10% were identified as recombinant chromosomes between the two speciesS. officinarum andS. spontaneum. This demonstrated for the first time the occurrence of recombination between the chromosomes of these two species. The rDNA sites were located by in situ hybridization in these two species and the cultivar R570. This supported different basic chromosome numbers and chromosome structural differences between the two species and provided a first bridge between physical and genetical mapping in sugarcane.     

Molecular investigation of the genetic base of sugarcane cultivars

 Molecular diversity was analysed among 162 clones of sugarcane using DNA restriction fragment length polymorphism (RFLP). One hundred and nine of them were modern cultivars of interspecific origin; most of them were bred in Barbados or in Mauritius. Fifty three were from Saccharum officinarum species, which is the major source of genes in modern cultivars, prevailing over the part of the genome incorporated from the wild species Saccharum spontaneum. Twelve low-copy nuclear DNA probes scattered over the genome were used in combination with one or two restriction enzymes. A total of 399 fragments was identified, 386 of which were polymorphic. Each sugarcane clone displayed a high number of fragments per probe/enzyme combination, illustrating the polyploid constitution of the genome. Among the S. officinarum clones, those from New Guinea had the largest variability and encompassed that present among clones collected from the Indonesian Islands and those known to have been involved in the parentage of modern cultivars. This is in agreement with the hypothesis that New Guinea is the centre of origin of this species. The clones from New Caledonia formed a separate group and could correspond to S. officinarum clones modified through introgression with other members of the ‘Saccharum complex’. Despite the low number of S. officinarum clones used for breeding cultivars, more than 80% of the markers present in the whole S. officinarum sample were also found in modern cultivars due probably to a high heterozygosity related to polyploidy. Among the cultivars, the two main groups, originating from Barbados and Mauritius, were clearly separated. This appeared essentially due to S. spontaneum alleles present in Mauritian cultivars and absent in Barbadan ones, probably in relation to the regular use of early generation interspecific hybrids in the breeding program employed in Mauritius. Received: 9 November 1998 / Accepted: 19 November 1998     

Young,intact and nested retrotransposons are abundant in the onion and asparagus genomes

Background and Aims

Although monocotyledonous plants comprise one of the two major groups of angiosperms and include >65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots.

Methods

To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Specifically, several available onion and asparagus bacterial artificial chromosomes (BACs) with contig sizes >35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons.

Key Results

The results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particularly abundant, as high as 4–5 % (asparagus) or 3–4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize.

Conclusions

Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae.     

Haplotype structure around Bru1 reveals a narrow genetic basis for brown rust resistance in modern sugarcane cultivars

Modern sugarcane cultivars (Saccharum spp., 2n?=?100-130) are high polyploid, aneuploid and of interspecific origin. A major gene (Bru1) conferring resistance to brown rust, caused by the fungus Puccinia melanocephala, has been identified in cultivar R570. We analyzed 380 modern cultivars and breeding materials covering the worldwide diversity with 22 molecular markers genetically linked to Bru1 in R570 within a 8.2?cM segment. Our results revealed a strong LD in the Bru1 region and strong associations between most of the markers and rust resistance. Two PCR markers, that flank the Bru1-bearing segment, were found completely associated with one another and only in resistant clones representing efficient molecular diagnostic for Bru1. On this basis, Bru1 was inferred in 86?% of the 194 resistant sugarcane accessions, revealing that it constitutes the main source of brown rust resistance in modern cultivars. Bru1 PCR diagnostic markers should be particularly useful to identify cultivars with potentially alternative sources of resistance to diversify the basis of brown rust resistance in breeding programs.     

Gypsy-like retrotransposons in Pyrenophora: an abundant and informative class of molecular markers.

This paper describes the development of S-SAP (sequence-specific amplified polymorphism) using a primer derived from the LTR (long terminal repeat) of the Pyggy retrotransposon isolated from Pyrenophora graminea. Fragments were amplified by S-SAP from different Pyrenophora spp., indicating the presence of Pyggy-like sequences in these genomes. The bands were highly polymorphic between isolates and the number of bands differed by as much as 10-fold between species, demonstrating the potential of this method for genetic analysis in fungi. The phylogenetic relationship among the isolates as deduced using S-SAP data is presented, and shows evidence of genetic exchange between P. graminea and P. teres.     

Experimental assessment of the accuracy of genomic selection in sugarcane

Sugarcane cultivars are interspecific hybrids with an aneuploid, highly heterozygous polyploid genome. The complexity of the sugarcane genome is the main obstacle to the use of marker-assisted selection in sugarcane breeding. Given the promising results of recent studies of plant genomic selection, we explored the feasibility of genomic selection in this complex polyploid crop. Genetic values were predicted in two independent panels, each composed of 167 accessions representing sugarcane genetic diversity worldwide. Accessions were genotyped with 1,499 DArT markers. One panel was phenotyped in Reunion Island and the other in Guadeloupe. Ten traits concerning sugar and bagasse contents, digestibility and composition of the bagasse, plant morphology, and disease resistance were used. We used four statistical predictive models: bayesian LASSO, ridge regression, reproducing kernel Hilbert space, and partial least square regression. The accuracy of the predictions was assessed through the correlation between observed and predicted genetic values by cross validation within each panel and between the two panels. We observed equivalent accuracy among the four predictive models for a given trait, and marked differences were observed among traits. Depending on the trait concerned, within-panel cross validation yielded median correlations ranging from 0.29 to 0.62 in the Reunion Island panel and from 0.11 to 0.5 in the Guadeloupe panel. Cross validation between panels yielded correlations ranging from 0.13 for smut resistance to 0.55 for brix. This level of correlations is promising for future implementations. Our results provide the first validation of genomic selection in sugarcane.     

A family of retrotransposons and associated genomic variation in wheat.

A family of related retroelements was characterized in the genomes of some Graminease species. The structure of these retroelements indicates that they are retrotransposons containing reading frames with sequence similarity to the polyproteins of copia and Ty. This family of retroelements (termed WIS-2) occurs in the genomes of barley, wheat, rye, oats, and Aegilops species. Ongoing genomic variation both within individual plants of a wheat variety and within and between varieties of wheat is associated with some members of the WIS-2 family.     

Response of eight sugarcane cultivars to glyphosine and glyphosate ripeners

Studies were conducted on eight sugarcane (Saccharum spp. hydrid) cultivars during the 1982–83 (plant crop) and 1983–84 (ratoon crop) growing seasons to determine the effects of glyphosine (Polaris) (N,N-bis (phosphonomethyl) glycine) and glyphosate (Polado) (sodium-N-(phosphonomethyl) glycine) on stalk sucrose content and yield. Difference due to crops (plant vs. ratoon) for sugarcane quality, kilograms of sugar per ton of cane (S/T), sugarcane yield, tons of cane per hectare (TCH), and sugar yield, tons of sugar per hectare (TSH) were significant. Significant differences were found in quality for the ratoon crop and cane and sugar yield in both crops due to ripener treatment. Cultivars in both crops differed significantly in quality and yield. Harvest dates were significantly different for all plant characteristics. Interactions of cultivar by treatment for the plant crop, harvest date by treatment for the ratoon crop, and cultivar by harvest date for both crops for cane quality also were significant. Time from ripener application to achievement of maximum sugar concentration also depended on cultivar. This is important in determining the economic benefits of a ripener treatment. Climatic conditions may also affect the benefits of such applications.Mention of trade name or proprietary product does not imply or constitute an endorsement or recommendation by the USDA or the University of Florida.     

Response of eight sugarcane cultivars to glyphosine and glyphosate ripeners

Studies were conducted on eight sugarcane (Saccharum spp. hydrid) cultivars during the 1982–83 (plant crop) and 1983–84 (ratoon crop) growing seasons to determine the effects of glyphosine (Polaris) (N,N-bis (phosphonomethyl) glycine) and glyphosate (Polado) (sodium-N-(phosphonomethyl) glycine) on stalk sucrose content and yield. Difference due to crops (plant vs. ratoon) for sugarcane quality, kilograms of sugar per ton of cane (S/T), sugarcane yield, tons of cane per hectare (TCH), and sugar yield, tons of sugar per hectare (TSH) were significant. Significant differences were found in quality for the ratoon crop and cane and sugar yield in both crops due to ripener treatment. Cultivars in both crops differed significantly in quality and yield. Harvest dates were significantly different for all plant characteristics. Interactions of cultivar by treatment for the plant crop, harvest date by treatment for the ratoon crop, and cultivar by harvest date for both crops for cane quality also were significant. Time from ripener application to achievement of maximum sugar concentration also depended on cultivar. This is important in determining the economic benefits of a ripener treatment. Climatic conditions may also affect the benefits of such applications.     

Mosquitoes LTR retrotransposons: a deeper view into the genomic sequence of Culex quinquefasciatus

A set of 67 novel LTR-retrotransposon has been identified by in silico analyses of the Culex quinquefasciatus genome using the LTR_STRUC program. The phylogenetic analysis shows that 29 novel and putatively functional LTR-retrotransposons detected belong to the Ty3/gypsy group. Our results demonstrate that, by considering only families containing potentially autonomous LTR-retrotransposons, they account for about 1% of the genome of C. quinquefasciatus. In previous studies it has been estimated that 29% of the genome of C. quinquefasciatus is occupied by mobile genetic elements.The potential role of retrotransposon insertions strictly associated with host genes is described and discussed along with the possible origin of a retrotransposon with peculiar Primer Binding Site region. Finally, we report the presence of a group of 38 retrotransposons, carrying tandem repeated sequences but lacking coding potential, and apparently lacking "master copy" elements from which they could have originated. The features of the repetitive sequences found in these non-autonomous LTR retrotransposons are described, and their possible role discussed.These results integrate the existing data on the genomics of an important virus-borne disease vector.     

Use of population structure and parentage analyses to elucidate the spread of native cultivars of Japanese chestnut

The Japanese chestnut (Castanea crenata Siebold et Zucc.) is naturally distributed throughout Japan and is cultivated for its fruit (nuts) throughout the country. Many native cultivars have cultivation records going back more than 100 years. Researchers have speculated that native cultivars that originated in the Tanba region, the most important region of cultivation, were spread throughout Japan. To clarify the breeding history and spreading pattern of Japanese chestnut cultivars, we estimated the population structure of a set of 60 native chestnut cultivars via hierarchical clustering and Bayesian model-based clustering. Both analyses gave similar results. The cultivars were divided into two main clusters: one with cultivars from the Tanba region, the other with cultivars from other areas of Japan. However, there were some exceptions to this pattern, suggesting that propagation of clones and seeds by humans was a part of the spreading process. Additionally, parent–offspring relationships were estimated from the data obtained for 175 simple sequence repeat markers. Out of the 60 genotypes, nine putative parent–offspring pairs and eight putative parent–offspring trios were identified. These results suggest that native cultivars are likely to have been selected from crosses of older native cultivars. In particular, some native cultivars from outside the Tanba region had parent–offspring relationships with cultivars from the Tanba region. This result suggests that cultivars from outside the Tanba region had been crossed with cultivars from the Tanba region and then selected as a means of introducing favorable traits from the Tanba cultivars.     

Source gene composition and gene conversion of the AluYh and AluYi lineages of retrotransposons

Background  

Alu elements are a family of SINE retrotransposons in primates. They are classified into subfamilies according to specific diagnostic mutations from the general Alu consensus. It is now believed that there may be several retrotranspositionally-competent source genes within an Alu subfamily. In this study, subfamilies falling on the AluYi and AluYh lineages, and the AluYg6 subfamily, are assessed for the presence of secondary source genes, and the influence of gene conversion on the AluYh and AluYi lineages is also described.     

Mononucleotide repeats are an abundant source of length variants in mouse genomic DNA

Microsatellite sequences, such as dinucleotide repeats, show a high degree of polymorphism in eukaryotic DNA. These sequences are convenient as genetic markers and can be analyzed by the polymerase chain reaction (PCR). We have assessed the frequency of length variants in 18 mononucleotide repeats in mouse DNA and find that the variability is similar to that reported for dinucleotide repeats. Nine of the 18 repeat sequences (50%) have three or more alleles in the strains tested. Ten of these repeat sequences have been mapped using strain distribution patterns (SDPs) in recombinant inbred (RI) strains.     

Analysis of the features and source gene composition of the AluYg6 subfamily of human retrotransposons

Background  

Alu elements are a family of SINE retrotransposons in primates. They are classified into subfamilies according to specific diagnostic mutations from the general Alu consensus. It is now believed that there may be several retrotranspositionally-competent source genes within an Alu subfamily. To investigate the evolution of young Alu elements it is critical to have access to complete subfamilies, which, following the release of the final human genome assembly, can now be obtained using in silico methods.     

Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa

The known genomic islands of Pseudomonas aeruginosa clone C strains are integrated into tRNA(Lys) (pKLC102) or tRNA(Gly) (PAGI-2 and PAGI-3) genes and differ from their core genomes by distinctive tetranucleotide usage patterns. pKLC102 and the related island PAPI-1 from P. aeruginosa PA14 were spontaneously mobilized from their host chromosomes at frequencies of 10% and 0.3%, making pKLC102 the most mobile genomic island known with a copy number of 30 episomal circular pKLC102 molecules per cell. The incidence of islands of the pKLC102/PAGI-2 type was investigated in 71 unrelated P. aeruginosa strains from diverse habitats and geographic origins. pKLC102- and PAGI-2-like islands were identified in 50 and 31 strains, respectively, and 15 and 10 subtypes were differentiated by hybridization on pKLC102 and PAGI-2 macroarrays. The diversity of PAGI-2-type islands was mainly caused by one large block of strain-specific genes, whereas the diversity of pKLC102-type islands was primarily generated by subtype-specific combination of gene cassettes. Chromosomal loss of PAGI-2 could be documented in sequential P. aeruginosa isolates from individuals with cystic fibrosis. PAGI-2 was present in most tested Cupriavidus metallidurans and Cupriavidus campinensis isolates from polluted environments, demonstrating the spread of PAGI-2 across habitats and species barriers. The pKLC102/PAGI-2 family is prevalent in numerous beta- and gammaproteobacteria and is characterized by high asymmetry of the cDNA strands. This evolutionarily ancient family of genomic islands retained its oligonucleotide signature during horizontal spread within and among taxa.