Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae Griseb. subtribe of the Andropogoneae Dumort. tribe

Evaluation of genome size and phylogenetic relationships of the Saccharum complex species

"Saccharum complex" is a hypothetical group of species, which is supposed to be involved in the origin of modern sugarcane, and displays large genomes and complex chromosomal alterations. The utilization of restricted parents in breeding programs of modern cultivated sugarcane has resulted in a genetic blockage, which controlled its improvement because of the limited genetic diversity. The use of wild relatives is an effective way to broaden the genetic composition of cultivated sugarcane. Due to the infrequent characterization of genomes, the potential of wild relatives is diffused in improving the cultivated sugarcane. To characterize the genomes of the wild relatives, the genome size and phylogenetic relationships among eight species, including Saccharum spontaneum, Erianthus arundinaceus, E. fulvus, E. rockii, Narenga porphyrocoma, Miscanthus floridulus, Eulalia quadrinervis, and M. sinensis were evaluated based on flow cytometry, genome surveys, K-mer analysis, chloroplast genome sequencing, and whole-genome SNPs analysis. We observed highly heterozygous genomes of S. spontaneum, E. rockii, and E. arundinaceus and the highly repetitive genome of E. fulvus. The genomes of Eulalia quadrinervis, N. porphyrocoma, M. sinensis, and M. floridulus were highly complex. Phylogenetic results of the two approaches were dissimilar, however, both indicate E. fulvus displayed closer relationships to Miscanthus and Saccharum than other species of Saccharum complex. Eulalia quadrinervis was more closely related to M. floridulus than M. sinensis; E. arundinaceus differ significantly from Miscanthus, Narenga, and Saccharum, but was relatively close to Erianthus. We proved the point of E. rockii and E. fulvus should not be classified as one genus, and E. fulvus should be classified as the Saccharum genus.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03338-5.

Assessment of Gene Flow to Wild Relatives and Nutritional Composition of Sugarcane in Brazil

The commercial release of genetically modified organisms (GMO) requires a prior environmental and human/animal health risk assessment. In Brazil, the National Biotechnology Technical Commission (CTNBio) requires a survey of the area of natural occurrence of wild relatives of the GMO in the Brazilian ecosystems to evaluate the possibility of introgressive hybridization between sexually compatible species. Modern sugarcane cultivars, the focus of this study, derive from a series of hybridization and backcrossing events among Saccharum species. The so-called "Saccharum broad sense" group includes around 40 species from a few genera, including Erianthus, found in various tropical regions, particularly South-Eastern Asia. In Brazil, three native species, originally considered to belong to Erianthus, were reclassified as S. angustifolium (Nees) Trin., S. asperum (Nees) Steud., and S. villosum Steud., based on inflorescence morphology. Thus, we have investigated the potential occurrence of gene flow among the Brazilian Saccharum native species and commercial hybrids as a requisite for GMO commercial release. A comprehensive survey was carried out to map the occurrence of the three native Saccharum species in Brazil, concluding that they are sympatric with sugarcane cultivation only from around 14°S southwards, which precludes most Northeastern sugarcane-producing states from undergoing introgression. Based on phenology, we concluded that the Brazilian Saccharum species are unable to outcross naturally with commercial sugarcane since the overlap between the flowering periods of sugarcane and the native species is limited. A phylogenomic reconstruction based on the full plastid genome sequence showed that the three native Saccharum species are the taxa closest to sugarcane in Brazil, being closer than introduced Erianthus or Miscanthus. A 2-year study on eight nutritional composition traits of the 20 main sugarcane cultivars cultivated in Brazil was carried out in six environments. The minimum and maximum values obtained were, in percent: moisture (62.6-82.5); sucrose (9.65-21.76); crude fiber (8.06-21.03); FDN (7.20-20.68); FDA (4.55-16.90); lipids (0.06-1.59); ash (0.08-2.67); and crude protein (0.18-1.18). Besides a considerable amount of genetic variation and plastic responses, many instances of genotype-by-environment interaction were detected.

Cytogenetic and agronomic characterization of intergeneric hybrids between Saccharum spp. hybrid and Erianthus arundinaceus

In sugarcane (Saccharum spp. hybrid) breeding, introgression of useful genes via intergeneric hybridization is a powerful strategy for improving the crop productivity. Erianthus arundinaceus shows great potential in terms of useful traits; however, little is known about the cytogenetic and agronomic characteristics of intergeneric hybrids between these two species. Here, we examine the cytogenetic and agronomic characteristics, and relationships between the two in intergeneric F₁ hybrids between modern sugarcane cultivar and E. arundinaceus identified by amplification of 5S rDNA markers and morphological characteristics. The nuclear DNA content of the hybrids varied from 6.07 to 8.94 pg/2C, with intra-clonal variation in DNA content and 5S rDNA sites. Genomic in situ hybridization revealed 53 to 82 chromosomes in the hybrids, with 53 to 56 derived from sugarcane and 1 to 29 from E. arundinaceus. There were significant positive correlations between the number of E. arundinaceus chromosomes and dry matter yield, millable stalk weight, single stalk weight, and stalk diameter, but not sucrose content, reducing sugar content, sucrose/reducing sugar ratio or fiber content. This detailed information on intergeneric F₁ hybrids between modern sugarcane cultivar and E. arundinaceus will contribute to effective utilization of E. arundinaceus in sugarcane breeding.

Complete Chloroplast Genomes of Erianthus arundinaceus and Miscanthus sinensis: Comparative Genomics and Evolution of the Saccharum Complex

The genera Erianthus and Miscanthus, both members of the Saccharum complex, are of interest as potential resources for sugarcane improvement and as bioenergy crops. Recent studies have mainly focused on the conservation and use of wild accessions of these genera as breeding materials. However, the sequence data are limited, which hampers the studies of phylogenetic relationships, population structure, and evolution of these grasses. Here, we determined the complete chloroplast genome sequences of Erianthus arundinaceus and Miscanthus sinensis by using 454 GS FLX pyrosequencing and Sanger sequencing. Alignment of the E. arundinaceus and M. sinensis chloroplast genome sequences with the known sequence of Saccharum officinarum demonstrated a high degree of conservation in gene content and order. Using the data sets of 76 chloroplast protein-coding genes, we performed phylogenetic analysis in 40 taxa including E. arundinaceus and M. sinensis. Our results show that S. officinarum is more closely related to M. sinensis than to E. arundinaceus. We estimated that E. arundinaceus diverged from the subtribe Sorghinae before the divergence of Sorghum bicolor and the common ancestor of S. officinarum and M. sinensis. This is the first report of the phylogenetic and evolutionary relationships inferred from maternally inherited variation in the Saccharum complex. Our study provides an important framework for understanding the phylogenetic relatedness of the economically important genera Erianthus, Miscanthus, and Saccharum.

Characterization of Chromosome Inheritance of the Intergeneric BC2 and BC3 Progeny between Saccharum spp. and Erianthus arundinaceus

Erianthus arundinaceus (E. arundinaceus) has many desirable agronomic traits for sugarcane improvement, such as high biomass, vigor, rationing ability, tolerance to drought, and water logging, as well as resistance to pests and disease. To investigate the introgression of the E. arundinaceus genome into sugarcane in the higher generations, intergeneric BC2 and BC3 progeny generated between Saccharum spp. and E. arundinaceus were studied using the genomic in situ hybridization (GISH) technique. The results showed that the BC2 and BC3 generations resulted from n + n chromosome transmission. Furthermore, chromosome translocation occurred at terminal fragments from the E. arundinaceus chromosome in some progeny of Saccharum spp. and E. arundinaceus. Notably, the translocated chromosomes could be stably transmitted to their progeny. This study illustrates the characterization of chromosome inheritance of the intergeneric BC2 and BC3 progeny between Saccharum spp. and E. arundinaceus. This work could provide more useful molecular cytogenetic information for the germplasm resources of E. arundinaceus, and may promote further understanding of the germplasm resources of E. arundinaceus for sugarcane breeders to accelerate its progress in sugarcane commercial breeding.

Biofuel and energy crops: high-yield Saccharinae take center stage in the post-genomics era

The Saccharinae, especially sugarcane, Miscanthus and sorghum, present remarkable characteristics for bioenergy production. Biotechnology of these plants will be important for a sustainable feedstock supply. Herein, we review knowledge useful for their improvement and synergies gained by their parallel study.

Phylogenetic relationships among Saccharum clones in Pakistan revealed by RAPD markers

Forty sugarcane genotypes (clones), including elite lines, commercial cultivars of Saccharum officinarum and S. barberi clones, were fingerprinted with 30 RAPD markers, using a PCR-based marker assay. The genetic distance for RAPD data was determined according to Nei, and relationships between accessions were graphed in a dendrogram. Genetic distance values ranging from 16.2 to 86.3% were observed among the 40 sugarcane accessions. The lowest genetic distance was found between genotypes US-406 and US-186. These two genotypes differed from each other in only 25 bands with 15 different primers. Genotypes Col-54 and CP-72-2086 were the second most similar group, with a genetic distance of 19.46%. The most dissimilar of all the accessions were CP-77-400 and US-133, with a genetic distance of 86.3%. RAPD fingerprints help sugarcane breeders clarify the genetic pedigree of commercial sugarcane varieties and can be used to evaluate the efficiency of conventional breeding methods.

Development of genome-wide simple sequence repeat markers using whole-genome shotgun sequences of sorghum (Sorghum bicolor (L.) Moench)

Simple sequence repeat (SSR) markers with a high degree of polymorphism contribute to the molecular dissection of agriculturally important traits in sorghum (Sorghum bicolor (L.) Moench). We designed 5599 non-redundant SSR markers, including regions flanking the SSRs, in whole-genome shotgun sequences of sorghum line ATx623. (AT/TA)_n repeats constituted 26.1% of all SSRs, followed by (AG/TC)_n at 20.5%, (AC/TG)_n at 13.7% and (CG/GC)_n at 11.8%. The chromosomal locations of 5012 SSR markers were determined by comparing the locations identified by means of electronic PCR with the predicted positions of 34 008 gene loci. Most SSR markers had a similar distribution to the gene loci. Among 970 markers validated by fragment analysis, 67.8% (658 of 970) markers successfully provided PCR amplification in sorghum line BTx623, with a mean polymorphism rate of 45.1% (297 of 658) for all SSR loci in combinations of 11 sorghum lines and one sudangrass (Sorghum sudanense (Piper) Stapf) line. The product of 5012 and 0.678 suggests that ∼3400 SSR markers could be used to detect SSR polymorphisms and that more than 1500 (45.1% of 3400) markers could reveal SSR polymorphisms in combinations of Sorghum lines.

Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome

Modern sugarcane (Saccharum spp.) is an important grass that contributes 60% of the raw sugar produced worldwide and has a high biofuel production potential. It was created about a century ago through hybridization of two highly polyploid species, namely S. officinarum and S. spontaneum. We investigated genome dynamics in this highly polyploid context by analyzing two homoeologous sequences (97 and 126 kb) in a region that has already been studied in several cereals. Our findings indicate that the two Saccharum species diverged 1.5-2 million years ago from one another and 8-9 million years ago from sorghum. The two sugarcane homoeologous haplotypes show perfect colinearity as well as high gene structure conservation. Apart from the insertion of a few retrotransposable elements, high homology was also observed for the non-transcribed regions. Relative to sorghum, the sugarcane sequences displayed colinearity, with the exception of two genes present only in sorghum, and striking homology in most non-coding parts of the genome. The gene distribution highlighted high synteny and colinearity with rice, and partial colinearity with each homoeologous maize region, which became perfect when the sequences were combined. The haplotypes observed in sugarcane may thus closely represent the ancestral Andropogoneae haplotype. This analysis of sugarcane haplotype organization at the sequence level suggests that the high ploidy in sugarcane did not induce generalized reshaping of its genome, thus challenging the idea that polyploidy quickly induces generalized rearrangement of genomes. These results also confirm the view that sorghum is the model of choice for sugarcane.

AFLP analysis of genetic diversity within Saccharum officinarum and comparison with sugarcane cultivars

Molecular diversity among 421 clones of cultivated sugarcane and wild relatives was analysed using AFLP markers. Of these clones, 270 were Saccharum officinarum and 151 were either cultivars produced by the Australian breeding program or important parents used in the breeding program. The S. officinarum clones were obtained from a collection that contained clones from all the major regions where S. officinarum is grown. Five AFLP primer combinations generated 657 markers of which 614 were polymorphic. All clones contained a large number of markers; a result of the polyploid nature and heterozygosity of the genome. S. officinarum clones from New Guinea displayed greater diversity than S. officinarum clones from other regions. This is in agreement with the hypothesis that New Guinea is the centre of origin of this species. The S. officinarum clones from Hawaii and Fiji formed a separate group and may correspond to clones that have been introgressed with other members of the ‘Saccharum complex’. Greater diversity was found in the cultivars than in the S. officinarum clones due to the introgression of S. spontaneum chromatin. These cultivars clustered as expected based on pedigree. The major contribution of clones QN66-2008 and Nco310 to Australian sugarcane cultivars divided the cultivars into 2 main groups. Although only a few S. officinarum clones are known to have been used in the breeding of current cultivars, about 90% of markers present in the S. officinarum clone collection (2n = 80) were also present in the cultivar collection. This suggests that most of the observed genetic diversity in S. officinarum has been captured in Australian sugarcane germplasm.

Very close relationship of the chloroplast genomes among Saccharum species

We recently determined the complete sequence of the sugarcane chloroplast genome. Here, we have used the information for a comprehensive phylogenetic analysis of the genus Saccharum, using all six species (13 accessions). The polymorphisms between sugarcane and maize in 26 chloroplast genome regions were used for the analysis. In 18 of the 26 regions (a total of 5,381 bp), we found 41 mutations involving 17 substitutions, three inversions, six insertion/deletion mutations, and 15 simple sequence repeat length polymorphisms. Based on these results, we calculated a phylogenetic tree of the genus Saccharum, in which all six species are clearly separated. By the analysis, (1) S. sinense and S. barberi, which have identical sequences, belong to the same clade, whereas the other four species, S. officinarum, S. robustum, S. edule, and S. spontaneum, form an independent clade; (2) S. spontaneum has a paraphyletic relationship with the other five species; and (3) no or very low intraspecific variation was observed in S. officinarum, S. robustum, S. sinense, S. barberi, and S. edule, whereas higher intraspecific variation was observed in S. spontaneum. Based on the number of nucleotide substitutions, the divergence time between S. officinarum and S. spontaneum, and between S. officinarum and maize were calculated to be about 730-780 thousand years ago and about 5.9 million years ago, respectively. These results suggest that the cytoplasm of Saccharum species are very closely related.

Species-specific accumulation of interspersed sequences in genus Saccharum

The genus Saccharum consists of two wild and four cultivated species. Novel interspersed sequences were isolated from cultivated sugar cane S. officinarum. These sequences were accumulated in all four cultivated species and their wild ancestral species S. robustum, but were not detected in the other wild species S. spontaneum and the relative Erianthus arundinaceus. The species-specific accumulation of interspersed sequences would correlate to the domestication of sugar canes.

Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome

The complete nucleotide sequence of the chloroplast genome of sugarcane (Saccharum officinarum) was determined. It consists of 141,182 base-pairs (bp), containing a pair of inverted repeat regions (IR(A), IR(B)) of 22,794 bp each. The IR(A) and IR(B) sequences separate a small single copy region (12,546 bp) and a large single copy (83,048 bp) region. The gene content and relative arrangement of the 116 identified genes (82 peptide-encoding genes, four ribosomal RNA genes, 30 tRNA genes), with the 16 ycf genes, are highly similar to maize. Editing events, defined as C-to-U transitions in the mRNA sequences, were comparable with those observed in maize, rice and wheat. The conservation of gene organization and mRNA editing suggests a common ancestor for the sugarcane and maize plastomes. These data provide the basis for functional analysis of plastid genes and plastid metabolism within the Poaceae. The sugarcane chloroplast DNA sequence is available at GenBank under accession NC005878.

A High-Density Genetic Recombination Map of Sequence-Tagged Sites for Sorghum, as a Framework for Comparative Structural and Evolutionary Genomics of Tropical Grains and Grasses

We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0.4 cM (∼300 kb) intervals based on 2050 RFLP probes, including 865 heterologous probes that foster comparative genomics of Saccharum (sugarcane), Zea (maize), Oryza (rice), Pennisetum (millet, buffelgrass), the Triticeae (wheat, barley, oat, rye), and Arabidopsis. Mapped loci identify 61.5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of ≤50 cM. Significant variations in DNA marker density are related to possible centromeric regions and to probable chromosome structural rearrangements between Sorghum bicolor and S. propinquum, but not to variation in levels of intraspecific allelic richness. While cDNA and genomic clones are similarly distributed across the genome, SSR-containing clones show different abundance patterns. Rapidly evolving hypomethylated DNA may contribute to intraspecific genomic differentiation. Nonrandom distribution patterns of multiple loci detected by 357 probes suggest ancient chromosomal duplication followed by extensive rearrangement and gene loss. Exemplifying the value of these data for comparative genomics, we support and extend prior findings regarding maize-sorghum synteny—in particular, 45% of comparative loci fall outside the inferred colinear/syntenic regions, suggesting that many small rearrangements have occurred since maize-sorghum divergence. These genetically anchored sequence-tagged sites will foster many structural, functional and evolutionary genomic studies in major food, feed, and biomass crops.

Cold tolerance of C4 photosynthesis in Miscanthus x giganteus: adaptation in amounts and sequence of C4 photosynthetic enzymes

Field-grown Miscanthus x giganteus maintains high photosynthetic quantum yields and biomass productivity in cool temperate climates. It is related to maize (Zea mays) and uses the same NADP-malic enzyme C(4) pathway. This study tests the hypothesis that M. x giganteus, in contrast to maize, forms photosynthetically competent leaves at low temperatures with altered amounts of pyruvate orthophosphate dikinase (PPDK) and Rubisco or altered properties of PPDK. Both species were grown at 25 degrees C/20 degrees C or 14 degrees C/11 degrees C (day/night), and leaf photosynthesis was measured from 5 degrees C to 38 degrees C. Protein and steady-state transcript levels for Rubisco, PPDK, and phosphoenolpyruvate carboxylase were assessed and the sequence of C(4)-PPDK from M. x giganteus was compared with other C(4) species. Low temperature growth had no effect on photosynthesis in M. x giganteus, but decreased rates by 80% at all measurement temperatures in maize. Amounts and expression of phosphoenolpyruvate carboxylase were affected little by growth temperature in either species. However, PPDK and Rubisco large subunit decreased >50% and >30%, respectively, in cold-grown maize, whereas these levels remained unaffected by temperature in M. x giganteus. Differences in protein content in maize were not explained by differences in steady-state transcript levels. Several different M. x giganteus C(4)-PPDK cDNA sequences were found, but putative translated protein sequences did not show conservation of amino acids contributing to cold stability in Flaveria brownii C(4)-PPDK. The maintenance of PPDK and Rubisco large subunit amounts in M. x giganteus is consistent with the hypothesis that these proteins are critical to maintaining high rates of C(4) photosynthesis at low temperature.

Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane

The use of maize microsatellite markers as a potential cost-effective method for molecular analysis of sugarcane was evaluated. Of the 34 primer pairs obtained from maize genomic libraries, 14 showed repeatable amplifications in Saccharum species clones, commercial hybrids, and the related genera Erianthus, accounting for 41.17% cross transferability. Complex banding patterns were encountered in sugarcane with the number of amplified fragments ranging from 7 to 14 with an average of 10 per primer, indicating the high polyploidy and heterozygosity existing in sugarcane. Phenetic analysis of the SSR polymorphisms produced by nine primers could clearly differentiate the different species of Saccharum and Erianthus and revealed the relationships that existed between them. Genetic similarity co-efficient indicated low diversity existing among the S. officinarum clones (82%) and a relatively higher level of diversity in the S. spontaneum clones (69.7%). Higher level of divergence of Erianthus from Saccharum was also clearly estabilished. Five primers produced genus- and species-specific fragments for Erianthus, S. spontaneum, S. officinarum, and S. barberi. The polymorphic primers, when tested on a panel of 30 commercial sugarcane cultivars, revealed a broad range (32.4-83.3%) of pair-wise similarity values, indicating their ability to detect high levels of polymorphism. A combination of two primers could differentiate all the varieties, further emphasizing their potential in fingerprinting and varietal identification.

A search for markers of sugarcane evolution

To determine the phylogenetic relationship between sugarcane cultivars and other members of the Saccharinae subtribe, we identified the fast evolving ITS1-5.8S-ITS2 (ITS = internal transcribed spacer; 5.8S = 5.8S ribosomal DNA) region of the sugarcane genome in the Sugarcane Expressed Sequence Tag (SUCEST) genome project database. Parsimony analysis utilizing this region and homologs belonging to the 23 closely related Andropogoneae currently deposited in the GenBank database has shown sugarcane as the sister group of Saccharum sinense. However, because there are few parsimony-informative characters and high homoplasy in the ITS1-5.8S-ITS2 region we were not able to determine with confidence the phylogenetic relationship between sugarcane and some of the remaining members of Saccharine subtribe. To find alternatives for the phylogenetic reconstruction of sugarcane evolutionary history, we selected 17 markers (nuclear, chloroplastic or mitochondrial) from the SUCEST database of which apha-tubulin, ribosomal protein L16 (rpl16) and DNA-directed RNA polymerase beta chain (rpoC2) were found to have a low incidence of polymorphism and comparable, or even faster, rates of evolution than the ITS1-5.8S-ITS2 region. We suggest that these markers should be considered as preferential choices for phylogenetic studies of Saccharinae subtribe.

Genetic maps of Saccharum officinarum L. and Saccharum robustum Brandes & Jew. ex grassl

Genetic analysis was performed in a population composed of 100 F1 individuals derived from a cross between a cultivated sugarcane (S. officinarum `LA Purple') and its proposed progenitor species (S. robustum `Mol 5829'). Various types (arbitrarily primed-PCR, RFLPs, and AFLPs) of single-dose DNA markers (SDMs) were used to construct genetic linkage maps for both species. The LA Purple map was composed of 341 SDMs, spanning 74 linkage groups and 1,881 cM, while the Mol 5829 map contained 301 SDMs, spanning 65 linkage groups and 1,189 cM. Transmission genetics in these two species showed incomplete polysomy based on the detection of 15% of SDMs linked in repulsion in LA Purple and 13% of these in Mol 5829. Because of this incomplete polysomy, multiple-dose markers could not be mapped for lack of a genetic model for their segregation. Due to inclusion of RFLP anchor probes, conserved in related species, the resulting maps will serve as useful tools for breeding, ecology, evolution, and molecular biology studies within the Andropogoneae.

Detailed alignment of saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes

The complex polyploid genomes of three Saccharum species have been aligned with the compact diploid genome of Sorghum (2n = 2x = 20). A set of 428 DNA probes from different Poaceae (grasses) detected 2460 loci in F1 progeny of the crosses Saccharum officinarum Green German x S. spontaneum IND 81-146, and S. spontaneum PIN 84-1 x S. officinarum Muntok Java. Thirty-one DNA probes detected 226 loci in S. officinarum LA Purple x S. robustum Molokai 5829. Genetic maps of the six Saccharum genotypes, including up to 72 linkage groups, were assembled into "homologous groups" based on parallel arrangements of duplicated loci. About 84% of the loci mapped by 242 common probes were homologous between Saccharum and Sorghum. Only one interchromosomal and two intrachromosomal rearrangements differentiated both S. officinarum and S. spontaneum from Sorghum, but 11 additional cases of chromosome structural polymorphism were found within Saccharum. Diploidization was advanced in S. robustum, incipient in S. officinarum, and absent in S. spontaneum, consistent with biogeographic data suggesting that S. robustum is the ancestor of S. officinarum, but raising new questions about the antiquity of S. spontaneum. The densely mapped Sorghum genome will be a valuable tool in ongoing molecular analysis of the complex Saccharum genome.

Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize

Comparative genetic maps of Papuan Saccharum officinarum L. (2n = 80) and S. robustum (2n = 80) were constructed by using single-dose DNA markers (SDMs). SDM-framework maps of S. officinarum and S. robustum were compared with genetic maps of sorghum and maize by way of anchor restriction fragment length polymorphism probes. The resulting comparisons showed striking colinearity between the sorghum and Saccharum genomes. There were no differences in marker order between S. officinarum and sorghum. Furthermore, there were no alterations in SDM order between S. officinarum and S. robustum. The S. officinarum and S. robustum maps also were compared with the map of the polysomic octoploid S. spontaneum 'SES 208' (2n = 64, x = 8), thus permitting relations to homology groups ("chromosomes") of S. spontaneum to be studied. Investigation of transmission genetics in S. officinarum and S. robustum confirmed preliminary results that showed incomplete polysomy in these species. Because of incomplete polysomy, multiple-dose markers could not be mapped for lack of a genetic model for their segregation. To coalesce S. officinarum and S. robustum linkage groups into homology groups (composed of homologous pairing partners), they were compared with sorghum (2n = 20), which functioned as a synthetic diploid. Groupings suggested by comparative mapping were found to be highly concordant with groupings based on highly polymorphic restriction fragment length polymorphism probes detecting multiple SDMs. The resulting comparative maps serve as bridges to allow information from one Andropogoneae to be used by another, for breeding, ecology, evolution, and molecular biology.

Identification and characterisation of sugarcane intergeneric hybrids, Saccharum officinarum x Erianthus arundinaceus, with molecular markers and DNA in situ hybridisation

Molecular markers were used to characterise sugarcane intergeneric hybrids between S. officinarum and E. arundinaceus. Very simple diagnostic tools for hybrid identification among the progeny were derived from isozyme electrophoresis and a sequence-tagged PCR. Two enzyme systems (GOT and MDH B) and PCR amplification revealing spacer-size variation in the 5s-rDNA cluster were found most convenient. Specific characterisation of the two genomic components was possible using RFLP and in situ hybridisation. The strong molecular differentiation between S. officinarum and E. arundinaceus allows the identification of numerous Erianthus-specific RFLP bands in the hybrids. Genomic DNA in situ hybridisation allows for the differentiation of the chromosomes contributed by S. officinarum and E. arundinaceus in chromosome preparations of the hybrids. In situ hybridisation with the 18s-5.8s-25s rDNA probe highlights the basic chromosome numbers in the two parental species. The potential of these techniques to monitor the Erianthus genome during the introgression process is discussed.

Chromosome assortment in Saccharum

Recent work has revealed random chromosome pairing and assortment in Saccharum spontaneum L., the most widely distributed, and morphologically and cytologically variable of the species of Saccharum. This conclusion was based on the analysis of a segregating population from across between S. spontaneum 'SES 208' and a spontaneously-doubled haploid of itself, derived from anther culture. To determine whether polysomic inheritance is common in Saccharum and whether it is observed in a typical biparental cross, we studied chromosome pairing and assortment in 44 progeny of a cross between euploid, meiotically regular, 2n=80 forms of Saccharum officinarum 'LA Purple' and Saccharum robustum ' Mol 5829'. Papuan 2n=80 forms of S. robustum have been suggested as the immediate progenitor species for cultivated sugarcane (S. officinarum). A total of 738 loci in LA Purple and 720 loci in Mol 5829 were amplified and typed in the progeny by arbitrarily primed PCR using 45 primers. Fifty and 33 single-dose polymorphisms were identified in the S. officinarum and S. robustum genomes, respectively (χ 2 at 98%). Linkage analysis of single-dose polymorphisms in both genomes revealed linkages in repulsion and coupling phases. In the S. officinarum genome, a map hypothesis gave 7 linkage groups with 17 linked and 33 unlinked markers. Four of 13 pairwise linkages were in repulsion phase and 9 were in coupling phase. In the S. robustum genome, a map hypothesis gave 5 linkage groups, defined by 12 markers, with 21 markers unlinked, and 2 of 9 pairwise linkages were in repulsion phase. Therefore, complete polysomic inheritance was not observed in either species, suggesting that chromosomal behavior is different from that observed by linkage analysis of over 500 markers in the S. spontaneum map. Implications of this finding for evolution and breeding are discussed.

Phylogenetic analysis of organellar DNA sequences in the Andropogoneae: Saccharinae

To study the phylogenetics of sugarcane (Saccharum officinarum L.) and its relatives we sequenced four loci on cytoplasmic genomes (two chloroplast and two mitochondrial) and analyzed mitochondrial RFLPs generated using probes for COXI, COXII, COXIII, Cob, 18S+5S, 26S, ATPase 6, ATPase 9, and ATPase α (D'Hont et al. 1993). Approximately 650 bp of DNA in the intergenic spacer region between rbcL and atpB and approximately 150 bp from the chloroplast 16S rDNA through the intergenic spacer region tRNA(val) gene were sequenced. In the mitochondrial genome, part of the 18S rRNA gene and approximately 150 bp from the 18S gene 3' end, through an intergenic spacer region, to the 5S rRNA gene were sequenced. No polymorphisms were observed between maize, sorghum, and 'Saccharum complex' members for the mitochondrial 18S internal region or for the intergenic tRNA(val) chloroplast locus. Two polymorphisms (insertion-deletion events, indels) were observed within the 18S-5S mitochondrial locus, which separated the accessions into three groups: one containing all of the Erianthus, Eccoilopus, Imperata, Sorghum, and 1 Miscanthus species; a second containing Saccharum species, Narenga porphyrocoma, Sclerostachya fusca, and 1 presumably hybrid Miscanthus sp. from New Guinea; and a third containing maize. Eighteen accessions were sequenced for the intergenic region between rbcL and atpB, which was the most polymorphic of the regions studied and contained 52 site mutations and 52 indels, across all taxa. Within the Saccharum complex, at most 7 site mutations and 16 indels were informative. The maternal lineage of Erianthus/Eccoilopus was nearly as divergent from the remaining Saccharum complex members as it was from sorghum, in agreement with a previous study. Sequences from the rbcL-atpB spacer were aligned with GENBANK sequences for wheat, rice, barley, and maize, which were used as outgroups in phylogenetic analyses. To determine whether limited intra-complex variability was caused by under sampling of taxa, we used seven restriction enzymes to digest the PCR-amplified rbcL-atpB spacer of an additional 36 accessions within the Saccharum complex. This analysis revealed ten restriction sites (none informative) and eight length variants (four informative). The small amount of variation present in the organellar DNAs of this polyploid complex suggests that either the complex is very young or that rates of evolution between the Saccharum complex and outgroup taxa are different. Other phylogenetic information will be required to resolve systematic relationships within the complex. Finally, no variation was observed in commercial sugarcane varieties, implying a world-wide cytoplasmic monoculture for this crop.