A search for markers of sugarcane evolution (original) (raw)
Related papers
Genetics and Molecular Research, 2014
A striking characteristic of modern sugarcane is that all sugarcane cultivars (Saccharum spp) share a common cytoplasm from S. officinarum. To explore the potential value of S. spontaneum cytoplasm, new Saccharum hybrids with an S. spontaneum cytoplasm were developed at the United States Department of Agriculture-Agricultural Research Service, Sugarcane Research Laboratory, through a combination of conventional and molecular breeding approaches. In this study, we analyzed the genetic variability among the chloroplast genomes of four sugarcane cultivars, eight S. spontaneum clones, and three F 1 progeny containing an S. spontaneum cytoplasm. Based on the complete chloroplast J.-R. Zhu et al. ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 13 (2): 3037-3047 (2014) genome sequence information of two sugarcane cultivars (NCo 310 and SP 80-3280) and five related grass species (barley, maize, rice, sorghum, and wheat), 19 polymerase chain reaction primer pairs were designed targeting various chloroplast DNA (cpDNA) segments with a total length varying from 4781 to 4791 bp. Ten of the 19 cpDNA segments were polymorphic, harboring 14 mutation sites [a 15-nt insertion/deletion (indel), a 5-nt indel, two poly (T) tracts, and 10 single nucleotide polymorphisms]. We demonstrate for the first time that the chloroplast genome of S. spontaneum was maternally inherited. Comparative sequence homology analyses clustered sugarcane cultivars into a distinctive group away from S. spontaneum and its progeny. Three mutation sites with a consistent, yet species-specific, nucleotide composition were found, namely, an A/C transversion and two indels. The genetic variability among cpDNA of sugarcane cultivars and S. spontaneum will be useful information to determine the maternal origin in the Saccharum genus.
Genetics and Molecular Research, 2016
We analyzed 80 plants of the sugarcane (Saccharum spp) variety 'RB867515' in order to investigate its diversity and genetic structure at the molecular level. Four simple sequence repeat (SSR) loci (UGSM51, SMC1237, SEGMS1069, and UGSM38) and five expressed sequence tag (EST)-SSR loci (ESTA68, ESTB92, ESTB145, ESTC66, and ESTC84) were used as molecular markers. The polymorphic loci rate was 66.6%. A total of 17 alleles and an average of 1.88 alleles/locus were detected. The number of alleles in the EST-SSR loci was lower than the number of alleles in the SSRs of non-expressed loci. The mean observed heterozygosity among the nine SSR loci was 0.3291. Genetic structure analysis showed that 'RB867515' contains alleles from three ancestral groups (K = 3), but there is little admixing of alleles in the same plant (from 0.8 to 17.3%); only 1.88% of the plants shared alleles from two or three groups. ESTB92, ESTC84, and UGSM38 were monomorphic, but there was evidence of polymorphism in ESTA68, ESTB145, ESTC66, UGSM51, SMC1237, and SEGMS1069, indicating that 'RB867515' has variability at the molecular level and the potential to be used as a parent in breeding programs. The molecular variability observed in 'RB867515' indicates that the clone terminology that is used to identify this cultivar is inconsistent with the original meaning of "clone", which is defined as a sample of genetically identical plants.
Molecular investigation of the genetic base of sugarcane cultivars
TAG Theoretical and Applied Genetics, 1999
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 interspeci"c origin; most of them were bred in Barbados or in Mauritius. Fifty three were from Saccharum o.cinarum 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 identi"ed, 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. o.cinarum 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. o.cinarum clones modi"ed Communicated by H. F. Linskens
Agronomy
Sugarcane (Saccharum spp. hybrids) is one of the most important commercial crops for sugar, ethanol, and other byproducts production; therefore, it is of great significance to carry out genetic research. Assessing the genetic population structure and diversity plays a vital role in managing genetic resources and gene mapping. In this study, we assessed the genetic diversity and population structure among 196 Saccharum accessions, including 34 S. officinarum, 69 S. spontaneum, 17 S. robustum, 25 S. barberi, 13 S. sinense, 2 S. edule, and 36 Saccharum spp. hybrids. A total of 624 polymorphic SSR alleles were amplified by PCR with 22 pairs of fluorescence-labeled highly polymorphic SSR primers and identified on a capillary electrophoresis (CE) detection system including 109 new alleles. Three approaches (model-based clustering, principal component analysis, and phylogenetic analysis) were conducted for population structure and genetic diversity analyses. The results showed that the 196...
A draft chromosome-scale genome assembly of a commercial sugarcane
Scientific Reports, 2022
Sugarcane accounts for a large portion of the worlds sugar production. Modern commercial cultivars are complex hybrids of S. officinarum, S. spontaneum, and several other Saccharum species, resulting in an auto-allopolyploid with 8-12 copies of each chromosome. The current genome assembly gold standard is to generate a long read assembly followed by chromatin conformation capture sequencing to scaffold. We used the PacBio RSII and chromatin conformation capture sequencing to sequence and assemble the genome of a South East Asian commercial sugarcane cultivar, known as Khon Kaen 3. The Khon Kaen 3 genome assembled into 104,477 contigs totalling 7 Gb, which scaffolded into 56 pseudochromosomes containing 5.2 Gb of sequence. Genome annotation produced 242,406 genes from 30,927 orthogroups. Aligning the Khon Kaen 3 genome sequence to S. officinarum and S. spontaneum revealed a high level of apparent recombination, indicating a chimeric assembly. This assembly error is explained by high nucleotide identity between S. officinarum and S. spontaneum, where 91.8% of S. spontaneum aligns to S. officinarum at 94% identity. Thus, the subgenomes of commercial sugarcane are so similar that using short reads to correct long PacBio reads produced chimeric long reads. Future attempts to sequence sugarcane must take this information into account. Sugarcane is an important crop species and is the major source of processed sugar in the world. The name sugarcane does not refer to a single species, but rather refers to any of several species in the genus Saccharum. Taxonomic classification of these species is difficult, confounded by many years of cultivation and cross breeding, which makes phenotypic classification unreliable, and has been a topic of much debate. It was originally considered that six species exist: S. spontaneum, S. robustum, S. officinarum, S. sinense, S. edule and S. barberi 1. Although, now it is common for S. edule to be excluded from this genus because in situ hybridisation revealed it to be a likely hybrid between S. officinarum and S. robustum, leaving only five species 1. Only two of these species, S. robustum and S. spontaneum, are considered wild species, and the remaining species are all cultivated 2,3. Modern commercial cultivars of sugarcane are complex hybrids of S. officinarum as the maternal donor crossed with S. spontaneum and, to a lesser extent, some other species and hybrids (for review see 1,4,5). Sugarcane is believed to have originated in the South Pacific, but was widely dispersed by early explorers making it difficult to pinpoint the exact origin. It is believed that S. spontaneum originates from India, but can be found growing wild from eastern and northern Africa, through the Middle East, to India, China, South East Asia, and through the Pacific to New Guinea. The other wild species, S. robustum, is indigenous to New Guinea and can be found along river banks. It is considered that S. officinarum also most likely originated in New Guinea and was likely derived from S. robustum. Modern commercial cultivars have complex polyploid genomes as a result of many generations of hybridisation.
A Survey Sequence Comparison of Saccharum Genotypes Reveals Allelic Diversity Differences
Tropical Plant Biology, 2014
Sugarcane (Saccharum spp.) is a crop of substantial international significance for both food and fuel, however its highly polyploid nature challenges investigation of its genetic composition. Efforts to generate the full sugarcane genome sequence are underway, however in the meantime crop improvement efforts are somewhat limited by the lack of genome sequence resources available for physiological characterization. Low-coverage survey sequence data was generated and assembled for six sugarcane genotypes representing a range of significant S. spontaneum, S. officinarum, and S. hybrid cultivar accessions from around the world. These data were explored to investigate the composition of repetitive sequences and variations in chloroplast genome sequence, as well as assembled into a conglomerate monoploid genome sequence for polymorphism comparison between the genotypes. Almost half (47 %) of the inter-genomic polymorphisms analysed in these data represented poly-allelic variations which cannot be applied in traditional present/absent marker analysis, suggesting that new approaches are required to better understand and access genetic diversity within the Saccharum genus. These results support previous assertions that S. spontaneum is both less repetitive (62 % repetitive kmers in Mandalay vs. 65 % in IJ76-514) and more highly polymorphic (17 % poly-alleles in Mandalay vs. 10 % polyalleles in IJ76-514) than S. officinarum, with S. hybrids being intermediate between the two. However, contrary to previous analysis the monoploid genome size of S. spontaneum does not appear to differ significantly from that of S. officinarum as had been expected. This genomic survey assembly will be a very useful resource for sugarcane genomics in the absence of a monoploid or polyploid genome sequence, and will be made available upon request.
A rapid DNA extraction method for sugarcane and its relatives
1992
A simple DNA extraction method based on CTAB precipitation was used to obtain DNA from members of the genus Saccharum and related species. DNA yields and purities were similar for all Saccharum species sampled. The method described here resulted in high quality total DNA suitable for polymerase chain reaction (PCR)-basecl techniques as well as restriction endonuclease digestion, Southern hybridization, and DNA cycle-sequencing.
2012
Background: Sugarcane breeding has significantly progressed in the last 30 years, but achieving additional yield gains has been difficult because of the constraints imposed by the complex ploidy of this crop. Sugarcane cultivars are interspecific hybrids between Saccharum officinarum and Saccharum spontaneum. S. officinarum is an octoploid with 2n = 80 chromosomes while S. spontaneum has 2n = 40 to 128 chromosomes and ploidy varying from 5 to 16. The hybrid genome is composed of 70-80% S. officinaram and 5-20% S. spontaneum chromosomes and a small proportion of recombinants. Sequencing the genome of this complex crop may help identify useful genes, either per se or through comparative genomics using closely related grasses. The construction and sequencing of a bacterial artificial chromosome (BAC) library of an elite commercial variety of sugarcane could help assembly the sugarcane genome. Results: A BAC library designated SS_SBa was constructed with DNA isolated from the commercial sugarcane variety SP80-3280. The library contains 36,864 clones with an average insert size of 125 Kb, 88% of which has inserts larger than 90 Kb. Based on the estimated genome size of 760-930 Mb, the library exhibits 5-6 times coverage the monoploid sugarcane genome. Bidirectional BAC end sequencing (BESs) from a random sample of 192 BAC clones sampled genes and repetitive elements of the sugarcane genome. Forty-five per cent of the total BES nucleotides represents repetitive elements, 83% of which belonging to LTR retrotransposons. Alignment of BESs corresponding to 42 BACs to the genome sequence of the 10 sorghum chromosomes revealed regions of microsynteny, with expansions and contractions of sorghum genome regions relative to the sugarcane BAC clones. In general, the sampled sorghum genome regions presented an average 29% expansion in relation to the sugarcane syntenic BACs.
Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize
Proceedings of the National Academy of Sciences, 1997
Comparative genetic maps of Papuan Saccharum officinarum L. (2 n = 80) and S. robustum (2 n = 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’ (2 n = 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 in...
Comparative genome mapping of sugar cane with other species within the Andropogoneae tribe
Heredity, 1994
Comparative mapping within the tribe Andropogoneae has recently progressed with the development of mapped maize genomic probes that can be used for sorghum and sugar cane genomes. In the present study, data from previous reports were used to locate various linkage groups of sugar cane and sorghum on the genomic map of maize. Syntenic genome regions in the three plants were determined according to existing bridge-loci. The distribution of these synteny clusters closely matched the duplication pattern in maize. In several cases, the two arms of a single maize chromosome corresponded to at least two synteny clusters. There seem to be common chromosome rearrangements between maize and sugar cane and between maize and sorghum. In this respect, sugar cane and sorghum appear to be more closely related than either one with maize. A more detailed analysis of two synteny clusters was undertaken using recent sugar cane data to compare gene orders and recombination rates of the three plants. The three genomes showed colinearity in these regions. Distances between genes were similar in maize and sorghum, whereas sugar cane tended to display less recombination, at least in the varietal progeny investigated.