Abstract
BackgroundSugarcane 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.ResultsA 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.ConclusionThe SS_SBa BAC library represents a new resource for sugarcane genome sequencing. An analysis of insert size, genome coverage and orthologous alignment with the sorghum genome revealed that the library presents whole genome coverage. The comparison of syntenic regions of the sorghum genome to 42 SS_SBa BES pairs revealed that the sorghum genome is expanded in relation to the sugarcane genome.
Highlights
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
Construction and characterisation of the SP80-3280 bacterial artificial chromosome (BAC) library The sugarcane variety SP80-3280 was chosen to construct the BAC library because it has been widely cultivated in Brazil
Sequencing a BAC library from this variety may reveal allelic composition involved in crop performance, and by comparing with genome sequence from other sugarcane BAC libraries may reveal genomic regions responsible for crop adaptation to different environments
Summary
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. Sugarcane has been grown as a sugar source for a century, but in recent years, extensive industrial plantations have demonstrated this crop’s value for the production of sustainable energy [2]. In industrial plantations, when sugarcane is harvested, its leaves are left in the field, contributing to the improvement of soil conservation and fertility. Sugarcane juice has been used as a carbon source by the synthetic biology industry to produce other fuels and high value molecules [3]. The worldwide use of sugarcane for sustainable energy production depends, on the development of superior varieties that are able to grow in less fertile soils, in stress-inducing biotic and abiotic conditions in a range of tropical and sub-tropical environments
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