Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Abstract

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.

Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance

“…Sugarcane is an important source of income worldwide, especially due to its efficiency in the manufacturing of biofuel and sugar-related products in most tropical and subtropical areas of the world 1,2 . Although this crop has great energetic potential, its breeding process has generated high genomic complexity across bred varieties, exceeding that of most if not all other crops 3 .…”

“…Modern sugarcane cultivars are derived from a process of hybridization that has occurred over a century between Saccharum spontaneum (2n = 5x = 40 to 16x = 128; x = 8) 3,4 and Saccharum officinarum (2n = 8x = 80, x = 10) 3,4 . S. officinarum has a more efficient process of sugar production but is susceptible to several biotic and abiotic stresses, in contrast to S. spontaneum, which has a low sucrose content but is resistant to different types of stress 1,3,5 . Sugarcane cultivars have unique chromosome sets (with numbers ranging from 80 to 130) 6 with highly complex genomic organization 1 , a polyploid genome (with overall ploidy estimated to be between 6 and 14) 7 , a frequent occurrence of aneuploidy at the locus level depending on the number of homologous chromosomes in hybrid cultivars 8 , an estimated whole-genome size of 10 Gb 9 , and a high content of repetitive regions (50% of genome size) 10 .…”

Bulked segregant RNA-Seq reveals differential genes and non-synonymous genetic variants linked to sucrose accumulation in sugarcane

“…hybrid) that has been aligned on the gene rich part of the sorghum genome (Garsmeur et al 2018). Recently, an allele-defined reference genome has also been published for S. spontaneum (Zhang et al 2018). Schneeberger and Weigel (2011) suggested that even in absence of complete genome sequence, it might be possible to identify genes underlying traits of interest using bulked segregant RNA seq (BSR-seq) approach.…”

Transcriptome Profile Analysis of Twisted Leaf Disease Response in Susceptible Sugarcane with Narenga porphyrocoma Genetic Background

“…Cultivated sugarcane is an important industrial crop with 3 a high sugar yield and has become a major energy crop worldwide (Grivet and Arruda 2001; 4 Yang et al 2010). It is cultivated in ~26 million hectares in tropical and subtropical regions 5 of the world, producing up to 1.8 billion metric tons of crushable stems (Zhang et al 2018). 6 Sugarcane provides around 80% of the world's sugar, with the secondary production as raw 7 materials for pulp, ethanol and bioplastics (Lam et al 2009; Li and Yang 2015).…”

“…Saccharum spontaneum L. as reference(Zhang et al 2018), the average mapping ratio of 20 twelve samples was 76.74%. The annotation of aligned reads showed 91,386 genes expressed 21 (65,391 known and 25,995 novel), and 96,101 annotated transcripts, including 53,481 novel 22 alternative splicing subtypes encode known proteins, 27,151 novel protein coding genes, and 23 15,469 long non-coding RNAs.…”