Genomic analysis of Saccharum species and interspecific hybrids

Sugarcane is the primary sugar crop and widely cultivated in tropical and subtropical regions. Saccharum officinarum and S. spontaneum are the parental species of modern sugarcane interspecific hybrid cultivars, which were selected from hybridization between high sugar content and biomass yield in S. officinarum and low sugar content and biomass yield but stress-tolerance in S. spontaneum followed by backcrossing to S. officinarum. The genomes of these hybrid cultivars were allo-autopolyploid with variable polyploidy and chromosome numbers, unusually complex even compared with genomes of other polyploid crops. Classical genetic studies of sugarcane lagged behind other major crops because of the complexity of the hybrid sugarcane genomes. In this dissertation, we utilized current genetic and genomic resources of sugarcane, developed species-specific markers, and discovered the relationship between modern sugarcane cultivars and their ancestral species. The reference genomes of S. spontaneum AP85-441 and S. officinarum LA Purple were used to dissect the genomes of hybrid sugarcane cultivars. S. officinarum-specific and S. spontaneum-specific single nucleotide polymorphisms (SNP) markers were developed to identify the fractions of the parental genomes in these hybrids. Enriched genomic regions with S. officinarum- and S. spontaneum-specific markers containing genes associated with agronomic traits, plant height, tillering, and disease resistance. The developed species-specific markers could be applied in marker-assisted selection (MAS) in sugarcane breeding programs. Sugarcane flowering is required for a breeding program to create new cultivars, but the flowering of hybrid cultivars terminates plant growth and reduces sugar yield. Most S. officinarum accessions are male sterile, which is a desirable trait for a maternal parent in sugarcane breeding, whereas S. spontaneum accessions have robust and viable pollen. Studies of gene expression profiles during flowering in these two species will facilitate sugarcane breeding. We performed transcriptomic analysis between S. spontaneum accession SES208 and S. officinarum accession LA Purple using flower tissue. Transcriptomic analysis showed that 988 genes and 2888 alleles were differentially expressed between the two species at three developmental stages. Ten genes and thirty alleles shared homology with male sterility (MS) genes in Arabidopsis and rice, providing candidate genes for male sterility in sugarcane. Plant hormone pathways were also involved in this process. WGCNA revealed different regulatory networks between the two species, with a candidate MS gene Sspon.03G0027010 (ACA7) correlated with other genes regulating male sterility in sugarcane. The construction of a genetic map serves as a vital requirement for exploring sugarcane genetics. In this study, our objective was to develop a genetic map for the selfed progeny (S1) of cultivar LCP 85-384 using RADseq. Three sets of SNP markers were generated from the reference genomes of LCP54-384, S. officinarum LA purple, and S. spontaneum AP85-441. However, the construction of an SNP-based high-density genetic map using simplex markers proved to be discouraging. Only 15-21% of the markers followed the expected segregation ratio (1:1), and these markers were clustered together in a single group, which contradicts the anticipated structure for polyploids with an estimated basic chromosome number of x = 10. The challenges faced in constructing the genetic map can be attributed to the high complexity of the sugarcane genome, a significant amount of missing data, genotyping errors, and an insufficient number of markers. To overcome these obstacles, alternative technologies, such as whole genome sequencing, should be explored to generate more extensive and reliable simplex markers for constructing a genetic map in sugarcane. To conclude, we reviewed studies of the sugarcane genome, collected the genetic and genomic resources of sugarcane, dissected the contributions of S. officinarum and S. spontaneum genomes in modern cultivars by hybrid genome analysis, identified candidate male-sterile genes in S. officinarum by transcriptome analysis, and attempted to construct a genetic map for a sugarcane cultivar LCP 85-384 using RADseq analysis. The generated genomic resources will expand our knowledge of modern sugarcane hybrid genomes and male sterility-related genes and generate resources to improve sugarcane breeding efficiency.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Plant Biology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2023

Author dc:creator

• Song, Jinjin

Contributors dc:contributor

• Ming, Ray
• Sacks, Erik
• Juvik, John
• Burgess, Steven

• Saccharum
• Hybrid Genome
• Male Sterility
• Genetic Map

Statement dc:rights

• Copyright 2023 Jinjin Song

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/121247

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F121247