GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane

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Almeida Balsalobre, Thiago Willian ; Pereira, Guilherme da Silva ; Alves Margarido, Gabriel Rodrigues ; Gazaffi, Rodrigo ; Barreto, Fernanda Zatti ; Anoni, Carina Oliveira ; Cardoso-Silva, Claudio Benicio ; Costa, Estela Araujo ; Mancini, Melina Cristina ; Hoffmann, Hermann Paulo ; de Souza, Anete Pereira ; Franco Garcia, Antonio Augusto ; Carneiro, Monalisa Sampaio

• Document type: Journal article
• Source: BMC Genomics; v. 18, JAN 11 2017.
• Web of Science Citations: 22

Abstract

Background: Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection. High-throughput next-generation sequencing (NGS) technologies have opened new opportunities for discovering molecular markers, especially single nucleotide polymorphisms (SNPs) and insertion-deletion (indels), at the genome-wide level. The objectives of this study were to (i) establish a pipeline for identifying variants from genotyping-by-sequencing (GBS) data in sugarcane, (ii) construct an integrated genetic map with GBS-based markers plus target region amplification polymorphisms and microsatellites, (iii) detect QTLs related to yield component traits, and (iv) perform annotation of the sequences that originated the associated markers with mapped QTLs to search putative candidate genes. Results: We used four pseudo-references to align the GBS reads. Depending on the reference, from 3,433 to 15,906 high-quality markers were discovered, and half of them segregated as single-dose markers (SDMs) on average. In addition to 7,049 non-redundant SDMs from GBS, 629 gel-based markers were used in a subsequent linkage analysis. Of 7,678 SDMs, 993 were mapped. These markers were distributed throughout 223 linkage groups, which were clustered in 18 homo(eo)logous groups (HGs), with a cumulative map length of 3,682.04 cM and an average marker density of 3.70 cM. We performed QTL mapping of four traits and found seven QTLs. Our results suggest the presence of a stable QTL across locations. Furthermore, QTLs to soluble solid content (BRIX) and fiber content (FIB) traits had markers linked to putative candidate genes. Conclusions: This study is the first to report the use of GBS for large-scale variant discovery and genotyping of a mapping population in sugarcane, providing several insights regarding the use of NGS data in a polyploid, non-model species. The use of GBS generated a large number of markers and still enabled ploidy and allelic dosage estimation. Moreover, we were able to identify seven QTLs, two of which had great potential for validation and future use for molecular breeding in sugarcane. (AU)

• FAPESP's process: 12/25236-4 - Comparative QTL mapping and genomic synteny between sweet sorghum and sugarcane
• Grantee: Guilherme da Silva Pereira
• Support type: Scholarships in Brazil - Doctorate
• FAPESP's process: 08/52197-4 - Genomic-assisted breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection
• Grantee: Anete Pereira de Souza
• Support type: Program for Research on Bioenergy (BIOEN) - Thematic Grants
• FAPESP's process: 12/11109-0 - In silico analysis of transcriptome and genome sequences in sugarcane: SNPs identification, allele specific expression analysis and, development and characterization of microsatellite markers
• Grantee: Cláudio Benício Cardoso da Silva
• Support type: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 08/57908-6 - National Institute of Science and Technology of Bioethanol
• Grantee: Marcos Silveira Buckeridge
• Support type: Program for Research on Bioenergy (BIOEN) - Thematic Grants