Abstract
Sugarcane is one of the most important industrial crops globally. It is the second largest source of bioethanol, and a major crop for biomass-derived electricity and sugar worldwide. Smut, caused by Sporisorium scitamineum, is a major sugarcane disease in many countries, and is managed by smut-resistant varieties. In China, smut remains the single largest constraint for sugarcane production, and consequently it impacts the value of sugarcane as an energy feedstock. Quantitative trait loci (QTLs) associated with smut resistance and linked diagnostic markers are valuable tools for smut resistance breeding. Here, we developed an F1 population (192 progeny) by crossing two sugarcane varieties with contrasting smut resistance and used for genome-wide single nucleotide polymorphism (SNP) discovery and mapping, using a high-throughput genotyping method called “specific locus amplified fragment sequencing (SLAF-seq) and bulked-segregant RNA sequencing (BSR-seq). SLAF-seq generated 148,500 polymorphic SNP markers. Using SNP and previously identified SSR markers, an integrated genetic map with an average 1.96 cM marker interval was produced. With this genetic map and smut resistance scores of the F1 individuals from four crop years, 21 major QTLs were mapped, with a phenotypic variance explanation (PVE) > 8.0%. Among them, 10 QTLs were stable (repeatable) with PVEs ranging from 8.0 to 81.7%. Further, four QTLs were detected based on BSR-seq analysis. aligning major QTLs with the genome of a sugarcane progenitor Saccharum spontaneum, six markers were found co-localized. Markers located in QTLs and functional annotation of BSR-seq-derived unigenes helped identify four disease resistance candidate genes located in major QTLs. 77 SNPs from major QTLs were then converted to Kompetitive Allele-Specific PCR (KASP) markers, of which five were highly significantly linked to smut resistance. The co-localized QTLs, candidate resistance genes, and KASP markers identified in this study provide practically useful tools for marker-assisted sugarcane smut resistance breeding.
Highlights
Sugarcane (Saccharum spp. hybrids) is world’s largest sugar and the second largest bioethanol crop (FAOSTAT, 2020)
The specific aims of our research reported here are: (i) SLAF-seq based integrated genetic map construction with single nucleotide polymorphism (SNP) and additional simple sequence repeats (SSRs) markers from the biparental mapping population described above, (ii) identification of quantitative trait locus (QTL) and SNP markers stably associated with smut resistance based on the integrated (SNP and SSR markers) genetic map, (iii) detection of QTLs and candidate gene mining for smut resistance via the bulked segregant RNA sequencing (BSR-seq) method, which was used for the first time in sugarcane, and (iv) development and evaluation of Kompetitive Allele-Specific Polymerase chain reaction (PCR) (KASP) markers assay with potential for screening large populations
Marker-assisted selection could be an effective strategy for disease resistance screening in breeding programs
Summary
Sugarcane (Saccharum spp. hybrids) is world’s largest sugar and the second largest bioethanol crop (FAOSTAT, 2020). In response to the growing sugar and biofuel demand, sugarcane production rose by about 45% in the last few decades globally, mostly through the expansion of cultivation in Brazil and India, the two largest sugarcane producers (FAOSTAT, 2020). In China, sugarcane is a major strategic crop and forms a component of expanding renewable energy portfolio underpinning government policies aimed at transitioning China to a carbon neutral country by 2050. It is grown in the Southern tropical and sub-tropical regions with ∼68% of cultivation located in Guangxi Province (Li, 2010)
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