Correction to: High-throughput miRNA deep sequencing in response to drought stress in sugarcane.

[This corrects the article DOI: 10.1007/s13205-021-02857-x.].

High-throughput miRNA deep sequencing in response to drought stress in sugarcane.

Drought is a major factor which reduces cane growth and productivity. In the present study, we sequenced drought susceptible (V1) and drought tolerant (V2) sugarcane varieties using high-throughput miRNA deep sequencing method to study the regulation of gene expression by miRNAs during drought stress in sugarcane. A total of 1224 conserved miRNAs which belong to 89 miRNA families were identified and 38% of the differentially regulated miRNAs were common for both varieties. Additionally 435 novel miRNAs were also identified from four small RNA libraries. We identified 145 miRNAs that were differentially expressed in susceptible variety (V1-31) and 143 miRNAs differentially expressed in the tolerant variety (V2-31). Target prediction revealed that the genes mainly encoded transcription factors, proteins, phosphatase and kinases involved in signal transduction pathways, integral component of membrane and inorganic ion transport metabolism, enzymes involved in carbohydrate transport and metabolism and drought-stress-related proteins involved in defense mechanisms. Pathway analysis of targets revealed that "General function prediction only" was the most significant pathway observed in both tolerant and susceptible genotypes followed by "signal transduction mechanisms". Functional annotation of the transcripts revealed genes like calcium-dependent protein kinase, respiratory burst oxidase, caffeic acid 3-O-methyltransferase, peroxidase, calmodulin, glutathione S-transferase and transcription factors like MYB, WRKY that are involved in drought tolerant pathways. qRT-PCR was used to verify the expression levels of miRNAs and their potential targets obtained from RNA sequencing results. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02857-x.

Informative genomic microsatellite markers for efficient genotyping applications in sugarcane.

Genomic microsatellite markers are capable of revealing high degree of polymorphism. Sugarcane (Saccharum sp.), having a complex polyploid genome requires more number of such informative markers for various applications in genetics and breeding. With the objective of generating a large set of microsatellite markers designated as Sugarcane Enriched Genomic MicroSatellite (SEGMS), 6,318 clones from genomic libraries of two hybrid sugarcane cultivars enriched with 18 different microsatellite repeat-motifs were sequenced to generate 4.16 Mb high-quality sequences. Microsatellites were identified in 1,261 of the 5,742 non-redundant clones that accounted for 22% enrichment of the libraries. Retro-transposon association was observed for 23.1% of the identified microsatellites. The utility of the microsatellite containing genomic sequences were demonstrated by higher primer designing potential (90%) and PCR amplification efficiency (87.4%). A total of 1,315 markers including 567 class I microsatellite markers were designed and placed in the public domain for unrestricted use. The level of polymorphism detected by these markers among sugarcane species, genera, and varieties was 88.6%, while cross-transferability rate was 93.2% within Saccharum complex and 25% to cereals. Cloning and sequencing of size variant amplicons revealed that the variation in the number of repeat-units was the main source of SEGMS fragment length polymorphism. High level of polymorphism and wide range of genetic diversity (0.16-0.82 with an average of 0.44) assayed with the SEGMS markers suggested their usefulness in various genotyping applications in sugarcane.

Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene (Bru1) in highly polyploid sugarcane (2n approximately 12x approximately 115).

The genome of modern sugarcane cultivars is highly polyploid (approximately 12x), aneuploid, of interspecific origin, and contains 10 Gb of DNA. Its size and complexity represent a major challenge for the isolation of agronomically important genes. Here we report on the first attempt to isolate a gene from sugarcane by map-based cloning, targeting a durable major rust resistance gene (Bru1). We describe the genomic strategies that we have developed to overcome constraints associated with high polyploidy in the successive steps of map-based cloning approaches, including diploid/polyploid syntenic shuttle mapping with two model diploid species (sorghum and rice) and haplotype-specific chromosome walking. Their applications allowed us (i) to develop a high-resolution map including markers at 0.28 and 0.14 cM on both sides and 13 markers cosegregating with Bru1 and (ii) to develop a physical map of the target haplotype that still includes two gaps at this stage due to the discovery of an insertion specific to this haplotype. These approaches will pave the way for the development of future map-based cloning approaches for sugarcane and other complex polyploid species.

Evidence for the dispersal of a unique lineage from Asia to America and Africa in the sugarcane fungal pathogen Ustilago scitaminea.

The basidiomycete Ustilago scitaminea Sydow, which causes sugarcane smut disease, has been spreading throughout Africa and America since the 1940s. The genetic diversity and structure of different populations of this fungus worldwide was investigated using microsatellites. A total of 142 single-teliospore were isolated from 77 distinct whips (sori) collected in 15 countries worldwide. Mycelium culture derived from on generation of selfing of these single teliospores were analysed for their polymorphisms at 17 microsatellite loci. All these strains but one were homozygous at all loci, indicating that selfing is likely the predominant reproductive mode of U. scitaminea. The genetic diversity of either American or African U. scitaminea populations was found to be extremely low and all strains belong to a single lineage. This lineage was also found in some populations of Asia, where most U. scitaminea genetic diversity was detected, suggesting that this fungal species originated from this region. The strong founder effect observed in U. scitaminea African and American populations suggests that the fungus migrated from Asia to other continents on rare occasions through movement of infected plant material.