Molecular Diversity Among Members of the Saccharum Complex Assessed Using TRAP Markers Based on Lignin-Related Genes

Suman, Andru; Ali, Kazim; Arro, Jie; Parco, Arnold; Kimbeng, C. A.; Baisakh, Niranjan

doi:10.1007/s12155-011-9123-9

Cited by 30 publications

(34 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The arbitrary primers were adapted of Li and Quiros [85]. Two fixed primers were designed from sucrose phosphate synthase (SuPS) [86, 87], and one primer each was designed from caffeic acid 3-O-methyltransferase (COMT) and cinnamoyl-CoA reductase (CCR) [88] gene sequences. PCRs were performed in a final volume of 20 μL [89].…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2017

View full text Add to dashboard Cite

BackgroundSugarcane (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.ResultsWe 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3383-x) contains supplementary material, which is available to authorized users.

show abstract

Section: Methodsmentioning

confidence: 99%

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

et al. 2017

View full text Add to dashboard Cite

show abstract

“…These markers have also been used to study the following: genetic maps of wheat (Liu et al, 2005), germplasm in spinach (Hu et al, 2007), and sugarcane (Suman et al, 2012); polymorphisms in cassava (Carmo et al, 2015); and the design and optimization of castor bean (Simões et al, 2017). The elite lineages used in this study were obtained from crossing parents (BRS Nordestina, Sipeal, EBDA MPA-17, Mirante, and Paraguaçu) developed by the genetic improvement program at the Núcleo de Melhoramento Genético e Biotecnologia in the Universidade Federal do Recôncavo da Bahia (NBIO-UFRB), in the city of Cruz das Almas, Bahia, Brazil.…”

Section: Introductionmentioning

confidence: 99%

Research Article Genetic divergence in elite castor bean lineages based on TRAP markers.

et al. 2017

View full text Add to dashboard Cite

ABSTRACT. Castor bean (Ricinus communis L.) is a tropical plant of great commercial interest and a potential source of biodiesel. The development of genetically improved cultivars with high amounts of oil in the seeds and low ricin toxicity is crucial to increase the productivity of this crop. The use of TRAP (target region amplification polymorphism) markers to develop elite lineages and study genetic divergence is fundamental to advance the genetic improvement of this species. The goal of this study was to evaluate the genetic divergence among 40 elite lineages of R. communis, which belong to the NBIO-UFRB Genetic Improvement Program, using TRAP markers involved in the biosynthesis of oil and ricin. Total DNA was extracted and quantified from the leaf tissue of the castor bean plants, and 70 TRAP combinations (fixed and arbitrary primers) were used to genotype the 40 lineages. Of the 580 fragments amplified, 335 were polymorphic (58%). The genetic dissimilarity among the lineages was calculated by the Jaccard dissimilarity index using the UPGMA grouping method. A dendrogram was generated, and four groups formed, showing divergence among the elite lineages that favors selection. The TRAP 2 K.S. Simões et al. Genetics and Molecular Research 16 (3): gmr16039776 molecular markers were efficient at characterizing the genetic variability among the lineages and, because TRAP markers are functional markers involved in the biosynthesis of oil and ricin, they are important when studying the association between a marker and a candidate gene.

show abstract

“…Moreover, other molecular classification methods, such as random amplified polymorphic DNA (RAPD) (Nair & Mary, 2006), amplified fragment length polymorphism (AFLP), microsatellites, and chloroplast genome analysis, all showed that sweetcane should be classified either as Erianthus or within a new genus (Feng, Wu, & Chen, 1997;Tsuruta, Ebina, Kobayashi, & Takahashi, 2017). Lignin gene-based TRAP markers also showed that sweetcane genotypes clustered as a distinct group that was highly divergent from the Saccharum (Suman et al, 2012). Thus, we use the Latin name Erianthus arundinaceus for sweetcane in this paper.…”

Section: Taxonomy and Genetic Diversitymentioning

confidence: 99%

Sweetcane (Erianthus arundinaceus) as a native bioenergy crop with environmental remediation potential in southern China: A review

Wang

et al. 2019

GCB Bioenergy

View full text Add to dashboard Cite

Sweetcane (Erianthus arundinaceus [Retzius] Jeswiet) is an ecologically dominant warm‐season perennial grass native to southern China. It traditionally plays an important role in sugarcane breeding due to its excellent biological traits and genetic relatedness to sugarcane. Recent studies have shown that sweetcane has a great potential in bioenergy and environmental remediation. The objective of this paper is to review the current research on sweetcane biology, phenology, biogeography, agronomy, and conversion technology, in order to explore its development as a bioenergy crop with environmental remediation potential. Sweetcane is resistant to a variety of stressors and can adapt to different growth environments. It can be used for ecological restoration, soil and water conservation, contaminated land repairing, nonpoint source pollutants barriers in buffer strips along surface waters, and as an ornamental and remediation plant on roadsides and in wetlands. Sweetcane exhibits higher biomass yield, calorific value and cellulose content than other bioenergy crops under the same growth conditions, thereby indicating its superior potential in second‐generation biofuel production. However, research on sweetcane as a bioenergy plant is still in its infancy. More works need be conducted on breeding, cultivation, genetic transformation, and energy conversion technologies.

show abstract

Molecular Diversity Among Members of the Saccharum Complex Assessed Using TRAP Markers Based on Lignin-Related Genes

Cited by 30 publications

References 35 publications

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

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

Research Article Genetic divergence in elite castor bean lineages based on TRAP markers.

Sweetcane (Erianthus arundinaceus) as a native bioenergy crop with environmental remediation potential in southern China: A review

Contact Info

Product

Resources

About