A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

Abstract

Background: The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO 2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results: The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of cosegregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization.

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

“…Sugarcane is predominantly an autopolyploid plant, and the understanding of its genome organization is limited [4, 7]. One possible way to increase knowledge of the genome organization of this species is by using genetic maps.…”

“…Several genetic linkage maps of sugarcane have been generated since a methodology based on single-dose markers (SDMs) was proposed by Wu et al [23]. SDMs that segregate 1:1 and 3:1 in full-sib progenies (F 1 populations) [24] or 3:1 in populations created by selfing an individual are commonly used for constructing genetic maps in sugarcane [4, 25–35]. An integrated map of sugarcane with different types of molecular markers, such as microsatellites or single sequence repeats (SSRs) and target region amplification polymorphism (TRAP), extended the characterization of polymorphic variation throughout the entire genome [36–38].…”

QTL mapping including codominant SNP markers with ploidy level information in a sugarcane progeny

“…This lack of saturation can probably be attributed to the low level of polymorphism found in some regions of the S. officinarum genome, from which a large part of the genome of modern sugarcane varieties originated as a consequence of the nobilization process (Alwala and Kimbeng 2010). Grivet et al (1996), Ming et al (1998), Hoarau et al (2001), Aitken et al (2005), Garcia et al (2006), Oliveira et al (2007), Palhares et al (2012) and Pastina et al (2012) also observed small LGs with few linked markers in their genetic maps. Although the genetic map not be completely saturated, the number of LGs agrees with the chromosome number expected in modern sugarcane varieties derived from S. officinarum (2n = 80) and S. spontaneum (2n = 40-128), which have a genome composed of approximately 70-80 % S. officinarum, 10-20 % S. spontaneum and 5-17 % recombinant chromosomes Grivet et al 1996;D'Hont and Glaszmann 2001).…”

“…Integrated linkage maps are advantageous because more saturated maps are obtained, allowing for better estimates of QTL locations and the ability to estimate linkage and linkage phases more accurately. This approach was also used for the sugarcane linkage map presented by Oliveira et al (2007), Palhares et al (2012) and Pastina et al (2012).…”

Sugarcane biotechnology: tapping unlimited potential

“…However, high inbreeding depression caused by endogamy limits the production of experimental mapping populations as noted in F2, BC, recombinant inbred lines (RILs), and double haploid (DH) lines (Palhares et al 2012). The S. spontaneum "SES 208" (2n = 64) linkage map was the first map constructed directly from a complex polyploid species based on single-dose markers (SDMs), which Potential promoters identified for constitutive, tissue-specific, or inducible transgene expression in sugarcane.…”