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 CO2 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 co-segregation 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.

Conclusions: Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.

Figure 1

Linkage map of the population ‘IAC66-6’ x ‘TUC71-7′. Genetic distances between adjacent markers are shown on the left of each co-segregation group (CG). AFLPs constitute the map scaffold; EST-SSR loci appear in bold with asterisk symbols, and scIvana_1-based markers are depicted in bold in a gray box. The final map was constructed with 546 markers associated with 92 CGs (in Arabic numerals). Forty-one CGs (42.7%) were assembled into seven putative independent HGs (in Roman numerals). Other CGs (51) were denoted as unassigned groups (U). Note the clustered tendency of some scIvana_1-based markers.

Figure 2

Structure of sugarcane retrotransposons scIvana_1 and scAle_1.  Retrotransposons are LTR (long terminal repeats) consisting of elements within transcription initiation and termination sequences and detected as Gag, Pol, and Int domains that code for CP (capsid-like proteins), PR (protease), RT (reverse transcriptase), RNAase-H (ribonuclease H), and INT (integrase). Other sequences featured are PBS (primer binding sites), and PPT (polypurine tracts). Arrows indicate the primers designed for amplifying each of the elements, and synthesis direction. 1: scIvana_1-SSAP1; 2: scIvana_1-GagRev; 3: scIvana_1-LTR1; 4: scIvana_1-LTR2; 5: scAle_1-LTRr; 6: scAle_1-RT; 7: scAle_1-LTR1; 8: scAle_1-LTR2. Figures were not drawn to scale and were adapted from Kumar and Bennetzen [79].