, Volume 164, Issue 1, pp 37-51

First online:

Linkage mapping and genome analysis in a Saccharum interspecific cross using AFLP, SRAP and TRAP markers

  • Sreedhar AlwalaAffiliated withSchool of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center
  • , Collins A. KimbengAffiliated withSchool of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center Email author 
  • , John C. VeremisAffiliated withUSDA-ARS, SRRC, Sugarcane Research UnitUSDA-APHIS-PPQ
  • , Kenneth A. GravoisAffiliated withSugar Research Station, Louisiana Agricultural Experiment Station, Louisiana State University Agricultural Center

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Framework genetic linkage maps of two progenitor species of cultivated sugarcane, Saccharum officinarum ‘La Striped’ (2n = 80) and S. spontaneum ‘SES 147B’ (2n = 64) were constructed using amplified fragment length polymorphism (AFLP), sequence related amplified polymorphism (SRAP), and target region amplification polymorphism (TRAP) markers. The mapping population was comprised of 100 F1 progeny derived from the interspecific cross. A total of 344 polymorphic markers were generated from the female (S. officinarum) parent, out of which 247 (72%) were single-dose (segregating in a 1:1 ratio) and 33 (9%) were double-dose (segregating in a 3.3:1 ratio) markers. Sixty-four (19%) markers deviated from Mendelian segregation ratios. In the S. spontaneum genome, out of a total of 306 markers, 221 (72%) were single-dose, 43 (14%) were double-dose, and 42 markers (14%) deviated from Mendelian segregation ratios. Linkage maps with Kosambi map distances were constructed using a LOD score ≥5.0 and a recombination threshold of 0.45. In Saccharum officinarum, 146 markers were linked to form 49 linkage groups (LG) spanning 1732 cM whereas, in S. spontaneum, 121 markers were linked to form 45 LG spanning 1491 cM. The estimated genome size of S. officinarum ‘La Striped’ was 2448 cM whereas that of S. spontaneum ‘SES 147B’ was 3232 cM. Based on the two maps, genome coverage was 69% in S. officinarum and 46% in S. spontaneum. The S. officinarum parent ‘La Striped’ behaved like an auto-allopolyploid whereas S. spontaneum ‘SES 147B’ behaved like a true autopolyploid. Although a large disparity exists between the two genomes, the existence of simple duplex markers, which are heterozygous in both parents and segregate 3:1 in the progeny, indicates that pairing and recombination can occur between the two genomes. The study also revealed that, compared with AFLP, the SRAP and TRAP markers appear less effective at generating a large number of genome-wide markers for linkage mapping in sugarcane. However, SRAP and TRAP markers can be useful for QTL mapping because of their ability to target gene-rich regions of the genome, which is a focus of our future research.


Saccharum AFLP SRAP TRAP markers Linkage map Segregation distortion