Construction of a genetic linkage map forSaccharum officinarumincorporating both simplex and duplex markers to increase genome coverage

Abstract

Saccharum officinarum L. is an octoploid with 80 chromosomes and a basic chromosome number of x = 10. It has high stem sucrose and contributes 80% of the chromosomes to the interspecific sugarcane cultivars that are grown commercially for sucrose. A genetic linkage map was developed for S. officinarum (clone IJ76-514) using a segregating population generated from a cross between Q165 (a commercial sugarcane cultivar) and IJ76-514. In total, 40 AFLP and 72 SSR primer pairs were screened across the population, revealing 595 polymorphic bands inherited from IJ76-514. These 595 markers displayed a frequency distribution different from all other sugarcane genetic maps produced, with only 40% being simplex markers (segregated 1:1). Of these 240 simplex markers, 178 were distributed on 47 linkage groups (LGs) and 62 remained unlinked. With the addition of 234 duplex markers and 80 biparental simplex markers (segregating 3:1), 534 markers formed 123 LGs. Using the multi-allelic SSR markers, repulsion phase linkage, and alignment with the Q165 linkage map, 105 of the 123 LGs could be grouped into 10 homology groups (HGs). These 10 HGs were further assigned to the 8 HGs observed in cultivated sugarcane and S. spontaneum. Analysis of repulsion phase linkage indicated that IJ76-514 is neither a complete autopolyploid nor an allopolyploid. Detection of 28 repulsion linkages that occurred between 6 pairs of LGs located in 4 HGs suggested the occurrence of limited preferential chromosome pairing in this species.

Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane

“…A very low level of single-dose markers (Wu et al 1992), the only type of markers easily used for mapping in sugarcane, was obtained for the female parent IJ76-514. This signiWcantly hampered construction of the IJ76-514 genetic map and was interpreted as a low level of heterozygosity in this S. oYcinarum clone (Aitken et al 2007). Our results clearly revealed that 2n transmission has occurred in this population; the implications of this should also be considered in the analysis of mapping data.…”

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

“…Comparable number of LG and map length were found in the female (S. officinarum ' La Striped'; 49 LG with 1732 cM) and male (S. spontaneum 'SES 147B';45 LG with 1491 cM) maps in our study. Recently Aitken et al (2007) constructed a linkage map of S. officinarum with 123 LG spanning 4306 cM with 534 linked SD, DD, TD and QD markers. To our knowledge, this is the first attempt to use AFLP in combination with either SRAP and/or TRAP markers for constructing linkage maps in these progenitor species of sugarcane.…”

“…Recently, Edmé et al (2006) developed a S. spontaneum and S. officinarum map using SSR markers. AFLP markers have so far been used to construct genetic linkage maps of commercial sugarcane (Hoarau et al 2001;Aitken et al 2005;Reffay et al 2005) and recently of S. officinarum (Aitken et al 2007).…”

Sugarcane Genetics and Genomics

“…Two linkage maps were constructed from this F 1 segregating population with 344 polymorphic markers from the female parent La Striped and 306 markers from the male parent SES 147B, yielding 49 and 45 linkage groups, respectively (Aitken et al 2007). …”