A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar

Abstract

Sugarcane varieties are complex polyploids carrying in excess of 100 chromosomes and are derived from interspecific hybridisation between the domesticated Saccharum officinarum and the wild relative S. spontaneum. A map was constructed in Denotes variety covered by Australian plant breeding rights., an Australian cultivar, from a segregating F1 population, using 40 amplified fragment length polymorphism (AFLP) primer combinations, five randomly amplified DNA fingerprints (RAF) primers and 72 simple sequence repeat (SSR) primers. Using these PCR-based marker systems, we generated 1,365 polymorphic markers, of which 967 (71%) were single-dose (SD) markers. Of these SD 967 markers, 910 were distributed on 116 linkage groups (LGs) with a total map length of 9,058.3 cM. Genome organisation was significantly greater than observed in previously reported maps for Saccharum spp. With the addition of 123 double-dose markers, 36 (3:1) segregating markers and a further five SD markers, 1,074 markers were mapped onto 136 LGs. Repulsion phase linkage detected preferential pairing for 40 LGs, which formed 11 LG pairs and three multi-chromosome pairing groups. Using SSRs, double-dose markers and repulsion phase linkage, we succeeded in forming 127 of the 136 LGs into eight homo(eo)logy groups (HG). Two HGs were each represented by two sets of LGs. These sets of LGs potentially correspond to S. officinarum chromosomes, with each set aligning to either end of one or two larger LGs. The larger chromosomes in the two HGs potentially correspond to S. spontaneum chromosomes. This suggestion is consistent with the different basic chromosome number of the two species that are hybridised to form sugarcane cultivars, S. spontaneum (x=8) and S. officinarum (x=10), and illustrates the structural relationship between the genomes of these two species. The discrepancy of coverage between HGs highlights the difficulty in mapping large parts of the genome.

Single strand conformation polymorphism of genomic and EST-SSRs marker and its utility in genetic evaluation of sugarcane

“…SSRs are ideal markers that exhibit great precision in polymorphism, reproducibility, multi-allelic nature and their transferability across genera (Parida et al 2010;Devarumath et al 2012). It also helps in breeding process including germplasm fingerprinting, genetic mapping and marker-assisted selection (Aitken et al 2005). Recently, microsatellites have been used to set up the genetic map in Saccharum spp.…”

“…Recently, microsatellites have been used to set up the genetic map in Saccharum spp. (Aitken et al 2005) as well as other poacea crops. Microsatellites or SSRs are categorized into the genomic (gSSR) and gene based Expressed Sequence Tags (EST-SSRs).…”

Genotype-Specific Microsatellite (SSR) Markers for the Sugarcane Germplasm from the Karst Region of Guizhou, China

“…Due to high level of heterozygosity and complexity of its genome, sugarcane molecular research has been confronted with unique challenges not encountered in other major crops, resulting in a slow progress in sugarcane molecular breeding. Nonetheless, many researchers have made an effort to evaluate different sources of sugarcane germplasm with various DNA markers, including 5S rRNA intergenic transcribed spacer (ITS) [1], restriction fragment length polymorphism (RFLP) [2] [3], random amplified polymorphic DNA (RAPD) [4] [5] [6] [7], amplified fragment length polymorphism (AFLP) [8] [9] [10], simple sequence repeats (SSR) [8] [11] [12] [13] [14], target region amplification polymorphism (TRAP) [15] [16], conserved-intron scanning marker (CISP) [17] [18] and single nucleotide polymorphism (SNP) [19] [20]. Sugarcane breeders have successfully found some cultivarspecific, species-specific and trait-specific DNA makers to accelerate the breeding process [13] Among PCR-based marker systems, SSR is a powerful marker system once developed for a particular organism due to its ubiquitous distribution across the entire genome, high polymorphism, and reliability.…”

Assessment of Genetic Relationship and Diversity among Chinese Sugarcane Parental Clones using SCoT and ISSR Markers

“…Molecular markers are widely used in plant genetic diversity as a result of not affected by environment. So far, different molecular markers, such as target region amplified polymorphism (Que et al, 2009), restriction fragment length polymorphism (Daugrois et al, 1996;Grivet et al, 1996), amplified fragment length polymorphism (Cai et al, 2005;Aitken et al, 2005Aitken et al, , 2006, random amplified polymorphic DNA (RAPD) (Mudge et al, 1996;Tabasum et al, 2010), and simple sequence repeat (SSR) (Pan, 2006;Santos et al, 2012), have been used in studies on the genetic diversity of sugarcane. As we know, single molecular markers are more often used when developing this research; very few studies on genetic diversity of sugarcane have reported using a combination of two or more molecular markers, especially in China.…”