Identification of molecular markers associated with sugar-related traits in a Saccharum interspecific cross

Abstract

The cultivated sugarcane (Saccharum spp. hybrids, 2n = 100-130) is one crop for which interspeciWc hybridization involving wild germplasm has provided a major breakthrough in its improvement. Few clones were used in the initial hybridization event leading to a narrow genetic base for continued cultivar development. Molecular breeding would facilitate the identiWcation and introgression of novel alleles/genes from the wild germplasm into cultivated sugarcane. We report the identiWcation of molecular markers associated with sugar-related traits using an F 1 population derived from a cross between S. oYcinarum 'Louisiana Striped' £ S. spontaneum 'SES 147B', the two major progenitor species of cultivated sugarcane. Genetic linkage maps of the S. oYcinarum and S. spontaneum parents were produced using the AFLP, SRAP and TRAP molecular marker techniques. The mapping population was evaluated for sugar-related traits namely, Brix (B) and pol (P) at the early (E) and late (L) plant growing season in the plant cane (04) and Wrst ratoon (05) crops (04EB, 04LB, 04LP, 05EB and 05EP). For S. oYcinarum, combined across all the traits, a total of 30 putative QTLs was observed with LOD scores ranging from 2.51 to 7.48. The phenotypic variation (adj. R 2 ) explained by all QTLs per trait ranged from 22.1% (04LP) to 48.4% (04EB). For S. spontaneum, a total of 11 putative QTLs was observed with LOD scores ranging from 2.62 to 4.70 and adj. R 2 ranging from 9.3% (04LP) to 43.0% (04LB). Nine digenic interactions (iQTL) were observed in S. oYcinarum whereas only three were observed in S. spontaneum. About half of the QTLs contributed by both progenitor species were associated with eVects on the trait that was contrary to expectations based on the phenotype of the parent contributing the allele. Quantitative trait loci and their associated eVects were consistent across crop-years and growing seasons with very few QTLs being unique to the early season. When the data were reanalyzed using the non-parametric discriminant analysis (DA) approach, signiWcant marker-trait associations were detected for markers that were either identical to or in the vicinity of markers previously identiWed using the traditional QTL approach. Discriminant analysis also pointed to previously

Development and Use of Simple Sequence Repeats (SSRs) Markers for Sugarcane Breeding and Genetic Studies

“…This narrow genetic base could restrict advancement in sugarcane breeding programs. A interspecific hybridization strategy used in the early 1900s introgessed genes and traits of choice from wild relatives into sugarcane cultivars to increase the genetic variability, resulting in significant improvements in sugarcane breeding and genetics [105]. For this introgression, plants of the F 1 and first backcross (BC 1 ) generations receive diploid gametes from a female S. officinarum, and haploid gametes from male S. spontaneum.…”

Simultaneously accounting for population structure, genotype by environment interaction, and spatial variation in marker–trait associations in sugarcaneThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

“…For example, Wei et al (2006) found that 11 AFLP markers could account for 59% of smut rating variation. For a biparental population, Alwala et al (2009) reported that 35.5%-48.4% of phenotypic variation for Brix or 22.1%-36.2% of phenotypic variation for pol could be explained by five to seven markers.…”

Marker-trait association study for sucrose and yield contributing traits in sugarcane (Saccharum spp. hybrid)

“…The highly heterozygous nature of sugarcane allows one to use the F 1 progeny of two highly heterozygous parents or the selfed progeny of a clone as the mapping population provided the progeny segregates for the trait in question (Selvi and Nair 2010). Linkage mapping has been done in sugarcane using low frequency marker alleles as it is possible to detect their segregation in a multiallelic system, and partial genetic maps have been produced for S. spontaneum (Al-Janabi et al 1993;daSilva et al 1993daSilva et al , 1995Ming et al 1998), S. officinarum (Mudge et al 1996;Guimaraes et al 1997;Aitken et al 2006), interspecific hybrids (Daugrois et al 1996;Ming et al 2001;Alwala et al 2009) and modern cultivars of sugarcane (Hoarau et al 2001;Edme et al 2006;Garcia et al 2006;Raboin et al 2006;Alwala et al 2008;Pastina et al 2012). However, the predominant mapping strategy based on single dose loci involves a biased genome sampling (Garcia et al 2013).…”