QTL analysis in a complex autopolyploid: genetic control of sugar content in sugarcane

Abstract

QTL mapping in autopolyploids is complicated by the possibility of segregation for three or more alleles at a locus and by a lack of preferential pairing, however the subset of polymorphic alleles that show simplex segregation ratios can be used to locate QTLs. In autopolyploid Saccharum, 36 significant associations between variation in sugar content and unlinked loci detected by 31 different probes were found in two interspecific F(1) populations. Most QTL alleles showed phenotypic effects consistent with the parental phenotypes, but occasional transgressive QTLs revealed opportunities to purge unfavorable alleles from cultivars or introgress valuable alleles from exotics. Several QTLs on homologous chromosomes appeared to correspond to one another-multiple doses of favorable 'alleles' at such chromosomal region(s) yielded diminishing returns-such negative epistasis may contribute to phenotypic buffering. Fewer sugar content QTLs were discovered from the highest-sugar genotype than from lower-sugar genotypes, perhaps suggesting that many favorable alleles have been fixed by prior selection, i.e. that the genes for which allelic variants (QTLs) persist in improved sugarcanes may be a biased subset of the population of genes controlling sugar content. Comparison of these data to mutations and QTLs previously mapped in maize hinted that seed and biomass crops may share a partly-overlapping basis for genetic variation in carbohydrate deposition. However, many QTLs do not correspond to known candidate genes, suggesting that other approaches will be necessary to isolate the genetic determinants of high sugar content of vegetative tissues.

Figure 1

Comparative mapping of sugar content QTLs. Bars and whiskers indicate 1 and 2 LOD likelihood intervals. Solid lines connect homologous loci on different sugarcane and sorghum linkage groups. Arrows indicate the inferred locations of markers used to align the homologous linkage groups among maize, sorghum, and sugarcane based on published (Ming et al. 1998) and unpublished data (M. McMullen and E. Coe, pers. comm.). Individual sorghum linkage groups are represented by LGs A to J. Sugarcane linkage groups from four parental varieties are indicated by the last letter of the marker name: G (Green German); M (Muntok Java); I (IND 81–146); P (PIN 84–1). Approximate map positions of double-dose (#) markers are inferred by the method of Da Silva (1995). The letters in parentheses following the marker name represent the sorghum linkage groups where the marker mapped, if different from the corresponding location shown. Only regions that contain, or are homologous to, QTLs are shown. Twenty-eight of the 36 sugar content QTLs are shown on this figure, along with nine putative QTLs. The markers associated with the remaining eight sugar content QTLs could not be mapped in sorghum.

Figure 2

Dosage effects of QTLs for sugar content and plant height (HT). Lowercase letters after the probe name represent the loci detected by this probe; the capital letter M or P represents parental variety MJ or PIN. Phenotypic effects of allele substitution at each locus are shown next to the locus (letter); the asterisk indicates the significant level at P < 0.01. Pl, Pq, Pc, and Pqt are the probabilities that linear, quadratic, cubic, and quartic components of the dosage curve are equal to zero.