Abstract

Media summary

Keywords

Sugarcane, S. officinarum, molecular markers, QTL, stalk weight, stalk number

Introduction

Sugarcane is a highly complex polyploid derived from interspecific hybridisation between S. officinarum and its wild relative S. spontaneum (Roach 1984). A major focus of sugarcane variety improvement programs is obtaining higher sugar yields. The components of sugar yield are stalk weight, stalk number and sugar content. Stalk diameter is an important factor affecting stalk weight. In recent decades the increase in sugar yield has been achieved primarily by increasing cane yield rather than sugar content (Moore et al. 1997). Both stalk weight and stalk number have been identified as important predictors of cane and sugar yield (Sunil and Lawrence 1996; Milligan et al. 1990). Molecular marker have been used to determine the location of QTL for a number of agronomic traits in sugarcane including plant height and flowering (Ming et al. 2002a), stalk length, stalk diameter and stalk number (Hoarau et al. 2002). QTL analysis has also been carried out on a number of other traits, related to sucrose content (Hoarau et al. 2002; Ming et al. 2001; 2002b). In this study we report the identification of molecular markers linked to stalk weight over two years, and stalk diameter and stalk number for one year of data. The research reported here is part of a project aiming to determine if and how DNA markers may be used in introgression of exotic germplasm in sugarcane breeding programs.

Materials and Methods

The S. officinarum clone IJ76-514 was crossed with the commercial variety Q165^A. A field trial in a randomised complete block design with four replicates containing 230 progeny was established at Ayr, Queensland in 2001 and again in an independent trial in 2002. AFLP, SSR, and RAF marker analysis following established procedures was used to characterise all progeny in the population. Markers present as a single copy in either parent i.e. single dose markers (Wu et al. 1992) were used to construct a genetic linkage map. The number of millable stalks (stalk number) was counted for each individual plot. Four stalks per plot were selected at random and stalk weight and stalk diameter were measured. Stalk diameter was measured mid-length of the stalk. QTL analysis (single marker regression and interval mapping) was carried out using QTL Cartographer for Windows Version 2.0 (Wang et al. 2004).

Results and Discussion

A genetic linkage map consisting of 1074 SSR and AFLP markers was constructed for the commercial cultivar Q165^A. Markers formed 136 linkage groups which were condensed into 8 homo(eo)logous groups. Far fewer single dose markers were identified for the S. officinarum parent than the sugarcane parent. This could be due to higher numbers of multicopy alleles present in this octoploid species compared to the sugarcane parent. For IJ76-514, 150 single dose markers formed 44 linkage groups, which could be aligned with the Q165^A linkage map. Marker-trait associations were identified for all traits tested. For all traits numerous QTL of small effect were identified consistent with other studies in sugarcane (Ming et al. 2002b; Hoarau et al. 2002). In total 16 QTL were identified for stalk weight in Q165^A, which explained from 3 to 9% of the variation (Table 1). Of these, 11 (69%) were identified in both years in totally independent field trials. This is in contrast to other studies in sugarcane where there were low levels of consistency between data collected in different years (Hoarau et al. 2002). The effect of the QTL was consistent over both years and both positive and negative effects were identified. Nine putative QTL were identified for stalk diameter in Q165^A (Table 2). These explained from 3% to 7% of the variation. In total 8 putative QTL were identified for stalk number in Q165^A (Table 2) and each explained from 3% to 9% of the variation. Again, QTL with both positive and negative effects were identified. Of the 16 QTL identified for stalk weight, 7 QTL were identified for stalk diameter in the same region. These could be either epistatic effects or different QTL located in close proximity to each other. In contrast only one of the QTL identified for stalk number also had an effect on the other traits.

The lower number of markers available for analysis in IJ76-514 meant that a smaller part of the genome could be analysed resulting in detection of fewer QTL. Four QTL were identified for stalk weight, 2 of which were significant in both years’ data and explained from 3% to 5% of the variation. For stalk diameter, 4 QTL were again identified which explained from 3% to 6% of the variation. Three of these were also significant for stalk weight. Two QTL were identified for stalk number, which both explained 5% of the variation; both were also significant for the other traits. Interestingly, all QTL identified were on homology group 2 which could partly be a result of more markers being mapped on this group. These QTL could be alleles of a single gene that effects stem morphology but with such small numbers of markers on the IJ76-514 map it is impossible to line up the linkage groups precisely. QTL on linkage groups 41, 6 and 27 had a consistently negative effect on the traits. Whereas the QTL identified on linkage group 11 has a negative effect on stalk diameter and a positive effect on stalk number. Data for stalk diameter and number were scored in 2002 only; further analysis will be carried out when data from a second year is available.

The most significant marker identified using CIM for each location is reported in Table 1. The p-value (P) (P≤ 0.01 in at least one year), the percent variation explained by the marker (%var) and the additive effect (kg/stalk), which was the average difference in phenotype of individuals differing by one copy of the indicated allele (single dose versus zero dose), (effect).

Table 1. Markers linked to QTL for stalk weight (kg/stalk) in Q165^A and IJ76-514

Marker associated with stalk diameter (mm) and stalk number (stalks/m²) from one year’s data. The p-value (P) (P≤ 0.01), the percent variation explained by the marker (%var) and the additive effect, which was the average difference in phenotype of individuals differing by one copy of the indicated allele (single dose versus zero dose), (effect).

Table 2 QTL identified for stalk diameter (mm) and stalk number (stalks/m²) in Q165^A and IJ76-514

Conclusion

Using a cross between a sugarcane cultivar and a S. officinarum clone, we have identified molecular markers for yield traits. Markers were identified for stalk weight, most of which were repeatable in independent environments, and for stalk diameter and stalk number measured in a single environment. Further work is required, and is underway, to examine the repeatability of these marker associations with QTL in populations derived from progeny used in this cross, and how DNA markers may best be used in introgression breeding programs in sugarcane.

Acknowledgements

This work is funded by a grant from the Sugarcane Research and Development Corporation (SRDC) of Australia. We acknowledge the competent supervision and input by Terry Morgan (CSR Ltd) and his team at Kalamia, and John Foreman (CSIRO), in conducting the field trials associated with this research.

References

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