A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers

Abstract

Background: Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers.

Results: The six component maps were constructed using the MultiPoint software. The lengths of the resulting maps varied between 910 and 1528 cM. The order of the 498 markers that segregated in more than one population was highly consistent between the six individual mapping data sets. The framework consensus map was constructed using a "Neighbours" approach and contained 251 integrated bridge markers on the 10 sorghum chromosomes spanning 1355.4 cM with an average density of one marker every 5.4 cM, and were used for the projection of the remaining markers. In total, the sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci (1190 DArT loci and 839 other loci) spanning 1603.5 cM and with an average marker density of 1 marker/0.79 cM. In addition, 35 multicopy markers were identified. On average, each chromosome on the consensus map contained 203 markers of which 58.6% were DArT markers. Non-random patterns of DNA marker distribution were observed, with some clear marker-dense regions and some marker-rare regions.

Conclusion: The final consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. In addition to overall general consistency of marker order across individual component maps, good agreement in overall distances between common marker pairs across the component maps used in this study was determined, using a difference ratio calculation. The obtained consensus map can be used as a reference resource for genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources. DArT markers represent an affordable, high throughput marker system with great utility in molecular breeding programs, especially in crops such as sorghum where SNP arrays are not publicly available.

Figure 1

Scatter plot representing the distribution of marker skewness of the six component sorghum maps, each dot representing one molecular marker. Vertical solid bars distinguish the 10 chromosomes, along the total map distance (x axis). The y axis details the log2 value of the ratio of the number of individuals carrying the A allele on the number of individuals carrying the B allele. Markers outside the two horizontal dotted lines are significantly skewed as calculated by the Chi-square test.

Figure 2

Colinearity of locus order in component maps. Loci that are common between pairs of populations are connected by lines. Population codes as in Table 1.

Figure 3

Total number and proportion of DArT vs non-DArT markers used as bridge markers on the consensus map, per chromosome.

Figure 4

A consensus map of sorghum derived from six component maps. Marker type is indicated by colour; DArT (black), SSR/STS (red), RFLP (green) and gene (blue). Bridge markers are underlined; attached markers are in italics and multicopy markers have an * suffix. The bar on the left hand side shows the distance in centiMorgans from the top of each chromosome. Heterochromatic regions are indicated by a bar to the left of each chromosome.