Large Scale Development Of SSR Markers And Its Application In Sorghum

Sorghum bicolor (L.) Moench is an important grain and forage crop grown worldwide in the semi-arid and arid tropics, ranked as the world's fifth most commonly cultivated cereal crop after wheat, rice, maize, and barley. Sorghum is also a good model for plant genomics study due to its adaptation to harsh environments, diverse germplasm collection, relatively small genome size, potential bio-fuel application and close relationship with maize, sugarcane and other cereal crops.Compared with other molecular marker techniques, SSR has additional advantages such as high polymorphism, reproducibility and reliability. The objectives of this study are firstly to explore SSR markers throughout whole genome and then utilize the markers in different areas involved in plant genetic improvement. The main results from 4 different parts:1) development of SSR makers; 2) construction of a genetic map,3) genetic mapping of SbPLS and 4) diversity study are summarized as follows.(1) We have developed 19057 SSR markers through whole genome based on the result of whole sorghum genome sequence. We selected 1061 markers for the polymorphism detection among three sorghum varieties (654, LTR108 and BTx623) and found that nearly 56.7% of markers showed polymorphism among them. The polymorphism rate is diffident among ten chromosomes. Some markers are clustering in some regions among ten chromosomes. Polymorphism rate was positively correlated with length of SSR markers, but not motif type. Among three varieties, the polymorphism rate is highest between 654 and LTR108.(2) Two hundred and forty-five markers were selected to construct a sorghum linkage map for a F2 population with 184 individuals derived from a cross between the 654 and LTR108. A total of 259 SSR loci were polymorphic and 252 SSRs were mapped to 11 linkage groups. These mapped SSR loci were distributed throughout 10 chromosomes and spanned a genetic distance of 1514 cM. There are a few gaps in some part of linkages groups while some markers are clustering in some regions among ten linkages groups. Segregation distortions were found in some regions of the map.(3) Two differences leaf sheath color, purple and white were observed in the F2 population used for map construction. Genetic mapping of SbPLS (sorghum bicolor purple leaf sheath) was conducted and the SbPLS was located on chromosome 6 between SSR markers sm06072 and sm06075. The gene was further fine mapped in the region between the two newly developed SSR markers SB3660 and SB3675, with a genetic distance of 2.5 cM.(4)Genetic diversity in 41 sorghum varieties was investigated using 52 developed SSR markers and 6 phenotypes characteristics including plant height, leaf number, Brix, spike length, spike type and sheath color. A total of 277 alleles were detected from SSR markers and the average allele of each locus was 5.3 with a range of 2-9. The result from cluster analysis showed that the 41 sorghum varieties were grouped into two clusters. Two types of sorghum can be separated distinctively as the majority of grain sorghum was grouped in the first cluster while the most sweet sorghum varieties in the second cluster. This result suggested that sweet sorghum is of polyphyletic origin within S. bicolor ssp. bicolor.