Location: Sugarcane ResearchTitle: Genetic analysis of the sugarcane (Saccharum spp.) cultivar LCP 85-384. I. linkage mapping using AFLP, SSR, and TRAP markers) Author
Submitted to: Theoretical and Applied Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 3/11/2011
Publication Date: 5/16/2011
Citation: Andru, S., Pan, Y.-B., Thongthawee, S., Burner, D.M., Kimbeng, C.A. 2011. Genetic analysis of the sugarcane (Saccharum spp.) cultivar LCP 85-384. I. linkage mapping using AFLP, SSR, and TRAP markers. Theoretical and Applied Genetics. 123(1):77-93. Interpretive Summary: Modern sugarcane varieties are derived from crosses between two ancestral species, namely, Saccharum officinarum L. and S. spontaneum L. Unlike other crops, sugarcane varietys have complex genomes with 100 to 130 chromosomes belonging to ten homo(eo)logous groups (HGs) with 10 to 13 chromosomes within each group. The genetic makeup of these chromosomes may differ to a great extent among varieties grown in different geographical areas. This makes sugarcane genetic research very difficult and as result, no classical chromosome (gene linkage) maps are available in sugarcane. Nor is information on the inheritance of these genes. Since the last decade, the advent of several molecular marker technologies has stimulated sugarcane genome research resulting in several molecular gene linkage maps and a few quantitative trait linkage (QTL) markers. Nonetheless, none of these advancements were based on Louisiana sugarcane. This paper reports the first genetic linkage map for Louisiana’s popular variety LCP 85-384 using a 300 self-pollinated offspring population and 95 polymerase chain reaction (PCR) primer pairs belonging to three classes of DNA markers, namely, amplified fragment length polymorphism (AFLP, 64), simple sequence repeats (SSR, 16) and targeted region amplification polymorphism (TRAP, 12). These 95 primer pairs produced 1,111 markers segregating among the mapping population, of which 773 segregated in a 3:1 fashion and therefore were single dose (SD) molecular markers eligible for constructing a lingkage map using software JoinMap 3.0. Aside from 55 SD markers that remained unlinked, 718 SD markers were assigned into 108 co-segregation groups (CGs) with a cumulative map length of 5,387 cM and a density of 7.5 cM per marker. In addition, 65 of the 108 CGs were further cross-linked into eight HGs based on information from both locus-specific SSR markers and repulsion phase linkages detected between CGs. With an estimated genome size of 12,313 cM for the variety LCP 85-384, the map covered approximately 43.7 % of the genome. The genetic linkage map may help find QTL markers associated with important agronomic traits to facilitate marker-assisted selection in Louisiana sugarcane breeding programs. However, more markers, SSR markers in particular, are needed on the map to render it more useful for QTL discovery.
Technical Abstract: Sugarcane hybrids are complex aneu-polyploids (2n = 100 to 130) derived from inter-specific hybridization between ancestral polyploid species, namely S. officinarum L. and S. spontaneum L. Efforts in understanding the sugarcane genome have recently been enhanced through the use of new molecular marker technologies. A framework genetic linkage map of Louisiana’s popular cultivar LCP 85-384 was constructed using the selfed progeny and based on 64 AFLP, 19 SSR and 12 TRAP primer pairs. Of 1,111 polymorphic markers detected, 773 were single dose (SD) markers (segregated in 3:1 ratio) which were used to construct the map. The linkage map was constructed using a LOD value of = 4.0 and recombination threshold of 0.44. The genetic distances between pairs of markers linked in the coupling phase was computed using the Kosambi mapping function. Of the 773 SD markers, 718 were assigned onto 108 co-segregation groups (CGs) with a cumulative map length of 5,387 cM and a density of 7.5 cM per marker. Fifty-five SD markers remained unlinked. With an estimated genome size of 12, 313 cM for LCP 85-384, the map covered approximately 43.7 % of the genome. Sixty -five of the 108 CGs were assigned into 8 homo(eo)logous groups (HGs) based on information from the locus-specific SSR markers and repulsion phase linkages detected between CGs. Detection of repulsion phase linkages in this study inferred the existence of preferential as well as multiple chromosome pairing behavior in LCP 85-384. The framework map in this study will provide an important background for mapping QTLs associated with important agronomic traits and this information will be useful for crossing and selecting of clones in the breeding program. However, more markers are needed on the map to render it more resourceful for QTL discovery.