Location: Sugarcane ResearchTitle: Identification of quantitative trait loci controlling sucrose content based on an enriched genetic linkage map of sugarcane (Saccharum spp. hybrids) cultivar ‘LCP 85-384’
|LIU, PINGWU - Guangxi Academy Of Agricultural Sciences|
|CHANDRA, AMARESH - Indian Institute Of Sugarcane Research|
|QUE, YOUXIONG - Fujian Agricultural & Forestry University|
|CHEN, PINGHUA - Fujian Agricultural & Forestry University|
|DALLEY, CALEB - Former ARS Employee|
|TEW, THOMAS - Retired ARS Employee|
Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/12/2015
Publication Date: 1/1/2016
Publication URL: https://handle.nal.usda.gov/10113/63055
Citation: Liu, P., Chandra, A., Que, Y., Chen, P.-H., Grisham, M.P., White, W.H., Dalley, C.D., Tew, T.L., Pan, Y.-B. 2016. Identification of quantitative trait loci controlling sucrose content based on an enriched genetic linkage map of sugarcane (Saccharum spp. hybrids) cultivar ‘LCP 85-384’. Euphytica. 207:527-549. doi:10.1007/s10681-015-1538-5.
Interpretive Summary: With multiple sets of chromosomes, the genetic makeup of sugarcane cultivars is so complicated that sugarcane is probably the most difficult crop to breed. Identification of quantitative trait loci or QTL markers that are associated with high sugar content is considered the best option to improve sugarcane productivity, because it would be more economical for sugar mills to process the same sugar yield from less cane with higher sugar content than from more cane with lower sugar content. In this study, we identified 24 such QTL markers by the enrichment of a foundation genetic linkage map of cultivar LCP 85-384 with 65 additional PCR primer pairs of a molecular marker class called SSR. Combining the results of other 19 SSR primer pairs from a prior study, these 84 SSR primer pairs produced 456 markers, of which 441 were segregating among the self-progenies of LCP 85-384. The SSR marker data were joined with segregation data from two other molecular marker classes called AFLP and TRAP to form the database to construct an enriched linkage map of LCP 85-384 using a computer software program “JoinMap”. The enriched linkage map contains 108 co-segregated groups (CGs, or chromosomes] under eight homologous groups (HGs or sets). Based on this enriched genetic linkage map, 24 putative sugar content-associated QTLs were identified. Although five QTLs were not linked to any chromosome, the other 19 QTLs were located on nine chromosomes belonging to four homologous sets (HGI, HGIII, HGV, and HGVII). Upon verification, these 19 QTL markers will be used to assist sugarcane breeders in selecting clones with high sugar content.
Technical Abstract: Since sugarcane cultivars possess >100 chromosomes (2n = 100-130) and are genetically complex polyploid and aneuploids, identification of quantitative trait loci (QTLs) associated with sugar content is considered the best option to improve sugar content through molecular breeding. Also, improving sugar content in sugarcane stalks is a more economical approach over improvement of cane yield. In this study, the foundation genetic linkage map of cultivar ‘LCP 85-384’ was enriched using 65 additional polymorphic SSR primer pairs to identify more co-segregated and homologous groups (CGs and HGs) and quantitative trait loci (QTLs) controlling sugar content. Combining the results of 19 SSR primer pairs from a prior study, the 84 SSR primer pairs produced 456 markers, of which 441 were polymorphic. Nine hundred and ninety-three simplex and 225 duplex AFLP and TRAP markers reported previously were also included to construct an enriched linkage map of LCP 85-384. Altogether, 967 simplex and duplex markers were assigned to 108 CGs using JoinMap program. The enriched linkage map had a cumulative genome length of 7,406.3 cM that included 675 AFLP (69.8%), 90 TRAP (9.3%), and 202 SSR (20.9%) markers. The 202 SSR markers were assigned to 65 CGs and eight HGs. The number of CGs per HG ranged from as few as two to as many as 36. Based on this enriched genetic linkage map, 24 putative QTLs were identified that accounted for sugar content variation within the LCP 85-384 self-progeny mapping population. Five QTLs were unlinked and the other 19 QTLs were located on nine CGs within four HGs (HGI, HGIII, HGV, and HGVII).