Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci) analysis in a Flint x Flint maize recombinant inbred line population.

Background: Cell-wall digestibility is the major target for improving the feeding value of forage maize. An understanding of the molecular basis for cell-wall digestibility is crucial towards breeding of highly digestible maize.

Results: 865 candidate ESTs for cell-wall digestibility were selected according to the analysis of expression profiles in 1) three sets of brown-midrib isogenic lines in the genetic background of inbreds 1332 (1332 and 1332 bm3), 5361 (5361 and 5361 bm3), and F2 (F2, F2 bm1, F2 bm2, and F2 bm3), 2) the contrasting extreme lines of FD (Flint x Dent, AS08 x AS 06), DD1 (Dent x Dent, AS11 x AS09), and DD2 (Dent x Dent, AS29 x AS30) mapping populations, and 3) two contrasting isogenic inbreds, AS20 and AS21.