The genetic basis for three grain yield components of rice, 1000 kerne
l weight (KW), grain number per panicle (GN), and grain weight. per pa
nicle (GWP), was investigated using restriction fragment length polymo
rphism markers and F-4 progeny testing from a cross between lice subsp
ecies japonica (cultivar Lemont from USA) and indica (cv. Teqing from
China). Following identification of 19 QTL affecting these traits, we
investigated the role of epistasis in genetic control of these phenoty
pes. Among 63 markers distributed throughout the genome that appeared
to be involved in 79 highly significant (P < 0.001) interactions, most
(46 or 73%) did not appear to have ''main'' effects on the relevant t
raits, but influenced the trait(s) predominantly through interactions.
These results indicate that epistasis is an important genetic basis f
or complex traits such as yield components, especially traits of low h
eritability such as GN and GWP. The identification of epistatic loci i
s an important step toward resolution of discrepancies between quantit
ative trait loci mapping and classical genetic dogma, contributes to b
etter understanding of the persistence of quantitative genetic variati
on in populations, and impels reconsideration of optimal mapping metho
dology and marker-assisted breeding strategies for improvement of comp
lex traits.