ARS | Publication request: QTL mapping for milling quality in elite western U.S. rice germplasm

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 19, 2011
Publication Date: October 31, 2011
Citation: Nelson, J.C., Jodari, F., Roughton, A.I., McKenzie, K.S., McClung, A.M., Fjellstrom, R.G., Scheffler, B.E. 2012. QTL mapping for milling quality in elite western U.S. rice germplasm. Crop Science. 52:242-252.

Interpretive Summary: The amount of whole versus broken kernels in harvested rice is a key crop value component, and the genetic control of grain breakage after milling (commonly called milling yield or head rice yield) is poorly understood. The goal of our studies was to characterize the mode of inheritance and determine rice gene regions providing control of milling yield, as well as identify DNA markers in these gene regions. We pursued these goals by making crosses between a high milling yield rice variety, called L-204, with a high grain yield, but low milling yield, breeding line, called 01Y110, and then measuring milling yields in progeny families derived from these genetic crosses. The progeny families were grown for two years, 2007 to 2008, in California, using replicated trials, and, after harvesting, tested for milling yield and other grain characteristics. Significant gene regions controlling milling yield were identified, although no single gene was responsible for a majority of the differences seen in milling yield. Our results show that milling yield is primarily controlled by gene effects and secondarily by environmental effects, and that the inheritance of milling yield is complex, influenced by several genes.

Technical Abstract: Rice (Oryza sativa L.) milling yield is a key export and domestic grain quality trait whose genetic control is poorly understood. To identify genomic regions influencing grain quality, quantitative-trait-locus (QTL) mapping was carried out for quality-related traits including head-rice yield (HR) in 205 recombinant inbred lines (RILs) derived from a cross of L-204, a high-HR long-grain cultivar, with 01Y110, a low-HR advanced breeding line with high yield potential, in the temperate US rice-growing region. In replicated trials planted in California during 2007–2008, three QTLs carrying the HR-increasing allele from L-204 and one from 01Y110 were consistently expressed. Multi-QTL models accounted for 30% of the genetic variation for HR and up to 58% for other quality-related traits. Measures of kernel damage, though correlated with HR, were poor predictors of HR. Heading time, kernel dimension, amylose content, and other highly heritable traits showed no correlation with HR. Stable QTLs for HR are likely to be revealed best by multi-environment experiments employing larger population sizes or more direct measurement of kernel structure and development traits involved in kernel breakage.