Abstract
BackgroundChalkiness is a major constraint in rice production because it is one of the key factors determining grain quality (appearance, processing, milling, storing, eating, and cooking quality) and price. Its reduction is a major goal, and the primary purpose of this study was to dissect the genetic basis of grain chalkiness. Using five populations across two environments, we also sought to determine how many quantitative trait loci (QTL) can be consistently detected. We obtained an integrated genetic map using the data from five mapping populations and further confirmed the reliability of the identified QTL.ResultsA total of 79 QTL associated with six chalkiness traits (chalkiness rate, white core rate, white belly rate, chalkiness area, white core area, and white belly area) were mapped on 12 chromosomes using five populations (two doubled haploid lines and three recombinant inbred lines) across two environments (Hainan in 2004 and Wuhan in 2004). The final integrated map included 430 markers; 58.3% of the QTL clustered together (QTL clusters), 71.4% of the QTL clusters were identified in two or more populations, and 36.1% of the QTL were consistently detected in the two environments. The QTL could be detected again and showed dominance (qWBR1, qWBR8, qWBR12, and qCR5) or overdominance effects (qWCR7) for the rate of the white belly or white core, respectively, and all four QTL clusters derived from Zhenshan 97 controlling white belly rate were stably and reliably identified in an F2 population.ConclusionsOur results identified 79 QTL associated with six chalkiness traits using five populations across two environments and yielded an integrated genetic map, indicating most of the QTL clustered together and could be detected in different backgrounds. The identified QTL were stable and reliable in the F2 population, and they may facilitate our understanding of the QTL related to chalkiness traits in different populations and various environments, the relationships among the various chalkiness QTL, and the genetic basis for chalkiness. Thus, our results may be immediately used for map-based cloning of important QTL and in marker-assisted breeding to improve grain quality in rice breeding.
Highlights
Chalkiness is a major constraint in rice production because it is one of the key factors determining grain quality and price
There was a smaller amount of chalkiness area in H94, and the endosperms were relatively transparent; Zhenshan 97 (ZS97) and WYJ had a larger amount of chalkiness area, and grain white core (WC) was readily distinguishable from grain white back (WB)
After the grain WC analysis of WB and other chalkinessrelated traits, we found that the variation coefficient of chalkiness rate (CR) and chalkiness area (CA) became greater than that before the traits’ subdivision (Table 1)
Summary
Chalkiness is a major constraint in rice production because it is one of the key factors determining grain quality (appearance, processing, milling, storing, eating, and cooking quality) and price. Its reduction is a major goal, and the primary purpose of this study was to dissect the genetic basis of grain chalkiness. Using five populations across two environments, we sought to determine how many quantitative trait loci (QTL) can be consistently detected. Rice grain quality is a complex determines grain quality and price, and its reduction is an important goal of artificial breeding in rice. Previous studies have shown that chalkiness is a complex quantitative trait that is controlled by polygenes and readily influenced by environmental factors [12,13,14]. Great progress has already been made toward understanding the genetic basis of chalkiness; no gene controlling the trait has been cloned, and not much is known about the genetic mechanisms for crop genetic improvement
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