QTL clusters reflect character associations in wild and cultivated rice

Abstract

The genetic basis of character association related to differentiation found in the primary gene pool of rice was investigated based on the genomic distribution of quantitative trait loci (QTLs). Major evolutionary trends in cultivated rice of Asiatic origin ( Oryza sativa) and its wild progenitor ( O. rufipogon) are: (1) differentiation from wild to domesticated types (domestication), (2) ecotype differentiation between the perennial and annual types in wild races, and (3) the Indica versus Japonica type differentiation in cultivated races. Using 125 recombinant inbred lines (RILs) derived from a cross between an Indica cultivar of O. sativa and a strain of O. rufipogon carrying some Japonica-like characteristics, we mapped 147 markers, mostly RFLPs, on 12 chromosomes. Thirty-seven morphological and physiological quantitative traits were evaluated, and QTLs for 24 traits were detected. The mapped loci showed a tendency to form clusters that are composed of QTLs of the domestication-related traits as well as Indica/Japonica diagnostic traits. QTLs for perennial/annual type differences did not cluster. This cluster phenomenon could be considered "multifactorial linkages" followed by natural selection favoring co-adapted traits. Further, it is possible that the clustering phenomenon is partly due to pleiotropy of some unknown key factor(s) controlling various traits through diverse metabolic pathways. Chromosomal regions where QTL clusters were found coincided with the regions harboring genes or gene blocks where the frequency of cultivar-derived alleles in RILs is higher than expected. This distortion may be partly due to unconscious selection favoring cultivated plant type during the establishment of RILs.

Mapping QTLs influencing rice floral morphology using recombinant inbred lines derived from a cross between Oryza sativa L. and Oryza rufipogon Griff

“…Moreover, The two QTLs, qANL-5 and qANL-9, were also identified near regions where Xiong et al (1999) detected two of the seven QTLs for ANL using simple interval mapping based on a LOD score > 2.4. The results from this study, together with those reported by Xiong et al (1999) and Cai and Morishima (2002), suggest that the variation in anther length between cultivated rice and its wild relatives was controlled by a relatively large number of QTLs compared to pistil traits. Comparative mapping among different populations is needed to confirm this hypothesis, since different field conditions and thresholds were used to detect QTLs in these studies.…”

“…All QTLs increased anther length at the wild rice allele. Three out of four QTLs were identified in the vicinity of QTL regions previously detected for ANL using simple interval mapping based on a LOD score > 3.0 (Cai and Morishima 2002). Moreover, The two QTLs, qANL-5 and qANL-9, were also identified near regions where Xiong et al (1999) detected two of the seven QTLs for ANL using simple interval mapping based on a LOD score > 2.4.…”

“…We used a linkage map constructed by Cai and Morishima (2002) using MAPMANAGER 3.0 (Manly 1993) based on the segregation data set of 147 markers in the F 6 RILs. To determine the primary linkage group, we referred to the known maps (Causse et al 1994;Harushima et al 1998).…”

“…The RILs were developed by a single-seed descent method from an F 2 population between a Taiwanese Indica cultivar (O. sativa), Peikuh, and an Asian wild rice (O. rufipogon), W1944, which is a perennial and exhibits partial outcrossing (Cai and Morishima 2002). Five plants of each RIL and parental lines were grown using pots in the field at the Agricultural and Forestry Research Center at the University of Tsukuba, Japan, in 1998.…”

“…To understand the genetic relationships of these organs, a detailed evaluation of the flowering stage is necessary. Cai and Morishima (2002) detected 6, 1 and 20 QTLs for the width and length-width ratio of the filled glume and anther length, respectively, using recombinant inbred lines (RILs) derived from a cross between O. sativa cv Pei-kuh and O. rufipogon W1944. This population could be expected to show wide segregation for floral traits, allowing detection of loci responsible for differences in mating system between cultivated rice and its wild relatives.…”