Mapping of Quantitative Trait Loci for Cold Tolerance in Weedy Rice

Abstract

A quantitative trait locus (QTL) analysis was carried out with a recombinant inbred line (RIL) population to identify the chromosomal regions responsible for cold tolerance of rice (Oryza sativa L.). The RIL population, consisting of 80 lines, was developed from a cross between the indica cultivar, Milyang 23 and the japonica weedy rice, Hapcheonaengmi 3. The population was genotyped with 2 morphological and 132 DNA markers, providing an average interval size of 11.3 cM, and was also evaluated for traits related to agricultural performance in cold water and in control plots. The RILs showed delayed heading and reduced culm length in the cold water plot and the differences in heading date and culm length between two plots were statistically significant. Cold tolerance was measured as days to heading, culm length, spikelet fertility, leaf discoloration, and panicle exsertion in the cold water plot, and difference in days to heading and the reduction ratio of culm length between two plots. A total of 14 QTLs for 7 traits were identified using single point and composite interval analysis. The number of QTLs per trait ranged from one to three. Phenotypic variation associated with each QTL ranged from 5.8 to 32.8 %. No digenic interaction was detected. Several QTLs associated with cold tolerance were clustered in a few chromosomal blocks. For 11 (78.6 %) of the QTLs identified in this study, the Hapcheonaengmi 3-derived alleles contributed desirable effects and favorable alleles were detected for difference in days to heading, spikelet fertility, panicle exsertion and leaf discoloration. From this study, it can be concluded that weedy rice is useful as a source of valuable alleles for breeding cold tolerance in rice.

Morphological and gene expression analysis under cool temperature conditions in rice anther development

“…To compare our results with the results of other researchers, who have reported QTLs involved in cool temperature tolerance (Takeuchi et al, 2001;Andaya and Mackill, 2003;Oh et al, 2004;Saito et Fig. 3.…”

“…We then compared our results with the results of other researchers who have reported QTLs involved in cool temperature tolerance (Takeuchi et al, 2001;Andaya and Mackill, 2003;Oh et al, 2004;Saito et al, 2004;Kuroki et al, 2007). A few genes in Group 1 were located in QTL regions for cool temperature tolerance of Hitomebore (Fig.…”

Detection of a novel quantitative trait locus for cold tolerance at the booting stage derived from a tropical japonica rice variety Silewah

“…Interestingly, the chromosomal segment of Silewah near the centromeric region of chromosome 11 was co-introgressed with qCTB3-Silewah into three cold tolerant strains (J501, J502 and J214). Although in this study a significant QTL for cold tolerance was not detected at this region of chromosome 11, QTLs for cold tolerance were reported on similar genomic regions not only at the reproductive stage (Oh et al 2004) but also at the vegetative stage (Oh et al 2004, Zhang et al 2005. The chromosomal segment of Silewah on chromosome 11 might have minor effect for cold tolerance at the booting stage and might be selected during breeding of cold tolerant strains.…”

“…Tolerance to cold at the booting stage is one of the most genetically complex traits in rice. To date, about 40 quantitative trait loci (QTLs) located on all chromosomes have been reported in various cross combinations (Andaya and Mackill 2003, Dai et al 2004, Kuroki et al 2007, Li et al 1997, Oh et al 2004, Saito et al 1995, Suh et al 2010, Takeuchi et al 2001, Xu et al 2008. Detection of QTLs with large effects has made it possible to transfer the target QTL (or gene) into elite varieties by marker-assisted selection (MAS); however, breeding for cold tolerance has been mainly by artificial selection with conventional breeding methods because of its complex pattern of inheritance.…”

Inheritance of pinacle exsertion in rice

“…More recently, 44 QTLs located on 11 of the 12 rice chromosomes were associated with increased panicle exsertion and described as major genes with overdominance (Han et al, 2006). In a recombinant inbred line population derived from an Indica ´ Japonica cross, however, a lower number of QTLs clustered in a few chromosomal blocks explained a small portion of the variation on this trait (Oh et al, 2004), discarding the involvement of major genes in panicle exsertion. In a diallel study, the general combining ability effects were more important than the specific combining ability effects for panicle exsertion (Han et al, 2004), showing that inheritance studies are highly dependent on the genetic material.…”