Characterization of QTL for unique agronomic traits of new-plant-type rice varieties using introgression lines of IR64

To enhance the yield potential of an elite indica rice cultivar, an introgression (BC3-derived) line of IR64, YTH288, was developed using a new-plant-type cultivar, IR66215-44-2-3, as a donor parent. YTH288 has agronomically valuable characteristics such as large panicles, few unproductive tillers, and large leaves inherited from NPT. To identify the genetic basis of these traits, we used 167 F2 plants derived from a cross between IR64 and YTH288 to conduct QTL analysis for five agronomic traits: days to heading (DTH), culm length (CL), flag leaf length (FLL), flag leaf width (FLW), and filled spikelet number per panicle (FSN). Six putative QTL were detected: four on chromosome 4 (for CL, FLL, FLW, and FSN) and two on chromosome 2 (for DTH and FLL). All QTL with the IR66215-44-2-3 allele, except that for FLL on chromosome 2, had positive effects on each trait. To confirm the effects of these putative QTL, we developed NILs with the IR64 genetic background by marker-assisted selection. We observed significant differences in several agronomic traits between IR64 and NILs that carried these QTL on chromosomes 2 and 4. Additionally, four IR64-NILs carrying chromosomal segments derived from different NPT varieties on the long arm of chromosome 4 exhibited similar pleiotropic effects for unique agronomic traits. These NILs can be used as research materials for studying each trait and as breeding materials for yield improvement of indica rice cultivars

Fine mapping of a gene for low-tiller number, Ltn, in japonica rice (Oryza sativa L.) variety Aikawa 1

Tillering is one of the most important agronomic traits related to grain production in rice (Oryza sativa L.). A japonica-type variety, Aikawa 1, is known to have low-tiller number. The detailed location of a lowtillering gene, Ltn, which has been localized on chromosome 8 in Aikawa 1, was conWrmed by molecular mapping. Using BC5F2 individuals derived from a cross between IR64 and Aikawa 1, the low-tillering gene was mapped to an interval deWned by SSR markers ssr5816-3 and A4765. This was designated as Ltn because there was no reported gene for tillering in the region of chromosome 8. Through high-resolution linkage analysis, the candidate region of Ltn was located between DNA markers ssr6049-23 and ind6049-1 corresponding to 38.6 kbp on the Nipponbare genome sequence. These DNA markers, which were tightly linked to Ltn, are useful for marker-assisted selection in breeding studies. (Résumé d'auteur

Estimation of genes in blast resistance in elite indica-type rice (Oryza sativa L.) varieties-bred at the International Rice Research Institute

The presence of blast resistance genes in the elite Indica-type rice (Oryza sativa L.) varieties bred at the International Rice Research Institute (IRRI) was estimated based on a differential system using Philippines isolates of the rice blast fungus Pyricularia grisea (Cooke) Sacc., according to the gene-for-gene theory. Based on the presence of the three resistance genes, Pi20, Pita and one of the Pik alleles (other than Pik-s), the 42 varieties were classified into seven groups. A group that did not harbor these three genes contained seven varieties derived from the progenies of the hybrids with IR24 as a parental variety. The largest group harboring Pita consisted of 17 varieties, including IR36 and its sister lines or progenies. The group harboring by Pi20 had seven varieties that included IR8, IR24 and their hybrid progenies. Thus, most of the IRRI varieties were classified into these three groups that included IR8, IR24, IR36 or their hybrid progenies in their pedigree. The presence of a total of seven resistance genes Pib, Pita, Piz-t, Pi20, Pik-s, one of the Pik alleles (other than Pik-s) and one of the two genes, Pii or Pi3, was estimated in these varieties. In some cases, the presence of genes like Pib, Pik-s and Piz-t could not be confirmed due to the masking effect of Pita, Pik allele, or Pi20. The number and kind of blast resistance genes in IRRI varieties were limited compared with previously reported blast resistance genes. Since the presence of Pik-s and another Pik allele was estimated in 17 varieties belonging to five groups, and that of Pib in 38 varieties belonging to four groups, it appeared that these genes were widely distributed in IRRI-bred varieties

Development of introgression lines of an indica-type rice variety, IR64, for unique agronomic traits and detection of the responsible chromosomal regions

A total of 334 introgression lines (INLs: BC3-derived lines) derived from crosses between a recurrent parent of Indica rice cultivar IR64 and 10 donor parents, including new plant type (NPT) lines IR65600-87-2-2-3, IR65598-112-2, IR65564-2-2-3, IR69093-41-2-3-2, IR69125-25-3-1-1, Hoshiaoba, IR66215-44-2-3, IR68522-10-2-2, IR71195-AC1, and IR66750-6-2-1, have been developed. These INLs with IR64 genetic background were characterized for eight agronomic traits: days to heading, culm length, leaf width, leaf length, panicle length, panicle number, 100-grain weight, and total spikelet number per panicle at the International Rice Research Institute from 2005 to 2007. To identify introgressed segments from the donor parents, genotypes of the 334 INLs were detected using more than 200 polymorphic simple sequence repeat markers. These segments detected on chromosomes 1, 2, 4, 5, and 6 were commonly introgressed across the INLs from more than four donor varieties. Based on the data of phenotype and genotype for the 334 INLs, associations between agronomic traits and introgressed chromosomal segments in the 334 INLs were investigated. A total of 54 regions for the eight traits were detected: seven regions for days to heading, eight regions for culm length, eight regions for leaf width, four regions for leaf length, six regions for panicle length, three regions for panicle number per plant, seven regions for 100-grain weight, and 11 regions for total spikelet number per panicle. Among them, the region on the long arm of chromosome 4 was associated with characteristics of the NPT such as long leaf, broad leaf, and high spikelet number. The developed 334 INLs with the IR64 genetic background will be useful materials for genetic analysis of agronomic traits