This paper summarizes results from a decade of collaborative research using advanced backcross (AB) populations to a) identify quantitative trait loci (QTL) associated with improved performance in rice and to b) clone genes underlying key QTLs of interest. We demonstrate that AB-QTL analysis is capable of (1) successfully uncovering positive alleles in wild germ-plasm that were not obvious based on the phenotype of the parent (2) offering an estimation of the breeding value of exotic germplasm, (3) generating near isogenic lines that can be used as the basis for gene isolation and also as parents for further crossing in a variety development program and (4) providing gene-based markers for targeted introgression of alleles using marker-assisted-selection (MAS). Knowledge gained from studies examining the population structure and evolutionary history of rice is helping to illuminate a long-term strategy for exploiting and simultaneously preserving the well-partitioned gene pools in rice.

Introgression has been achieved from wild species Oryza grandiglumis (2n = 48, CCDD, Acc. No. 101154) into O. sativa subsp. japonica cv. Hwaseongbyeo as a recurrent parent. An advanced introgression (backcross) line, HG101, produced from a single plant from BC5F3 families resembled Hwaseongbyeo, but it showed differences from Hwaseongbyeo in several traits, including days to heading and culm length. To detect the introgressions, 450 microsatellite markers of known chromosomal position were used for the parental survey. Of the 450 markers, 51 (11.3%) detected O. grandiglumis segments in HG101. To characterize the effects of alien genes introgressed into HG101, an F(2:3) population (150 families) from the cross Hwaseongbyeo/HG101 was developed and evaluated for 13 agronomic traits. Several lines outperformed Hwaseongbyeo in several traits, including days to heading. Genotypes were determined for 150 F2 plants using simple sequence repeat markers. Qualitative trait locus (QTL) analysis was carried out to determine the relationship between marker genotype and the traits evaluated. A total of 39 QTL and 1 gene conferring resistance to blast isolate were identified using single-point analysis. Phenotypic variation associated with each QTL ranged from 4.2 to 30.5%. For 18 (46.2%) of the QTL identified in this study, the O. grandiglumis-derived alleles contributed a desirable agronomic effect despite the overall undesirable characteristics of the wild phenotype. Favorable wild alleles were detected for days to heading, spikelets per panicle, and grain shape traits. Grain shape QTL for grain weight, thickness, and width identified in the F(2:3) lines were further confirmed based on the F4 progeny test. The confirmed locus, tgw2 for grain weight is of particular interest because of its independence from undesirable height and maturity. Several QTL controlling amylose content and grain traits have not been detected in the previous QTL studies between Oryza cultivars, indicating potentially novel alleles from O. grandiglumis. The QTL detected in this study could be a rich source of natural genetic variation underlying the evolution and breeding of rice.

A high-resolution physical map targeting a cluster of yield-related QTLs on the long arm of rice chromosome 9 has been constructed across a 37.4 kb region containing seven predicted genes. Using a series of BC3F4 nearly isogenic lines (NILs) derived from a cross between the Korean japonica cultivar Hwaseongbyeo and Oryza rufipogon (IRGC 105491), a total of seven QTLs for 1,000-grain weight, spikelets per panicle, grains per panicle, panicle length, spikelet density, heading date and plant height were identified in the cluster (P

Asian cultivated rice was domesticated from ihe wild rice, Oryza rufi/iDgon and throughout the domesiiealion process, a wide range of morphological and physiological changes altered the ancestral form. This study was conducted lo idenlify the genetic basis of changes associiiied wilh the domestication process. An recombinanl Inbred line (RIL) population consisting of 120 lines w:is developed from a cross bciwccn ihc inpouica cultivar. 'Hwayeongbyeo' and a presumed wild progenitor. O. riijipof^on Griff. Acc.01944. The population was genotyped with 124 simple sequence length repeat (SSR) markers, providing an average interval size of 15 cM. and also evaluated for 20 [rails related to domestication and agricultural performance. A total of 63 quantitative (rail locus (QTLs) and one locus associated with qualitative variation for pericarp coloration were identified using single poini and composite interval analysis. The number of QTLs per trait ranged from one lo seven. Phenoiypic variation associated with each QTL ranged from ?.! to 40.4%. with an average of 15.3%. The results indicated thai most domestication-related traits clustered in chromosomal blocks, and the positions of many of ihese clusters were consistent with those reported in previous studies and with skewed segregation ratios in ihese BCjFv RILs. For LI (20.6%) ofthe QTLs identified in this study, the O. rufipogoii-denved allele contributed a desirabie agronomic effect despite the overall undesirable characteristics of the wild phenotype. Favourable alleles from O. rtifipogoii were detected for panicle length, spikelets per panicle, days to heading and leaf discoloration associated with cold stress. When compared with previous studies involving interspecific crosses, it can be concluded that O. riifipogon is useful as a source of valuable alleles for rice improvement and that many of the introgressed regions contain genes that have a favourable impact on phenotype in different genetic backgrounds and different environments.

A quantitative trait locus (QTL) for grain weight (GW) was detected near SSR marker RM210 on chromosome 8 in backcross populations derived from a cross between the Korean japonica cultivar Hwaseongbyeo and Oryza rufipogon (IRGC 105491). The O. rufipogon allele increased GW in the Hwaseongbyeo background despite the fact that O. rufipogon was the small-seeded parent. Using sister BC(3)F(3) near-isogenic lines (NILs), gw8.1 was validated and mapped to a 6.1 cM region in the interval between RM42 and RM210 (P < or = 0.0001). Substitution mapping with eight BC(3)F(4) sub-NILs further narrowed the interval containing gw8.1 to about 306.4 kb between markers RM23201.CNR151 and RM30000.CNR99. A yield trial using homozygous BC(3)F(4) sister sub-NILs and the Hwaseongbyeo recurrent parent indicated that the NIL carrying an O. rufipogon chromosome segment across the entire gw8.1 target region out-yielded its sister NIL (containing Hwaseongbyeo chromosome in the RM42-RM210 interval) by 9% (P=0.029). The higher-yielding NIL produced 19.3% more grain than the Hwaseongbyeo recurrent parent (P=0.018). Analysis of a BC(3)F(4) NIL indicated that the variation for GW is associated with variation in grain shape, specifically grain length. The locus, gw8.1 is of particular interest because of its independence from undesirable height and grain quality traits. SSR markers tightly linked to the GW QTL will facilitate cloning of the gene underlying this QTL as well as marker-assisted selection for variation in GW in an applied breeding program.