Sang-Ho Chu

Characterization and Mapping of a Shattering Mutant in Rice That Corresponds to a Block of Domestication Genes

Easy shattering reduces yield due to grain loss during harvest in cereals. Shattering is also a hindrance in breeding programs that use wild accessions because the shattering habit is often linked to desirable traits. We characterized a shattering mutant line of rice, Hsh, which was derived from a nonshattering japonica variety, Hwacheong, by N-methyl-N-nitrosourea (MNU) treatment. The breaking tensile strength (BTS) of the grain pedicel was measured using a digital force gauge to evaluate the degree of shattering of rice varieties at 5, 10, 15, 20, 25, 30, 35, and 40 days after heading (DAH). The BTS of Hwacheong did not decrease with increasing DAH, maintaining a level of 180–240 gf, while that of Hsh decreased greatly during 10–20 DAH and finally stabilized at 50 gf. Optical microscopy revealed that Hsh had a well-developed abscission layer similar to the wild rice Oryza nivara (accession IRGC105706), while Hwacheong did not produce an abscission layer, indicating that the shattering of Hsh was caused by differentiation of the abscission layer. On the basis of the BTS value and morphology of the abscission layer of F1 plants and segregation data in F2 populations, it was concluded that the easy shattering of Hsh was controlled by the single recessive gene sh-h. The gene sh-h was determined to be located on rice chromosome 7 by bulked segregant analysis. Using 14 SSR markers on rice chromosome 7, the gene sh-h was mapped between the flanking markers RM8262 and RM7161 at distances of 1.6 and 2.0 cM, respectively. An SSR marker Rc17 cosegregated with the gene sh-h. The locus sh-h for shattering was tightly linked to the Rc locus conferring red pericarp, as well as a QTL qSDs-7-1 for seed dormancy, implying that this region might represent a domestication block in the evolutionary pathway of rice.

PCR Marker-Based Evaluation of the Eating Quality of Japonica Rice (Oryza sativa L.)

Evaluation of eating quality in early breeding generations of rice is critical to developing varieties with better palatability. This paper reports DNA markers associated with eating quality of temperate japonica rice and an evaluation method aided by multiple regression analysis. A total of 30 markers comprising STSs, SNPs, and SSRs were tested for their association with palatability using 22 temperate japonica varieties with different palatability values. Eating quality-related traits of the 22 varieties were also measured. Of the 30 markers, 18 were found to be significantly associated with palatability and, consequently, a model regression equation with an R2 value of 0.99 was formulated to estimate the palatability by the marker data set. Validation of the model equation using selected breeding lines indicated that the marker set and the equation are highly applicable to evaluation of the palatability of cooked rice in temperate japonica varieties.

Fine mapping and candidate gene analysis of hwh1 and hwh2 , a set of complementary genes controlling hybrid breakdown in rice

Hybrid breakdown (HB), a phenomenon of reduced viability or fertility accompanied with retarded growth in hybrid progenies, often arises in the offspring of intersubspecific hybrids between indica and japonica in rice. We detected HB plants in F8 recombinant inbred lines derived from the cross between an indica variety, Milyang 23, and a japonica variety, Tong 88-7. HB plants showed retarded growth, with fewer tillers and spikelets. Genetic analysis revealed that HB was controlled by the complementary action of two recessive genes, hwh1 and hwh2, originating from each of both parents, which were fine-mapped on the short arm of chromosome 2 and on the near centromere region of the long arm of chromosome 11, respectively. A comparison of the sequences of candidate genes among both parents and HB plants revealed that hwh1 encoded a putative glucose-methanol-choline oxidoreductase with one amino acid change compared to Hwh1 and that hwh2 probably encoded a putative hexose transporter with a six amino acid insertion compared to Hwh2. Investigation of the distribution of these alleles among 54 japonica and indica cultivars using candidate gene-based markers suggested that the two loci might be involved in developing reproductive barriers between two subspecies.

Analysis of segregation distortion and its relationship to hybrid barriers in rice

BackgroundSegregation distortion (SD) is a frequently observed occurrence in mapping populations generated from crosses involving divergent genotypes. In the present study, ten genetic linkage maps constructed from reciprocal F2 and BC1F1 mapping populations derived from the parents Dasanbyeo (indica) and Ilpumbyeo (japonica) were used to identify the distribution, effect, and magnitude of the genetic factors underlying the mechanisms of SD between the two subspecies.ResultsSD loci detected in the present study were affected by male function, female function, and zygotic selection. The most pronounced SD loci were mapped to chromosome 3 (transmitted through male gametes), chromosome 5 (transmitted through male gametes), and chromosome 6 (transmitted through female gametes). The level of SD in BC1F1 populations which defined by chi-square value independence multiple tests was relatively low in comparison to F2 populations. Dasanbyeo alleles were transmitted at a higher frequency in both F2 and BC1F1 populations, suggesting that indic a alleles are strongly favored in inter-subspecific crosses in rice. SD loci in the present study corresponded to previously reported loci for reproductive barriers. In addition, new SD loci were detected on chromosomes 2 and 12.ConclusionThe identification of the distribution of SD and the effect of genetic factors causing SD in genetic mapping populations provides an opportunity to survey the whole genome for new SD loci and their relationships to reproductive barriers. This provides a basis for future research on the elucidation of the genetic mechanisms underlying SD in rice, and will be useful in molecular breeding programs.

Identification of QTLs for hybrid fertility in inter-subspecific crosses of rice (Oryza sativa L.)

Two subspecies in rice, japonica and indica, have their own ecotypic traits. However, reproductive barriers such as spikelet sterility in hybrid progenies between subspecies have been an obstacle in breeding programs for combining desirable traits from both subspecies through inter-subspecific hybridization. The 166 F9 RILs and two BC1F1s’ were analyzed for spikelet and pollen fertility with the parents and F1 between Dasanbyeo (DS, indica) / TR22183 (TR, japonica). A frame map was constructed using a total of 218 polymorphic STS and SSR markers. In both BC1F1s’ of DS//DS/TR and TR//DS/TR, clusters of significant QTLs for spikelet and pollen fertility were identified on the short arm of chromosome 5 and chromosome 8. Nine and ten digenic epistatic interactions for DS//DS/TR and TR//DS//TR were identified, respectively. HF-QTLs were detected at the similar position with subspecies-specific markers and segregation distortion loci, implying that HF-QTLs might be associated with the differentiation of indica and japonica. Hybrid fertility/sterility and its relationship with other traits are discussed in relation to the reproductive barriers between subspecies of rice.

Isolation and characterization of a dominant dwarf gene, d-h, in rice.

Plant height is an important agronomic trait that affects grain yield. Previously, we reported a novel semi-dominant dwarfmutant, HD1, derived from chemical mutagenesis using N-methyl-N-nitrosourea (MNU) on a japonica rice cultivar, Hwacheong. In this study, we cloned the gene responsible for the dwarf mutant using a map-based approach. Fine mapping revealed that the mutant gene was located on the short arm of chromosome 1 in a 48 kb region. Sequencing of the candidate genes and rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR) analysis identified the gene, d-h, which encodes a protein of unknown function but whose sequence is conserved in other cereal crops. Real-time (RT)-PCR analysis and promoter activity assays showed that the d-h gene was primarily expressed in the nodes and the panicle. In the HD1 plant, the d-h gene was found to carry a 63-bp deletion in the ORF region that was subsequently confirmed by transgenic experiments to be directly responsible for the gain-of-function phenotype observed in the mutant. Since the mutant plants exhibit a defect in GA response, but not in the GA synthetic pathway, it appears that the d-h gene may be involved in a GA signaling pathway.

QTL analyses of heterosis for grain yield and yield-related traits in indica-japonica crosses of rice (Oryza sativa L.)

Two sets of rice materials, 166 RILs derived from a cross between Milyang 23 (Korean indica-type rice) and Tong 88-7 (japonica Rice), and BC1F1 hybrids derived from crosses between the RILs and the female parent, Milyang 23, were produced to identify QTLs for heterosis of yield and yield-related traits. The QTLs were detected from three different phenotype data sets including the RILs, BC1F1 hybrids, and mid-parental heterosis data set acquired from the definition of mid-parental heterosis. A total of 57 QTLs were identified for nine traits. Of eight QTLs detected for yield heterosis, five overlapped with other heterosis QTLs for yield-related traits such as spikelet number per panicle, days to heading, and spikelet fertility. Four QTLs for yield heterosis, gy1.1, py6, gy10, and py11, were newly identified in this study. We identified a total of 17 EpQTLs for yield heterosis that explain 21.4 ∼ 59.0 % of total phenotypic variation, indicating that epistatic interactions may play an important role in heterosis.