Joong Hyoun Chin

Inactivation of the UGPase1 gene causes genic male sterility and endosperm chalkiness in rice (Oryza sativa L.).

A rice genic male-sterility gene ms-h is recessive and has a pleiotropic effect on the chalky endosperm. After fine mapping, nucleotide sequencing analysis of the ms-h gene revealed a single nucleotide substitution at the 3′-splice junction of the 14th intron of the UDP-glucose pyrophosphorylase 1 (UGPase1; EC2.7.7.9) gene, which causes the expression of two mature transcripts with abnormal sizes caused by the aberrant splicing. An in vitro functional assay showed that both proteins encoded by the two abnormal transcripts have no UGPase activity. The suppression of UGPase by the introduction of a UGPase1-RNAi construct in wild-type plants nearly eliminated seed set because of the male defect, with developmental retardation similar to the ms-h mutant phenotype, whereas overexpression of UGPase1 in ms-h mutant plants restored male fertility and the transformants produced T1 seeds that segregated into normal and chalky endosperms. In addition, both phenotypes were co-segregated with the UGPase1 transgene in segregating T1 plants, which demonstrates that UGPase1 has functional roles in both male sterility and the development of a chalky endosperm. Our results suggest that UGPase1 plays a key role in pollen development as well as seed carbohydrate metabolism.

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.

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.

Application of indica–japonica single-nucleotide polymorphism markers for diversity analysis of Oryza AA genome species

High-throughput genotyping using single-nucleotide polymorphisms (SNP) is one tool that can be used to study the genetic relationships between wild rice relatives and cultivated rice. In this study, a set of 96 indica–japonica SNP markers, which can differentiate indica and japonica subspecies of rice, were used to characterize 227 Oryza accessions including 93 AA genome accessions from seven wild Oryza species. A total of 72 markers of the 96 markers were selected for the phylogenetic study and allele polymorphism survey. A subset of SNP markers were present only in Oryza sativa and evolutionarily close species, Oryza nivara and Oryza rufipogon. These markers can be used for distinguishing cultivated rice from the other species and vice versa. Eight clusters were generated through phylogenetic analysis, and Oryza meridionalis and Oryza longistaminata appeared to be the most distantly related species to cultivated rice. In this study, Oryza barthii and Oryza glaberrima accessions were found to exhibit high genetic similarity. Across the wild species, more indica-type alleles were detected for most accessions. In this study, a set of markers selected to be informative across O. sativa accessions were used, but it will be interesting to compare the results of this study with SNP data obtained through next-generation sequencing in the future.

Brief History and Perspectives on Plant Breeding

Following the rediscovery of Mendel’s principles of heredity in 1900, plant breeding has made tremendous progress in developing diverse methodologies to create and select variation by using genetic principles. Since the beginning of the twenty-first century, plant breeding has been systematized with state-of-the-art technologies aided by transgenic and genomics approaches. In the future, breeders will be able to assemble desirable alleles or genes into promising varieties with optimized performance using an approach that integrates scientific fields. Recent concerns about global warming, abnormal weather patterns, and unfavorable environments have pushed breeders to speed up the breeding process. In this chapter, the history of plant breeding, methods for creating variation, selection and generation advance strategies, and challenges and perspectives are briefly reviewed and discussed.

Characterization of Selected Rice Varieties Adapted in Africa

Rice varieties developed through the inter-specific crosses between Asian (Oryza sativa L.) and African cultivated rice (O. glaberrima Steud.) have contributed to yield enhancement of African rice. However, the genetic diversity and genetic structure of the African varieties have rarely been reported. In this study, we characterized 40 rice varieties including rice released in Africa based on eleven yield related agronomic traits and 96 single nucleotide polymorphism (SNP) markers. They were grouped into three categories based on the cluster analysis using agronomic traits. Meanwhile, they were grouped into two distinct clusters, indicaand japonica-type, based on the genetic distance using 96 SNP markers. CG14, which belongs to O. glaberrima, was found to be an admixture type between indica and japonica. The number of secondary branches (SBs) was the only agronomic trait which was significantly different between two groups. The results of this study provide basic agronomic and genomic information of cultivated and tested rice varieties for Africa, that would be helpful for further rice varietal improvement in Africa.