Masahiro Yano

Mapping and characterization of seed dormancy QTLs using chromosome segment substitution lines in rice

Seed dormancy—the temporary failure of a viable seed to germinate under favorable conditions—is a complex characteristic influenced by many genes and environmental factors. To detect the genetic factors associated with seed dormancy in rice, we conducted a QTL analysis using chromosome segment substitution lines (CSSLs) derived from a cross between Nona Bokra (strong dormancy) and Koshihikari (weak dormancy). Comparison of the levels of seed dormancy of the CSSLs and their recurrent parent Koshihikari revealed that two chromosomal regions—on the short arms of chromosomes 1 and 6—were involved in the variation in seed dormancy. Further genetic analyses using an F2 population derived from crosses between the CSSLs and Koshihikari confirmed the allelic differences and the chromosomal locations of three putative QTLs: Sdr6 on chromosome 1 and Sdr9 and Sdr10 on chromosome 6. The Nona Bokra alleles of the three QTLs were associated with decreased germination rate. We discuss the physiological features of the CSSLs and speculate on the possible mechanisms of dormancy in light of the newly detected QTLs.

Well-ordered monolayers of alkali-doped coronene and picene: Molecular arrangements and electronic structures

Adsorptions of alkali metals (such as K and Li) on monolayers of coronene and picene realize the formation of ordered phases, which serve as well-defined model systems for metal-intercalated aromatic superconductors. Upon alkali-doping of the monolayers of coronene and picene, scanning tunneling microscopy and X-ray absorption spectroscopy revealed the rearrangement of the entire molecular layer. The K-induced reconstruction of both monolayers resulted in the formation of a structure with a herringbone-like arrangement of molecules, suggesting the intercalation of alkali metals between molecular planes. Upon reconstruction, a shift in both the vacuum level and core levels of coronene was observed as a result of a charge transfer from alkali metals to coronene. In addition, a new density of states near the Fermi level was formed in both the doped coronene and the doped picene monolayers. This characteristic electronic feature of the ordered monolayer has been also reported in the multilayer picene films, ensuring that the present monolayer can model the properties of the metal-intercalated aromatic hydrocarbons. It is suggested that the electronic structure near the Fermi level is sensitive to the molecular arrangement, and that both the strict control and determinations of the molecular structure in the doped phase should be important for the determination of the electronic structure of these materials.

Genomics-Assisted Allele Mining and its Integration Into Rice Breeding

Understanding the association between nucleotide changes and phenotypic changes is necessary for germplasm enhancement but has been a significant challenge in the molecular genetics and breeding of rice. In this article, we summarize our efforts to develop plant materials such as chromosome segment substitution lines to enhance the genetic analysis of traits of interest. The power of genetic dissection of phenotypic traits by use of novel populations is illustrated by our genetic analysis of heading date. We also present examples of the discovery of useful alleles involved in disease resistance and drought avoidance. Finally, we describe the discovery of genome-wide single-nucleotide polymorphism, which facilitate genetic analysis. This new type of genetic marker has allowed us to uncover the genome architecture of modern cultivars in Japan. These areas of progress will gradually change the landscape of selection in rice breeding.

Genetic and Molecular Dissection of Flowering Time Control in Rice

Flowering time is one of the most important agronomic traits in rice (Oryza sativa L.) and is primarily controlled by quantitative trait loci (QTLs) that are associated with a photoperiodic response, particularly in short-day (SD) plants such as rice. Since the early twentieth century, rice breeders and researchers have been interested in clarifying the genetic control of flowering time because its modification is important for regional adaptation. The sequencing of the rice genome has facilitated genome-wide mapping of loci and gene cloning; thus, more progress has been made in elucidating the genetic control pathways of flowering. In this chapter, we provide an overview of the studies investigating rice flowering.

Genetic dissection of pre-harvest sprouting resistance in an upland rice cultivar

Seed dormancy is important in rice breeding because it confers resistance to pre-harvest sprouting (PHS). To detect quantitative trait loci (QTLs) for pre-harvest sprouting resistance, we used chromosome segment substitution lines (CSSLs) derived from a cross between the Japanese upland rice cultivar ‘Owarihatamochi’ and the lowland rice cultivar ‘Koshihikari’. In the CSSLs, several chromosomal regions were associated with PHS resistance. Among these, the chromosome 9 segment from ‘Owarihatamochi’ had the greatest association with increased PHS resistance. Further QTL analysis using an advanced backcross population (BC4F2) derived from a ‘Koshihikari’ × ‘Owarihatamochi’ cross revealed two putative QTLs, here designated qSDR9.1 (Seed dormancy 9.1) and qSDR9.2, on chromosome 9. The ‘Owarihatamochi’ alleles of the two QTLs reduced germination. Further fine mapping revealed that qSDR9.1 and qSDR9.2 were located within 4.1-Mb and 2.3-Mb intervals (based on the ‘Nipponbare’ reference genome sequence) defined by the simple sequence repeat marker loci RM24039 and RM24260 and Indel_2 and RM24540, respectively. We thus identified two QTLs for PHS resistance in ‘Owarihatamochi’, even though resistance levels are relatively low in this cultivar. This unexpected finding suggests the advantages of using CSSLs for QTL detection.

Genetic Dissection and Mapping of Genes Conferring Field Resistance to Rice Blast in Japanese Upland Rice

Field resistance to rice blast in Japanese upland was analyzed genetically. Chromosomal regions that are involved in field resistance were detected by quantitative trait loci (QTL) analysis using F4 lines of a cross between resistant upland rice variety Owarihatamochi and susceptible irrigated rice variety Nipponbare. At two QTLs on chromosome 4 and one on chromosome 12, alleles from Owarihatamochi were resistant, while an allele from Nipponbare was resistant at one QTL on chromosome 9. Backcrossed progeny lines with each of the resistant alleles from upland rice were developed using the highly susceptible irrigated rice cultivar Aichiasahi as the recurrent parent. At all three QTLs, the lines with the Owarihatamochi allele showed a significantly higher level of field resistance than did those with the Aichiasahi allele. The differences in resistance between two genotypes were largest at the QTL on chromosome 4 and smallest at the QTL on chromosome12, in good accordance with the result of QTL analysis. The QTL of largest effect on chromosome 4 was mapped as a single recessive gene designated as pi21 by genetic linkage analysis. Using a mapping population consisting of 82 lines, we located pi21 between marker loci G271 and G317 at a distance of 5.0 cM and 8.5 cM, respectively. High-resolution genetic linkage analysis using 1104 individuals identified several DNA markers tightly linked with the pi21locus. These markers are being used to identify P1 artificial chromosome (PAC) clones containing this locus for positional cloning of pi21.