Fine-scale genetic structure of the rice landrace population in Japan.

Rice cultivation was introduced into Japan 3000 years ago and has expanded across the country and encompasses a wide variety of environmental conditions. Here, we elucidated the differentiation of the genetic population structure of 1037 rice landraces across Japan. Using 4451 polymorphisms derived from genome-wide analysis of double-digest restriction-site-associated DNA analysis, population genomics including ADMIXTURE and principal component analysis was carried out.

Artificial selection in the expansion of rice cultivation.

Gene distributions and population genomics suggest artificial selection of ghd7 osprr37, for extremely early heading date of rice, in the Tohoku region of Japan. The ranges of cultivated crops expanded into various environmental conditions around the world after their domestication. Hokkaido, Japan, lies at the northern limit of cultivation of rice, which originated in the tropics.

Translation of continuous artificial selection on phenotype into genotype during rice breeding programs.

Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the genetic relationships of rice varieties in Hokkaido, Japan, one of the northern limits of rice cultivation around the world. Furthermore, artificial selection during rice breeding programs has been characterized using genome sequences.

Genetic effect of a new allele for the flowering time locus in rice.

The optimization of flowering time is a key aspect in maximizing grain productivity in rice. Allelic variations in genes for flowering time are major drivers in the wide adaptability of cultivated rice around the world. Here, we identified a novel allele of flowering time gene ().

Days to heading, controlled by the heading date genes, and , limits rice yield-related traits in Hokkaido, Japan.

A key aspect of rice breeding programs is the optimization of days to heading (DTH) for maximizing grain productivity in cultivation areas. Here, the effects of genotypes for heading date on yield-related traits in rice (culm and panicle length (CL and PL), panicle number (PN), and total number of seeds) were investigated. () and () are the main controllers of the variation in heading date in the rice population of Hokkaido, Japan.

A novel genotype DATTO5 developed using the five genes exhibits the fastest heading date designed in rice.

The optimization of heading date is a key aspect for maximizing grain productivity in cereal crops including rice. The combinations of genes for heading date, a quantitative trait, are a major driver in the wide adaptability of cultivated rice worldwide. Here, we identified a novel QTL, (quantitative trait locus for days-to-heading on chromosome 3), for early flowering time in the F population derived from a cross between Hoshinoyume (HS) and Daichinohoshi (DH) among local rice populations with extremely early heading date.

Marker-assisted selection in rice breeding programs in Hokkaido.

Rice breeding programs in Hokkaido over the past 100 years have dramatically increased productivity and improved the eating quality of rice. Commercial varieties with high yield and good eating quality, such as Kirara 397, Hoshinoyume, and Nanatsuboshi, have been continuously registered since 1990. Furthermore, varieties with better eating quality using , which reduces amylose content to improve the taste of sticky rice, such as Oborozuki and Yumepirika, were registered in 2006 and 2008, respectively.

Switching genetic effects of the flowering time gene in LD conditions by and in rice.

Flowering time control in plants is a major limiting factor on the range of species. Day length, perceived via the photoperiodic pathway, is a critical factor for the induction of flowering. The module of -- in the long day (LD) plant is conserved in diverse plant species including the short day (SD) plant rice, where this module comprises ()-.

Introgression of the chromosomal region with the Pi-cd locus from Oryza meridionalis into O. sativa L. during rice domestication.

The genotype of the Pi-cd locus found in blast-resistant rice variety Kitakurin, which is a cultivated rice from Japan belonging to Oryza sativa japonica, is identical to that of its wild relative O. meridionalis. Crop domestication from wild relatives to cultivated species has encompassed significant phenotypic changes.

Establishment of adaptability to the northern-limit of rice production.

The domestication of cultivated crops from their wild relatives narrowed down their genetic diversity in a bottleneck effect. Subsequently, the cultivation areas of crops have expanded all over the world into various environmental conditions from the original area along with human migration after domestication. Here, we demonstrated the genetic changes in the adaptation of rice to Hokkaido (41°2-45°3N latitude), Japan, from the tropics of their origin in Asian cultivated rice, Oryza sativa L.

Colocalization of QTLs for hull-cracked rice and grain size in elite rice varieties in Japan.

The control of insects that consume cereal grains is important for the production and storage of grains. Hull-cracked rice, which has splits in the hull, becomes more susceptible to insects both in the paddy field and during storage. The development of varieties with a low frequency of hull-cracked rice is the most economical and effective strategy to avoid insect damage and the environmental risks from agricultural chemical entering rice grains.

Phenotypic changes during 100-year rice breeding programs in Hokkaido.

Plant breeding programs in local regions may have genetic and phenotypic variations that are desirable and shape adaptability during the establishment of local populations. Despite the characterization of genetic population structures in various kinds of populations, the effects of variations in phenotype on agro-economical traits currently remain unclear. In the present study, we evaluated phenotypic changes in 26 agro-economical traits among the local population during rice breeding programs in Hokkaido.

Genome-wide association mapping focusing on a rice population derived from rice breeding programs in a region.

Plant breeding programs in local regions may generate genetic variations that are desirable to local populations and shape adaptability during the establishment of local populations. To elucidate genetic bases for this process, we proposed a new approach for identifying the genetic bases for the traits improved during rice breeding programs; association mapping focusing on a local population. In the present study, we performed association mapping focusing on a local rice population, consisting of 63 varieties, in Hokkaido, the northernmost region of Japan and one of the northern limits of rice cultivation worldwide.

Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping.

Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits.

[Serum ALP elevation early after treatment is a predictor for response in myeloma patients treated with bortezomib].

Several studies have shown the predictive value of elevated serum alkaline phosphatase (ALP) level in multiple myeloma (MM) patients treated with bortezomib (BTZ). We assessed the relationship between changes in ALP levels during treatment and response. Thirty patients treated with BTZ in our hospital were analyzed retrospectively.

Genetic shift in local rice populations during rice breeding programs in the northern limit of rice cultivation in the world.

The rapid accumulation of pre-existing mutations may play major roles in the establishment and shaping of adaptability for local regions in current rice breeding programs. The cultivated rice, Oryza sativa L., which originated from tropical regions, is now grown worldwide due to the concerted efforts of breeding programs.

Diversification of the plant-specific hybrid glycine-rich protein (HyGRP) genes in cereals.

Plant-specific hybrid proline- or glycine-rich proteins (HyP/GRPs) are involved in diverse gene functions including plant development and responses to biotic and abiotic stresses. The quantitative trait locus, qLTG3-1, enhances seed germination in rice under low-temperature conditions and encodes a member with a glycine-rich motif of the HyP/GRP family. The function of this gene may be related to the weakening of tissue covering the embryo during seed germination.

QTL pyramiding for improving of cold tolerance at fertilization stage in rice.

Vigorous cold tolerance at the fertilization stage (CTF) is a very important characteristic for stable rice production in cold temperature conditions. Because CTF is a quantitatively inherited trait, pyramiding quantitative trait loci (QTLs) using marker-assisted selection (MAS) is effective for improving CTF levels in rice breeding programs. We previously identified three QTLs controlling CTF, qCTF7, qCTF8 and qCTF12, using backcrossed inbred lines derived from a cross between rice cultivar Eikei88223 (vigorous CTF) and Suisei (very weak CTF).

Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation.

The rice local population was clearly differentiated into six groups over the 100-year history of rice breeding programs in the northern limit of rice cultivation over the world. Genetic improvements in plant breeding programs in local regions have led to the development of new cultivars with specific agronomic traits under environmental conditions and generated the unique genetic structures of local populations. Understanding historical changes in genome structures and phenotypic characteristics within local populations may be useful for identifying profitable genes and/or genetic resources and the creation of new gene combinations in plant breeding programs.

Genetical and morphological characterization of cold tolerance at fertilization stage in rice.

Cold temperature during the reproductive phase leads to seed sterility, which reduces yield and decreases the grain quality of rice. The fertilization stage, ranging from pollen maturation to the completion of fertilization, is sensitive to unsuitable temperature. Improving cold tolerance at the fertilization stage (CTF) is an important objective of rice breeding program in cold temperature areas.

Roles of the Hd5 gene controlling heading date for adaptation to the northern limits of rice cultivation.

During the diversification of cultivated rice after domestication, rice was grown in diverse geographic regions using genetic variations attributed to the combination of alleles in loci for adaptability to various environmental conditions. To elucidate the key gene for adaptation in rice cultivars to the northern limit of rice cultivation, we conducted genetic analyses of heading date using extremely early-heading cultivars. The Hd5 gene controlling heading date (flowering time) generated variations in heading date among cultivars adapted to Hokkaido, where is the northernmost region of Japan and one of the northern limits of rice cultivation in the world.

Selection for low-temperature germinability on the short arm of chromosome 3 in rice cultivars adapted to Hokkaido, Japan.

In plant breeding with intensive selection, the haplotype patterns in the targeted chromosomal regions may become monogenic among local populations with the most desirable combination of loci. This study demonstrated that the chromosomal region surrounding qLTG3-1 was under selection during rice breeding programs in a local region of Japan, Hokkaido. qLTG3-1 is a major quantitative trait loci controlling tolerance to low-temperature at the seed germination stage in rice, termed low-temperature germinability.

Transposition behavior of nonautonomous a hAT superfamily transposon nDart in rice (Oryza sativa L.).

Transposable elements (TEs) have a significant impact on the evolution of gene function and genome structures. An endogenous nonautonomous transposable element nDart was discovered in an albino mutant that had an insertion in the Mg-protoporphyrin IX methyltransferase gene in rice. In this study, we elucidated the transposition behavior of nDart, the frequency of nDart transposition and characterized the footprint of nDart.

Genetic effects of major QTLs controlling low-temperature germinability in different genetic backgrounds in rice (Oryza sativa L.).

The effects of QTLs are demonstrated basically within the population used in the original QTL analysis as the difference between the alleles of the parental varieties. For the efficient use of QTLs in breeding programs, it is necessary to assess whether the QTL exhibits its genetic effect when it is introgressed into different genetic backgrounds. Extensive studies of tolerance to low temperature at the seed germination stage (called low-temperature germinability) in rice revealed that 2 major QTLs on chromosomes 3 and 11, qLTG3-1 and qLTG11, have large effects.

Origins of functional nucleotide polymorphisms in a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice.

qLTG3-1 is a major quantitative trait locus (QTL) controlling tolerance to low-temperature at the seed germination stage (termed low-temperature germinability) in rice using a population derived from the cross between Italica Livorno from Italy and Hayamasari from Japan. Map-based cloning identified that qLTG3-1 encodes a protein of unknown function. The molecular identification of this major QTL could make it possible to identify allelic variation and favorable alleles for rice breeding programs.