Identification of genetic loci for seed shattering in Italian ryegrass (Lolium multiflorum Lam.).

We have identified a unique genetic locus for seed shattering in Italian ryegrass that has an exceedingly large effect and shows partial dominance for reduced seed shattering. Genetic improvement of seed retention in forage grasses can contribute to improving their commercial seed production. The objective of this study was to identify the genetic loci responsible for seed shattering in Italian ryegrass (Lolium multiflorum Lam.

Development of SNP genotyping assays for heading date in rice.

Heading date (HD) is a crucial agronomic trait, controlled by multiple loci, that conditions a range of geographical and seasonal adaptations in rice ( L.). Therefore, information on the HD genotypes of cross parents is essential in marker-assisted breeding programs.

Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice.

Many agronomic traits that are important in rice breeding are controlled by multiple genes. The extensive time and effort devoted so far to identifying and selecting such genes are still not enough to target multiple agronomic traits in practical breeding in Japan because of a lack of suitable plant materials in which to efficiently detect and validate beneficial alleles from diverse genetic resources. To facilitate the comprehensive analysis of genetic variation in agronomic traits among Asian cultivated rice, we developed 12 sets of chromosome segment substitution lines (CSSLs) with the background, 11 of them in the same genetic background, using donors representing the genetic diversity of Asian cultivated rice.

Rapid DNA-genotyping system targeting ten loci for resistance to blast disease in rice.

The fungal pathogen causes blast, a severe disease of rice ( L.). Improving blast resistance is important in rice breeding programs.

Panicle blast 1 (Pb1) resistance is dependent on at least four QTLs in the rice genome.

Background: Rice blast is the most serious disease afflicting rice and there is an urgent need for the use of disease resistance (R) genes in blast tolerance breeding programs. Pb1 is classified as a quantitative resistance gene and it does not have fungal specificity. Pb1-mediated resistance develops in the latter stages of growth.

Detection of QTLs for cold tolerance of rice cultivar 'Kuchum' and effect of QTL pyramiding.

A QTL for cold tolerance at the booting stage of rice cultivar 'Kuchum' was detected and delimited into a 1.36 Mb region, and a cold-tolerant line was developed by QTL pyramiding. Low temperature in summer causes pollen sterility in rice, resulting in a serious loss of yield.

Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross.

Grain shape is an important trait for improving rice yield. A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F2 mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations. In this study, we developed two advanced mapping populations (chromosome segment substitution lines [CSSLs] and BC4F2 lines consisting of more than 2000 individuals) in the genetic backgrounds of two improved cultivars: a japonica cultivar (Koshihikari) with short, round grains, and an indica cultivar (IR64) with long, slender grains.

Genetic architecture of variation in heading date among Asian rice accessions.

Background: Heading date, a crucial factor determining regional and seasonal adaptation in rice (Oryza sativa L.), has been a major selection target in breeding programs. Although considerable progress has been made in our understanding of the molecular regulation of heading date in rice during last two decades, the previously isolated genes and identified quantitative trait loci (QTLs) cannot fully explain the natural variation for heading date in diverse rice accessions.

QTLs underlying natural variation of root growth angle among rice cultivars with the same functional allele of DEEPER ROOTING 1.

Background: The functional allele of the rice gene DEEPER ROOTING 1 (DRO1) increases the root growth angle (RGA). However, wide natural variation in RGA is observed among rice cultivars with the functional DRO1 allele. To elucidate genetic factors related to such variation, we quantitatively measured RGA using the basket method and analyzed quantitative trait loci (QTLs) for RGA in three F2 mapping populations derived from crosses between the large RGA-type cultivar Kinandang Patong and each of three accessions with varying RGA: Momiroman has small RGA and was used to produce the MoK-F2 population; Yumeaoba has intermediate RGA (YuK-F2 population); Tachisugata has large RGA (TaK-F2 population).

A QTL for root growth angle on rice chromosome 7 is involved in the genetic pathway of DEEPER ROOTING 1.

Background: Root growth angle (RGA) is an important trait that influences the ability of rice to avoid drought stress. DEEPER ROOTING 1 (DRO1), which is a major quantitative trait locus (QTL) for RGA, is responsible for the difference in RGA between the shallow-rooting cultivar IR64 and the deep-rooting cultivar Kinandang Patong. However, the RGA differences between these cultivars cannot be fully explained by DRO1.

A major QTL controlling deep rooting on rice chromosome 4.

Drought is the most serious abiotic stress that hinders rice production under rainfed conditions. Breeding for deep rooting is a promising strategy to improve the root system architecture in shallow-rooting rice cultivars to avoid drought stress. We analysed the quantitative trait loci (QTLs) for the ratio of deep rooting (RDR) in three F₂ mapping populations derived from crosses between each of three shallow-rooting varieties ('ARC5955', 'Pinulupot1', and 'Tupa729') and a deep-rooting variety, 'Kinandang Patong'.

Relationship between transmission ratio distortion and genetic divergence in intraspecific rice crosses.

The strength of reproductive isolation often correlates positively with parental divergence in both animals and plants. Here, we assess the relationship between transmission ratio distortion (TRD) of marker loci and parental divergence in intraspecific rice (Oryza sativa L.) crosses.

Uncovering of major genetic factors generating naturally occurring variation in heading date among Asian rice cultivars.

To dissect the genetic factors controlling naturally occurring variation of heading date in Asian rice cultivars, we performed QTL analyses using F(2) populations derived from crosses between a japonica cultivar, Koshihikari, and each of 12 cultivars originating from various regions in Asia. These 12 diverse cultivars varied in heading date under natural field conditions in Tsukuba, Japan. Transgressive segregation was observed in 10 F(2) combinations.

Development of genome-wide simple sequence repeat markers using whole-genome shotgun sequences of sorghum (Sorghum bicolor (L.) Moench).

Simple sequence repeat (SSR) markers with a high degree of polymorphism contribute to the molecular dissection of agriculturally important traits in sorghum (Sorghum bicolor (L.) Moench). We designed 5599 non-redundant SSR markers, including regions flanking the SSRs, in whole-genome shotgun sequences of sorghum line ATx623.

The genome sequence and structure of rice chromosome 1.

The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence.