A prolific and robust whole-genome genotyping method using PCR amplification via primer-template mismatched annealing.

Whole-genome genotyping methods are important for breeding. However, it has been challenging to develop a robust method for simultaneous foreground and background genotyping that can easily be adapted to different genes and species. In our study, we accidently discovered that in adapter ligation-mediated PCR, the amplification by primer-template mismatched annealing (PTMA) along the genome could generate thousands of stable PCR products.

Genetic Dissection of Rice Ratooning Ability Using an Introgression Line Population and Substitution Mapping of a Pleiotropic Quantitative Trait Locus .

Ratooning ability is a key factor that influences ratoon rice yield, in the area where light and temperature are not enough for second season rice. In the present study, an introgression line population derived from Minghui 63 as the recipient parent and 02428 as the donor parent was developed, and a high-density bin map containing 4568 bins was constructed. Nine ratooning-ability-related traits were measured, including maximum tiller number, panicle number, and grain yield per plant in the first season and ratoon season, as well as three secondary traits, maximum tiller number ratio, panicle number ratio, and grain yield ratio.

Morphological and physiological factors contributing to early vigor in the elite rice cultivar 9,311.

Huanghuazhan (HHZ) and 9,311 are two elite rice cultivars in China. They have achieved high yield through quite different mechanisms. One of the major features that gives high yield capacity to 9,311 is its strong early vigor, i.

Hairy Leaf 6, an AP2/ERF Transcription Factor, Interacts with OsWOX3B and Regulates Trichome Formation in Rice.

Trichome formation has been extensively studied as a mechanistic model for epidermal cell differentiation and cell morphogenesis in plants. However, the genetic and molecular mechanisms underlying trichome formation (i.e.

Genome-wide study of an elite rice pedigree reveals a complex history of genetic architecture for breeding improvement.

Improving breeding has been widely utilized in crop breeding and contributed to yield and quality improvement, yet few researches have been done to analyze genetic architecture underlying breeding improvement comprehensively. Here, we collected genotype and phenotype data of 99 cultivars from the complete pedigree including Huanghuazhan, an elite, high-quality, conventional indica rice that has been grown over 4.5 million hectares in southern China and from which more than 20 excellent cultivars have been derived.

Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding.

Analyses of genome variations with high-throughput assays have improved our understanding of genetic basis of crop domestication and identified the selected genome regions, but little is known about that of modern breeding, which has limited the usefulness of massive elite cultivars in further breeding. Here we deploy pedigree-based analysis of an elite rice, Huanghuazhan, to exploit key genome regions during its breeding. The cultivars in the pedigree were resequenced with 7.

Diversity and selective sweep in the OsAMT1;1 genomic region of rice.

Background: Ammonium is one of the major forms in which nitrogen is available for plant growth. OsAMT1;1 is a high-affinity ammonium transporter in rice (Oryza sativa L.), responsible for ammonium uptake at low nitrogen concentration.

A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice.

Rice yield and heading date are two distinct traits controlled by quantitative trait loci (QTLs). The dissection of molecular mechanisms underlying rice yield traits is important for developing high-yielding rice varieties. Here, we report the cloning and characterization of Ghd8, a major QTL with pleiotropic effects on grain yield, heading date, and plant height.

Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice.

The gene GS3 has major effect on grain size and plays an important role in rice breeding. The C to A mutation in the second exon of GS3 was reported to be functionally associated with enhanced grain length in rice. In the present study, besides the C-A mutation at locus SF28, three novel polymorphic loci, SR17, RGS1, and RGS2, were discovered in the second intron, the last intron and the final exon of GS3, respectively.

Linking differential domain functions of the GS3 protein to natural variation of grain size in rice.

Grain yield in many cereal crops is largely determined by grain size. Here we report the genetic and molecular characterization of GS3, a major quantitative trait locus for grain size. It functions as a negative regulator of grain size and organ size.

A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker.

Comparative sequencing of GS3, the most important grain length (GL) QTL, has shown that differentiation of rice GL might be principally due to a single nucleotide polymorphism (SNP) between C and A in the second exon. A total of 180 varieties representing a wide range of rice germplasm were used for association analysis between C-A mutation and GL in order to confirm the potential causal mutation. A cleaved amplified polymorphic sequence (CAPS) marker, SF28, was developed based on the C-A polymorphism in the GS3 gene.