AveDissR: An R function for assessing genetic distinctness and genetic redundancy.

PREMISE OF THE STUDY: Assessing genetic distinctness or redundancy is an important part of plant germplasm characterization. We previously introduced a new marker-based approach using the average dissimilarity of an accession to assess genetic distinctness or redundancy. However, this approach has not been widely applied, largely due to the lack of software to integrate separate analyses involving dissimilarity calculation, analysis of molecular variance, and principal coordinates analysis. METHODS AND RESULTS: An R function, AveDissR, was developed to integrate three separate analyses into one package for assessing genetic distinctness or redundancy. It can analyze large data sets of dominant or codominant markers such as amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), or single-nucleotide polymorphisms (SNPs), generate a useful set of output files for germplasm assessment, and run in an R environment on any computer platform. CONCLUSIONS: AveDissR can make the assessment of genetic distinctness or redundancy in plant germplasm more feasible and useful.

Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding.

Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding.

Genotyping-by-Sequencing and Its Application to Oat Genomic Research.

Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for sampling genome-wide genetic variation, performing genome-wide association mapping, and conducting genomic selection. It is a combined one-step process of SNP marker discovery and genotyping through genome reduction with restriction enzymes and SNP calling with or without a sequenced genome. This approach has the advantage of being rapid, high throughput, cost effective, and applicable to organisms without sequenced genomes. It has been increasingly applied to generate SNP genotype data for plant genetic and genomic studies. To facilitate a wider GBS application, particularly in oat genetic and genomic research, we describe the GBS approach, review the current applications of GBS in plant species, and highlight some applications of GBS to oat research. We also discuss issues in various applications of GBS and provide some perspectives in GBS research. Recent developments of bioinformatics pipelines in high-quality SNP discovery for polyploid crops will enhance the application of GBS to oat genetic and genomic research.

Multiplexed shotgun sequencing reveals congruent three-genome phylogenetic signals for four botanical sections of the flax genus Linum.

A genome-wide detection of phylogenetic signals by next generation sequencing (NGS) has recently emerged as a promising genomic approach for phylogenetic analysis of non-model organisms. Here we explored the use of a multiplexed shotgun sequencing method to assess the phylogenetic relationships of 18 Linum samples representing 16 species within four botanical sections of the flax genus Linum. The whole genome DNAs of 18 Linum samples were fragmented, tagged, and sequenced using an Illumina MiSeq. Acquired sequencing reads per sample were further separated into chloroplast, mitochondrial and nuclear sequence reads. SNP calls upon genome-specific sequence data sets revealed 6143 chloroplast, 2673 mitochondrial, and 19,562 nuclear SNPs. Phylogenetic analyses based on three-genome SNP data sets with and without missing observations showed congruent three-genome phylogenetic signals for four botanical sections of the Linum genus. Specifically, two major lineages showing a separation of Linum-Dasylinum sections and Linastrum-Syllinum sections were confirmed. The Linum section displayed three major branches representing two major evolutionary stages leading to cultivated flax. Cultivated flax and its immediate progenitor were formed as its own branch, genetically more closely related to L. decumbens and L. grandiflorum with chromosome count of eight, and distantly apart from six other species with chromosome count of nine. Five species of the Linastrum and Syllinum sections were genetically more distant from cultivated flax, but they appeared to be more closely related to each other, even with variable chromosome counts. These findings not only provide the first evidence of congruent three-genome phylogenetic pathways within the Linum genus, but also demonstrate the utility of the multiplexed shotgun sequencing in acquisition of three-genome phylogenetic signals of non-model organisms.

[Response of leaf anatomical characteristics of Cyclobalanopsis gilva seedlings to drought stress].

In this study, the leaf anatomical characteristics and transpiration rate of one-year-old seedlings from three study areas including Qingyuan of Zhejiang Province, Dongkou and Jingzhou of Hunan Province were investigated using a pot planting experiment in which relative soil water content was kept as 75%-80% (control), 55%-60% (mild drought stress), 45%-50% (moderate drought stress), 30%-35% (severe drought stress), respectively. The results showed that drought stress significantly reduced the total thickness of the seedling leaves, the thickness of their upper and lower epidermis and the thickness of palisade tissue. The ratio of the palisade tissue to spongy tissue, stomatal length and width also decreased significantly, while the stomatal density increased significantly as the drought stress became more intense. The treatments of drought stress had no significant effect on the thickness of the main veins of the leaves although their xylem thickness varied depending on the seedlings from the different study sites. The change of leaf structure caused the change of physiological function. As drought stress was intensified, the transpiration rate of C. gilva seedlings decreased significantly. The ratio of the palisade tissue to spongy tissue, the thickness of the lower epidermis and stomatal density of the seedlings from Dongkou of Hunan Province were significantly greater, while the transpiration rate was significantly lower than those from other two study sites for all the drought stress treatments, implying that the C. gilva seedlings from Dongkou of Hunan Province had a stronger drought-resistance ability.