Search

Products from peanut seeds are nutritious for human and/or animal consumption. Peanut seed nutritional quality is determined by the genotype (G) of cultivars or accessions, environmental conditions (E), and their interactions (G × E). To evaluate the effects of genotype, environment, and their interactions on seed nutritional quality, 52 peanut germplasm accessions, which vary in oil content and fatty acid composition, were planted at three locations (Citra, FL; Byron, GA; and Clovis, NM) for 2 years (2017 and 2018). The harvested seeds were analyzed for protein, oil, and fatty acid composition using an N analyzer, nuclear magnetic resonance, and gas chromatography, respectively. Significant effects of accession, FAD2 gene, where FAD is fatty acid desaturase, location, year, and their interactions on the investigated traits were evaluated. The average oil content from accessions grown in Florida (51.1%) or Georgia (50.7%) was significantly higher than those grown in New Mexico (45.8%), whereas the average protein content from accessions grown in Florida (23.2%) was significantly lower than those grown in New Mexico (25.4%) or Georgia (24.8%). This is expected as there is a negative correlation between oil and protein content. After genotyping and classification (A/A, A/W, and G/W) for the FAD2A/FAD2B genes, the nutritional quality variations were further evaluated at the levels of the specific haplotype of FAD2A/FAD2B and explicit environmental index. The average prediction accuracy of seed nutritional quality trait values from the prediction model demonstrated that predicting trait values in new environments is feasible. The results of this study provide insights into the seed nutritional analysis, germplasm evaluation, and peanut breeding, cultivation, and production to peanut breeders, curators, farmers, and product processors. Core Ideas: Genotype, environment, and their interactions affect peanut seed nutritional quality.The FAD2A/FAD2B gene (F) effect significantly alters seed fatty acid composition.Location (L) effect significantly changes seed oil and protein content.Photothermal time may be a good parameter for representing the growing location environmental conditions for data analysis.Recommendation was given to farmers and processors on how to cultivate the right peanut varieties and purchase the right seeds from specific regions. [ABSTRACT FROM AUTHOR]

Recently, the Cas9-CRISPR system has proven to be a useful tool for genome editing in eukaryotes, which repair the double stranded breaks made by Cas9 with non-homologous end joining or homologous recombination. Escherichia coli lacks non-homologous end joining and has a very low homologous recombination rate, effectively rendering targeted Cas9 activity lethal. We have developed a heat curable, serializable, plasmid based system for selectionless Cas9 editing in arbitrary E. coli strains that uses synthetic CRISPRs for targeting and -red to effect repairs of double stranded breaks. We have demonstrated insertions, substitutions, and multi-target deletions with our system, which we have tested in several strains.

Paired-end library sequencing has been proven useful in scaffold construction during de novo whole genome shotgun assembly. The ability of generating mate pairs with > 8 Kb insert sizes is especially important for genomes containing long repeats. To make mate paired libraries for next generation sequencing, DNA fragments need to be circularized to bring the ends together. There are several methods that can be used for DNA circulation, namely ligation, hybridization and Cre-LoxP recombination. With higher circularization efficiency with large insert DNA fragments, Cre-LoxP recombination method generally has been used for constructing >8 kb insert size paired-end libraries. Second fragmentation step is also crucial for maintaining high library complexity and uniform genome coverage. Here we will describe the following three fragmentation methods: restriction enzyme digestion, random shearing and nick translation. We will present the comparison results for these three methods. Our data showed that all three methods are able to generate paired-end libraries with greater than 20 kb insert. Advantages and disadvantages of these three methods will be discussed as well.

Fosmid or BAC end sequencing plays an important role in de novo assembly of large genomes like fungi and plants. However construction and Sanger sequencing of fosmid or BAC libraries are laborious and costly. The current 454 Paired-End (PE) Library and Illumina Jumping Library construction protocols are limited with the gap sizes of approximately 20 kb and 5 kb, respectively. In the attempt to understand the limitations of constructing PE libraries with greater than 30Kb gaps, we have purified 18, 28, 45, and 65Kb sheared DNA fragments from yeast and circularized the ends using the Cre-loxP approach described in the 454 PE Library protocol. With the increasing fragment sizes, we found a general trend of decreasing library quality in several areas. First, redundant reads and reads containing multiple loxP linkers increase when the average fragment size increases. Second, the contamination of short distance pairs (

Long insert size paired-end (PE) sequences play a key role in de novo assemblies of complex genomes. There is no reliable method, however, for generating 30Kb or longer insert size PE libraries that is suitable for 454 or Illumina sequencing. In the attempt to understand the limitations of constructing greater than 30Kb PE libraries, we have purified 18, 28, 45, and 65Kb sheared DNA fragments from yeast and circularized the ends using the Cre-loxP approach described in the 454 Titanium long paired-end library protocol. With the increasing insert sizes, we found a general trend of decreasing library quality in several areas. First, the portion of redundant pairs increases from 18percent to almost 40percent of the total pairs when the average fragment size increases from 18Kb to 45Kb. Second, the contamination of short insert size pairs (