Genome-wide association mapping of date palm fruit traits

Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform genome-wide association studies (GWAS) of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor VIRESCENS gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crops, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species

The genomic landscape of molecular responses to natural drought stress in Panicum hallii

© 2018, The Author(s). Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory networks are more likely to have opposing effects than expected under neutral evolution, supporting a strong influence of compensatory evolution and stabilizing selection. These results implicate trans-regulatory evolution as a driver of drought responses and demonstrate the potential for crop improvement in drought-prone regions through modification of gene regulatory networks

Understanding the effect of Raphanus sativus extract on the pathogenesis of chronic myeloid leukemia, breast and colon cancer through mathematical modeling

Chronic myeloid leukemia (CML), breast, and colon cancer are among the most prevalent types of cancer in the Philippines. In most of the cancer cases reported annually, cancer is only detected when it is on its advance stage due to the lack of early detection and limited options of targeted therapies. There are studies that show different effects of Raphanus sativus (radish) extract on different cancer diseases. However, it is still unknown why it has different effects on different cancer diseases. Therefore, understanding disease dynamics would help in improving prognosis and diagnosis. In this study, we propose a mathematical model that would explain the effect of Raphanus sativus extract on the pathogenesis of CML, breast and colon cancer. Since p53 is one of the most extensively studied gene in the field of cancer research and Cyclin D1-CDK complex is one of the more frequently altered cell cycle regulators in cancers, these genes are the focus for the basis of the effectiveness of the drug. Based on our simulations, we have showed that a 99.99%, 99.68%, and 98.96% decrease in the steady-state concentration of p53 are observed in breast cancer, colon cancer, and CML, respectively, after the drug was inserted in the model. Moreover, Cyclin D1-CDK complex\u27s steady-state concentration is decreased by 99.91% in breast cancer, 99.89% in colon cancer, and 98.50% in CML. Hence, the model suggests that Raphanus sativus extract is highly effective on breast cancer followed by colon cancer and CML

A Bac Library Of The Sp80-3280 Sugarcane Variety (saccharum Sp.) And Its Inferred Microsynteny With The Sorghum Genome

Background: Sugarcane breeding has significantly progressed in the last 30 years, but achieving additional yield gains has been difficult because of the constraints imposed by the complex ploidy of this crop. Sugarcane cultivars are interspecific hybrids between Saccharum officinarum and Saccharum spontaneum. S. officinarum is an octoploid with 2n=80 chromosomes while S. spontaneum has 2n=40 to 128 chromosomes and ploidy varying from 5 to 16. The hybrid genome is composed of 70-80%S. officinaram and 5-20%S. spontaneum chromosomes and a small proportion of recombinants. Sequencing the genome of this complex crop may help identify useful genes, either per se or through comparative genomics using closely related grasses. The construction and sequencing of a bacterial artificial chromosome (BAC) library of an elite commercial variety of sugarcane could help assembly the sugarcane genome. Results: A BAC library designated SS-SBa was constructed with DNA isolated from the commercial sugarcane variety SP80-3280. The library contains 36,864 clones with an average insert size of 125 Kb, 88% of which has inserts larger than 90 Kb. Based on the estimated genome size of 760-930 Mb, the library exhibits 5-6 times coverage the monoploid sugarcane genome. Bidirectional BAC end sequencing (BESs) from a random sample of 192 BAC clones sampled genes and repetitive elements of the sugarcane genome. Forty-five per cent of the total BES nucleotides represents repetitive elements, 83% of which belonging to LTR retrotransposons. Alignment of BESs corresponding to 42 BACs to the genome sequence of the 10 sorghum chromosomes revealed regions of microsynteny, with expansions and contractions of sorghum genome regions relative to the sugarcane BAC clones. In general, the sampled sorghum genome regions presented an average 29% expansion in relation to the sugarcane syntenic BACs. Conclusion: The SS-SBa BAC library represents a new resource for sugarcane genome sequencing. An analysis of insert size, genome coverage and orthologous alignment with the sorghum genome revealed that the library presents whole genome coverage. 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