Next-generation Sequencing of restriction-Site-Associated DNA (RAD-Seq) from 1300 Miscanthus Genotyp

Descriptions

The global demands for food and renewable energy are increasing at currently unsustainable rates that are expected to accelerate in the future. A major challenge for plant breeders is therefore to develop bioenergy crops that ideally (1) are highly productive, but carbon negative; (2) can be grown under a wide range of environmental conditions, including marginal lands, but with minimal agronomic inputs (e.g., fertilisers, pesticides, irrigation); (3) produce biomass that can efficiently be converted to biofuels; and (4) can be deployed very rapidly. However, most existing energy crops fail to meet at least one of these requirements. Furthermore, traditional breeding approaches, while certain to be effective, tend to be relatively slow. One way to accelerate breeding cycles is to use diagnostic molecular markers (DNA polymorphisms) to select superior plants at a juvenile age, instead of having to wait for years before direct evaluations can be made. However, an emerging consensus from studies that aim to identify such marker-trait correlations is that genetic variation for most phenotypic traits is underpinned by hundreds of DNA polymorphisms, making it impossible to cherry-pick superior germplasm based on a handful of markers. A more practical approach is therefore to use very large numbers of molecular markers, or even entire genome sequences, to predict phenotypes. This approach, known as genomic selection, is becoming increasingly affordable because of recent breakthroughs in sequencing technology and is believed to have great potential for accelerating crop development and optimisation.As part of two BBSRC-funded projects, we will take advantage of an extensive germplasm collection and apply marker-assisted approaches to accelerate a world-leading breeding programme for the promising energy crop Miscanthus. To achieve this goal, we will first acquire prerequisite information on genome-wide patterns of DNA polymorphism. Then, we will characterise the genomic architectures of phenotypic traits targeted by breeders (i.e., determine the approximate number of DNA polymorphisms underlying genetic variation for each trait and quantify the phenotypic effect of each polymorphism) using state of the art statistical models. Finally, we will apply the genomic selection approach described above to Miscanthus, potentially accelerating breeding cycles 2-3 times and benefitting not only plant scientists and breeders, but also farmers and the general public.To complete the objectives of these projects, we require extensive DNA polymorphism data that should meet the following criteria:1. Data should be obtained through next-generation sequencing of restriction-site-associated DNA (RAD-Seq) from 1300 Miscanthus genotypes;2. Data should be based on 10-15K RAD-Seq tags;3. Data should be delivered as standard bioinformatics output (.fastq) files within 25 weeks of receiving DNA templates;4. Average sequence coverage per tag per individual should exceed 10-fold.The above quote will be assessed 70% on Price and 30% on Quality from a total available score of 1000, 700 marks available for the commercial element and 300 marks available for the technical element. Please see attached schedule of prices for your completion. The technical element of the overall score will be assed based on the following questions and criteria:The following three questions each account for 10% of your overall score or 100 available marks per question:Q1 - Data should be based on 10-15K RAD-Seq tags; possible answers and related scores:Under 10-15K = 0 marks or 0%10-15K = 20 marks or 20%15-20K = 30 marks or 30%20-25K = 40 marks or 40%25-30K = 50 marks or 50%30-35K = 60 marks or 60%35-40K = 70 marks or 70%40-40K = 80 marks or 80%45-50K = 100 marks or 100%Q2 - Data should be delivered as standard bioinformatics output (.fastq) files within 25 weeks of receiving DNA templates; possible answers and related scores:Over 35 weeks = 0 marks or 0%35 weeks = 25 marks or 25%30 weeks = 50 marks or 50%25 weeks = 75 marks or 75%20 weeks = 100 marks or 100%Q3 - Average sequence coverage per tag per individual should exceed 10-fold; possible answers and related scores:Less than 10-fold = 0 marks or 0%10-fold = 20 marks or 20%20-fold = 40 marks or 40%30-fold = 60 marks or 60%40-fold = 80 marks or 80%50-fold = 100 marks or 100%Commercial Response Notes and Guidance:The pricing schedule that you will need to complete is based on services we have been provided in the past and is not intended to show favouritism or provide any advantage to any particular bidder. We will accept alternatives to the products/services described in the pricing schedule on the understanding that equivalence is demonstrated by the bidder.