Finger Millet Whole Genome Sequencing Project

Transcription

1 Finger Millet Whole Genome Sequencing Project Scien&sts: DA Odeny (ICRISAT- Nairobi), Katrien Devos (UGA, USA), Allen van Deynze (UC Davis), F Stomeo (BecA- ILRI), Y Nasser (BecA- ILRI), A Djikeng (BecA- ILRI), K Tesfaye (UAA, Ethiopia), M Dida (UM, Kenya), E Mneney (MARI, Tanzania), E Bongkam- Rudloff (SLU, Sweden), S de Villiers (PU, Kenya) Fellows: Jus&n Ringo, Dagnachew Lule, Davis Gimode, Erick Owuor

2 Finger millet A small but highly nutri0ous grain Good storage quality Superior mal0ng quality Adapted to diverse agro- ecologies Na0ve to eastern Africa

3 However: Finger millet an orphan cereal crop ü Li>le research investment ü Lack of genomic resources Finger millet allotetraploid ü Hybridiza0on of two different species (AABB) ü True progenitors not known with certainty

4 Bio- Innovate Established in 2010, based at ILRI Funded mainly by SIDA Support mul0- disciplinary product oriented innova0on ac0vi0es Operates in eastern African countries Currently supports 9 projects Sorghum and millet africa.org

5 Sorghum and Millet ConsorCum Members: Moi and Maseno University, MARI, EIAR, ICRISAT, Makerere University, Addis Ababa University (PI) ICRISAT ac0vi0es (biotechnology) Sorghum Stay- green trait mapping Finger millet Regional gene0c diversity Ini0ate marker- assisted selec0on for drought and blast resistance

6 Challenges Independent marker development expensive Microsatellite markers: Genome/transcript sequence required Single nucleo0de polymorphisms (SNPs) markers: SNP assays or representa0ve reference genome required: Genome/transcript sequence required Whole genome sequencing best op0on Other global ini0a0ves exist: AOCC

7 African Orphan Crops ConsorCum

8 African Orphan Crops ConsorCum Read all about AOCC here: h>p:// orphan- crops.aspx An interna0onal effort to improve nutri0on, produc0vity and climate adaptability of Africa s food crops Goal: Sequence, assemble and annotate 100 genomes For each genome sequenced, 100 accessions re- sequenced Sequencing informa0on publicly available

9 Bio- Innovate/AOCC Bio- Innovate interest and investment in finger millet AOCC has finger millet in the list of 100 crops to be sequenced

10 Re- sequencing 1. Wild accessions 2. Drought tolerance 3. Blast resistance 1. Lines grown in Africa 2. Lines with important nutri0onal & produc0vity/resistant traits 4. Lines must be publicly available 3. Sampling of diversity worldwide Bio- Innovate AOCC

11 Whole Genome Sequencing Started/launched in April 2014 Objec0ves 1. To create a representa0ve reference genome that will facilitate rou0ne use of marker- assisted and genomics- assisted selec0on of advanced finger millet for superior varietal development 2. To develop a robust set of molecular markers to facilitate the u0liza0on of the promising desirable gene0c resources selected under Project 1 3. To build capacity in the applica0on of genomics in finger millet breeding and the u0liza0on of the Integrated Breeding Plaborm

12 ObjecCve 1: CreaCng RepresentaCve AcCviCes Reference Genome Genera0ng whole genome sequence of KNE796 (ICRISAT/AOCC) Whole genome de novo sequence assembly (AOCC/SLU) Genera0ng comprehensive transcriptome data and genome annota0on (BecA/AOCC) Anchoring and refining assembly with dense gene0c map(s) (ICRISAT/UGA)

13 ObjecCve 2: To develop a robust set AcCviCes of molecular markers Re- sequencing 35 blast resistant and 5 blast suscep0ble finger millet accessions selected from the field screening ac0vity in Maseno University (MU/ UGA) Re- sequencing 35 drought tolerant and 5 drought tolerant finger millet accessions selected from the field screening ac0vity in Tanzania (MARI) Re- sequencing 20 wild (10 from Ethiopia, 5 from Kenya, 5 from Tanzania) accessions of finger millet (AAU)

14 ObjecCve 3: To build capacity (BecA) AcCviCes Train finger millet breeders in the prac0cal u0liza0on of molecular markers in their breeding programs Integrate conven0onal and molecular breeding in finger millet using the Genera0on Challenge Program s Integrated Breeding Plaborm (IBP) Train finger millet breeders in the use of IBP Training young upcoming scien0sts in the applica0on of genomics in finger millet breeding through ABCF

15 Progress DNA has been sent to BGI and sequencing of small libraries completed First assembly done by BGI and genome size es0ma0on done Two ABCF fellows recruited by BecA and both started in June 2014 Transcriptome analysis in response to blast disease/striga infesta0on: M Dida/ICRISAT Capacity Building: 1 st Bioinforma0cs training from 18 th to 29 th August: par0cipants from partner ins0tu0ons

16 Summary This is a joint ini0a0ve between AOCC and Bio- Innovate Most contribu0ons are in- kind given the expensive nature of WGS Strong capacity building component Most proposed ac0vi0es should be completed by end of year Purely Africa- driven

17 Acknowledgement

18 Thank You