Is faba bean on the threshold of a golden era of gene identification?

Transcription

1 School of Agriculture, Policy and Development Is faba bean on the threshold of a golden era of gene identification? Donal O Sullivan 29 th January 2015, Copenhagen University of Reading

2 In brief Why faba bean? It s not all genetics. But it is, really.. An entirely SNP-based consensus map for faba bean Exploitation of simple patterns of synteny with Medicago Mutagenesis 2

3 Why faba bean? 1. Faba bean is the broadacre grain legume best placed (in UK) to provide: sustainably produced protein for food and feed return N to soil in a sustainable rotation 2. We have identified several researchable topics that can be readily addressed IF we have the right tools to do so. Stem nematode resistance More reliable pod set Nutritional quality For humans (VC) For animals (protein content, aa comp, low tannins) Herbicide resistance

4 We are addicted to Haber-Bosch N From: Erisman et al (2008) Nature Geoscience

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6 Erith (1930) Genetica 6

7 Hc hc Erith (1930) Genetica 7

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9 SNP DISCOVERY

10 23.2k contigs ALBUS nematode-susceptible white flower 454 sequence of RNA From 10-day old seedlings Alignment of 14k gene transcripts present in both lines to Mt3.5 predicted CDSs 26.7k contigs BPL10 nematode resistant normal flower 40,000 putative SNPs >ALBUS AGGACTTGTACGTACG >BPL10 AGGACATGTACGTACG >Mt3.5 ACGACTTGTAGGTACG 888 new KASPAR assays designed Validation on 37 reference lines

11 MAPPING

12 Populations used ALBUS x BPL10 (anchor) 136 F 2 s Segregates for white flower (zero tannin) NV657 x NV F 2 s Segregates for ZT NV644 x NV F 2 s Segregates for dwarfism, hilum colour, ZT NV639 x NV F 2 s Segregates for closed flower mutation Mélodie x ILB F4s Segregates for stipule spotting, hilum colour and vicine-convicine Côte D Or/1 x BPL4628/ RILs Segregates for frost tolerance Call rate across pops ranged from 98-99%

13 A consensus faba bean SNP linkage map 687 high quality SNPs mapped Map length 1,404 cm 6 linkage groups = haploid chromosome number each LG cross-linked to previous gene-based maps Chr Mt synteny # Markers Map length (cm) I 2>7>6> II 3> Mapped traits Cf vc, Hc SSP1 Zt1 qsd,qct Webb et al (2015) Plant Biotechnology Journal, in press References unpublished Khazaei et al (2015) Mol Breed; Khazaei et al (2014) Mol Breed Webb et al (2015) Plant Biotech J; Khazaei et al (2014) TAG III ; IV 4>8> Sc Khazaei et al (2014) TAG V 7>5> Dwf1 unpublished VI 8> qsw Khazaei et al (2014) TAG

14 SYNTENY

15 From Choi (2004) PNAS 15

16 Mt1 Vf1 (4) Mt2 Vf2 (2) Mt3 Mt4 Vf3 (1) Mt5 Mt6 Mt7 Vf4 Vf5 (2) (3) Mt8 Vf6 (2)

17 Faba Medicago Lentil synteny Vf2 = Mt2 = Lc3 Vf5 = Mt7 = Lc6 17

18 ALBUS white flower BPL10 normal flower? The Vicia faba orthologue of the WD40 TF AtTTG1/Pisum A2 gene is a good positional and biological candidate for ZT

19 VfWD40-1 = ZT1 PCR BPL10 Zt1 normal flower ALBUS zt1 white flower Genome walking ALBUS (zt1) 19

20 Vicine and convicine anti-nutritional compounds Causes favism in G6PD-deficient humans (400 million worldwide) Lowers weight gain and egg weight/number in laying hens 20

21 How much VC in our germplasm? Mélodie/2 Betty Disco ILB938/2 Mélodie/2 x ILB938/2 RIL (Khazaei & Stoddard) Khamassi et al (2013) PGRCU 21

22 qv-c qc qv Linked Vc and Hc loci Vf_Mt2g005900_001 Vf_Mt1g083330_001 Vf_Mt2g007220_001 hc Hc 4.4 Vf_Mt2g010740_001 Vf_Mt2g010880_ HC 12.5 Vf_Mt2g015010_001 Vicine Convicine Vicine-convicine 26.3 Vf_Mt2g021130_ Vf_Mt2g026550_ Vf_Mt2g028620_ Vf_Mt2g030200_ Vf_Mt2g033460_001 Khazaei et al, 2015, Mol Breed, online 22

23 Mt2 kb SNP mining in the VC region

24 New validation populations for VC Hedin/2 x Disco 167 x F2 Albus/3 x Disco 150 x F2 Disco x NV x F2 Disco x NV x F2 Hedin/2 x Betty/3 41 x F2 Total 539 F2s 24

25 MUTAGENESIS

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27 Hedin/2 inbred line ~Medium-small seeds Spring habit Highly autofertile Highly inbred Summer 2013 multiplication 2x pollinator-free cages Isolation distance 2 x single inbred plant progenies 300 plants total c. 25,000 seeds 27

28 Mutagenesis next steps Spring 2014 >10,000 M 0 harvest bulk of >1,000,000 M 1 Spring 2015 screen batches of 50,000 M 2 using a high density seedling screen every 10 days Herbicide targets amidosulfuron (Bayer Eagle) TBC 28

29 Sebastien 1992 sulfonylurea-resistant soybean patent 29

30 Acknowledgements: University of Reading Laurence Hansen, Caroline Hadley, Deepti Angra NIAB Jane Thomas, Amanda Cottage, Anne Webb, Krystyna Gostciewicz, Douglas Hobbs Visiting Scientist (INAT,Tunisia) - Khalil Khamassi Wherrys - Peter Smith NPZ-Lembke Olaf Sass Collaborators Ana Maria Torres (IFAPA), Wolfgang Link (Goettingen), Fred Stoddard (Helsinki), Gérard Duc (INRA-Dijon), Fouad Maalouf, Francis Ogbonnaya (ICARDA), Mahmoud Zeid (Alexandria)

31 THANK YOU! TAK!