Understanding the genetic control of flowering time to create adapted and high yielding narrow-leafed lupins

Transcription

1 Understanding the genetic control of flowering time to create adapted and high yielding narrow-leafed lupins Candy Taylor UWA School of Agriculture and Environment

2 Acknowledgements Supervisors Prof Wallace Cowling Dr Matthew Nelson Dr Lars Kamphuis Dr Jens Berger CSIRO Agriculture & Food Mr Gagan Garg Prof Karam Singh & lab group Berger lab group Funding GRDC (DAW00238) UWA School of Agriculture & Environment Mike Carroll Travelling Fellowship Farrer Memorial Trust Travelling Scholarship GRS Overseas Travel Award Research Training Program Stipend UWA Mr Robert Creasy Mr Bill Piasini Ms Weilu Zhang Dr Federico Ribalta Ms Simmone Wells Ms Sabrina Tischern Dr Janine Croser Ms Mahsa Mousavi Ms Anita Severn-Ellis Dr Katia Stefanova Dr Philipp Bayer Prof Dave Edwards

3 Narrow-leafed lupin Break crop Pest and disease management Fixes nitrogen and mobilises phosphorus Pulse crop Excellent nutritional properties: High protein and fibre Gluten free, low GI and fat content Livestock and aquaculture feed Emerging as a human health food

4 Lupin production in Australia Global production = 1.3 million tonnes Ukraine Germany 2% 4% Morocco 5% Other 8% WA produces 70-80% of Australia s lupins Russian Federation 14% Poland 16% Australia 51% Northern WA wheatbelt produces the majority

5 We need early flowering in Northern WA Short season environments Lupins are the only break crop option for sandy and acidic soils WA Lupin Agzones Need early flowering to escape terminal drought

6 But we don t need early flowering elsewhere in Australia Long season environments (LSE) WA Lupin Agzones Alternative break crops are more profitable Lupins flower too early to capitalise on favourable climatic conditions

7 Later flowering varieties could help increase lupin adoption CSIRO modelling indicates later flowering is needed in LSE environments in southern WA and the eastern states 15 day delay = 7% yield increase in LSE 22 day delay = 16% yield increase in LSE

8 Goal of my research To find new genetic variation for flowering time To help us breed later flowering, better adapted, higher yielding crops in LSE To help make lupins a viable option for ALL production areas in Australia

9 Three approaches 1. Characterise the main early flowering time gene in Australian crops 2. Map an intermediate flowering time gene 3. Explore genome-wide variation for flowering time

10 1. Characterising the main early flowering time gene in Australian crops

11 Background LanFTc1 is the main gene controlling flowering time in lupin Vernalisation: prolonged exposure to cold temperatures that induces flowering ku = vernalisation responsive and flowers too late

12 No (or partial) vernalisation in ku types can create undesirable phenotypes

13 Background LanFTc1 is the main gene controlling flowering time in lupin Vernalisation: prolonged exposure to cold temperatures that induces flowering ku = vernalisation responsive and flowers too late Ku = vernalisation unresponsive and flowers early Are there more variations of LanFTc1?

14 LanFTc1 at the molecular level 5 5 Regulatory Region CDS 3 ku Ku Jul Kb Kb Kb 5 3

15 LanFTc1 variants are associated with different flowering times Variant Vernalised (days) 0 Kb ku Kb Ku Kb Jul Kb 49

16 LanFTc1 variants are associated with different flowering times Variant Vernalised (days) Non-vernalised (days) Difference (days) 0 Kb ku *** Kb Ku *** Kb Jul *** Kb *** 18

17 LanFTc1 variants are associated with different flowering times Variant Vernalised (days) Non-vernalised (days) Difference (days) 0 Kb ku *** Kb Ku *** Kb Jul *** Kb *** 18 This is valuable variation for medium-high rainfall LSE

18 LanFTc1 variants are associated with different gene expression profiles 45 Non-vernalised 40 Relative gene expression (log2 scale) bp deletion 0 V 0 Quad Kb (ku) 1.4 V Quad Sampling time (degree-days)

19 LanFTc1 variants are associated with different gene expression profiles 45 Non-vernalised 40 Relative gene expression (log2 scale) Kb (ku) Sampling time (degree-days)

20 LanFTc1 variants are associated with different gene expression profiles 45 Non-vernalised 40 Relative gene expression (log2 scale) Kb (ku) 1.4 Kb (Ku) Sampling time (degree-days)

21 LanFTc1 variants are associated with different gene expression profiles 45 Non-vernalised 40 Relative gene expression (log2 scale) Sampling time (degree-days) 0 Kb (ku) 1.4 Kb (Ku) 5.2 Kb (Jul)

22 LanFTc1 variants are associated with different gene expression profiles 45 Non-vernalised 40 Relative gene expression (log2 scale) Kb (ku) 1.4 Kb (Ku) 5.2 Kb (Jul) 1.2 Kb Sampling time (degree-days)

23 1. Characterising the main early flowering time gene in Australian crops Summary 1. We found two new variations of LanFTc1 that affect flowering time 2. The first variant (Jul) is very early, like Ku 3. The second variant delays flowering by 2.5 weeks relative to Ku and is valuable for breeding

24 2. Mapping an intermediate flowering time gene

25 Background efl is another gene that facilitates mid-late flowering We don t know where it is found in the genome or what the underlying gene is Knowing these things can help us manage flowering time using marker-assisted selection

26 Broadly mapping efl using an F2 population Chittick (efl) X Geebung (Efl) F2 F2 F1 F2 F2 F2

27 Broadly mapping efl using an F2 population Frequency Chittick (efl) Geebung (Efl) efl-like bulk Efl-like bulk Days to flowering

28 efl maps to chromosome Kb region 9 genes 1 flowering-related 757 Kb region 48 genes 2 flowering-related ΔSNP-index Chromosome position

29 Next step? Fine mapping using a more powerful population Speed breeding: 7 months months per generation

30 2. Mapping an intermediate flowering time gene Summary 1. We have broadly mapped efl to chromosome We are about to complete fine mapping in an F6 population

31 3. Exploring genome-wide variation for flowering time

32 Background The only flowering time genes we know of and use in breeding are LanFTc1 (Ku and Jul) and efl How much other variation exists (with and without vernalisation) in cultivars and wild populations? Which parts of the genome are associated with this variation?

33 Measuring species-wide diversity in 380 narrow-leafed lupins Vernalisation treatments: full (4 weeks) and mild (1 week)

34 There is plenty of flowering time variation in wild germplasm (Early) AUS Full vernalisation (Late) Mild vernalisation (Early)

35 There is plenty of flowering time variation in wild germplasm (Early) Australia Poland AUS POL Full vernalisation ku efl Ku, Jul (Late) Mild vernalisation (Early)

36 There is plenty of flowering time variation in wild germplasm (Early) Australia Spain AUS ESP POL PRT Poland Portugal Full vernalisation ku efl Ku, Jul (Late) Mild vernalisation (Early)

37 There is plenty of flowering time variation in wild germplasm (Early) Australia Spain France AUS ESP FRA ITA POL PRT Poland Portugal Italy Full vernalisation ku efl Ku, Jul (Late) Mild vernalisation (Early)

38 There is plenty of flowering time variation in wild germplasm (Early) Australia Spain France Greece AUS ESP FRA GRC ITA POL PRT Poland Portugal Italy Full vernalisation ku efl Ku, Jul (Late) Mild vernalisation (Early)

39 There is plenty of flowering time variation in wild germplasm (Early) Australia Spain France Greece AUS ESP FRA GRC ISR ITA POL PRT Poland Portugal Italy Israel Full vernalisation ku efl 1.2 Kb del Ku, Jul (Late) Mild vernalisation (Early)

40 There is plenty of flowering time variation in wild germplasm (Early) Australia Spain France Greece Morocco AUS ESP FRA GRC ISR ITA MAR POL PRT Poland Portugal Italy Israel Full vernalisation ku efl 1.2 Kb del Ku, Jul (Late) Mild vernalisation (Early)

41 3. Exploring genome-wide variation for flowering time Summary 1. The narrow-leafed lupin germplasm collection has diverse flowering times 2. Genome-wide association analyses are underway to find new genes responsible for flowering time control

42 Take home message Understanding the genetic control of flowering time can help improve crop adaptation and yield potential for ALL Australian production areas