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FR-H3: A New QTL to Assist in the Development of Fall-Sown Barley with Superior Low Temperature Tolerance.

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Presentation on theme: "FR-H3: A New QTL to Assist in the Development of Fall-Sown Barley with Superior Low Temperature Tolerance."— Presentation transcript:

1 FR-H3: A New QTL to Assist in the Development of Fall-Sown Barley with Superior Low Temperature Tolerance

2 Outline Introduction Germplasm Linkage Maps Phenotyping & QTL Analysis Conclusions and Implications

3 Introduction

4 Fall-Sown Malting Barley New to the U.S. Two varieties approved by AMBA ◦Both two-row, lack LTT 49% malting barley planted has been six- row over the past 5 years Most selection has been done within a spring growth habit framework Advantages ◦Higher Yielding ◦Conserves Water

5 Adaptation to Target Regions Winter Hardiness Disease Resistance

6 Winter Hardiness Complex Trait Vernalization Sensitivity Photoperiod Sensitivity Low Temperature Tolerance

7 Vernalization Sensitivity The requirement of a period of low temperature in order to transition from the vegetative to reproductive state

8 Photoperiod Sensitivity Flowering is dependent on sufficient day length ◦Short Day ◦Long Day

9 Low Temperature Tolerance The capacity to survive low temperatures Induced response Reduced after reproductive transition

10 Defined by LTT, VS, & PS Winter ◦Varying LTT, VS, PS varies Facultative ◦Varying LTT, No VS, PS varies Spring ◦Lack LTT and VS, Short PS irrelevant Growth Habits

11 Winter Hardiness: VS Winter Genotype: Vrn-H2_/vrn-H1vrn-H1/vrn-H3vrn-H3

12 Winter Hardiness: PS PPD-H1 ◦Recessive Allele Insensitivity to long photoperiods PPD-H2 ◦Deletion Short PS

13 Winter Hardiness: LTT FR-H1 ◦VRN-H1? FR-H2 ◦≥11 C-repeat binding factor genes ◦Copy number variation

14 Low Temperature Tolerance Studies FR-H1 first reported Dicktoo x Morex (Hayes et al. 1993) FR-H2 discovered Nure x Tremois (Francia et al. 2004) FR-H1 and FR-H2 validated through GW- AM (von Zitzewitz et al. 2011) Galiba et al Skinner et al Francia et al Stockinger et al Galiba et al. 2009

15 Is LTT due only to FR-H1 and FR- H2 or are there other, undiscovered determinants of this critical trait?

16 Resistance to Biotic Stresses Barley Stripe Rust ◦Incited by Puccinia striiformis f. sp. hordei ◦Prominent in Pacific NW  First reported in Oregon in 1995 ◦Spread by wind QTL and Genes Identifies Chen et al Hayes et al Toojinda et al Castro et al Vales et al Rossi et al. 2006

17 Scald ◦Incited by Rhynchosporium secalis ◦Spread by splashing rain ◦Reduce functional green leaf tissue on plant Many Genes and QTL identified Fungicides effective but more effective to deploy resistance genes Pyramiding resistance genes ◦Effective and durable Resistance to Biotic Stresses Abbott et al Garvin et al Jensen et al Cheong et al Li and Zhou 2011

18 Overall Scheme Two doubled haploid populations Genotyping ◦Custom 384-OPA Linkage Maps (JoinMap 4) Phenotyping ◦LTT ◦VS (FT & FLN) ◦BSR ◦Scald QTL analysis (Windows QTL Cartographer) Pooled data when appropriate

19 Germplasm Two doubled haploid populations (half-sibs) ◦NB3437f/OR71 (N=111) and NB713/OR71 (N=124) OR71 ◦Facultative, Moderate LTT, BSR resistant, good malting quality NB3437f ◦Facultative, High LTT, BSR susceptible, poor malting quality NB713 ◦Winter, High LTT, BSR susceptible, poor malting quality

20 NB3437f NB3437 bulk seed lot grown <1% flowered without vernalization VRN-H2 deletion confirmed

21 Genotyping Parents previously genotyped with Barley OPA 1 & 2 (Barley CAP) ◦3,072 SNPs total Custom 384-OPA ◦Barley consensus map (Close et al. 2009) ◦Maximize polymorphism, genome coverage, focus on specific regions/genes of interest  Concurrent MAS study

22 Linkage Mapping NB3437f/OR71 (220 SNPs) NB713/OR71 (217 SNPs) Combined population (157 SNPs)

23 NB3437f/OR71 3_ _ _ _ _08391_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ H2H 3H4H5Ha6H7H 5Hb 5Hc 5Hd 5He

24 NB713/OR71 2_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _0510 2_0974 3_0385 1_1233 2_1210 3_0889 3_0006 3_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ H2H 3H4H5Ha6H7Ha 5Hb 7Hb

25 Combined Population 2_ _ _ _ _ _ _ _ _0293 1_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Hb 2_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ H2H 3H4Ha5Ha6H7H 5Hd 4Hb 3_ _ Hc

26 Phenotyping LTT ◦Controlled Environment  MRI ◦Field Conditions  SPMN, LNE, FCCO, FMT Final Leaf Number ◦GH: V+/V- Flowering Time ◦GH: V+/V- ◦Field: COR Disease Resistance ◦BSR and Scald  COR

27 LTT: MRI and SPMN

28 LTT: LNE & FCCO

29 LTT QTL Results FR-H3 FR-H2 VRN-H2

30 5H and MRI QTL Scans

31 Final Leaf Number

32 FLN QTL Results VRN-H2 VRN-H3 VRN-H2

33

34 Flowering Time

35 FT QTL Results VRN-H3 VRN-H2 PPD-H2

36 Disease: BSR and Scald

37 BSR & Scald QTL Results Rps4 Rrs15 Rrs2

38 Combined Population QTL Analysis VRN -H3 Rps4 FR-H3 FR-H2

39 Conclusions and Implications

40 LTT: Challenges and Opportunities Assessing LTT is challenging Lowest Temperatures ◦SPMN: -27°C; LNE: -26°C; FCCO: -25°C; FMT: -32°C; MRI: -13.5°C  No Survival at FMT  Nearly complete survival FCCO Other factors Controlled Freeze Tests $$ SPMN has been informative

41 FR Loci Expectations FR-H1 ◦~24cM region between flanking markers  All parents monomorphic within 5 cM (n = 27 markers) FR-H2 ◦Expected QTL  Marker polymorpisms  Differences in LTT ◦Complicated by 5H fragmentation

42 5H Fragmentation Chromosome rearrangements ◦e.g. Inversion Copy Number ◦CBF genes related to degree of LTT (Stockinger et al. 2007) Heterozygosity in Parents ◦Genotyping of parents revealed no heterozygosity ◦Multiple plants used for crossing not all were genotyped ◦Retention of heterozygosity? High density mapping, cytogenetics

43 FR-H3 Discovery Genetic basis of superior LTT in NE unknown: necessary for molecular breeding Previous Reports on 1H (Hayes et al. 2003) ◦Dicktoo x Morex  Pleiotropic effect of PPD-H2  PPD-H2 distal to FR-H3 SPMN ◦Additive effect of 29% in combined population

44 Vernalization Sensitivity: validation and discovery Role of VRN-H2 Confirmed ◦NB3437f x OR71  All progeny flowered under V- conditions  VRN-H2 deletions ◦NB713 x OR71  Segregated for VS  VRN-H2 presence/absence

45 Unexpected role of VRN-H3 Variation in exotic germplasm Wong ◦Released: China 1941 ◦Pedigrees of NB3437f & NB713 NE contributed the early flowering allele VRN Model ◦Recessive vrn-H3 required for VS ◦Dominant Vrn-H3 flowers very early ◦NB713 has VS  alternative recessive allele ◦Recessive allele triggered only under long days Vernalization Sensitivity: validation and discovery

46 LTT and VS: uncoupled NB3437f x OR71 and NB713 x OR71 similar LTT values NB713 x OR71 ◦High survival with and without VS ◦VRN-H2 QTL was detected in MRI  VS may have delayed vegetative to reproductive transition through critical times

47 NB713 x OR71: Facultative Vs. Winter

48 BSR Resistance First report in fall-sown barley background Resistance donors ◦Kold or Strider  Winter six-rows released by OSU  Effective resistance since BSR first reported in the area in 1995 Large-effect QTL on 1H ◦58-88% variation Favorable 1H LTT and BSR alleles in repulsion ◦Progeny with high survival and BSR resistance ◦~20 cM apart in combined map

49 Combined Population QTL Scan

50 Scald Resistance All parents have some resistance ◦Selected for “field resistance” NB3437f x OR71 ◦Favorable alleles on 4H and 7H contributed by NB3437f NB713 x OR71 ◦Favorable alleles on 2H and 7HL contributed by OR71 Results confounded by year effect ≥4 loci segregating

51 Prospects for Disease Resistant, LT Tolerant Fall-Sown Barley Fall-sown barley advantages ◦e.g. Yield and water conservation Pre-requisites ◦Sufficient LTT, disease resistance, grain with a premium Assessment of malting quality not possible ◦BSR (COR) and LT injury (SPMN)

52 OrNe Germplasm Continuation Used in crossing ◦LTT and scald resistance Limited number incorporated in breeding program ◦OBELT Included in association mapping panel in the TCAP (http://triticeaecap.org/) ◦Assessed for multiple phenotypes including malt quality

53 Final Thoughts Multitude of favorable alleles discovered for future MAS and GS schemes Newly discovered FR-H3 and superior Nebraska FR-H2 ◦Targets for LTT introgression Finding undiscovered QTL shows that the search for more LTT QTL should continue as well as identifying candidate genes and causal polymorphisms

54 Acknowledgements OSU Barley Project ◦Patrick Hayes ◦Alfonso Cuesta-Marcos ◦Ann Corey ◦Tanya Filichkin ◦Yada Chutimanitsakun ◦Natalie Graham Committee Members ◦Glenn Howe, Tony Chen, James Hermes Collaborators ◦CSIS: Luis Cistue ◦UNL: Stephen Baenziger ◦UM: Kevin Smith ◦Anheuser-Busch: G. Hanning, J. Heward ◦MRI: Ildikó Karsai, Zoltan Bedo ◦JHI: J. Russell, Robbie Waugh USDA/AFRI

55 Questions

56 Are You Feeling OrNe Baby?


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