Improving barley and wheat germplasm for changing environments

Transcription

1 AWARD NUMBER: Improving barley and wheat germplasm for changing environments Triticeae CAP (T-CAP) 56 participants, 28 institutions, 21 states

2 Integration of wheat and barley research communities The T-CAP includes: 56 participants 28 institutions 21 states. Most have previous experience in the BarleyCAP and WheatCAP projects States with former BarleyCAP and WheatCAP programs States with WheatCAP programs States with BarleyCAP programs Project-wide resources and activities Genotyping labs, SNP development, KS also GBS National Small Grain Collection Database, web resources & tools Project direction Education coordination Industry liaison coordination

3 Objectives Discover and deploy beneficial alleles from diverse wheat and barley germplasm (NSGC cores and elite materials). Accelerate breeding through marker-assisted selection and genomic selection. Implement sequence-based genotyping methodologies to discover new allelic diversity. Implement web-based tools to integrate marker-assisted selection and genomic selection strategies into breeding programs. Develop and implement a Plant Breeding Training Network to train the next generation of plant breeders.

4 Management structure

5 Germplasm and populations Objective 1: Discover and deploy beneficial alleles from diverse wheat and barley germplasm Barley and wheat NSGC cores 2,571 H. vulgare; 4,231 wheat (hexaploid and tetraploid) accessions Five NAM populations Barley and wheat elite AM panels Collaborative winter wheat breeding populations Wheat and barley breeding program germplasm Wild barley introgression population Specialized genetic stocks and populations (NILS and RILs)

6 Wheat core collection NSGC 3129 Triticum aestivum subsp. aestivum 6x BA u D Domesticated, Free threshing 11 Triticum aestivum subsp. compactum 6x BA u D Domesticated, Free threshing 11 Triticum aestivum subsp. sphaerococcum 6x BA u D Domesticated, Free threshing 9 Triticum aestivum subsp. macha 6x BA u D Domesticated, Hulled 130 Triticum aestivum subsp. spelta 6x BA u D Domesticated, Hulled 1 Triticum vavilovii 6x BA u D Domesticated, Hulled Triticum turgidum subsp. durum 4x BA u Domesticated, Free threshing 61 Triticum turgidum subsp. turgidum 4x BA u Domesticated, Free threshing 13 Triticum turgidum subsp. carthlicum 4x BA u Domesticated, Free threshing 26 Triticum turgidum subsp. polonicum 4x BA u Domesticated, Free threshing 22 Triticum turgidum subsp. turanicum 4x BA u Domesticated, Free threshing 83 Triticum turgidum subsp. dicoccon 4x BA u Domesticated, Hulled 3 Triticum turgidum subsp. paleocolchicum 4x BA u Domesticated, Hulled 3 Triticum ispahanicum 4x BA u Domesticated, Hulled 89 Triticum turgidum subsp. dicoccoides 4x BA u Wild, Hulled 19 Triticum timopheevii subsp. armeniacum 4x GA u Wild, Hulled 25 Triticum timopheevii subsp. timopheevii 4x GA u Wild, Hulled Seed increases from single plants were grown and phenotyped in ID Aberdeen for height and heading time.

7 Barley core collection NSGC all H. vulgare Growth habit Spike Source 2,100 spring; 376 winter; 95 facultative 639 two-row; 1,213 six-row; 46 mixed; 673 no data 1,033 cultivars & breeding lines; 1,150 land races; 31 genetic stocks; 357 undetermined. Total 2,571 accessions from 105 countries and regions Seed increases from single plants ( 2500) were grown and phenotyped in ID for height and heading time. This project will change the paradigm of how we utilize germplasm resources for barley and wheat improvement from a view centered on the characterization of accessions to one centered on the discovery and deployment of valuable alleles

8 96 Accessions Barley NAM 200 Accessions in total Capture 86% of polymorphisms with MAF 0.01 Baronesse Rasmusson 96 Accessions 2-row Elite 6-row Elite 96 Lines / Pop 8 Accessions chosen for diversity Test allele x background interaction

9 25 Accessions Wheat NAM 75 Accessions in total (selected based on diversity) Capture polymorphisms with MAF Accessions Spring Elite Hard Winter 100 Lines / Pop. Start with ~300 Trim height and heading date extremes Soft Winter 25 Accessions

10 Association mapping populations BARLEY AM POPULATIONS Spring six-row barley: 256 advanced breeding lines and cultivars -Developed and genotyped. Will be evaluated for NUE, WUE and yield. Spring two-row barley: 256 advanced breeding lines and cultivars -Developed and genotyped. Will be evaluated for NUE, WUE and yield. Winter six-row barley: 256 advanced breeding lines and cultivars -Developed and genotyped. Will be evaluated for NUE, WUE and yield. Barley LTT panel: 384 lines from international collections WHEAT AM POPULATIONS Spring wheat: 300 lines for drought tolerance (10% in common with CIMMYT AM and 10% Canada AM). Wheat diseases: 384 lines for leaf rust and 384 lines for stripe rust. Hard winter wheat: 300 hard wheat lines. NUE, WUE and yield. Soft winter wheat: 300 soft wheat lines. NUE and yield

11 Cooperative Winter Wheat Breeding Present uniform tests: Evaluate lines over environments Genomics era tests: Evaluate alleles & genetic models over environments, programs, genetic backgrounds 3 adaptation regions, each with 4 breeding programs, each contributing 200 lines. Test own 50 lines & 150 exchanged lines. Provides large pops, leverage all phenotyping of breeding, genetic variation. Each program accesses alleles from other programs that may be rare in theirs. A C B D Example: equal exchange among four programs. Each arrow is exchange of 50 lines

12 Other germplasm and populations BARLEY Wild barley introgression population 900 BC 2 lines derived from 25 wild barley accessions crossed to Rasmusson Otis (drought tolerant) x Garnet (drought susceptible) RIL population (200 lines) WHEAT Isogenic lines: for stem solidness, long grain fill period, Rht8 height, 1RS rye translocation Wild Triticeae introgressions in wheat: 300 alien Triticeae translocation and substitution lines into Chinese Spring wheat Wheat Backcross RILs for drought tolerance BC 2 from C306 (drought tolerant)/2*pbw534 Hexaploid x tetraploid RIL Choteau (6x) x Mountrail (4x)

13 Traits Disease resistance Barley and wheat stem, stripe and leaf rust Barley spot blotch & spot-form net blotch Water and Nitrogen use efficiency, yield Regular agronomic traits Protein (and minerals) Canopy spectral reflectance (heading + grain filling) WUE productivity under water stress / non-stressed conditions. NWI-1 (R970 R900)/(R970+R900), NWI-3 (R970 R850)/(R970+R850) CID (carbon isotope discrimination) Biomass: NDVI (R900 R680)/(R900+R680)] NUE productivity under N limiting/ non-stressed conditions Protein content Sdr /Sdv (need 680/760 and 490/530) complex formula GPC-B1 LTT (barley only)

14 LD in Wheat and Barley LD in barley LD in wheat Barley: 2010 Hamblin et al. Crop Science 50% decay 2-4 cm (1816 lines, 1536 SNP) (6cM in OR) Wheat: 2010.Akhunov et al. BMC Genomics 50% decay 6-9 cm, (478 lines, 1536 SNP) Barley genetic map ~ 1250 cm (3000 SNPs provides ~2-3 SNP/cM; 9,000 SNPs provides ~7SNPs/cM; GBS provides many more SNPs/cM) Wheat genetic map ~ 3500 cm (3000 SNPs provides ~1 SNP/cM; 9,000 SNPs provides ~3 SNPs/cM; GBS provides many more)

15 Genotyping 48 SNP platforms for MAS 384 SNP platforms for GS and barley NAM populations 9,000 SNP platforms for NSGC cores, elite wheat panels, and barley low temperature tolerance panel 1536 SNPs plus genotyping by sequencing for spring wheat NAM, collaborative winter wheat programs Genotyping by sequencing for NAM parents and winter wheat NAM populations Gene capture for selected accessions of the wheat and barley NSGC cores

16 The Hordeum Toolbox (Developed by barley CAP) Data: Trait SNP marker Maps Pedigrees Lines Data is accessible using a variety of queries Data download for TASSEL and FLAPJACK Database is web accessible Hosted by GrainGenes

17 T3: The Triticeae Toolbox Database hosted by GrainGenes Personnel and activities: Project curator will monitor data quality and provide support to participants Web site programmer will develop the web site capabilities, interface data analysis and manipulation tools useful to breeders Database programmer will develop and implement data visualization tools, test new applications and develop new algorithms for AM and GS

18 Marker Assisted Selection

19 Genomic (Genome-Wide) Selection

20 Genomic selection Advance lines informative for model improvement (Training population) Test varieties and release Advance lines with highest GEBV Phenotype (lines have already been genotyped) Model Training Cycle Updated Model Genomic Selection Line Development Cycle Make crosses and advance generations Train prediction model Genotype selection candidates New Germplasm Heffner, Sorrells, Jannink, Crop Science 2009

21 NSGC barley/ wheat cores Elite barley panels Elite wheat panels Winter wheat cooperative breeding Specialized stocks and populations Barley LTT panel Wild barley introgression lines Phenotyping Genotyping (SNP and gene capture) Phenotyping Phenotyping SNP genotyping T3 database Phenotyping SNP genotyping T3 database Phenotyping SNP genotyping T3 database Phenotyping Phenotyping SNP genotyping T3 database T3 database T3 database + GRIN NAM populations Association mapping train GS models Association mapping train GS models Linkage mapping Association mapping Phenotyping genotyping MAS and GS MAS NAM founders GBS T3 database Wheat breeding programs Barley breeding programs Association mapping and linkage mapping MAS GS Improved wheat and barley germplasm

22 Project funded by NIFA CAP grant