CALIFORNIA CROP IMPROVEMENT ASSOCIATION COMPREHENSIVE ANNUAL RESEARCH REPORT WHEAT BREEDING July 1, 2014 to June 30, 2015

CALIFORNIA CROP IMPROVEMENT ASSOCIATION COMPREHENSIVE ANNUAL RESEARCH REPORT WHEAT BREEDING July 1, 2014 to June 30, 2015 PROJECT TITLE: Development of wheat varieties for California PRINCIPAL INVESTIGATOR: Jorge Dubcovsky OTHER INVESTIGATORS: Oswaldo Chicaiza, Alicia del Blanco, Francisco Maciel, Marcelo Soria LEVEL OF 2014-2015 FUNDING: $97,000 (Regional Testing: $68,432) OBJECTIVES AND EXPERIMENTS CONDUCTED BY LOCATION TO ACCOMPLISH OBJECTIVES: This annual report is organized from the most advanced material evaluated in the regional trials, followed by the material evaluated in the elite, advanced and preliminary yield trials, observation plots, short rows screening nurseries, segregating generations and new hybrid combinations. VARIETY RELEASES Foundation seed: Breeder seed of the new hard red spring wheat UC1745 was delivered to the Foundation Seed Program to produce Foundation seed in the 2015 cycle. LINES IN REGIONAL TESTING Common wheat: The lines UC1768 and UC1769 were dropped from the regional trial for showing an unstable yield performance. The line UC1767 was the top yielding line in the regional trials but the bread quality was not satisfactory for the industry. Since it was the first year in the regional trial UC 1767 will be retested in 2015. Five new lines UC1789, UC1790, UC1791, UC1792 and UC1793 will be evaluated in the 2015 regional trial. Durum wheat: The line UC1758 was dropped from the regional trial because of low yield performance. The lines UC 1756, UC1770 and UC1771 showed high yield performance and acceptable pasta quality but since all three are high Cd, none of these lines will be released until the low Cd gene will be incorporated. UC1770 and UC1771 will be retested in the 2015 regional trial. Four new lines UC1796, UC1797, UC1798 and UC1799 selected for showing high yield performance, good pasta quality and low Cd will be tested in the 2015 regional trial. 1

ELITE YIELD TRIALS The elite yield trials of common wheat included 32 breeding lines and three control varieties and were planted in Davis, Colusa and Kings. The elite yield trials of durum wheat included 32 breeding lines and three control varieties and were planted in Davis, Kings and Imperial Valley. The experiments in Colusa and Kings were handled by Phil Mayo and the trial at Imperial Valley was handled by Francisco Maciel. Common wheat: During the growing cycle, notes of heading date, disease severity (stripe rust, leaf rust, and septoria), plant height, lodging, and shattering were scored at each location. The variables grain yield, test weight, 1000 kernel weight, and grain protein content were measured after harvest. 13 lines were selected and one sample from each location was sent to the CWC laboratory for a complete quality analysis. Based on the agronomic data, disease scores, grain yield and quality data, four lines (14010/17, 20, 22, 29) will be tested in the elite and regional trials as UC1789, UC1790, UC1791, and UC1792. 12 lines will be retested in the 2015 elite trial. Durum wheat: After selecting for agronomic characteristics, disease resistance, yield performance, protein content, and grain appearance, 18 lines were selected and sent to the CWC laboratory for a complete quality analysis. Adding the quality parameters to the selection, 12 lines will be retested in the 2015 elite trial. ADVANCED YIELD TRIALS Common wheat: 86 breeding lines and 3 control varieties were evaluated in the 2014 advanced yield trials at Davis. After selecting for agronomic characteristics, disease resistance, yield performance, protein content, and grain appearance, 26 lines were selected and sent to the CWC laboratory for a complete quality analysis. One line 14014/42 will be tested in the elite and regional trials as UC1793. 18 lines were selected and included in the 2015 elite trial. Durum wheat: 33 breeding lines and two control varieties were evaluated in Davis. 60 low Cd breeding lines and seven control varieties were evaluated in Davis and Imperial Valley. After selecting for agronomic characteristics, disease resistance, yield performance, protein content, and grain appearance, 24 lines were selected and sent to the CWC laboratory for a complete quality analysis. The best four lines (14215/9, 11, 14, 42) were selected and included in the 2015 regional and elite trials as UC1796, UC1797, UC1798, UC1799. 12 lines were included in the 2015 elite trial. PRELIMINARY YIELD TRIALS Common wheat: 216 breeding lines and three control varieties were evaluated in three preliminary yield trials. After selection for agronomic characteristics, disease resistance, yield performance, grain protein content, and grain appearance, 84 lines were selected and will be evaluated in the 2015 advanced yield trials. Durum wheat: 142 breeding lines and three control varieties of durum wheat were evaluated in two preliminary yield trials; based on agronomic characteristics, disease resistance, yield 2

performance, grain protein content, and grain appearance, the best 72 lines were selected and included in the 2015 advanced yield trials. OBSERVATION PLOTS Common wheat: 875 breeding lines and three varieties of common wheat were evaluated in observation plots, after selection for agronomic characteristics, disease reaction, grain yield, grain appearance, and grain protein content; 171 lines were advanced to the 2015 preliminary yield trials. Durum wheat: 541 breeding lines and four varieties of durum wheat were evaluated in observation plots, after selection for agronomic characteristics, disease reaction, grain yield, grain appearance, and grain protein content; the best 140 lines were included in the 2015 preliminary yield trials. New introductions: 909 breeding lines of common wheat and 155 breeding lines of durum wheat from the CIMMYT program were planted as screening rows. After selection for agronomic characteristics, disease resistance, grain appearance and grain protein content, 154 lines of common wheat and 58 breeding lines of durum wheat were selected and advanced to the 2015 observation plots. Also, 1180 breeding lines of common wheat and 207 advanced breeding lines of durum wheat from CIMMYT were cleared through quarantine during the winter 2014 and planted in the field as screening rows in 2015. NEW HYBRIDS AND SEGREGATING POPULATIONS New Hybrids: 97 crosses among common wheat (Table 1) and 98 crosses among durum wheat (Table 2) were made in the winter of 2014, the F 1 seeds were planted at Tulelake during the summer and the F 2 populations will be evaluated in the field in the 2015 cycle. Segregating generations: F 2 generation: this generation included 181 populations of common wheat and 111 populations of durum wheat. After selection, 152 populations of common wheat and 88 populations of durum wheat were selected and advanced to the F 3 generation. F 3 generation of common wheat included 153 F 3 families. After selection, 123 families were advanced to the F 4 generation. The F 3 generation of durum wheat included 127 F 3 families. 4000 DNA samples from 69 F 3 families from crosses high Cd x low Cd were sent to the USDA laboratory in Pullman, WA to select lines having the gene for low Cadmium content. 1911 homozygous low Cd lines were identified. 35 F 3 families from crosses low Cd x low Cd was selected. All the selected lines were planted in the field as F 4 families. The F 4 generation of common wheat included 149 families. After selection, 103 families were advanced to the F 5 generation. 3

The F 4 generation of durum wheat included 147 families. After selection, 103 families were advanced to the F 5 generation. The F 5 generation of common wheat included 96 families. After selection, 79 families were advanced to the F 6 generation. The F 5 generation of durum wheat included 96 families. After selection, 71families were advanced to the F 6 generation. The F 6 generation of common wheat included 96 families. After the field selection, the grain of each line was evaluated for its appearance and grain protein content. Finally, 582 breeding lines were advanced to observation plots. The F 6 generation of durum wheat included 67 families. After the field selection, the grain of each line was evaluated for its appearance and grain protein content. Finally, 335 breeding lines were advanced to observation plots. 4

Table 1. Experiment 14000 crossing block common wheat (97 crosses) Entry pedigree source 1 2 25 27 29 30 31 32 33 34 35 1 UC1419 Yr5 Yr15 Gpc= UC1743 13010/17 2 UC1128 Yr5 Yr15 Gpc= UC1744 13010/18 x x 3 UC1110/UC1037 Gpc GLU= UC1745 13010/22 4 UC1110/UC1037 Gpc GLU= UC1767 13010/23 x x x x x x x x x 5 EXPRESS 2NS Yr15/IRANIAN Yr33= UC1768 13010/31 x x 6 UC1296/UC1417 = UC1769 13010/34 x x x x x x x 7 EXPRESS 2NS Yr15/UC1107 5+10 2NS 13013/38 x x x x x x x 8 UC1493/UC1419 13016/11 x x x x x 9 13017/16 x x 10 EXPRESS (2NS, Yr15,B15)/KERN Yr5, Lr47, Lr37 13017/24 x x x x 11 SUMMIT/EXPRESS 2NS, Yr15, B15 13017/50 x x 12 UC1478//MADSEN/2*EXPRESS 13018/5 x x x x x x x 13 UC1478//MADSEN/2*EXPRESS 13018/7 x x x x x x 14 UC1478//MADSEN/2*EXPRESS 13018/8 x x x x x 15 UC1107/IDO377S//UC1107/3/MADSEN/2*EXPRESS 13018/23 x x x x 16 UC1107/IDO377S//UC1107/3/UC1107 5+10 2NS Yr15 13018/29 x x x 17 UC1128 Yr15 B15/SUMMIT 13018/43 x x 18 PFAU/MILAN/3/BABAX/LR42//BABAX 13018/72 x x x x 19 IDO694c (needs stripe & prot) 13009/14 x x 20 ATOMO (UC1723) 13100/29 x x 21 LG 08SB0738 (UC1726) Phil x x 22 LG 08SB0008 B (UC1727) Phil x x 23 APB 770229 (UC1746) Phil x 24 APB 430701 (UC1747) Phil x x 25 KERN 515 HP 2NS 13100/30 26 LASSIK Yr5 13100/31 27 CLEAR WHITE 515 HP 2NS 13100/32 28 UC1107 5+10 Yr5 Yr15 2NS 13100/33 29 UC1110 5+10 Yr5 Yr15 Gpc 13100/34 30 Blanca Grande 515 Gpc 13100/37 x 31 Summit 515 13100/38 32 Blanca Fuerte Gpc 13100/39 x x 33 F7 3 5 2/3*UC1041 (03020/80) 2NS 11100/21 x 34 UC1037 Gpc 5+10 2NS Yr5 Yr15 Gpc (BC7F2) 05660/38 x 35 Clear White D w/vrnd1 only Hope FT allele Rebeca x 5

Table 2. Experiment 14200 crossing block durum wheat (98 crosses). Entry Pedigree source 18 19 20 21 22 23 24 25 26 27 28 29 30 1 UC1375/KOFA HP= UC1756 13210/3 2 UC1375/UC1408 13210/4 x X 3 PLATINUM/UC1408= UC1770 13210/5 x x 4 CROWN/UC1408 13210/16 x X x x 5 KOFA//UC1113/PLATINUM= UC1758 13210/20 x 6 KOFA//UC1113/PLATINUM= UC1771 13210/21 x 7 DESERT KING/UC1452 13216/9 x x x x x x x x x x x 8 KOFA Gpc/UC1504 13216/11 x x x x x x x x x x x x 9 UC1452/UC1429 13216/25 x x x x x x x x x 10 UC1504//DESERT KING 13216/40 x x x x 11 UC1504/UC1452 13216/41 x x x x 12 KOFA/UC1113//DESERT KING 13216/49 x x x x x x x x x x x 13 KOFA/UC1113//UC1452 13216/55 x x x x x x x x 14 BICHENA/PLATA//UC1429 13217/14 x x x x x SOMAT_3/PHAX 15 1//TILO_1/LOTUS_4/3/UC1489 13217/23 x x x 16 UC1489/UC1505 13217/52 x x x x x 17 UC1489//KOFA/UC1113 13217/59 x x x x 18 WWWD6523/UC1308 = UC1690 Miwok low Cd 13210/32 19 Tipai (low Cd) 13215/6 X 20 WWW D6523/UC1308= 12210/10 (low Cd) 13215/15 21 Desert King (low Cd) Gpc 7B 6A 2013/5 TL x 22 UC1308 2+12 (low Cd) =UC1689 13200/4 23 03E25070 (low Cd) 13200/5 24 APB D00 627 (low Cd) 13200/6 25 DT557 (low Cd) Canada 13200/7 26 Kronos (low Cd) BC5F3 13200/8 27 D99 425 (low Cd Gpc) 13200/9 28 Helios low Cd 13200/12 29 Kiko Nick (UC1697) 13200/44 x x x x x 30 Havasu x 31 APB D7 12 (UC1753) x x 6

MAS BACKCROSSING FOR BIOTIC AND ABIOTIC STRESSES Summary Marker assisted selection: Leaf samples from 7925 F 3 durum lines were sent to the USDA laboratory in Pullman, WA to select lines having the gene for low Cadmium content. A total of 1110 lines homozygous for the low cadmium allele were identified and will be evaluated as F 4 lines in 2014. In addition to the low cadmium gene we advanced the introgression of genes for improved yellow color, and for increased gluten strength and protein content. We also combined the genes for increased resistant starch in our top durum varieties. In the common wheat we continue the introgression of stripe rust and septoria resistance genes. We also initiated the incorporation of novel low molecular weight glutenins alleles for gluten strength and elasticity and transferred the increased resistant starch mutations to common wheat. We have initiated the transfer of two recently discovered genes to increase grain seize and yield under water stress Drought tolerance: We completed the combination of the rye 1RS distal segment associated with improved drought tolerance with the stripe rust resistance genes Yr15 and the strong gluten allele 7Bx-over-expressor (7Bx OE ). We are initiation backcrossing of the engineered chromosome into CA adapted wheat breeding lines. We continued the mapping of the resistance gene. This year we sequenced the complete 1RS arm and the 1RS arm with the distal wheat translocation. We are currently analyzing the large amount of sequencing. The manuscript Mapping a region within the 1RS.1BL translocation in common wheat affecting grain yield and canopy water status was published this year in Theoretical and Applied Genetics documenting our progress in this area. Increased grain size: We completed a study in collaboration with the John Innes institute in the UK where we identified a gene that increases grain weight in both durum and common wheat. The wheat gene TaGW2 functions as a negative regulator of grain weight, so the disruption of this gene results in increased grain weight. We screened our mutant population and identified mutants in the A genome copy TaGW2-A1. We backcrossed the mutant gw2-a1 allele into tetraploid and hexaploid wheat and generated a series of backcross derived isogenic lines which were evaluated in greenhouse and field conditions. Across 10 experiments the gw2-a1 mutant allele significantly increased thousand-grain-weight (6.5%) in tetraploid and hexaploid wheat compared to the wild type isogenic line. The increase in grain size width and length was consistent across grains of different sizes, suggesting that the effect of the gw2-a1 mutation is stable across the ear and within spikelets. A molecular marker was developed to accelerate the deployment of the gw2-a1 allele into our breeding program. Stripe rust: We completed and published a multiyear study to identify novel sources of resistance to the new virulent races of stripe in a worldwide collection of 1,000 spring wheat accessions. The lines were evaluated in six environments in western USA, including two environments in California. The study revealed higher levels of stripe rust resistance in accessions from Southern Asia, the likely center of origin of this pathogen. Results from this study provided an integrated view of global stripe rust resistance resources in spring wheat and identify new resistance loci that will be useful to diversify the current resistance genes deployed to control this devastating disease. We selected seven of the lines with new resistance alleles and crossed them to California varieties for validation. 7

We are also combining slow rusting genes, which are effective at the adult plant stage and do not provide a complete protection against the pathogen but are more durable. In this area we completed five backcrossing cycles for the introgression of Yr18, Yr36 and Yr48 into Yecora Rojo. Homozygous lines for the different combinations will be selected in 2015 and evaluated in 2015-2016. These partial resistance genes are being combined with race-specific stripe rust resistance genes Yr15 and Yr5. We introgressed the Gpc-B1/Yr36 gene combination in Patwin-515 and completed the preliminary evaluation of the isogenic line with promising results. Patwin 515-HP is being considered as potential replacement of Patwin-515. In a separate project we completed the combination of the low-ppo allele with the linked Yr5 Pst resistance gene. This new pair of genes is being combined in a Clear White + Yr5, Yr15, Yr36, and Yr17 low-ppo allele. Seeds are being increased. Septoria tritici: In this area we continue the deployment of the septoria tritici resistance genes Stb4 (from Tadorna ), Stb7 (from Estanzuela Federal ) and Stb3 from Israel 493. A manuscript was published in 2015 reporting the genetic mapping of Stb3 and the development of linked markers to accelerate selection. Stem rust Ug99: A new race of Puccinia graminis f. sp. tritici, the causal pathogen of stem rust of wheat, designated Ug99, and its variants, are virulent to plants carrying stem rust resistance genes currently deployed in most wheat cultivars worldwide. Therefore, identification, mapping and deployment of effective resistance genes are critical to reduce this threat. In 2014 we completed and published the mapping of the Ug99 resistance gene Sr21. Resistance gene Sr21 identified in diploid wheat T. monococcum is effective against races from the Ug99 race group. We screened four monogenic lines with Sr21 and four susceptible controls with 16 Pgt isolates including 5 isolates of the Ug99 race group under three different temperatures and three different photoperiods. We observed that temperature influences the interaction between monogenic lines with Sr21 and Ug99 race group isolates, and may be the source of previous inconsistencies. This result indicates that, although Sr21 is a useful tool against Ug99, its effectiveness can be modulated by environmental conditions and should not be deployed alone. Using two large diploid wheat-mapping populations (total 3,788 F 2 plants) we mapped Sr21 approximately 50 cm from the centromere on the long arm of chromosome 2A m within a 0.20 cm interval. The closely linked markers identified in this study will be useful to reduce the T. monococcum segments introgressed into common wheat, accelerate Sr21 deployment in wheat breeding programs, and facilitate the map-based cloning of this gene. We also completed the introgression of the Ug99 resistance gene Sr35 into common wheat. This gene confers immunity to Ug99. To avoid negative effects of linked regions we used ph1b induced homoeologous recombination to reduce the T. monococcum chromosome regions surrounding the gene. A line with a small introgression is being increased for germplasm release. 8

MAS BACKCROSSING FOR QUALITY GENES HMW glutenins: We continued the use of protein SDS-PPAGE to select lines with strong gluten by favoring the HMW glutenin allele 5+10 and 1 or 2* and discarding the lines with the 2+12 or Glu-A1 null alleles in common wheat. In durum wheat, instead, we are introgressing the 2+12 allele to replace the null Glu-A1. Alicia del Blanco is completing a manuscript reporting the agronomic and quality evaluations of isogenic lines with and without the 2+12 allele. LMW glutenin alleles: We completed and published a study to characterize the effect of nine isogenic lines carrying different LWM glutenin alleles that contribute to wheat breadmaking quality. Using DNA markers and a backcross program we developed a set of nine near isogenic lines including different alleles in the genetic background of the Argentinean variety ProINTA Imperial. The nine NILs and the control were evaluated in three different environments. Significant genotype-by-environment interactions were detected for most quality parameters indicating that the effects of the LMW glutenin alleles are modulated by environmental differences. None of the lines showed differences in total flour protein content. On average, the Glu-A3f, Glu-B3b, Glu-B3g and Glu-B3i Man alleles were associated with the highest values in gluten strength-related parameters, while Glu-A3e, Glu-B3a and Glu-B3i Chu were consistently associated with weak gluten and low quality values. We selected the best alleles in the A and B genome from the variety Buck Manantial and initiated introgression of these LMW-glutenin alleles in the top yielding California varieties with weak gluten (e.g. UC1767). High protein gene Gpc-B1: We completed the introgression of this gene into Patwin-515 and continued its introgression into selected lines with high yield potential but low grain protein content. The introgression of this gene in Patwin 515 was completed as described above. Low Cadmium durum: We used the perfect marker for the Cdu1 gene to select lines for the presence of the low cadmium allele in our advanced and segregating populations. A total of 7,925 durum lines were genotyped and lines with the low Cd allele were selected. Near isogenic lines of our top yielding varieties Desert King and Tipai with low Cd were completed and are under seed increase. We also continued the marker assisted backcrossing of this gene into our elite durum lines. The Cdu1 low cadmium gene is being combined with the increased resistance starch genes and with two QTL for improved yellow color in Desert King. Durum wheat yellow pigment: We completed the introgression of two QTLs for improved yellow pigment on chromosomes 6A and 7B identified in a previous study into Dessert King. A line combining the two QTL for yield and the low Cd allele is almost ready for seed increase. We continue the introgression of these two QTL in multiple lines of our breeding program that show excellent yield potential but weak yellow color. Increased resistant starch: Increased amylose in wheat starch is associated with increased resistant starch, a fermentable dietary fiber. Fermentation of resistant starch in the large intestine produces short-chain fatty acids that provide human health benefits. To increase amylose content in both hexaploid and tetraploid wheat we generated mutants for the Starch branching Enzyme II, SBEIIa and SBEIIb, which are responsible for the 9

addition of the starch branches. Tetraploid lines with mutations in both genes showed a 9- to 10-fold increase in resistant starch. In 2014 we evaluated effect of these mutations on agronomic characteristics and quality in pasta wheat. In three replicated field trials, the presence of these four mutations was associated with an average 5% reduction in kernel weight and 15% reduction in grain yield compared to the wild-type, suggesting that premium prices will be required to grow these special varieties. Complete milling and pasta quality analysis showed that the mutant lines have an acceptable quality with positive effects on pasta firmness and negative effects on semolina extraction and pasta color. Positive fermentation responses were detected in rats fed diets incorporating mutant wheat flour. This study quantified benefits and costs associated with the deployment of the SBEIIa/b-AB mutations in durum wheat. This information will help breeders to develop realistic strategies to deploy durum wheat varieties with increased levels of amylose and resistant starch. We are also transferring the double SBEIIa-SBEIIb mutations to hexaploid wheat varieties Lassik and Patwin to increase resistant starch in common wheat. GRANTS 2014 California Wheat Commission (2014). $275,000. Development and Evaluation of Wheat Varieties for California. USDA-CAP (ends 01/16). $5,000,000. Renewal fourth year TCAP grant BARD grant (ends 11/16) $149,000. Cloning a new stripe rust resistance gene. Gates foundation (ends 03/16) $138,000. Grant for cloning resistance genes to Ug99 and to deploy them in Ethiopian varieties. USDA-NRI NIFA grant (ends 08/16) $135,000. Grant to characterize the mechanism of action of Sr35. PUBLICATIONS 2014 Papers generated by our research project were referred more than 1250 times during 2014 documenting the increasing impact of our research worldwide. We published 13 research articles in wheat and 1 in barley in peer-reviewed scientific journals and produced the Agronomy Progress Report documenting the performance of barley and wheat varieties and breeding lines across different California environments. 10

Peer-reviewed publications Pearce, S., F. Tabbita, D. Cantu, V. Buffalo, R. Avni, H. Vazquez-Gross, R. Zhao, C.J. Conley, A. Distelfeld, and J. Dubcovsky. 2015. Regulation of Zn and Fe transporters by the GPC1 gene during early wheat monocarpic senescence. BMC Plant Biol. 14:368. Maccaferri, M., A. Ricci, S. Salvi, S. Milner, E. Noli; P. Martelli, R. Casadio, A. Eduard, S. Scalabrin, V. Vendramin, K. Ammar, A. Blanco, F. Desiderio, A. Distelfeld, J. Dubcovsky, T. Fahima, J. Faris, A. Korol, A. Massi, A. Mastrangelo, M. Morgante, C. Pozniak, S. Xu, R. Tuberosa. 2014. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnology Journal doi: 10.1111/pbi.12288 Howell, T., I. Hale, D. L. Jankuloski, M. Bonafede, M. Gilbert, J. Dubcovsky. 2014 Mapping a region within the 1RS.1BL translocation in common wheat affecting grain yield and canopy water status. Theor Appl Genet 127: 2695-2709. Wang, X., X. Wang, L. Deng, H. Chang, J. Dubcovsky, H. Feng, Q. Han, L. Huang, Z. Kang. 2014. Wheat TaNPSN SNARE homologues are involved in vesicle-mediated resistance to stripe rust (Puccinia striiformis f. sp. tritici). J. Exp. Bot. 65: 4807-4820. Nitcher, R., S. Pearce, G. Tranquilli, X. Zhang, J. Dubcovsky. 2014. Effect of the Hope FT-B1 allele on wheat heading time and yield components. J. Heredity 105:666-675. Hazard B., X. Zhang, M. Naemeh, J. Dubcovsky. 2014. Registration of Durum Wheat germplasm lines with combined mutations in SBEIIa and SBEIIb genes conferring increased amylose and resistant starch. J. Crop Reg. 8:334 338. Chen, A., C. Li,, W. Hu, M. Lau, H. Lin, N.C. Rockwell, S.S. Martin, J.A. Jernstedt, J.C. Lagarias, and J. Dubcovsky. 2014. PHYTOCHROME C plays a major role in the acceleration of wheat flowering under long days. Proc. Natl. Acad. Sci. U.S.A. 111:10037-10044. Henry I.M., U. Nagalakshmi, M.C. Lieberman, K.J. Ngo, K.V. Krasileva, H. Vasquez-Gross, A. Akunova, E. Akhunov, J. Dubcovsky, T. H. Tai, L. Comai. 2014. Efficient genome-wide detection and cataloging of EMS-induced mutations using next-generation sequencing and exome capture. Plant Cell 26:1382 1397 Lv B., R. Nitcher, X. Han, S. Wang, F. Ni, K. Li, S. Pearce, J. Wu, J. Dubcovsky, D. Fu. 2014. Characterization of FLOWERING LOCUS T1 (FT1) gene in Brachypodium and wheat. PLoS One 9:e94171 Zhu J., S. Pearce, A. Burke, D.R. See, D.Z. Skinner, J. Dubcovsky, K. Garland-Campbell. 2013. Copy number variation at VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat. Theor Appl Genet 127:1183 1197. Avni R., R. Zhao, S. Pearce, Y. Jun, C. Uauy, F. Tabbita, T. Fahima, A. Slade, J. Dubcovsky, A. Distelfeld. 2014. Functional characterization of GPC-1 genes in hexaploid wheat. Planta 239:313 324. Kippes N., J. Zhu, A. Chen. L.S. Vanzetti, A. Lukaszewski, H. Nishida, K. Kato, J. Dvorak, J. Dubcovsky (2014) Fine mapping and epistatic interactions of the vernalization gene VRN-D4 in hexaploid wheat. Mol. Genet. Genomics 289: 47 62 11

Wang S., Wong D., Forrest K., Allen A., Chao S., Huang B., Maccaferri M., Salvi S., Milner S., Cattivelli L., Mastrangelo A., Whan A., Stephen S., Barker G., Wieseke R., Plieske J., IWGSC., Lillemo M., Mather D., Appels R., Dolferus R., Brown-Guedira G., Korol A., Akhunova A., Feuillet C., Salse J., Morgante M., Pozniak C., Luo M.-C., Dvorak J., Morell M., J. Dubcovsky, Ganal M., Tuberosa R., Lawley C., Mikoulitch I., Cavanagh C., Edwards K., Hayden M., Akhunov E. (2014) Characterization of polyploid wheat genomic diversity using a high-density 90,000 SNP array. Plant Biotechnol. J. 12:787-796. Presentations 2014 Dubcovsky, J. 2014. Identifying valuable gene variants for wheat improvement. Wolf Awards Conference, May 29, 2014, Jerusalem, Israel. Dubcovsky, J. 2014. Dissecting the Complex Flowering Pathway in Wheat Using Novel Reverse Genetic Resources. ASA, CSSA, and SSSA Conference, Nov. 2-5, 2014, Long Beach, CA. Keynote speaker at the Ron Phillips Plant Genetics Lectureship. Dubcovsky, J., 2014. Improving California Wheat for Grain and Forage. Alfalfa & Grains Symposium, Long Beach, CA December 10-12. Dubcovsky, J. 2015. Yr36 confers partial resistance to wheat stripe rust by a novel mechanism. "Plant Interactions with Pests and Pathogens Workshop", Plant and Animal Genome XXIII, January 10-14, San Diego. Carle, S., S. Pearce, D. Z. Skinner, J. Dubcovsky, K. Garland-Campbell. 2014. Measuring the genetic capacity of PNW winter wheat varieties for cold-tolerance. Plant and Animal Genome XXII, January 10-14, San Diego. Krasileva, K., S. Ayling, H. Vasquez-Gross, F. Paraiso, T. Howell1, C. Uauy and J. Dubcovsky. 2014. Exome capture and TILLING in tetraploid and hexaploid wheats. Plant and Animal Genome XXII, January 10-14, San Diego. W031. Maccaferri M., A. Ricci, S. Salvi, E. Akhunov, K. Ammar, A. Blanco, L. Cattivelli, A. Distelfeld, J. Dubcovsky, J. Dvorak, T. Fahima, J. Faris, A. Korol, M. Morgante, R. Papa, C. Pozniak, S. Xu, R. Tuberosa. 2014. Towards an SNP-based consensus map of durum wheat. Plant and Animal Genome XXII, January 10-14, San Diego. Jordan, K., S. Wang, L.J. Gardiner, Y. Lun, N. Hall, J. Dubcovsky, C. Pozniak, A. Akhunova, L. Talbert, A. Hall, E. Akhunov. 2014. A first generation haplotype map of wheat genome. Plant and Animal Genome XXII, January 10-14, San Diego. W444 J.-Y. Gou, D. Cantu, A. Dobon-Alonso, C. Uauy, T. Midorikawa, K. Inoue, D. Fu, A. Blechl, J. Dubcovsky. 2014. Resistance mechanism of Yr36 to wheat stripe rust. Plant and Animal Genome XXII, January 10-14, San Diego.W335. Jordan, K., S. Wang, L.J. Gardiner, Y. Lun, N. Hall, J. Dubcovsky, C. Pozniak, A. Akhunova, L. Talbert, A. Hall, E. Akhunov. 2014. A diversity map of the hexaploid wheat genome. Plant and Animal Genome XXII, January 10-14, San Diego. P211. 12

Hazard, B., X. Zhang, R. Naemeh, J. Dubcovsky. 2014. Combined mutations in SBEIIa and SBEIIb genes in durum wheat increase the amylose and resistant starch content in the grain. Plant and Animal Genome XXII, January 10-14, San Diego. P247. Salcedo, A., S. Wang, R.L. Bowden, X. Wang, D. Cantu, H. Liang, J. Dubcovsky, E. Akhunov. 2014. Evaluation of pathogen-protein effectors candidates responsible for triggering the Sr35-mediated response to Puccinia graminis f. sp. tritici (Pgt) infection. Plant and Animal Genome XXII, January 10-14, San Diego. P263. Cobo, N., Tomar, L., Alvarez, A., Pflüger, L., and J. Dubcovsky. 2014. Mapping and validation of two QTL conferring stripe rust resistance in hexaploid wheat. Borlaug Global Rust Initiative 2014 Workshop. March 22-28 2014, CIMMYT, Obregon, Mexico. Howell, T., I. Hale, L. Jankuloski, M. Bonafede, and J. Dubcovsky. 2014. Mapping increased yield and improved canopy water status to a region of a rye chromosome arm introgression in common wheat. 4 th Annual National Association of Plant Breeders Meeting, August 5-8, 2014 in Minneapolis, MN Gilbert, M.E., T. Howell, J. Zhang, S. Rowland, C. Qualset, and J. Dubcovsky. 2014. What information does canopy temperature provide about plant water use? ASA, CSSA, and SSSA Conference, Nov. 2-5, 2014, Long Beach, CA. Poster 392-4. Bonafede MD, MA Alvarez, SM Lewis, ML Appendino, J. Dubcovsky, GE Tranquilli. 2014. Use of genes from wild species transferred to Triticum aestivum through chromosome engineering. In: International Seminar 1914-2014: 100-years of wheat improvement in La Estanzuela, a valuable legacy for the future. August 27 29, 2014. INIA La Estanzuela, Uruguay. Howell, T., I. Hale, L. Jankuloski, M. Bonafede, and J. Dubcovsky. 2014. Mapping increased yield and improved canopy water status to a region of a rye chromosome arm introgression in common wheat. ASA, CSSA, and SSSA Conference, Nov. 2-5, 2014, Long Beach, CA. Poster 390-1. Krasileva, K.V., J. Hegarty, H. Vasquez-Gross, F. Paraiso, X. Wang, P. Bailey, S. Ayling, C. Uauy and J. Dubcovsky. 2014. Tilling for Disease Resistance Genes. Plant and Animal Genome XXIII, January 10-14, San Diego. SERVICES PROVIDED 2014 Organization of the 2014 Field Day at UC Davis, California. Organization and talks for the 2014 Quality Collaborators Meeting at UC Davis. Seeds of advanced breeding lines with pyramided resistance genes were provided to private and public breeders as requested. The germplasm and varieties developed by our program are publicly available and being used extensively by California growers and as parental lines in other public and private wheat breeding programs. MAS backcrossing programs for stripe rust resistance genes and low cadmium were continued in collaboration with Arizona Plant Breeders and World Wide Wheat. 13

SUMMARY OF 2014 RESEARCH (Major Accomplishments) CONCISE GENERAL SUMMARY OF CURRENT YEAR S RESULTS Variety releases: Breeder seed of the new hard red spring wheat UC1745 was delivered to the Foundation Seed Program to produce Foundation seed in the 2015 cycle. Regional trials Common wheat: The lines UC1768 and UC1769 were dropped from the regional trial for showing an unstable yield performance. The line UC1767 was the top yielding line in the regional trials but the bread quality was not satisfactory for the industry. Since it was the first year in the regional trial UC 1767 will be retested in 2015. Five new lines UC1789, UC1790, UC1791, UC1792 and UC1793 will be evaluated in the 2015 regional trial. Durum wheat: The line UC1758 was dropped from the regional trial because of low yield performance. The lines UC 1756, UC1770 and UC1771 showed good yield performance and acceptable pasta quality but since all three are high Cd, none of these lines will be released until the low Cd trait will be incorporated. Four new lines UC1796, UC1797, UC1798 and UC1799 selected for showing high yield performance, good pasta quality and low Cd will be tested in the 2015 regional trial. Quality Collaborators Program: Four lines UC1789, UC1790, UC1791 and UC1792 of common wheat and four lines UC1796, UC1797, UC1798 and UC1799 of durum wheat will be included in the 2015 quality collaborators testing program. Yield trials: 370 lines of common wheat and 287 lines of durum wheat were evaluated in elite, advanced, and preliminary yield trials in 2014. Grain samples from the best 46 lines (90 samples) of common wheat and 46 lines (83 samples) of durum wheat were sent to the CWC Quality Laboratory for a complete quality analysis. 30 lines of durum wheat were sent to the Dr. Dubcovsky laboratory to test for low Cd marker. 435 lines of common wheat and 294 lines of durum wheat will be evaluated in the elite, advanced, and preliminary yield trials in 2015. Observation plots: A total of 920 lines of common wheat and 555 lines of durum wheat were evaluated in observation plots in 2014. After selection for agronomic characteristics, yield performance and protein content, 300 lines of common wheat and 150 lines of durum wheat were selected and will be evaluated in the preliminary yield trials in 2015. Addition of new hybrids and segregating populations: 97 crosses among common wheat and 98 crosses among durum wheat were made in the winter of 2014, the F 1 seeds were planted at Tulelake during the summer and the F 2 populations will be evaluated in the field in the 2015 cycle. Also, 181 F 2 populations of common wheat, 111 F 2 populations of durum wheat, 497F 3 to F 6 families of common wheat and 437 F 3 to F 6 families of durum wheat were planted and evaluated in the field in 2014. After selection for agronomic characteristics, disease resistance, and grain appearance, 496 F 3 to F 6 families of common wheat, and 407 F 3 to F 6 families of durum wheat will be evaluated in the field in 2015. 14

Marker assisted selection: Leaf samples from 7925 F 3 durum lines were sent to the USDA laboratory in Pullman, WA to select lines having the gene for low Cadmium content. A total of 1110 lines homozygous for the low cadmium allele were identified and will be evaluated as F 4 lines in 2014. In addition to the low cadmium gene we advanced the introgression of genes for improved yellow color, and for increased gluten strength and protein content. We also combined the genes for increased resistant starch in our top durum varieties. In the common wheat we continue the introgression of stripe rust and septoria resistance genes. We also initiated the incorporation of novel low molecular weight glutenins alleles for gluten strength and elasticity and transferred the increased resistant starch mutations to common wheat. We have initiated the transfer of two recently discovered genes to increase grain weight and yield under water stress. Acknowledgements: I acknowledge here the major contributions that Dr. Oswaldo Chicaiza and Alicia del Blanco made to the breeding program and Phil Mayo to the Regional testing program, Marcelo Soria to the database, and Xiaoqin Zhang to the MAS backcrossing program. In addition I acknowledge the extremely valuable data provided by the CWC quality laboratory and Dr. Lee Jackson, as well as the continuous support of the CWC and CCIA. Jorge Dubcovsky, Distinguished Professor Dept. of Plant Sciences University of California, One Shields Avenue, Davis CA 95616-8515 Phone: (530) 752-5159, Fax: (530) 752-4361 E-mail: jdubcovsky@ucdavis.edu 15