Horticulture and Crop Science, the Ohio State University, Ohio Agricultural Research and Development Center, USA
Trait and trait stability are important for wheat breeding. Our objectives were to assess the relative efficiency of genomic selection (GS) for various wheat traits and trait stability using four different models. Genotyping was conducted with a 90K SNP chip panel. SNP tagging was used to obtain a subset of 3,919 relatively independent markers for downstream analysis. Phenotyping was conducted on a population consisting of 273 lines, from seven different soft red winter wheat breeding programs in the U.S.A. Eberhart and Russells’ regression and additive main effects and multiplicative interaction (AMMI) models were used to assess trait stability. GS accuracy (r) was assessed for ridge regression best linear unbiased prediction (rr-BLUP), Bayesian ridge regression (BRR), reproducing kernel hilbert space (RKHS), and elastic net (EN). Across all models, GS produced a wide range of accuracies for trait stability (0.1 to 0.65) that varied by trait and stability method. Accuracy was 0.35 for yield and 0.44 for yield stability using AMMI, indicating the viability of GS in selecting lines with both high and stable yield. Our findings lay the foundation for wheat breeding programs in northeastern U.S.A. to implement GS. It also provides useful information for wheat rust researchers: as phenotypic selection for rust resistance can be both expensive and time consuming and rapid evolution of rust pathogens require an emphasis on durable resistance controlled by multiple genes, the GS approach applicable for complex traits thus has potential to achieve higher gains per unit time than traditional breeding for rust resistance.
Ambo Plant Protection Research Center, Ethiopia
During the 2014/15 main crop season 831 wheat fields and experimental plots were assessed for diseases; 66.2% were in the Oromiya, 20.3% in Tigray and 13.4% in SNNP regions. The major diseases encountered include rusts, septoria leaf blotches, foot and root diseases, Fusarium head blight and smuts. The overall mean prevalence of stem rust was 61%, yellow rust 22%, leaf rust 18.8% and Septoria leaf blotches 52.9%. The incidence of the important diseases was highest in SNNP region. The mean incidence of yellow rust ranged from 5.7% in Oromiya to 39.2% in SNNP. The lowest incidence of stem rust, 15.9%, was noted in Tigray and the highest, 64.4%, in SNNP. The minimum mean Septoria incidence was 23% in Oromiya, and maximum was 66.7% in SNNP. Stem rust severities varied from 7 MR-MSS in Tigray to 36 MR-MSS in SNNP. Furthermore, the widely grown varieties Digelu and Danda’a were resistant to yellow rust, but susceptible to stem rust. Varieties Meda Wolbu, Hogona and Ogolcho were not affected by any of the rusts in Oromiya. Variety Hidase was susceptible in SNNP. Out of 115 Pgt cultures established from stem rust samples collected from the three regions, races TKTTF, RRTTF, TTKSK, TRTTF and JRCQC were identified. Stem rust samples were collected from varieties Digelu, Danda’a, Kakaba, and Hidase. Race TKTTF, virulent on Digalu and first identified in Oromiya region in 2013, is now present in all areas. Adapted varieties with durable stem rust resistance in Ethiopia remains an urgent requirement.
Campo Experimental Valle de México INIFAP, México
Yellow (stripe) rust continues to be an important disease of wheat in the irrigated EL Bajio region and northwestern Mexico, and in the High Plateau of Central Mexico. Isolate MEX 96.11, virulent to race-specific resistance genes Yr2, Yr3, Yr6, Yr7, Yr9 and Yr27, represented the most prevalent Pst race until 2001 and evolution of new virulences was slow. Several additional R-genes, including a gene in Pollmer triticale, are now defeated. The aggressive Pst race with Yr8 virulence, first detected in the United States in 2000, not only became widespread in Mexico by 2003 but continued to evolve at a more rapid rate with virulence to Yr1 occurring in 2003. However these races did not cause crop losses other than increased levels of head infections in some cultivars. Variants with virulences to Yr17 and Yr31 were detected in 2007 and 2008, respectively. These resistance genes are known to occur in some wheat varieties and breeding materials. 2010 disease data from trap nurseries that included the Avocet isolines and other varieties indicated the existence of virulence for Yr1, 2 (Siete Cerros), 3 (Tatara), 6, 7, 8, 9, 17, 27 and 31 (Rebeca F2000) in different Pst isolates. During the 2014 crop season, an epidemic occurred in farm fields and samples were collected and analyzed in greenhouse tests. Virulence combination V2, 3, 6, 7, 8, 9, 17, 27 and 31 first identified and represented in isolates CEVAMEX14.25 and MEX 14.141, and a similar isolate MEX14.146 virulent to Yr1 were the most frequent. These new virulence combinations caused yield losses in cultivar Nana F2007 grown in the Mexican highlands and Luminaria F2012, released for the irrigated areas of Bajio. Our results indicate a continuing evolution and accumulation of virulences in the aggressive Pst lineage. Determination of the defeated genes in Nana F2007 and Luminaria F2012 is underway.
Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, Canada
Most of the current stem rust resistance genes (Sr) in Canadian wheat varieties are ineffective against the Pgt race Ug99 lineage, which pose a major threat to wheat production worldwide. Several stem rust resistance genes, including Sr33, Sr35, Sr36, SrCad/Sr42 and Sr43, are effective against race TTKSK. Although Sr36 is ineffective against Ug99 race TTTSK, it is still potentially useful for pyramiding genes to develop germplasm with durable stem rust resistance. For this purpose, we made crosses among RL5405 (Sr33), RL6099 (Sr35), Lang (Sr36), AC Cadillac (SrCad/Sr42), and RWG34 (Sr43) containing the respective Sr genes. A total of 54 doubled haploid (DH) lines were produced from the F1 from AC Cadillac/Lang//RWG34/RL5405, and 82 DH lines were obtained from RWG34/RL5405//RL6099. The DH progeny were tested at the seedling stage with race TTKSK and susceptible lines were discarded. We putatively developed 12 genotypes with multiple Sr gene combinations, including Sr33+Sr36+SrCad/Sr42+Sr43, Sr33+Sr36+SrCad/Sr42, Sr33+Sr36+Sr43, Sr33+SrCad/Sr42+Sr43, Sr36+SrCad/Sr42+Sr43, Sr35+Sr33+Sr43, Sr33+Sr36, Sr33+Sr43, Sr36+SrCad/Sr42, Sr36+Sr43, Sr35+Sr33, and Sr35+Sr43, based on positive association with linked PCR markers. Another population with 63 DH lines was derived from (Hoffman*2/RL6099)//(Hoffman*2/Lang) to combine the Fusarium head blight (FHB) resistance of Hoffman (Fhb1) with Sr35 and Sr36. We found 17 of 63 DH lines containing both Sr35 and Sr36 based also on linked PCR markers. This indicated that the combination Sr35+Sr36 was pyramided into the Canadian cultivar Hoffman; this derivative will be useful for development of cultivars resistant to Ug99 and FHB in Canada.
National Research Council of Canada, Canada
Leaf rust is the most widely occurring disease of wheat worldwide. Resistance is the most practical and effective way to control the disease. Most leaf rust resistance genes are race-specific (“R”, qualitative resistance) and a relatively few are adult plant resistance genes, some of which have been described as slow rusting (“APR”, quantitative resistance). Due to limited knowledge, most resistance genes have been deployed in cultivars by an inefficient “blind” approach. This results in the well known “boom and bust cycle” (resistance followed by susceptibility) because the pathogen evolves rapidly and migrates over long distances. Therefore, a breeding-by-design approach is needed to achieve durable resistance. Pyramiding multiple R, APR or APR+R genes has been used successfully over many years to achieve durable resistance to leaf rust in Canada and some other countries. To further enhance this strategy we seek to understand the molecular mechanisms underlying key resistance genes. To identify the molecular mechanisms underlying rust resistance conferred by major R and APR genes, we performed an integrated systemic transcriptome analysis via RNA-seq on the Thatcher NILs with Lr16, Lr22a, Lr21, Lr34, Lr34+Lr16, and Lr67 challenged with Pt race BBBD. Sampling was conducted over a time series during the infection process of both seedlings and adult plants. Through RNA-seq we were able to capture the dynamic interactome of host-pathogen interactions conferred by these R and APR genes. Preliminary results revealed that resistance reactions conferred by R gene Lr21 and APR gene Lr67 were significantly different compared to other R and APR genes. Significantly, the Thatcher NIL line with Lr34+Lr16 showed the combines defense reactions of Lr16 and Lr34.